Publications

Author	Title	Year	Journal/Proceedings	Reftype
Babcock, M. S. & Olson, W. K.	The effect of mathematics and coordinate system on comparability and ependenciesof nucleic acid structure parameters. [Abstract] [BibTeX]	1994	Journal of Molecular Biology	article
Abstract: This paper critically examines the methodologies used to analyze nucleic acid three-dimensional structure based on guidelines set at a 1988 EMBO workshop. The implications of these analyses cannot be fully understood without a thorough knowledge of how the nos. are calcd. This paper addresses one aspect of the calcns., namely the obsd. correlations between various parameters. These correlations are addressed in the mathematics by explicitly incorporating the concept of a pivot point, which is the point about which a base rotates as it buckles, propeller twists and opens. Pivot points enable one to model the phys. motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters found in other approaches. The correlations that are reduced or eliminated are actually artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. The mathematics the authors have developed, including the mathematics of pivot points, are presented in the companion paper. Here, the authors explain how some of the obsd. correlations occur as a byproduct of the method of calcn., while others are truly structural, and the authors show how optimum pivot points can be detd. to minimize artifactual correlations. The observation that exptl. bases often rotate about the long axis in a ropellermotion as well as rotate about the Z-axis of each base, öpeninginto the major groove, is evident in the location of the optimum region for the pivot point as detd. in this study. The authors consider locating a pivot point as a calibration step to increase the agreement between phys. intuition and the mathematics of the authors' program. [on SciFinder (R)]
BibTeX: @article{RefWorks:431, author = {Marla S. Babcock and Wilma K. Olson}, title = {The effect of mathematics and coordinate system on comparability and \"dependencies\" of nucleic acid structure parameters.}, journal = {Journal of Molecular Biology}, year = {1994}, volume = {237}, number = {1}, pages = {98-124}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 3, 6; CODEN: JMOBAK; CAS Registry Numbers: 65-71-4 (Thymine); 71-30-7 (Cytosine); 73-24-5 (Adenine); 73-40-5 (Guanine) Role: PRP (Properties) (structure of, calcn. of, effect of mathematics and coordinate system on)} }
Babcock, M. S., Pednault, E. P. D. & Olson, W. K.	Nucleic acid structure analysis. Mathematics for local cartesian and helical structure parameters that are truly comparable between structures. [Abstract] [BibTeX]	1994	Journal of Molecular Biology	article
Abstract: Analyzing nucleic acid structures in a comparable manner has become increasingly important as the no. of solved structures had increased. This paper presents the concepts, mathematics, theorems, and proofs that form the basis of a new program to analyze three-dimensional DNA and RNA structures. The approach taken here provides numerical data in accordance with guidelines set at a 1988 EMBO workshop. Math. definitions are provided for all local structural parameters described in the guidelines. The definitions satisfy the guideline requirements while preserving the original phys. intuition of the parameters. In particular, the rotational parameters are true rotations based on a simple phys. model (net rotation at const. angular velocity), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the math. definitions are sym. with the property that a 5 Deg tilt is the same as a 5 Deg roll and a 5 Deg twist, except that the rotations take place about different axes. In other approaches, a 5 Deg tilt can mean a different amt. of net rotation than a 5 Deg roll or a 5 Deg twist. A second unique feature of the mathematics is that it explicitly incorporates the concept of a pivot point, which is the point about which a base in a base-pair rotates as it buckles, propeller twists, and opens. Pivot points enable one to model the phys. motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters that arise as math. induced artifacts in other approaches. This paper, together with the statistical anal. in the companion paper for detg. the locations of the pivot points, provides everything needed to understand the output of the program as it relates to individual structures. [on SciFinder (R)]
BibTeX: @article{RefWorks:430, author = {Marla S. Babcock and Edwin P. D. Pednault and Wilma K. Olson}, title = {Nucleic acid structure analysis. Mathematics for local cartesian and helical structure parameters that are truly comparable between structures.}, journal = {Journal of Molecular Biology}, year = {1994}, volume = {237}, number = {1}, pages = {125-156}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 3, 6; CODEN: JMOBAK} }
Babcock, M. S., Pednault, E. P. D. & Olson, W. K.	Nucleic acid structure analysis: a users guide to a collection of new analysis programs. [Abstract] [BibTeX]	1993	Journal of Biomolecular Structure & Dynamics	article
Abstract: Common nomenclature describing the geometry of nucleic acid structures was established at a 1988 EMBO Workshop on DNA Curvature and Bending [Diekmann, S. (1988); Diekmann, S. (1989); Sarma, R.H. (1988); Dickerson, R. E. (1989); Dickerson, R. E. et al. (1989)]. The authors have subsequently developed and incorporated sophisticated mathematics in a computer program to calc. the parameters described by the guidelines. The program calcs. all the local parameters relating complementary bases and neighboring base and base pairs in both Cartesian and helical coordinate frames. In addn., the main math. property requested by the EMBO guidelines - that the magnitude of the parameters be independent of strand or direction of measurement - is accomplished without the use of a midway coordinate frame for the rotational parameters. The mathematics preserve the phys. intuition used in defining the parameters; in particular, the rotational parameters are true rotations based on a simple phys. model (rotation at const. angular velocity for a unit amt. of time), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the math. equations are sym. with the property that a 5 Deg tilt is the same as a 5 Deg roll or a 5 Deg twist, except that the rotations take place about different axes. In other approaches, a 5 Deg tilt can mean a different amt. of net rotation from a 5 Deg roll or a 5 Deg twist. In addn., a great deal of flexibility is built into the program so that the user has control over the anal., including the input format, the coordinate frame used for the base pairing relationship, the point about which the rotations are performed, and which geometric relationships are analyzed. While there is a great deal of flexibility, the program is easy to use. Interactive queries and user accessible files make the options in the program very convenient to tailor to individual needs. In addn., there is also a program that calcs. bond lengths, valence angles, and torsion angles along the nucleic acid backbone, and within the sugar and base rings. Another program 'learns' the identities of the bond lengths, valence angles, and torsion angles that the user would like to det. This last program is esp. useful for calcg. the hydrogen bonds between atoms in complementary strands as well as the unusual hydrogen bonds found in recently detd. nucleic acid NMR structures or within protein/nucleic acid complexes. [on SciFinder (R)]
BibTeX: @article{RefWorks:307, author = {Marla S. Babcock and Edwin P. D. Pednault and Wilma K. Olson}, title = {Nucleic acid structure analysis: a users guide to a collection of new analysis programs.}, journal = {Journal of Biomolecular Structure & Dynamics}, year = {1993}, volume = {11}, number = {3}, pages = {597-628}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: JBSDD6} }
Benevides, J. M., Chan, G., Lu, X., Olson, W. K., Weiss, M. A. & Thomas, G. J.	Protein-Directed DNA Structure. I. Raman Spectroscopy of a High-Mobility-Group Box with Application to Human Sex Reversal. [Abstract] [BibTeX]	2000	Biochemistry	article
Abstract: Protein-directed reorganization of DNA underlies mechanisms of transcription, replication, and recombination. A mol. model for DNA reorganization in the regulation of gene expression is provided by the sequence-specific high-mobility-group (HMG) box. Structures of HMG-box complexes with DNA are characterized by expansion of the minor groove, sharp bending toward the major groove, and local unwinding of the double helix. The Raman vibrational signature of such DNA reorganization has been identified in a study of the SRY HMG box, encoded by the human male-detg. region of the Y chromosome. The authors observe in the human SRY-HMG:DNA complex extraordinarily large perturbations to Raman bands assocd. with vibrational modes of the DNA backbone and accompanying large increases in intensities of Raman bands attributable to base unstacking. In contrast, DNA major-groove binding, as occurs for the bZIP protein GCN4 [Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochem. 39, XXX-XXX], perturbs the Raman signature of DNA only marginally. Raman markers of minor-groove recognition in the human SRY-HMG:DNA complex are due primarily to perturbation of specific vibrational modes of deoxyribose moieties and presumably reflect desolvation at the nonpolar interface of protein and DNA. These Raman markers may be diagnostic of protein-induced DNA bending and are proposed as a baseline for comparative anal. of mutations in SRY that cause human sex reversal. [on SciFinder (R)]
BibTeX: @article{RefWorks:391, author = {James M. Benevides and Ging Chan and Xiang-Jun Lu and Wilma K. Olson and Michael A. Weiss and George J. Thomas}, title = {Protein-Directed DNA Structure. I. Raman Spectroscopy of a High-Mobility-Group Box with Application to Human Sex Reversal.}, journal = {Biochemistry}, year = {2000}, volume = {39}, number = {3}, pages = {537-547}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 3-4; CA Section Cross-references: 6; CODEN: BICHAW; CAS Registry Numbers: 257616-53-8 Role: BPR (Biological process), BSU (Biological study, unclassified), BIOL (Biological study), PROC (Process) (Raman spectroscopy of SRY high-mobility-group Box:DNA complex and possible application to diagnosis of human sex reversal)} }
Benevides, J. M., Li, T., Lu, X., Srinivasan, A. R., Olson, W. K., Weiss, M. A. & Jr, G. J. T.	Protein-Directed DNA Structure II. Raman Spectroscopy of a Leucine Zipper bZIP Complex. [Abstract] [BibTeX]	2000	Biochemistry	article
Abstract: Mechanisms of transcription may involve protein-directed changes in DNA structure and DNA-directed changes in protein structure. We have employed Raman spectroscopy to characterize vibrational signatures assocd. with such induced mol. fitting for two classes of transcription factors-the basic leucine-zipper (bZIP) motif and the high-mobility-group (HMG) box-each with a DNA target site. Results for bZIP are described here; findings for the HMG-box are reported in the preceding paper in this issue [Benevides, J. M., Chan, G., Lu, X.-J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochem. 39]. The yeast activator GCN4 provides a well-studied example of bZIP recognition, wherein B-DNA serves essentially as a template for protein folding. Anal. of Raman spectra of the 57-residue GCN4 bZIP domain, its AP-1 binding site, and their specific complex confirms a DNA-induced increase in a-helicity, attributable to folding of GCN4 basic arms with virtually no change in B-DNA structure, consistent with previous X-ray and NMR structure detns. The absence of DNA perturbations in the bZIP model contrasts sharply with the HMG box, where DNA structure perturbations predominate. The bZIP and HMG-box models represent two opposing extremes in a range of induced fits identifiable by Raman spectroscopy. Previously characterized l repressor/operator complexes [Benevides, J. M., Weiss, M. A., and Thomas, G. J. (1994) J. Biol. Chem. 269, 10869-10878] occupy an intermediate position within this range. A comprehensive tabulation of Raman markers proposed as diagnostic of different protein/DNA recognition motifs is presented. The results are analyzed in terms of available DNA crystal structures (Nucleic Acid Database) to identify details of DNA conformation that correlate with specific Raman recognition markers. [on SciFinder (R)]
BibTeX: @article{RefWorks:390, author = {James M. Benevides and Tiansheng Li and Xiang-Jun Lu and A. R. Srinivasan and Wilma K. Olson and Michael A. Weiss and George J. Thomas Jr}, title = {Protein-Directed DNA Structure II. Raman Spectroscopy of a Leucine Zipper bZIP Complex.}, journal = {Biochemistry}, year = {2000}, volume = {39}, number = {3}, pages = {548-556}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-7; CODEN: BICHAW} }
Berman, H. M., Clowney, L., Gelbin, A., Hsieh, S., Olson, W. K., Westbrook, J. & Zardecki, C.	The nucleic acid database: a research tool for the study of nucleic acid crystal structures. [BibTeX]	1996	Folding & design	article
BibTeX: @article{RefWorks:411, author = {Helen M. Berman and Lester Clowney and Anke Gelbin and Shu-Hsin Hsieh and Wilma K. Olson and John Westbrook and Christine Zardecki}, title = {The nucleic acid database: a research tool for the study of nucleic acid crystal structures.}, journal = {Folding & design}, year = {1996}, volume = {1}, number = {Suppl.}, pages = {S10}, note = {Copyright (C) 2007 ACS on SciFinder (R)); CODEN: FODEFH} }
Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R. & Schneider, B.	The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. [Abstract] [BibTeX]	1992	Biophysical journal	article
Abstract: A description is given of the Nucleic Acid Database which contains information on 192 DNA and RNA crystal structures, including 130 entries having at coordinates. Data prepn., database management, and information retrieval are described. [on SciFinder (R)]
BibTeX: @article{RefWorks:317, author = {Helen M. Berman and Wilma K. Olson and David L. Beveridge and John Westbrook and Anke Gelbin and Tamas Demeny and Shu Hsin Hsieh and A. R. Srinivasan and Bohdan Schneider}, title = {The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.}, journal = {Biophysical journal}, year = {1992}, volume = {63}, number = {3}, pages = {751-759}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 20-5; CA Section Cross-references: 6; CODEN: BIOJAU} }
Boschitsch, A. H., Fenley, M. O. & Olson, W. K.	A Fast Adaptive Multipole Algorithm for Calculating Screened Coulomb (Yukawa) Interactions. [Abstract] [BibTeX]	1999	Journal of Computational Physics	article
Abstract: The screened Coulomb (Yukawa or Debye-Huckel) potential, F=exp(-kr)/r, where r is the sepn. distance and k is the Debye-Huckel screening parameter, gives a good description of the electrostatic interactions in a variety of biol. and phys. important charged systems. It is well known that the direct calcn. of the energy and forces due to a collection of N charged particles involves the pairwise summation of all charged particle interactions and exhibits an O(N2) computational complexity which severely restricts max. problem size. This has prompted the development of fast summation algorithms that allow the electrostatic energy and forces to be obtained in only O(N log N) operations. To date, however, practically all such implementations have been limited exclusively to pure Coulombic potentials (k=0), and the central contribution of the present method is to extend this capability to the entire range of the inverse Debye length, k>=0. The basic formulation and computational implementation of the spherical modified Bessel function-based multipole expansions appropriate for the screened Coulomb kernel are first presented. Next, a simple model system consisting of a single source charged particle is studied to show that the max. electrostatic energy error incurred by an M-order multipole expansion for the Yukawa potential is bounded above by the error of the equiv. multipole expansion for the Coulombic potential. Finally, timing and accuracy studies are presented for a variety of charged systems including polyelectrolyte chains, random distributions of charges inside a cube, and face-centered-cubic lattice charge configurations contg. up to 103,823 charges. (c) 1999 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:396, author = {Alexander H. Boschitsch and Marcia O. Fenley and Wilma K. Olson}, title = {A Fast Adaptive Multipole Algorithm for Calculating Screened Coulomb (Yukawa) Interactions.}, journal = {Journal of Computational Physics}, year = {1999}, volume = {151}, number = {1}, pages = {212-241}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 65; CODEN: JCTPAH} }
Chalikian, T. V., Volker, J., Srinivasan, A. R., Olson, W. K. & Breslauer, K. J.	The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques. [Abstract] [BibTeX]	1999	Biopolymers	article
Abstract: Using high precision densimetric and ultrasonic measurements, we have detd., at 25 Deg, the apparent molar volumes jV and the apparent molar compressibilities jKs of four nucleic acid duplexes-namely, the DNA duplex, poly(dIdC).poly(dIdC); the RNA duplex, poly(rA).poly(rU); and the two DNA/RNA hybrid duplexes, poly(rA).poly(dT) and poly(dA).poly(rU). Using available fiber diffraction data on these duplexes, we have calcd. the mol. vols. as well as the solvent-accessible surface areas of the constituent charged, polar, and nonpolar at. groups. We found that the hydration properties of these nucleic acid duplexes do not correlate with the extent and the chem. nature of the solvent-exposed surfaces, thereby suggesting a more specific set of duplex-water interactions beyond general solvation effects. A comparative anal. of our volumetric data on the four duplexes, in conjunction with available structural information, suggests the following features of duplex hydration: (a) The four duplexes exhibit different degrees of hydration, in the order poly(dIdC).poly(dIdC) > poly(dGdC).poly(dGdC) > poly(dAdT).poly(dAdT) ~ poly(dA).poly(dT). (b) Repetitive AT and IC sequences within a duplex are solvated beyond general effects by a spine of hydration in the minor groove, with this sequence-specific water network involving about 8 addnl. water mols. from the second and, perhaps, even the third hydration layers. (c) Repetitive GC and IC sequences within a duplex are solvated beyond general effects by a atch of hydrationin the major groove, with this water network involving about 13 addnl. water mols. from the second and, perhaps, even the third hydration layers. (d) Random sequence, polymeric DNA duplexes, which statistically lack extended regions of repetitive AT, GC, or IC sequences, do not experience such specific enhancements of hydration. Consequently, consistent with our previous observations (T. V. Chalikian et al., 1994), duplexes with approx. 50% AT content exhibit the weakest hydration, while an increase or decrease from this AT content causes enhancement of hydration, either due to stronger hydration of the minor groove (an increase in AT content) or due to stronger hydration of the major groove (an increase in GC content). (e) In dil. aq. solns., a B-DNA duplex is more hydrated than an A-DNA duplex, a volumetric-based conclusion that is in agreement with previous results obtained on crystals, fibers, and DNA solns. in org. solvent-water mixts. (f) the A-like, RNA duplex poly(rA).poly(rU) and the structurally similar A-like, hybrid duplex poly(rA).poly(dT), exhibit similar hydration properties, while the structurally distinct A-like, hybrid duplex poly(rA).poly(dT) and non-A-like, hybrid duplex poly(dA).poly(rU) exhibit differential hydration properties, consistent with structural features dictating hydration characteristics. We discuss how volumetric characterizations, in conjunction with structural studies, can be used to describe, define, and resolve the general and sequence/conformation-specific hydration properties of nucleic acid duplexes. [on SciFinder (R)]
BibTeX: @article{RefWorks:393, author = {Tigran V. Chalikian and Jens Volker and A. R. Srinivasan and Wilma K. Olson and Kenneth J. Breslauer}, title = {The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques.}, journal = {Biopolymers}, year = {1999}, volume = {50}, number = {5}, pages = {459-471}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 24936-38-7; 27156-07-6 (Poly(rA).poly(dT); 33572-75-7 (Poly(dA).poly(rU); 34639-43-5 Role: BSU (Biological study, unclassified), PRP (Properties), BIOL (Biological study) (hydration of nucleic acid duplexes as assessed by combination of volumetric and structural techniques)} }
Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. K. & Berman, H. M.	Geometric Parameters in Nucleic Acids: Nitrogenous Bases. [Abstract] [BibTeX]	1996	Journal of the American Chemical Society	article
Abstract: Estd. bond-lengths and bond-angle parameters for the nitrogenous base side groups of nucleic acids are presented. These values are the result of a statistical survey of small mols. in the Cambridge Structural Database for which high-resoln. X-ray and neutron crystal structures are available. The statistics include arithmetic means and std. deviations for the different samples, as well as comparisons of the population distributions for sugar- and non-sugar-derivatized bases. These accumulated data provide appropriate target values for refinements of oligonucleotide structures, as well as sets of std. at. coordinates for the five common bases. [on SciFinder (R)]
BibTeX: @article{RefWorks:417, author = {Lester Clowney and Shri C. Jain and A. R. Srinivasan and John Westbrook and Wilma K. Olson and Helen M. Berman}, title = {Geometric Parameters in Nucleic Acids: Nitrogenous Bases.}, journal = {Journal of the American Chemical Society}, year = {1996}, volume = {118}, number = {3}, pages = {509-518}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 26-9; CA Section Cross-references: 22, 75; CODEN: JACSAT; CAS Registry Numbers: 65-71-4 (Thymine); 66-22-8 (Uracil); 71-30-7 (Cytosine); 73-24-5 (Adenine); 73-40-5 (Guanine); 18444-01-4 (Adenine conjugate monoacid); 20791-98-4 (Cytosine conjugate monoacid) Role: PRP (Properties) (statistical analyses of bond lengths and valence angles for neutral and protonated purine and pyrimidine bases)} }
Coleman, B. D., Olson, W. K. & Swigon, D.	Theory of sequence-dependent DNA elasticity. [Abstract] [BibTeX]	2003	Journal of Chemical Physics	article
Abstract: The elastic properties of a mol. of duplex DNA are strongly dependent on nucleotide sequence. In the theory developed here the contribution yn of the nth base-pair step to the elastic energy is assumed to be given by a function y~n of six kinematical variables, called tilt, roll, twist, shift, slide, and rise, that describe the relative orientation and displacement of the nth and (n+1)th base pairs. The sequence dependence of elastic properties is detd. when one specifies the way y~n depends on the nucleotides of the two base pairs of the nth step. Among the items discussed are the symmetry relations imposed on y~n by the complementarity of bases, i.e., of A to T and C to G, the antiparallel nature of the DNA sugar-phosphate chains, and the requirement that y~n be independent of the choice of the direction of increasing n. Variational equations of mech. equil. are here derived without special assumptions about the form of the functions y~n, and numerical solns. of those equations are shown for illustrative cases in which y~n is, for each n, a quadratic form and the DNA forms a closed, 150 base-pair, minicircle that can be called a DNA o-ring because it has a nearly circular stress-free configuration. Examples are given of noncircular equil. configurations of naked DNA o-rings and of cases in which the interaction with ligands induces changes in configuration that are markedly different from those undergone by a minicircle of intrinsically straight DNA. When a minicircle of intrinsically straight DNA interacts with an intercalating agent that upon binding to DNA causes a local redn. of intrinsic twist, the configuration that minimizes elastic energy depends on the no. of intercalated mols., but is independent of the spatial distribution of those mols. along the minicircle. In contrast, it is shown here that the configuration and elastic energy of a DNA o-ring can depend strongly on the spatial distribution of the intercalated mols. As others have obsd. in calcns. for Kirchhoff rods with intrinsic curvature, an o-ring that has its intrinsic twist reduced at a single base-pair step can undergo large deformations with localized untwisting and bending at remote steps, even when the amt. a of twist redn. is less than the amt. required to induce supercoiling in rings of intrinsically straight DNA. We here find that the presence in the functions y~n of cross-terms coupling twist to roll can amplify the configurational changes induced by local untwisting to the point where there can be a value of a at which a first-order transition occurs between two distinct stable noncircular configurations with equal elastic energy. [on SciFinder (R)]
BibTeX: @article{RefWorks:377, author = {Bernard D. Coleman and Wilma K. Olson and David Swigon}, title = {Theory of sequence-dependent DNA elasticity.}, journal = {Journal of Chemical Physics}, year = {2003}, volume = {118}, number = {15}, pages = {7127-7140}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 65; CODEN: JCPSA6} }
Czapla, L., Swigon, D. & Olson, W. K.	Sequence-Dependent Effects in the Cyclization of Short DNA. [Abstract] [BibTeX]	2006	Journal of Chemical Theory and Computation	article
Abstract: A new, computationally efficient Monte Carlo approach has been developed to est. the ring-closure properties of short, realistically modeled DNA chains. The double helix is treated at the level of base-pair steps using an elastic potential that accounts for the sequence-dependent variability in the intrinsic structure and elastic moduli of the base-pair steps, including the known coupling of conformational variables. Rather than using traditional Metropolis-Monte Carlo techniques to generate representative configurations, a Gaussian sampling method is introduced to construct three-dimensional structures from linear combinations of the rigid-body parameters defining the relative orientation and displacement of successive base pairs. The computation of the J factor, the well-known ratio of the equil. consts. for cyclization vs bimol. assocn. of a linear mol., takes into account restrictions on the displacement and directions of the base pairs joined in ring closure, including the probability that the end-to-end vector is null and the terminal base pairs coincide. The increased sample sizes needed to assess the likelihood that very short chains satisfy these criteria are attained using the Alexandrowicz half-chain sampling enhancement technique in combination with selective linkage of the two-half-chain segments. The method is used to investigate the cyclization properties of arbitrary-length DNA with greatly enhanced sampling sizes, i.e., O(1014) configurations, and to est. J factors lower than 0.1 pM with high accuracy. The methodol. has been checked against classic theor. predictions of the cyclization properties of an ideal, inextensible, naturally straight, DNA elastic rod and then applied to investigate the extent to which one can account for the unexpectedly large J factors of short DNA chains without the need to invoke significant distortions of double helical structure. Several well-known structural features of DNA-including the presence of intrinsic curvature, roll-twist coupling, or enhanced pyrimidine-purine deformability-bring the computed J factors in line with the obsd. data. Moreover, periodically distributed roll-twist coupling reduces the magnitude of oscillations in J, seen in plots of J vs chain length, to the extent found exptl. [on SciFinder (R)]
BibTeX: @article{RefWorks:370, author = {Luke Czapla and David Swigon and Wilma K. Olson}, title = {Sequence-Dependent Effects in the Cyclization of Short DNA.}, journal = {Journal of Chemical Theory and Computation}, year = {2006}, volume = {2}, number = {3}, pages = {685-695}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: JCTCCE} }
Erie, D. A., Breslauer, K. J. & Olson, W. K.	A Monte Carlo method for generating structures of short single-stranded DNA sequences. [Abstract] [BibTeX]	1993	Biopolymers	article
Abstract: A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Min. energy states of individual dinucleotide monophosphate mols. are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mol of the global min. in the resulting optimized states are then allowed to vary by +-10 Deg in an effort to est. the breadth of the different local min. The energies of a total of 2187 (37) angle combinations are examd. per local conformational min. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theor. sample match those found in NMR soln. studies. This last step is necessitated by limitations in the theor. methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from NMR coupling consts. and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150-325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CXnG) chains, were X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5' end of the chain using random nos. to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 106 conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar-phosphate backbone. The distributions of oligonucleotide conformations are examd. in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodol. is discussed and compared with other nucleic acid model building techniques. [on SciFinder (R)]
BibTeX: @article{RefWorks:313, author = {Dorothy A. Erie and Kenneth J. Breslauer and Wilma K. Olson}, title = {A Monte Carlo method for generating structures of short single-stranded DNA sequences.}, journal = {Biopolymers}, year = {1993}, volume = {33}, number = {1}, pages = {75-105}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: BIPMAA; CAS Registry Numbers: 1969-54-6; 4251-20-1; 4336-87-2; 4624-07-1; 4829-64-5; 23339-45-9; 75567-41-8; 75579-55-4; 77540-75-1; 92396-49-1; 144994-91-2; 144994-92-3 Role: PRP (Properties) (conformation of, Monte Carlo method for calcn. of)} }
Erie, D. A., Jones, R. A., Olson, W. K., Sinha, N. K. & Breslauer, K. J.	Melting behavior of a covalently closed, single-stranded, circular DNA. [Abstract] [BibTeX]	1989	Biochemistry	article
Abstract: A 26 residue deoxynucleotide sequence d(TTCCT5GGAATTCCT5GGAA), which folds intramolecularly to a dumbbell-shaped, double-hairpin structure with a gap between the 3' and the 5' ends, was synthesized. T4 polynucleotide kinase was used to phosphorylate the 5' end followed by T4 DNA ligase to close the 3' and 5' ends. Melting of the dumbbell structure formed by this ligated sequence produces a covalently closed, single-stranded, circular final state. Calorimetric and spectroscopic techniques were used to characterize thermodynamically the melting behavior of the ligated mol. and compared it with the corresponding melting behavior of its unligated precursor. This comparison enabled the characterization of the influence of single-stranded ring closure on intramol. duplex melting. The data reveal that ring closure produces a thermally more stable structure which exhibits significantly altered melting thermodn. These thermodn. differences are rationalized in terms of differential solvation and differential counterion assocn. between the ligated and unligated mols. The importance of such constrained dumbbell structures as models for hairpins, cruciforms, and locally melted domains with naturally occurring DNA polymers is also noted. [on SciFinder (R)]
BibTeX: @article{RefWorks:332, author = {Dorothy A. Erie and Roger A. Jones and Wilma K. Olson and Navin K. Sinha and Kenneth J. Breslauer}, title = {Melting behavior of a covalently closed, single-stranded, circular DNA.}, journal = {Biochemistry}, year = {1989}, volume = {28}, number = {1}, pages = {268-273}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BICHAW; CAS Registry Numbers: 117988-12-2 Role: BIOL (Biological study) (melting and phosphorylation of); 70755-49-6; 110743-49-2; 117982-68-0 Role: PROC (Process) (melting of); 117982-70-4P Role: SPN (Synthetic preparation), PREP (Preparation) (prepn. and ligation and melting of); 117982-69-1P Role: SPN (Synthetic preparation), PREP (Preparation) (prepn. and melting of, as model for closed circular single-stranded DNA)} }
Erie, D. A., Suri, A. K., Breslauer, K. J., Jones, R. A. & Olson, W. K.	Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data. [Abstract] [BibTeX]	1993	Biochemistry	article
Abstract: A computational procedure for generating conformations of DNA hairpin loop structures from a broad range of low-energy starting states is described. The starting point of the modeling is the distribution of oligonucleotide chain conformations obtained from Monte Carlo simulations of feasible dinucleotide steps. Structures that meet the spatial criteria for hairpin loop formation are selected from the distributions and subsequently minimized using all-atom mol. mechanics. Both d(CTnG) and d(CAnG) oligomers, where n = 3, 4, or 5, are modeled. These sequences are chosen because of the large no. of published NMR and thermodn. studies on DNA hairpins contg. thymine or adenine residues. The minimized three-dimensional hairpin loop structures are compared with one another as well as analyzed in terms of available exptl. data. The computational approach provides the first detailed anal. of DNA hairpin loop structure in terms of a multistate conformational model. Investigation of the minimized conformations reveals several interesting structural features. First, hairpin loops of the same sequence adopt several distinctly different conformations, as opposed to minor variants of the same equil. structure, that could potentially interconvert in soln. Second, in contrast to double-helical nucleic acids, the hairpin loop models exhibit hydrophobic and hydrophilic surfaces. The different disposition of hydrophobic groups in loops vs. duplexes could modulate both protein-nucleic acid interactions and nucleic acid self-assocn. Third, perpendicular arom. interactions of loop residues are obsd. in many of the computed hairpins. This sort of interaction might be important in the stabilization of non-hydrogen-bonded nucleic acid secondary and tertiary structures. The predicted structural features in the models help, in addn., to account for the unusual thermodn. properties of DNA hairpin loops. Comparison of the theor.-generated NOEs in different structures further reveals that very different mol. structures and interaction can, in principle, produce the same NOEs. The multistate description suggested by this observation differs from the conventional interpretation of DNA soln. structure in terms of the fluctuations about a single preferred chain conformation. There is not necessarily only one set of closely related structures consistent with the obsd. data. [on SciFinder (R)]
BibTeX: @article{RefWorks:315, author = {Dorothy A. Erie and Asif K. Suri and Kenneth J. Breslauer and Roger A. Jones and Wilma K. Olson}, title = {Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data.}, journal = {Biochemistry}, year = {1993}, volume = {32}, number = {2}, pages = {436-454}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: BICHAW; CAS Registry Numbers: 75567-41-8; 75579-55-4; 77540-75-1; 92396-49-1; 144994-91-2; 144994-92-3 Role: PRP (Properties) (hairpin loop conformation of, theor. prediction of, thermodn. and spectrometry in relation to); 111853-74-8; 111853-75-9; 117988-81-5; 117988-84-8; 118025-39-1; 129874-43-7; 129874-45-9 Role: PRP (Properties) (hairpin loop conformation of, thermodn. of)} }
Fenley, M. O., Manning, G. S., Marky, N. L. & Olson, W. K.	Excess counterion binding and ionic stability of kinked and branched DNA. [Abstract] [BibTeX]	1998	Biophysical chemistry	article
Abstract: The excess no. of counterions assocd. with kinked and branched DNA and the ionic stabilities of these structures as a function of chain length and both Na+ and Mg2+ salt concn., using numerical counterion condensation theory, are computed. The DNA structures are modeled as 2 or more finite lines of phosphate charges radiating from the kink or junction center. The no. of excess counterions around the (40-90 Deg) kinked duplex is very small (at most four). The geometries of large 3- and 4-way DNA junctions (with >50 base pairs per arm) in solns. contg. low to moderate NaCl concns., by contrast, accumulate a substantial no. of excess Na+ (>20) but ?15 Mg2+ counterions. The excess no. of counterions surrounding the kinked linear chain and the branched DNA structures either remains invariant or increases with chain length, tending to reach a plateau value. Open configurations, such as the planar Y-shaped 3-way junction (with 3 120 Deg inter-arm angles) and the 90 Deg cross-shaped four-way junction, are ionically more stable than compact geometries, such as pyramidal 3-way junctions and X-shaped 4-way junctions, over the entire range of salt concn. considered (10-5-10-1 M NaCl or MgCl2). The ionic stabilities of the compact forms increase with increasing salt concn. and become comparable to those of the extended geometries at high salt (esp. when Mg2+ is the supporting salt). [on SciFinder (R)]
BibTeX: @article{RefWorks:400, author = {Marcia O. Fenley and Gerald S. Manning and Nancy L. Marky and Wilma K. Olson}, title = {Excess counterion binding and ionic stability of kinked and branched DNA.}, journal = {Biophysical chemistry}, year = {1998}, volume = {74}, number = {2}, pages = {135-152}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BICIAZ; CAS Registry Numbers: 7439-95-4 (Magnesium); 7440-23-5 (Sodium) Role: BAC (Biological activity or effector, except adverse), BSU (Biological study, unclassified), BIOL (Biological study) (excess counterion binding and ionic stability of kinked and branched DNA)} }
Fenley, M. O., Manning, G. S. & Olson, W. K.	Electrostatic persistence length of a smoothly bending polyion computed by numerical counterion condensation theory. [Abstract] [BibTeX]	1992	Journal of Physical Chemistry	article
Abstract: Using numerical counterion condensation theory, the electrostatic component of the persistence length of DNA is computed for three models. In the line model, the phosphate charges are represented as points uniformly distributed on a line of zero radius. In the helical model, the phosphates are given the three-dimensional coordinates deduced from x-ray fiber diffraction; the helical model is considered with and without the dielec. satn. effect. For each model, the free energy of bending smoothly to a specified radius of curvature is calcd. All models exhibit strong end effects for finite-length DNA. The most reliable model is the helical model with dielec. satn. Persistence lengths calcd. for it are linearly correlated, to good numerical approxn., with the inverse concn. of salt. Comparison with exptl. data suggests that real thermal bending fluctuations of DNA in soln. may not be describable as the smooth length-invariant bending postulated by any of the models. [on SciFinder (R)]
BibTeX: @article{RefWorks:320, author = {Marcia O. Fenley and Gerald S. Manning and Wilma K. Olson}, title = {Electrostatic persistence length of a smoothly bending polyion computed by numerical counterion condensation theory.}, journal = {Journal of Physical Chemistry}, year = {1992}, volume = {96}, number = {10}, pages = {3963-3969}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 9, 68; CODEN: JPCHAX} }
Fenley, M. O., Manning, G. S. & Olson, W. K.	A numerical counterion condensation analysis of the B-Z transition of DNA. [Abstract] [BibTeX]	1990	Biopolymers	article
Abstract: The salt dependence of the B-Z transition in DNA was examd. by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference DG is computed for both the ZI and ZII conformations over broad ranges of NaCl and MgCl2 concns. and polymer lengths. For the solvent both a const.-dielec. model (dielec. const. set to 78.3) and a dielec. satn. model (distance-dependent const.) were employed. Where comparison can be made, the results for the const.-dielec. model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low-salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielec. model. The behavior of ZI and ZII are qual. similar throughout the entire salt range for the const.-dielec. model, but qual. different if dielec. satn. is simulated, as is necessary for a realistic description. The ionic DG, in the presence of dielec. satn., bears comparison with the high-salt trend of the measured total DG if Z-DNA is predominantly ZI, but not if it is predominantly ZII. [on SciFinder (R)]
BibTeX: @article{RefWorks:325, author = {Marcia O. Fenley and Gerald S. Manning and Wilma K. Olson}, title = {A numerical counterion condensation analysis of the B-Z transition of DNA.}, journal = {Biopolymers}, year = {1990}, volume = {30}, number = {13-14}, pages = {1205-1213}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 7439-95-4 (Magnesium); 7440-23-5 (Sodium) Role: BIOL (Biological study) (DNA binding of, ionic strength effect on, in counterion condensation study)} }
Fenley, M. O., Manning, G. S. & Olson, W. K.	Approach to the limit of counterion condensation. [Abstract] [BibTeX]	1990	Biopolymers	article
Abstract: According to counterion condensation theory, one of the contributions to the polyelectrolyte free energy is a pairwise sum of Debye-Hueckel potentials between polymer charges that are reduced by condensed counterions. When the polyion model is taken as an infinitely long and uniformly spaced line of charges, a simple closed expression for the summation, combined with entropy-derived mixing contributions, leads to the central result of the theory, a condensed fraction of counterions dependent only on the linear charge d. of the polyion and the valence of the counterion, stable against increases of salt up to concns. in excess of 0.1M. Here the sum is numerically evaluated for B-DNA models other than the infinite line of B-DNA charges. For a finite-length line there are end effects at low salt. The condensation limit is reached as a flat plateau by increasing the salt concn. At a fixed salt concn. the condensation limit is reached by increasing the length of the line. At moderate salt even very short B-DNA line-model oligomers have condensed fractions not far from the infinite polymer limit. For a long double-helical array with charge coordinates at the phosphates of B-DNA, the limiting condensed fraction appears to be approached at low salt. In contrast to the results for the line of charges, however, the computed condensed fraction varies strongly with salt in the range of exptl. typical concns. Salt invariance is restored, in agreement with both the line model and exptl. data, when dielec. satn. is considered by means of a distance-dependent dielec. function. For sufficiently long B-DNA line and helical models, at typical salt concns., the counterion binding fraction approaches the polymer limit as a linear function of 1/P, where P is the no. of phosphate groups of B-DNA. [on SciFinder (R)]
BibTeX: @article{RefWorks:326, author = {Marcia O. Fenley and Gerald S. Manning and Wilma K. Olson}, title = {Approach to the limit of counterion condensation.}, journal = {Biopolymers}, year = {1990}, volume = {30}, number = {13-14}, pages = {1191-1203}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 7439-95-4 (Magnesium); 7440-23-5 (Sodium) Role: PRP (Properties) (condensation limit of, with B DNA model oligomers, ionic strength effect on)} }
Fenley, M. O., Olson, W. K., Chua, K. & Boschitsch, A. H.	Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA. [Abstract] [BibTeX]	1996	Journal of Computational Chemistry	article
Abstract: This article presents a fast adaptive method for the computation of long-range electrostatic interactions in computer simulations of polyelectrolyte DNA. Classically, the computation of electrostatic energy involves a direct summation of all pairwise interactions due to the charges phosphate groups in the mol. This results in an N-body interaction problem with an asymptotic time complexity of O(N2) which is computationally very expensive and limits the no. of phosphate groups that can be used in computer simulations of polyelectrolyte DNA to at most several hundred. We describe an effort to speed up computer simulations of polyelectrolyte DNA with the use of a fast adaptive hierarchical algorithm for the computation of electrostatic energy (i.e., modified Debye-Huckel energy). The asymptotic time complexity is reduced to O(N) with the implementation of the fast hierarchical algorithm on serial computers. This is achieved by grouping phosphate groups into an adaptive hierarchical data structure and computing the interactions between groups using low order multipole and Taylor series expansions expressed in Cartesian coordinates. We first examine the accuracy and speed enhancements of the fast hierarchical method in the computation of the electrostatic energy of circular DNA at zero and high salt concns. The fast hierarchical method is further tested in a one-step Monte Carlo (MC) simulated annealing algorithm for closed circular supercoiled DNA. In all cases, we observe order of magnitude redns. in the computation time with negligible loss of numerical accuracy in the electrostatic energy computation. [on SciFinder (R)]
BibTeX: @article{RefWorks:413, author = {Marcia O. Fenley and Wilma K. Olson and Kiat Chua and Alexander H. Boschitsch}, title = {Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA.}, journal = {Journal of Computational Chemistry}, year = {1996}, volume = {17}, number = {8}, pages = {976-991}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JCCHDD} }
Fenley, M. O., Olson, W. K. & Manning, G. S.	Dependence of Counterion Binding on DNA Shape as Determined By Counterion Condensation Theory. [Abstract] [BibTeX]	2000	Macromolecules	article
Abstract: We have computed the fraction of DNA phosphate charge neutralized by condensed counterions for parallel pairs of linear DNA segments, DNA circles, and representative closed-circular supercoiled DNA configurations ranging in length from 42 to 3000 base pairs. We find significant but small uptake of condensed counterions for the more compact structures relative to an isolated linear DNA segment. [on SciFinder (R)]
BibTeX: @article{RefWorks:388, author = {Marcia O. Fenley and Wilma K. Olson and Gerald S. Manning}, title = {Dependence of Counterion Binding on DNA Shape as Determined By Counterion Condensation Theory.}, journal = {Macromolecules}, year = {2000}, volume = {33}, number = {5}, pages = {1899-1903}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: MAMOBX; CAS Registry Numbers: 7440-23-5 (Sodium) Role: BPR (Biological process), BSU (Biological study, unclassified), BIOL (Biological study), PROC (Process) (dependence of counterion binding on DNA shape as detd. by counterion condensation theory)} }
Fenley, M. O., Olson, W. K., Tobias, I. & Manning, G. S.	Electrostatic effects in short superhelical DNA. [Abstract] [BibTeX]	1994	Biophysical chemistry	article
Abstract: The authors present Monte Carlo simulations of the equil. configurations of short closed circular DNA that obeys a combined elastic, hard-sphere, and electrostatic energy potential. The authors employ a B-spline representation to model chain configuration and simulate the effects of salt on chain folding by varying the Debye screening parameter. The authors obtain global equil. configurations of closed circular DNA, with several imposed linking no. differences, at two salt concns. (specifically at the extremes of no added salt and the high salt regime), and for different chain lengths. Minimization of the composite elastic/long-range potential energy under the constraints of ring closure and fixed chain length is found to produce structures that are consistent with the configurations of short supercoiled DNA obsd. exptl. The structures generated under the constraints of an electrostatic potential are less compact than those subjected only to an elastic term and a hard-sphere constraint. For a fixed linking no. difference greater than a crit. value, the interwound structures obtained under the condition of high salt are more compact than those obtained under the condition of no added salt. In the case of no added salt, the electrostatic energy plays a dominant role over the elastic energy in dictating the shape of the closed circular DNA. The DNA supercoil opens up with increasing chain length at low salt concn. A branched three-leaf rose structure with a fixed linking no. difference is higher in energy than the interwound form at both salt concns. employed here. [on SciFinder (R)]
BibTeX: @article{RefWorks:427, author = {Marcia O. Fenley and Wilma K. Olson and Irwin Tobias and Gerald S. Manning}, title = {Electrostatic effects in short superhelical DNA.}, journal = {Biophysical chemistry}, year = {1994}, volume = {50}, number = {3}, pages = {255-271}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BICIAZ} }
Ge, W., Schneider, B. & Olson, W. K.	Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. [Abstract] [BibTeX]	2005	Biophysical journal	article
Abstract: Elastic ellipsoidal functions defined by the obsd. hydration patterns around the DNA bases provide a new basis for measuring the recognition of ligands in the grooves of double-helical structures. Here a set of knowledge-based potentials suitable for quant. description of such behavior is extd. from the obsd. positions of water mols. and amino acid atoms that form hydrogen bonds with the nitrogenous bases in high resoln. crystal structures. Energies based on the displacement of hydrogen-bonding sites on drugs in DNA-crystal complexes relative to the preferred locations of water binding around the heterocyclic bases are low, pointing to the reliability of the potentials and the apparent displacement of water mols. by drug atoms in these structures. The validity of the energy functions has been further examd. in a series of sequence substitution studies based on the structures of DNA bound to polyamides that have been designed to recognize the minor-groove edges of Watson-Crick base pairs. The higher energies of binding to incorrect sequences superimposed (without conformational adjustment or displacement of polyamide ligands) on obsd. high resoln. structures confirm the hypothesis that the drug subunits assoc. with specific DNA bases. The knowledge-based functions also account satisfactorily for the measured free energies of DNA-polyamide assocn. in soln. and the obsd. sites of polyamide binding on nucleosomal DNA. The computations are generally consistent with mechanisms by which minor-groove binding ligands are thought to recognize DNA base pairs. The calcns. suggest that the asym. distributions of hydrogen-bond-forming atoms on the minor-groove edge of the base pairs may underlie ligand discrimination of G.C from C.G pairs, in addn. to the commonly believed role of steric hindrance. The anal. of polyamide-bound nucleosomal structures reveals other discrepancies in the expected chem. design, including unexpected contacts to DNA and modified base pair targets of some ligands. The ellipsoidal potentials thus appear promising as a math. tool for the study of drug- and protein-DNA interactions and for gaining new insights into DNA-binding mechanisms. [on SciFinder (R)]
BibTeX: @article{RefWorks:371, author = {Wei Ge and Bohdan Schneider and Wilma K. Olson}, title = {Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids.}, journal = {Biophysical journal}, year = {2005}, volume = {88}, number = {2}, pages = {1166-1190}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-7; CODEN: BIOJAU; CAS Registry Numbers: 65-71-4 (Thymine) Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PYP (Physical process), BIOL (Biological study), PROC (Process) (base pair with adenine; knowledge-based elastic potentials for docking polyamide drugs or proteins with nucleic acid base pairs in relation to hydration patterns and hydrogen bonding properties); 73-40-5 (Guanine) Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PYP (Physical process), BIOL (Biological study), PROC (Process) (base pair with cytosine; knowledge-based elastic potentials for docking polyamide drugs or proteins with nucleic acid base pairs in relation to hydration patterns and hydrogen bonding properties); 71-30-7 (Cytosine) Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PYP (Physical process), BIOL (Biological study), PROC (Process) (base pair with guanine; knowledge-based elastic potentials for docking polyamide drugs or proteins with nucleic acid base pairs in relation to hydration patterns and hydrogen bonding properties); 73-24-5 (Adenine) Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PYP (Physical process), BIOL (Biological study), PROC (Process) (base pair with thymine; knowledge-based elastic potentials for docking polyamide drugs or proteins with nucleic acid base pairs in relation to hydration patterns and hydrogen bonding properties); 7732-18-5 (Water); 147859-82-3; 181028-22-8; 181028-25-1 Role: BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PYP (Physical process), BIOL (Biological study), PROC (Process) (knowledge-based elastic potentials for docking polyamide drugs or proteins with nucleic acid base pairs in relation to hydration patterns and hydrogen bonding properties)} }
Gelbin, A., Schneider, B., Clowney, L., Hsieh, S., Olson, W. K. & Berman, H. M.	Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents. [Abstract] [BibTeX]	1996	Journal of the American Chemical Society	article
Abstract: A statistical survey of the torsion angles, bond angles, and bond lengths in the sugar and phosphate groups of well-refined mononucleoside, mononucleotide, dinucleoside monophosphate, and trinucleoside diphosphate crystal structures contained in the Cambridge Structural Database and the Nucleic Acid Database is reported. The mean values of the geometrical parameters in these structures and their estd. std. deviations are sepd. according to their chem. and conformation. These new parameters serve as a basis for a dictionary of std. nucleic acid geometry. [on SciFinder (R)]
BibTeX: @article{RefWorks:416, author = {Anke Gelbin and Bohdan Schneider and Lester Clowney and Shu-Hsin Hsieh and Wilma K. Olson and Helen M. Berman}, title = {Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents.}, journal = {Journal of the American Chemical Society}, year = {1996}, volume = {118}, number = {3}, pages = {519-529}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-9; CA Section Cross-references: 75; CODEN: JACSAT} }
Goldman, C. & Olson, W. K.	DNA denaturation as a problem of translational-symmetry restoration. [Abstract] [BibTeX]	1993	Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics	article
Abstract: The authors study the quantum-mech. version of a model proposed by Peyrard and Bishop [Phys. Rev. Lett.62, 2755 (1989)] to describe the denaturation phenomenon on the DNA double helix. The authors characterize denaturation as a phase transition leading to the restoration of the translational invariance of the system. The problem is approached via a modified perturbative theory which incorporates also nonperturbative effects. These are accounted by an auxiliary random variable (u) describing the equil. positions of the constituting particles. The criticality of the model is revealed by analyzing equations involving the first and second cumulants of the u-distribution function. As a consequence, an anal. expression for the crit. temp. Tc is obtained as a function of all model parameters. [on SciFinder (R)]
BibTeX: @article{RefWorks:310, author = {Carla Goldman and Wilma K. Olson}, title = {DNA denaturation as a problem of translational-symmetry restoration.}, journal = {Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics}, year = {1993}, volume = {48}, number = {2}, pages = {1461-1468}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: PLEEE8} }
Gorin, A. A., Zhurkin, V. B. & Olson, W. K.	B-DNA twisting correlates with base-pair morphology. [Abstract] [BibTeX]	1995	Journal of Molecular Biology	article
Abstract: The obsd. sequence dependence of the mean twist angles in 38 B-DNA crystal structures can be understood in terms of simple geometrical features of the constituent base-pairs. Structures with low twist appear to unwind in response to severe steric clashes of large exocyclic groups (such as NH2-NH2) in the major and minor grooves, while those with high twist are subjected to lesser contacts (H-O and H-H). The authors offer a simple clash function that depends on base-pair morphol. (i.e. the chem. constitution of base-pairs) and satisfactorily accounts for the twist angles of the ten common Watson-Crick dimer steps both in the solid state and in soln. The twist-clash correlation that the authors find here still holds when extended to modified bases. In addn. to Calladine's purine-purine clashes, the authors add other close contacts between bases in the grooves, and consider the conformational restrictions on the geometry of the sugar-phosphate backbone (namely, the authors emphasize the tendency of DNA to conserve virtual backbone length). The significance of this finding is threefold: (1) sequence-dependent DNA twisting is directly involved with protein-DNA interactions; (2) strong correlation between Twist and Roll helps to elucidate the bending of the double helix as a function of base sequence; (3) it is possible to anticipate the effects of chem. modifications on twisting and bending. The mutual correlations of other structural parameters with the twist make this angle a primary determinant of DNA conformational heterogeneity. [on SciFinder (R)]
BibTeX: @article{RefWorks:423, author = {Andrey A. Gorin and Victor B. Zhurkin and Wilma K. Olson}, title = {B-DNA twisting correlates with base-pair morphology.}, journal = {Journal of Molecular Biology}, year = {1995}, volume = {247}, number = {1}, pages = {34-48}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK} }
Hao, M. H. & Olson, W. K.	Molecular modeling and energy refinement of supercoiled DNA. [Abstract] [BibTeX]	1989	Journal of Biomolecular Structure & Dynamics	article
Abstract: A method is presented for constructing the complete at. structure of supercoiled DNA starting from a linear description of the double-helical pathway. The folding pathway is defined by piecewise B-spline curves and the atoms are initially positioned with respect to the local Frenet trihedra detd. by the equations of the curves. The resulting chem. structure is cor. and refined with an energy minimization procedure based on std. potential expressions. The refined mol. structure is then used to study the effects of supercoiling on the local secondary structure of DNA. The minimized structure is found to differ from an isotropic elastic rod model of the double helix, with the base pairs bending in an asym. fashion along the supercoiled trajectory. The starting trajectory is chosen so that the refined supercoiled structure is either underwound (10.37 base pairs per turn) or overwound (9.65 base pairs per turn) compared to the std. ten-fold B-DNA fiber diffraction model. The underwound supercoil is also lower in energy than the overwound duplex. The variation of base pair sequence in poly(dA).poly(dT), poly(dAT).poly(dTA), and poly(dA5T5).poly(dT5A5) is addnl. found to influence the secondary structural features along a given supercoiled pathway. Finally, the detailed features of the refined structures are found to be in agreement with known x-ray crystallog. structures of DNA oligomers. [on SciFinder (R)]
BibTeX: @article{RefWorks:327, author = {Ming Hong Hao and Wilma K. Olson}, title = {Molecular modeling and energy refinement of supercoiled DNA.}, journal = {Journal of Biomolecular Structure & Dynamics}, year = {1989}, volume = {7}, number = {3}, pages = {661-92, 1 plate}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 9; CODEN: JBSDD6; CAS Registry Numbers: 26966-61-0; 114939-93-4 Role: BIOL (Biological study) (double-stranded, supercoiling of, sequence dependence of); 27156-07-6 Role: BIOL (Biological study) (supercoiling of, sequence dependence of)} }
Hao, M. H. & Olson, W. K.	The global equilibrium configurations of supercoiled DNA. [Abstract] [BibTeX]	1989	Macromolecules	article
Abstract: The equil. configurations of circular DNA with imposed linking no. differences are studied by computer simulation. The configurational energy of the double helix is described by an isotropic elastic deformation model together with a pairwise potential for calcg. the self-interaction between distant points along the chain. The axis of the closed double-helical trajectory of the polymer is represented by piecewise cyclic B-spline curves that are approximated by a finite no. of controlling points. The global min. of the total potential energy is obtained with an algorithm that combines Metropolis-Monte Carlo sampling with a simulated annealing procedure. Simulation conditions are examd. as are the effects of adjustable energy parameters. The dependence of the algorithm on temp. is related to the actual chain length of the DNA through the well-known relationship between persistence length and temp. The predicted 3-dimensional arrangements are consistent with the configurations of supercoiled DNA obsd. in electron micrographs. The most stable structures of the closed chain are interwound configurations that are also critically dependent on the specified linking no. difference. The toroidal configuration is unstable and, upon energy minimization, is transformed to an interwound form. The optimized trajectories of knotted structures, however, are independent of the linking difference over the range of values examd. [on SciFinder (R)]
BibTeX: @article{RefWorks:329, author = {Ming Hong Hao and Wilma K. Olson}, title = {The global equilibrium configurations of supercoiled DNA.}, journal = {Macromolecules}, year = {1989}, volume = {22}, number = {8}, pages = {3292-3303}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 9; CODEN: MAMOBX} }
Hao, M. H. & Olson, W. K.	Modeling DNA supercoils and knots with B-spline functions. [Abstract] [BibTeX]	1989	Biopolymers	article
Abstract: A method is offered to model the complex trajectories of closed circular DNA supercoils and knots. The trajectories are approximated by polygons and anal. expressions of the curves are generated from the polygons with B-spline functions. The resulting curves are used to evaluate the writhe and elastic energy of a series of interrelated supercoils, and to generate detailed at. models of the deformed double helix. [on SciFinder (R)]
BibTeX: @article{RefWorks:330, author = {Ming Hong Hao and Wilma K. Olson}, title = {Modeling DNA supercoils and knots with B-spline functions.}, journal = {Biopolymers}, year = {1989}, volume = {28}, number = {4}, pages = {873-900}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-15; CA Section Cross-references: 6; CODEN: BIPMAA} }
Hingerty, B. E., Broyde, S. B. & Olson, W. K.	The poly(rU) coil: a minimum-energy model that matches experimental observations. [Abstract] [BibTeX]	1982	Biopolymers	article
Abstract: A model of the randomly coiling form of poly(U) based on min.-energy conformers of UpU is described. The blend of conformers is chosen to fit the C-C rotational populations derived in NMR studies of UpU and poly(U) and to match the exptl. unperturbed dimensions of the poly(U) chain. In addn., ests. of loop closure based on the model are comparable to the sizes of loops most frequently seen in model oligonucleotides. Approx. 60% of the conformers constituting the model are characterized by stacked, extended C2'-endo w'wy = tg-g+ rotations. The remainder of the chain is described by equal nos. of C3'-endo A (w'wy = g-g-g+) and Watson-Crick (w'wy = g-tt) helical arrangements. [on SciFinder (R)]
BibTeX: @article{RefWorks:347, author = {Brian E. Hingerty and Suse B. Broyde and Wilma K. Olson}, title = {The poly(rU) coil: a minimum-energy model that matches experimental observations.}, journal = {Biopolymers}, year = {1982}, volume = {21}, number = {6}, pages = {1167-1188}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 27416-86-0 Role: PRP (Properties) (conformation of, UpU min. energy conformers in study of); 2415-43-2 Role: PRP (Properties) (min. energy conformation of, poly(U) coil in relation to)} }
Jin, E., Katritch, V., Olson, W. K., Kharatisvili, M., Abagyan, R. & Pilch, D. S.	Aminoglycoside Binding in the Major Groove of Duplex RNA: The Thermodynamic and Electrostatic Forces that Govern Recognition. [Abstract] [BibTeX]	2000	Journal of Molecular Biology	article
Abstract: We use a combination of spectroscopic, calorimetric, viscometric and computer modeling techniques to characterize the binding of the aminoglycoside antibiotic, tobramycin, to the polymeric RNA duplex, poly(rI).poly(rC), which exhibits the characteristic A-type conformation that is conserved among natural and synthetic double-helical RNA sequences. Our results reveal the following significant features: (i) CD-detected binding of tobramycin to poly(rI).poly(rC) reveals an apparent site size of four base-pairs per bound drug mol.; (ii) tobramycin binding enhances the thermal stability of the host poly(rI).poly(rC) duplex, the extent of which decreases upon increasing in Na+ concn. and/or pH conditions; (iii) the enthalpy of tobramycin- poly(rI).poly(rC) complexation increases with increasing pH conditions, an observation consistent with binding-induced protonation of one or more drug amino groups; (iv) the affinity of tobramycin for poly(rI).poly(rC) is sensitive to both pH and Na+ concn., with increases in pH and/or Na+ concn. resulting in a concomitant redn. in binding affinity. The salt dependence of the tobramycin binding affinity reveals that the drug binds to the host RNA duplex as trication. (v) The thermodn. driving force for tobramycin- poly(rI).poly(rC) complexation depends on pH conditions. Specifically, at pH?6.0, tobramycin binding is entropy driven, but is enthalpy driven at pH>6.0. (vi) Viscometric data reveal non-intercalative binding properties when tobramycin complexes with poly(rI).poly(rC), consistent with a major groove-directed mode of binding. These data also are consistent with a binding-induced redn. in the apparent mol. length of the host RNA duplex. (vii) Computer modeling studies reveal a tobramycin-poly(rI).poly(rC) complex in which the drug fits snugly at the base of the RNA major groove and is stabilized, at least in part, by an array of hydrogen bonding interactions with both base and backbone atoms of the host RNA. These studies also demonstrate an inability of tobramycin to form a stable low-energy complex with the minor groove of the poly(rI).poly(rC) duplex. In the aggregate, our results suggest that tobramycin-RNA recognition is dictated and controlled by a broad range of factors that include electrostatic interactions, hydrogen bonding interactions, drug protonation reactions, and binding-induced alterations in the structure of the host RNA. These modulatory effects on tobramycin-RNA complexation are discussed in terms of their potential importance for the selective recognition of specific RNA structural motifs, such as asym. internal loops or hairpin loop-stem junctions, by aminoglycoside antibiotics and their derivs. (c) 2000 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:387, author = {Emily Jin and Vsevolod Katritch and Wilma K. Olson and Malkhaz Kharatisvili and Ruben Abagyan and Daniel S. Pilch}, title = {Aminoglycoside Binding in the Major Groove of Duplex RNA: The Thermodynamic and Electrostatic Forces that Govern Recognition.}, journal = {Journal of Molecular Biology}, year = {2000}, volume = {298}, number = {1}, pages = {95-110}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK} }
Jin, R., Jr., W. H. C., Srinivasan, A. R., Olson, W. K., Breslow, R. & Breslauer, K. J.	Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5versus 3',5phosphodiester linkages. [Abstract] [BibTeX]	1993	Proceedings of the National Academy of Sciences of the United States of America	article
Abstract: The authors have used a combination of spectroscopic, calorimetric, and computational techniques to characterize the properties of nucleic acid complexes with 2',5 and 3',5phosphodiester linkages. Specifically, the authors have compared the properties of complexes formed by the assocn. of 3',5single-stranded 16-mers of adenylic acid (A16) and thymidylic acid (T16) with the complexes formed by the corresponding single-stranded 16-mers with 2',5phosphodiester linkages (A16 and T16). The authors' results reveal the following differential features: (i) the 3',5strands form either a duplex or a triplex, depending on the sodium ion concn., whereas the 2',5strands form either a triplex or no complex at all; (ii) the 2',5and 3',5triplexes exhibit significantly different CD spectra, suggesting that the two triplex states are conformationally nonequivalent; (iii) the 2',5triplex has a lower charge d. than the 3',5triplex; (i.v.) the thermal stability of the 3',5triplex, as expected, is concn. dependent, whereas the thermal stability of the 2',5triplex is concn. independent; (v) relative to their component single strands, the 2',5triplex is thermodynamically much less stable than the 3',5triplex, despite being thermally more stable; (vi) the reduced thermodn. stability of the 2',5triplex relative to the 3',5triplex is overwhelmingly enthalpic in origin. In the aggregate, the authors' results reveal and characterize significant differences in the properties of complexes formed by the assocn. of strands with identical base sequences but different phosphodiester linkages. The authors describe a structural model that is consistent with many of the differential properties obsd. The authors also speculate on how these differential properties may have provided an evolutionary advantage for 3',5linkages and how the properties of 2',5complexes might be exploited in antisense strategies. [on SciFinder (R)]
BibTeX: @article{RefWorks:309, author = {Renzhe Jin and William H. Chapman Jr. and Annankoil R. Srinivasan and Wilma K. Olson and Ronald Breslow and Kenneth J. Breslauer}, title = {Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5\"-versus 3',5\"-phosphodiester linkages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {1993}, volume = {90}, number = {22}, pages = {10568-10572}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: PNASA6; CAS Registry Numbers: 7440-23-5 (Sodium) Role: BIOL (Biological study) ((2'->5')- and (3'->5')-linked DNA response to); 152790-23-3; 152890-96-5 Role: PRP (Properties) (structure and thermodn. stability of, sodium effect on, (2'->5')-linked oligodeoxyribonucleotide structure in relation to)} }
Katritch, V., Bustamante, C. & Olson, W. K.	Pulling Chromatin Fibers: Computer Simulations of Direct Physical Micromanipulations. [Abstract] [BibTeX]	2000	Journal of Molecular Biology	article
Abstract: A low-resoln. mol. model, which combines the known mech. properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently obsd. findings in the non-destructive regime (<20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the expt. limits the equil. entry-exit angle of linker DNA on the chromatosome to W=50(+-10) Deg and the effective DNA linker length to Leff=40(+-5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estn. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in soln. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mech. stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small (<2kT) inter-nucleosomal attractions. (c) 2000 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:389, author = {Vsevolod Katritch and Carlos Bustamante and Wilma K. Olson}, title = {Pulling Chromatin Fibers: Computer Simulations of Direct Physical Micromanipulations.}, journal = {Journal of Molecular Biology}, year = {2000}, volume = {295}, number = {1}, pages = {29-40}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-3; CODEN: JMOBAK} }
Katritch, V., Olson, W. K., Pieranski, P., Dubochet, J. & Stasiak, A.	Properties of ideal composite knots. [Abstract] [BibTeX]	1997	Nature (London)	article
Abstract: The shortest tube of const. diam. that can form a given knot represents the 'ideal' form of the knot. Ideal knots provide an irreducible representation of the knot, and they have some intriguing math. and phys. features, including a direct correspondence with the time-averaged shapes of knotted DNA mols. in soln. Here we describe the properties of ideal forms of composite knots-knots obtained by the sequential tying of two or more independent knots (called factor knots) on the same string. We find that the writhe (related to the handedness of crossing points) of composite knots is the sum of that of the ideal forms of the factor knots. By comparing ideal composite knots with simulated configurations of knotted, thermally fluctuating DNA, we conclude that the additivity of writhe applies also to randomly distorted configurations of composite knots and their corresponding factor knots. We show that composite knots with several factor knots may possess distinct structural isomers that can be interconverted only by loosening the knot. [on SciFinder (R)]
BibTeX: @article{RefWorks:407, author = {Vsevolod Katritch and Wilma K. Olson and Piotr Pieranski and Jacques Dubochet and Andrzej Stasiak}, title = {Properties of ideal composite knots.}, journal = {Nature (London)}, year = {1997}, volume = {388}, number = {6638}, pages = {148-151}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: NATUAS} }
Katritch, V., Olson, W. K., Vologodskii, A., Dubochet, J. & Stasiak, A.	Tightness of random knotting. [Abstract] [BibTeX]	2000	Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics	article
Abstract: Long polymers in soln. frequently adopt knotted configurations. To understand the phys. properties of knotted polymers, it is important to find out whether the knots formed at thermodn. equil. are spread over the whole polymer chain or rather are localized as tight knots. We present here a method to analyze the knottedness of short linear portions of simulated random chains. Using this method, we observe that knot-detg. domains are usually very tight, so that, for example, the preferred size of the trefoil-detg. portions of knotted polymer chains corresponds to just seven freely jointed segments. [on SciFinder (R)]
BibTeX: @article{RefWorks:386, author = {Vsevolod Katritch and Wilma K. Olson and Alexander Vologodskii and Jacques Dubochet and Andrzej Stasiak}, title = {Tightness of random knotting.}, journal = {Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics}, year = {2000}, volume = {61}, number = {5-B}, pages = {5545-5549}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 36-7; CODEN: PLEEE8} }
Kosikov, K. M., Gorin, A. A., Lu, X., Olson, W. K. & Manning, G. S.	Bending of DNA by Asymmetric Charge Neutralization: All-Atom Energy Simulations. [Abstract] [BibTeX]	2002	Journal of the American Chemical Society	article
Abstract: DNA dodecamers of the alternating d(CG).d(CG) sequence with six phosphate groups either charge-neutralized or substituted by neutral methylphosphonates across the major or minor groove have been subjected to energy minimization to det. the conformational effect of the asym. elimination of phosphate charge. We report bending angles, directions of bending, and detailed structural characteristics such as groove widths and local base-pair parameters. Our principal results are that charge neutralization on one face of the DNA induces significant bending toward the neutralized face, in agreement with theor. predictions on a simplified model and exptl. data on a similar base-pair sequence, and that the DNA conformation averaged over all stereospecific methylphosphonate substitutions is nearly the same as the conformation produced by charge neutralization of the phosphates. Individual isomers, however, cover a wide range of structures, with the magnitude and direction of overall bending sensitive to the precise stereochem. pattern of neutralization. Our simulation does not explicitly contain counterions, and the results therefore suggest that counterions can influence DNA structure by neutralizing the phosphate charge. These data provide new hints into the mol. mechanisms which underlie the deformations of DNA structure induced by the binding of pos. charged proteins and other tightly assocd. cationic species. [on SciFinder (R)]
BibTeX: @article{RefWorks:380, author = {Konstantin M. Kosikov and Andrey A. Gorin and Xiang-Jun Lu and Wilma K. Olson and Gerald S. Manning}, title = {Bending of DNA by Asymmetric Charge Neutralization: All-Atom Energy Simulations.}, journal = {Journal of the American Chemical Society}, year = {2002}, volume = {124}, number = {17}, pages = {4838-4847}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JACSAT; CAS Registry Numbers: 25512-84-9 (Poly (dCdG) Role: PRP (Properties) (double-stranded; all-atom energy simulations of bending of DNA by asym. charge neutralization); 993-13-5 (Methylphosphonic acid) Role: PRP (Properties) (in DNA; all-atom energy simulations of bending of DNA by asym. charge neutralization)} }
Kosikov, K. M., Gorin, A. A., Zhurkin, V. B. & Olson, W. K.	DNA Stretching and Compression: Large-scale Simulations of Double Helical Structures. [Abstract] [BibTeX]	1999	Journal of Molecular Biology	article
Abstract: Computer-simulated elongation and compression of A- and B-DNA structures beyond the range of thermal fluctuations provide new insights into high energy activated forms of DNA implicated in biochem. processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG).poly(dC) and poly(dA).poly(dT) double helixes, stretched from compressed states of 2.0 .ANG. per base-pair step to highly extended forms of 7.0 .ANG. per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of double-helical DNA identified in single crystals as well as non-canonical forms, such as the original Watson-Crick duplex with trans conformations about the P-O5' and C5'-C4' backbone bonds. The lowest energy min. correspond to canonical A- and B-form duplexes. The calcns. further reveal a no. of unusual helical conformations that are energetically disfavored under equil. conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy vs. stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identified by direct stretching expts. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the obsd. sharp increase in force required to stretch single DNA mols. more than 1.6-1.65 times their canonical extension. Our extended duplexes also help to tie together a no. of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochem. model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The cryst. TBP-bound DNA steps follow the calcd. compression-elongation pattern of an unusual vertical duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition. Significantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy profiles show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy activated forms calcd. here are crit. for DNA processing, e.g. nucleo-protein recognition, DNA/RNA synthesis, and strand exchange. (c) 1999 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:395, author = {Konstantin M. Kosikov and Andrey A. Gorin and Victor B. Zhurkin and Wilma K. Olson}, title = {DNA Stretching and Compression: Large-scale Simulations of Double Helical Structures.}, journal = {Journal of Molecular Biology}, year = {1999}, volume = {289}, number = {5}, pages = {1301-1326}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK; CAS Registry Numbers: 24939-09-1 (Poly(dA).poly(dT); 25512-84-9 (Poly(dG).poly(dC) Role: BPR (Biological process), BSU (Biological study, unclassified), PEP (Physical, engineering or chemical process), PRP (Properties), BIOL (Biological study), PROC (Process) (DNA stretching and compression: large-scale simulations of double helical structures)} }
Langowski, J., Olson, W. K., Pedersen, S. C., Tobias, I., Westcott, T. P. & Yang, Y.	DNA supercoiling, localized bending and thermal fluctuations. [Abstract] [BibTeX]	1996	Trends in biochemical sciences	article
Abstract: A review, with 19 refs. The authors report here DNA supercoiling, localized bending and thermal fluctuations. [on SciFinder (R)]
BibTeX: @article{RefWorks:415, author = {Joerg Langowski and Wilma K. Olson and Scott C. Pedersen and Irwin Tobias and Timothy P. Westcott and Yang Yang}, title = {DNA supercoiling, localized bending and thermal fluctuations.}, journal = {Trends in biochemical sciences}, year = {1996}, volume = {21}, number = {2}, pages = {50}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-0; CODEN: TBSCDB} }
Li, T., Bathory, E., LaVoie, E. J., Srinivasan, A. R., Olson, W. K., Sauers, R. R., Liu, L. F. & Pilch, D. S.	Human Topoisomerase I Poisoning by Protoberberines: Potential Roles for Both Drug-DNA and Drug-Enzyme Interactions. [Abstract] [BibTeX]	2000	Biochemistry	article
Abstract: Protoberberines represent a structural class of org. cations that induce topoisomerase I-mediated DNA cleavage, a behavior termed topoisomerase I poisoning. We have employed a broad range of biophys., biochem., and computer modeling techniques to characterize and cross-correlate the DNA-binding and topoisomerase poisoning properties of four protoberberine analogs that differ with respect to the substituents on their A- and/or D-rings. Our data reveal the following significant features: (i) The binding of the four protoberberines unwinds duplex DNA by approx. 11 Deg, an observation consistent with an intercalative mode of interaction. (ii) Enthalpically favorable interactions, such as stacking interactions between the intercalated ligand and the neighboring base pairs, provide 2,3-dimethoxy .mchgt. 3,4-dimethoxy. These differences in topoisomerase I poisoning activity may reflect the differing abilities of the analogs to interact with specific functionalities on the enzyme, thereby stabilizing the enzyme in its cleavable state. In the aggregate, our results are consistent with a mechanistic model in which both ligand-DNA and ligand-enzyme interactions are important for the poisoning of topoisomerase I by protoberberines, with the DNA-directed interactions involving ring D and the enzyme-directed interactions involving ring A. It is reasonable to suggest that the poisoning of topoisomerase I by a broad range of other naturally occurring and synthetic ligands may entail a similar mechanism. [on SciFinder (R)]
BibTeX: @article{RefWorks:385, author = {Tsai-Kun Li and Eleanor Bathory and Edmond J. LaVoie and A. R. Srinivasan and Wilma K. Olson and Ronald R. Sauers and Leroy F. Liu and Daniel S. Pilch}, title = {Human Topoisomerase I Poisoning by Protoberberines: Potential Roles for Both Drug-DNA and Drug-Enzyme Interactions.}, journal = {Biochemistry}, year = {2000}, volume = {39}, number = {24}, pages = {7107-7116}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 1-12; CODEN: BICHAW; CAS Registry Numbers: 3486-67-7 (Palmatine); 19716-66-6; 178818-97-8; 286000-57-5 Role: BAC (Biological activity or effector, except adverse), BSU (Biological study, unclassified), BIOL (Biological study) (human topoisomerase I poisoning by protoberberines and potential roles for both drug-DNA and drug-enzyme interactions); 143180-75-0 Role: BPR (Biological process), BSU (Biological study, unclassified), BIOL (Biological study), PROC (Process) (human topoisomerase I poisoning by protoberberines: potential roles for both drug-DNA and drug-enzyme interactions)} }
Liu, G., Geurts, A. M., Yae, K., Srinivasan, A. R., Fahrenkrug, S. C., Largaespada, D. A., Takeda, J., Horie, K., Olson, W. K. & Hackett, P. B.	Target-site preferences of Sleeping Beauty transposons. [Abstract] [BibTeX]	2005	Journal of Molecular Biology	article
Abstract: The Sleeping Beauty (SB) transposon is a Tc1/mariner family transposon that has applications in vertebrate animals for gene transfer, gene-tagging, and human gene therapy. This study analyzed the target-site preferences of the SB transposon. At the genomic level, integration of SB transposons with respect to genes (exons and introns) and intergenic regions appears fairly random but not on a micro-scale. Although there appears to be a consensus sequence around the vicinity of the target sites, the primary sequence is not the detg. factor for target selection. When integrations were examd. over a limited topog., the sites used most often for integration did not match the consensus sequence. Rather, a unique deformation inherent in the sequence may be a recognition signal for target selection. The deformation is characterized by an angling of the target site such that the axis around the insertion site is off-center, the rotation of the helix (twisting) is non-uniform and there is an increase in the distance between the central base-pairs. These observations offer several hypothetical insights into the transposition process. These observations suggest that particular deformations of the double helix predicted by the Vstep algorithm can distinguish TA sites that vary by about 16-fold in their preferences for accommodating insertions of SB transposons. [on SciFinder (R)]
BibTeX: @article{RefWorks:372, author = {Geyi Liu and Aron M. Geurts and Kojiro Yae and A. R. Srinivasan and Scott C. Fahrenkrug and David A. Largaespada and Junji Takeda and Kyoji Horie and Wilma K. Olson and Perry B. Hackett}, title = {Target-site preferences of Sleeping Beauty transposons.}, journal = {Journal of Molecular Biology}, year = {2005}, volume = {346}, number = {1}, pages = {161-173}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 3-4; CA Section Cross-references: 13; CODEN: JMOBAK} }
Liu, G. & Olson, W. K.	Application of Fourier methods to computer simulation of supercoiled DNA. [Abstract] [BibTeX]	1995	Computational Polymer Science	article
Abstract: Fourier methods have been applied to model the overall geometry of a supercoiled DNA curve, the starting coordinates of which can be obtained from electron microscopy measurements or other theor. simulations. Evenly spaced points on a known DNA curve are selected and subsequently used to model the original curve in terms of a finite Fourier series. Hence, a simple anal. curve expression, which closely resembles the initial data, is obtained for anal. and optimization. Energy minimization of DNA supercoils represented by such finite Fourier series has been performed using an elastic energy model. Minimized configurations are identified for interwound supercoils of 1000 bp at various values of the linking no. difference, DLk. The configurational profiles of writhing nos. (Wr) and energy vs. DLk are similar to those of optimized structures previously found with a B-spline representation of the DNS supercoil. However, there are some notable differences that probably result from the more global nature of the Fourier modeling compared to the B-spline. At the same DLk, a higher value of the writhing no. and a lower energy of writhing no. and a lower energy are consistently obtained with the finite Fourier series representation. Unlike the B-spline minimized structures and the configurations identified earlier by finite element anal., only two families of supercoiled families, the figure-eight and the loose interwound forms at low DLK, are found to overlap; there is no overlapping of interwound configurational families at higher DLk. The optimized configurations of three-lobed 1000 bp branched DNA supercoils have also been identified. Different families of structures are found over a DLk range between -0.6 and 6.0. Family I, with three lobes of similar shape and size and with Wr ~ 0, occurs at low DLk values. Families II-VI also with three lobes of similar shape and size, exist over a range of DLK from 1.0 to 4.6. The structures in families IIa-Va with one lobe larger than the others have similar Wr values at the same DLk but are slightly higher in energy. Families VII and ViII of min. found between DLk of 3.2 and 6.0 are characterized by one interwound and two open lobes, the latter being similar to but smaller than the lobes in the simpler branched structures of families II-VI. The occurrence of branched interwound energy min. is consistent with the highly branched configurations of supercoiled DNA obsd. under the electron microscope. Configurational snapshots of long partially relaxed DNA plasmids (6400 bp) taken from electron microscopic images are found to optimize to closely related linear and branched interwound forms with writhing nos. comparable to those of the nearly planar projected starting states. The energy minimization tends to straighten and maximize nonbonded contacts between interwound double helical strands and to fix the size of the hairpin loops emerging from the interwound domains. The configurational similarities of these minimized andomstarting states with the families of optimized configurations systematically identified at shorter chain lengths affirm the completeness of the search of energy min. [on SciFinder (R)]
BibTeX: @article{RefWorks:421, author = {Guohua Liu and Wilma K. Olson}, title = {Application of Fourier methods to computer simulation of supercoiled DNA.}, journal = {Computational Polymer Science}, year = {1995}, volume = {5}, number = {1&2}, pages = {7-27}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: CPOSEJ} }
Liu, G., Schlick, T., Olson, A. J. & Olson, W. K.	Configurational transitions in Fourier series-represented DNA supercoils. [Abstract] [BibTeX]	1997	Biophysical journal	article
Abstract: A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the assocn. of closely spaced charged rods. The finite Fourier series-derived polymer formulation is an alternative to the piecewise B-spline curves used in past work to describe the motion of smoothly deformed supercoiled DNA in terms of a limited no. of independent variables. This study focuses on two large-scale configurational events: the interconversion between circular and figure-8 forms at a relatively low level of supercoiling, and the transformation between branched and interwound structures at a higher superhelical d. [on SciFinder (R)]
BibTeX: @article{RefWorks:404, author = {Guohua Liu and Tamar Schlick and Andrew J. Olson and Wilma K. Olson}, title = {Configurational transitions in Fourier series-represented DNA supercoils.}, journal = {Biophysical journal}, year = {1997}, volume = {73}, number = {4}, pages = {1742-1762}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIOJAU} }
Lu, X., Babcock, M. S. & Olson, W. K.	Overview of nucleic acid analysis programs. [Abstract] [BibTeX]	1999	Journal of Biomolecular Structure & Dynamics	article
Abstract: A review with 42 refs. We outline the math. distinctions among seven of the most popular computer programs currently used to analyze the spatial arrangements of bases and base pairs in nucleic acid helical structures. The schemes fall into three basic categories on the basis of their definitions of rotational parameters: matrix-based, projection-based, and combined matrix- and projection-based. The approaches also define and construct base and base-pair coordinate frames in a variety of ways. Despite these math. distinctions, the computed parameters from some programs are strongly correlated and directly comparable. By contrast, other programs which use identical methodologies sometimes yield very different results. The choice of ref. frame rather than the math. formulation has the greater effect on calcd. parameters. Any factor which influences the ref. frame, such as fitting or not fitting std. bases to the exptl. derived coordinates, will have a noticeable effect on both complementary base pair and dimer step parameters. [on SciFinder (R)]
BibTeX: @article{RefWorks:397, author = {Xiang-Jun Lu and Marla S. Babcock and Wilma K. Olson}, title = {Overview of nucleic acid analysis programs.}, journal = {Journal of Biomolecular Structure & Dynamics}, year = {1999}, volume = {16}, number = {4}, pages = {833-843}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-0; CODEN: JBSDD6} }
Lu, X. & Olson, W. K.	3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. [Abstract] [BibTeX]	2003	Nucleic acids research	article
Abstract: We present a comprehensive software package, 3DNA, for the anal., reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helixes, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The anal. routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended ref. frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calc. local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full at. models with the sugar-phosphate backbone and publication quality standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on x-ray diffraction measurements of various repeating sequences can also be generated within the program. [on SciFinder (R)]
BibTeX: @article{RefWorks:376, author = {Xiang-Jun Lu and Wilma K. Olson}, title = {3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.}, journal = {Nucleic acids research}, year = {2003}, volume = {31}, number = {17}, pages = {5108-5121}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: NARHAD} }
Lu, X. & Olson, W. K.	Resolving the Discrepancies Among Nucleic Acid Conformational Analyses. [Abstract] [BibTeX]	1999	Journal of Molecular Biology	article
Abstract: Growing interest in understanding the relationship between the global folding of nucleic acids and the sequence-dependent structure of individual base-pair steps has stimulated the development of new math. methods to define the geometry of the constituent base-pairs. Several approaches, designed to meet guidelines set by the nucleic acid community, permit rigorous comparative analyses of different three-dimensional structures, as well as allow for reconstruction of chain mols. at the base-pair level. The different computer programs, however, yield inconsistent descriptions of chain conformation. Here we report our own implementation of seven algorithms used to det. base-pair and dimer step parameters. Aside from reproducing the results of individual programs, we uncover the reasons why the different algorithms come to conflicting structural interpretations. The choice of mathematics has only a limited effect on the computed parameters, even in highly deformed duplexes. The results are much more sensitive to the choice of ref. frame. The disparate schemes yield very similar conformational descriptions if the calcns. are based on a common ref. frame. The current positioning of ref. frames at the inner and outer edges of complementary bases exaggerates the rise at distorted dimer steps, and points to the need for a carefully defined conformational std. (c) 1999 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:398, author = {Xiang-Jun Lu and Wilma K. Olson}, title = {Resolving the Discrepancies Among Nucleic Acid Conformational Analyses.}, journal = {Journal of Molecular Biology}, year = {1999}, volume = {285}, number = {4}, pages = {1563-1575}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK} }
Lu, X., Shakked, Z. & Olson, W. K.	A-form Conformational Motifs in Ligand-bound DNA Structures. [Abstract] [BibTeX]	2000	Journal of Molecular Biology	article
Abstract: Recognition and biochem. processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the mol. In addn. to the direct recognition elements embedded in the linear sequence of bases (i.e. hydrogen bonding sites), these mol. agents seemingly sense and/or induce an ïndirectconformational response in the DNA base-pairs that facilitates close intermol. fitting. As part of an effort to decipher this sequence-dependent structural code, we have analyzed the extent of B -> A conformational conversion at individual base-pair steps in protein and drug-bound DNA crystal complexes. We take advantage of a novel structural parameter, the position of the phosphorus atom in the dimer ref. frame, as well as other documented measures of local helical structure, e.g. torsion angles, base-pair step parameters. Our anal. pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in other studies of DNA structure. The collective data provide new structural details on the conformational pathway connecting A and B-form DNA and illustrate how both proteins and drugs take advantage of the intrinsic conformational mechanics of the double helix. Significantly, the base-pair steps which exhibit pure A-DNA conformations in the crystal complexes follow the scale of A-forming tendencies exhibited by synthetic oligonucleotides in soln. and the known polymorphism of synthetic DNA fibers. Moreover, most crystallog. examples of complete B-to-A deformations occur in complexes of DNA with enzymes that perform cutting or sealing operations at the (O3'-P) phosphodiester linkage. The B -> A transformation selectively exposes sugar-phosphate atoms, such as the 3'-oxygen atom, ordinarily buried within the chain backbone for enzymic attack. The forced remodeling of DNA to the A-form also provides a mechanism for smoothly bending the double helix, for controlling the widths of the major and minor grooves, and for accessing the minor groove edges of individual base-pairs. (c) 2000 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:383, author = {Xiang-Jun Lu and Zippora Shakked and Wilma K. Olson}, title = {A-form Conformational Motifs in Ligand-bound DNA Structures.}, journal = {Journal of Molecular Biology}, year = {2000}, volume = {300}, number = {4}, pages = {819-840}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 1; CODEN: JMOBAK} }
Marky, N. L. & Olson, W. K.	Configurational statistics of the DNA duplex: extended generator matrixes to treat the rotations and translations of adjacent residues. [Abstract] [BibTeX]	1994	Biopolymers	article
Abstract: The base-to-base virtual bond treatment of nucleic acids used in statistical mech. calcns. of polynucleotide chain properties has been refined by incorporating the six parameters that relate the positions and orientations of sequential rigid bodies. The scheme allows for the sequence-dependent bending, twisting, and displacement of base pairs as well as for asymmetry in the angular and translational fluctuations of individual residues. Expressions are developed for the generator matrixes required for the computation, as a function of chain length, of various parameters measuring the overall mean extension and shape of the DNA. Quantities of interest include the end-to-end vector r, the square of the end-to-end distance r2, the square radius of gyration s2, the center-of-gravity vector g, the second moments of inertia Sx2, and the higher moments of r and g. The matrix expressions introduced in the 1960s by Flory and co-workers for the detn. of configuration-dependent polymer chain avs. are decompd. into their translational and orientational contributions so that the methods can be extended to he rigid body anal. of chem. moieties. The new expressions permit, for the first time, examn. of the effects of sequence-dependent translations, such as the lateral sliding of residues in A- and B-helixes and the vertical opening of base pairs in drug-DNA complexes, on the av. extension and shape of the long flexible double helix. The approach is illustrated in the following paper using conformational energy ests. of the base sequence-dependent flexibility of successive B-DNA base pairs. [on SciFinder (R)]
BibTeX: @article{RefWorks:432, author = {Nancy L. Marky and Wilma K. Olson}, title = {Configurational statistics of the DNA duplex: extended generator matrixes to treat the rotations and translations of adjacent residues.}, journal = {Biopolymers}, year = {1994}, volume = {34}, number = {1}, pages = {109-120}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: BIPMAA} }
Marky, N. L. & Olson, W. K.	Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method. [Abstract] [BibTeX]	1994	Biopolymers	article
Abstract: The authors have used the elementary generator matrixes outlined in the preceding paper to examine the conformational plasticity of the nucleic acid double helix. Here the authors investigate kinked DNA structures made up of alternating B- and A-type helixes and intrinsically curved duplexes perturbed by the intercalation of ligands. The authors model the B-to-A transition by the lateral translation of adjacent base pairs, and the intercalation of ligands by the vertical displacement of neighboring residues. The authors report a complete set of av. configuration-dependent parameters, ranging from scalars (i.e., persistence lengths) to first- and second-order tensor parameters (i.e., av. second moments of inertia), as well as approxns. of the assocd. spatial distributions of the DNA and their angular correlations. The av. structures of short chains (of lengths less than 100 base pairs) with local kinks or intrinsically curved sequences are essentially rigid rods. At the smallest chain lengths (10 base pairs), the kinked and curved chains exhibit similar av. properties, although they are structurally perturbed compared to the std. B-DNA duplex. In contrast, at lengths of 200 base pairs, the curved and kinked chains are more compact on av. and are located in a different space from the std. B- or A-DNA helix. While A-DNA is shorter and thicker than B-DNA in x-ray models, the long flexible A-DNA helix is thinner and more extended on av. than its B-DNA counterpart because of more limited fluctuations in local structure. Curved polymers of 50 base pairs or longer also show significantly greater asymmetry than other DNAs (in terms of the distribution of base pairs with respect to the center of gravity of the chain). The intercalation of drugs in the curved DNA straightens and extends the smoothly deformed template. The dimensions of the av. ellipsoidal boundaries defining the configurations of the intercalated polymers are roughly double those of the intrinsically curved chain. The altered proportions and orientations of these d. functions reflect the changing shape and flexibility of the double helix. The calcns. shed new light on the possible structural role of short A-DNA fragments in long B-type duplexes and also offer a model for understanding how GC-specific intercalative ligands can straighten naturally curved DNA. The mechanism is not immediately obvious from current models of DNA curvature, which attribute the bending of the chain to a perturbed structure in repeating tracts of A.T base pairs. [on SciFinder (R)]
BibTeX: @article{RefWorks:433, author = {Nancy L. Marky and Wilma K. Olson}, title = {Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method.}, journal = {Biopolymers}, year = {1994}, volume = {34}, number = {1}, pages = {121-142}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 65-71-4 (Thymine) Role: PRP (Properties) (base pair with adenine, spatial translational motion of, of DNA, extended matrix generator method for study of); 73-40-5 (Guanine) Role: PRP (Properties) (base pair with cytosine, spatial translational motion of, of DNA, extended matrix generator method for study of); 71-30-7 (Cytosine) Role: PRP (Properties) (base pair with guanine, spatial translational motion of, of DNA, extended matrix generator method for study of); 73-24-5 (Adenine) Role: BIOL (Biological study) (base pair with thymine, spatial translational motion of, of DNA, extended matrix generator method for study of)} }
Marky, N. L. & Olson, W. K.	Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNAPhe. [Abstract] [BibTeX]	1987	Biopolymers	article
Abstract: The flexibility of tRNA hairpin loops contg. n bases (residues) was examd. by the theor. model of N. L. Marky and W. K. Olson (1982) for oligonucleotide loop closure. The study is based on correlated probabilities of chain sepn. and terminal residue orientation as outlined previously. The probabilities are calcd. using std. statistical mech. methods as functions of local conformational changes of the chain backbone. The results for an RNA chain of 9 residues suggest that the anticodon loop is a dynamic structure capable of assuming a variety of different spatial conformations. Free energy values related to the various conformations span a narrow range of values (2-4 kcal/mol) and compare well with exptl. observations in aq. soln. Conformational transitions between the loop conformations are within <0.5 kcal/mol in free energy. The different spatial loop conformations and the likely pathways between them may have potential relevance to the mol. translation of the genetic code. [on SciFinder (R)]
BibTeX: @article{RefWorks:339, author = {Nancy L. Marky and Wilma K. Olson}, title = {Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNAPhe.}, journal = {Biopolymers}, year = {1987}, volume = {26}, number = {3}, pages = {415-438}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Marky, N. L. & Olson, W. K.	Loop formation in polynucleotide chains. I. Theory of hairpin loop closure. [Abstract] [BibTeX]	1982	Biopolymers	article
Abstract: A model to det. the probability of loop formation, based on an elaborated form of the theory of cyclization equil. proposed by H. Jacobson and W. H. Stockmayer (1950) was developed and applied to RNA chains with homogeneous puckering and lengths of up to 27 residues. Equations relating to the probability of occurrence of hairpin loops in a particular chain are given and the phys. parameters involved are described. For randomly coiling models previously developed to reproduce polynucleotide unperturbed dimensions, loop closure probability is maximized with chains of length 22 residues. Larger hairpin loops of 24-25 residues, also favored in C3'-endo random coils of this type, are potential models of tRNA unfolding. Monte Carlo simulation was also performed. [on SciFinder (R)]
BibTeX: @article{RefWorks:346, author = {Nancy L. Marky and Wilma K. Olson}, title = {Loop formation in polynucleotide chains. I. Theory of hairpin loop closure.}, journal = {Biopolymers}, year = {1982}, volume = {21}, number = {12}, pages = {2329-2344}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Maroun, R. C. & Olson, W. K.	Base sequence effects in double-helical DNA. III. Average properties of curved DNA. [Abstract] [BibTeX]	1988	Biopolymers	article
Abstract: The matrix-generator methods set forth in the preceding paper for treating rodlike DNA are adapted here to the calcn. of av. chain extension, macroscopic flexibility, and terminal residue orientation in curved duplexes. The different characteristics of curved vs. rodlike chains are illustrated with the hypothetical poly[d(A5G5)] . poly[d(T5C5)] duplex. The curved helix is both more compact and macroscopically stiffer than either the poly(dA) . poly(dT) or the poly(dG) . poly(dC) chain. The calcns. were also extended to simple repetitive DNA sequences generated by synthetic ligation studies and the computed av. chain properties compared with obsd. gel mobilities. The predicted chain extension is also checked against the measured persistence lengths of the rodlike poly[d(GC)] and poly[d(AT)] alternating copolymers, and the known cyclization tendencies of selected repeating sequences. Chains are generated from local potential energy maps describing the morphol. and flexibility of adjacent base pairs. The energy maps, while approx., are more accurate descriptors of local structure than many of the intuitive models of DNA curvature offered to date. According to the energy surfaces, the intrinsic bending of curved DNA can be traced to asymmetry in the bending of the guanosine and cytidine residues that join half-helical turn stretches of adenines in these chains. The oligo (A) stretches are analogous to residues of a perfectly elastic DNA that bend with equal likelihood in opposing directions. In other models of DNA curvature, the (G . C) base pairs are presumed to adopt the classical B-DNA structure, whereas the (A . T) base pairs are thought to be in some perturbed conformation. [on SciFinder (R)]
BibTeX: @article{RefWorks:334, author = {Rachid C. Maroun and Wilma K. Olson}, title = {Base sequence effects in double-helical DNA. III. Average properties of curved DNA.}, journal = {Biopolymers}, year = {1988}, volume = {27}, number = {4}, pages = {585-603}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 26966-61-0; 36786-90-0; 98687-69-5; 98687-73-1; 114939-93-4; 114939-97-8; 114939-99-0; 114940-01-1; 114955-04-3; 114955-06-5; 114955-08-7; 114955-10-1 Role: BIOL (Biological study) (double-stranded, flexibility and bending tendencies and dimensions of, calcn. of); 24939-09-1; 25512-84-9; 114939-57-0; 114939-62-7; 114939-67-2; 114939-72-9; 114939-76-3; 114939-81-0; 114939-86-5; 114939-91-2; 114954-97-1; 114955-02-1; 114989-43-4; 115013-77-9; 115013-80-4; 115013-83-7; 115013-86-0; 115013-89-3 Role: BIOL (Biological study) (flexibility and bending tendencies and dimensions of, calcn. of)} }
Maroun, R. C. & Olson, W. K.	Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains. [Abstract] [BibTeX]	1988	Biopolymers	article
Abstract: Matrix generator techniques were adapted to account for precise structural features of the nucleotide repeating unit and to translate the primary sequence of DNA base pairs into 3-dimensional structures. Chains were constructed to reflect the local sequence-dependent differences of bending and twisting of adjacent residues and various overall chain properties, including the av. unperturbed moments of the end-to-end vector r, and the mean angular orientation (g between base pair normals, f1 between long axes, and f2 between short axes) of terminal chain residues, was computed. The chain backbone is treated implicitly in terms of the spatial fluctuations of successive base pairs. Motions are limited to low-energy perturbations of the std. B-DNA helix. Approx. potential energy schemes represent the rules governing the patterns of local base-base morphol. and flexibility. Theor. predictions are compared with exptl. observations at both the local and the macromol. level. Initial applications are limited to the rodlike poly(dA).poly(dT) and poly(dG).poly(dC) helices. The former duplex is more compressed and the latter more extended than random-sequence DNA of the same chain length. The flexibility of the duplexes as a whole is described in terms of the av. higher moments of the displacement vector r = r - r, where r is the avg. value of r, and the likelihood of chain cyclization is estd. from 3-dimensional Hermite series expansions of the displacement tensors. Emphasis is on theor. methodol. and the practical relevance of the calcd. chain moments to obsd. phys. properties. [on SciFinder (R)]
BibTeX: @article{RefWorks:335, author = {Rachid C. Maroun and Wilma K. Olson}, title = {Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains.}, journal = {Biopolymers}, year = {1988}, volume = {27}, number = {4}, pages = {561-584}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 24939-09-1 (Poly(dA)poly(dT); 25512-84-9 (Poly(dG)poly(dC) Role: BIOL (Biological study) (conformation and flexibility of, nucleotide chain length effect on, statistical model of)} }
Martino, J. A., Katritch, V. & Olson, W. K.	Influence of nucleosome structure on the three-dimensional folding of idealized minichromosomes. [Abstract] [BibTeX]	1999	Structure (London)	article
Abstract: The closed circular, multinucleosome-bound DNA comprising a minichromosome provides one of the best known examples of chromatin organization beyond the wrapping of the double helix around the core of histone proteins. This higher level of chain folding is governed by the topol. of the constituent nucleosomes and the spatial disposition of the intervening protein-free DNA linkers. By simplifying the protein-DNA assembly to an alternating sequence of virtual bonds, the organization of a string of nucleosomes on the minichromosome can be treated by analogy to conventional chem. depictions of macromol. folding in terms of the bond lengths, valence angles, and torsions of the chain. If the nucleosomes are evenly spaced and the linkers are sufficiently short, regular minichromosome structures can be identified from anal. expressions that relate the lengths and angles formed by the virtual bonds spanning the nucleosome-linker repeating units to the pitch and radius of the organized quaternary structures that they produce. The resulting models with 4-24 bound nucleosomes illustrate how a minichromosome can adopt the low-writhe folding motifs deduced from biochem. studies, and account for published images of the 30 nm chromatin fiber and the simian virus 40 (SV40) nucleohistone core. The marked sensitivity of global folding to the degree of protein-DNA interactions and the assumed nucleosomal shape suggest potential mechanisms for chromosome rearrangements upon histone modification. [on SciFinder (R)]
BibTeX: @article{RefWorks:394, author = {Jennifer A. Martino and Vsevolod Katritch and Wilma K. Olson}, title = {Influence of nucleosome structure on the three-dimensional folding of idealized minichromosomes.}, journal = {Structure (London)}, year = {1999}, volume = {7}, number = {8}, pages = {1009-1022}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-1; CODEN: STRUE6} }
Martino, J. A. & Olson, W. K.	Modeling chain folding in protein-constrained circular DNA. [Abstract] [BibTeX]	1998	Biophysical journal	article
Abstract: An efficient method for sampling equil. configurations of DNA chains binding one or more DNA-bending proteins is presented. The technique is applied to obtain the tertiary structures of minimal bending energy for a selection of dinucleosomal minichromosomes that differ in degree of protein-DNA interaction, protein spacing along the DNA chain contour, and ring size. The protein-bound portions of the DNA chains are represented by tight, left-handed supercoils of fixed geometry. The protein-free regions are modeled individually as elastic rods. For each random spatial arrangement of the two nucleosomes assumed during a stochastic search for the global min., the paths of the flexible connecting DNA segments are detd. through a numerical soln. of the equations of equil. for torsionally relaxed elastic rods. The minimal energy forms reveal how protein binding and spacing and plasmid size differentially affect folding and offer new insights into exptl. minichromosome systems. [on SciFinder (R)]
BibTeX: @article{RefWorks:401, author = {Jennifer A. Martino and Wilma K. Olson}, title = {Modeling chain folding in protein-constrained circular DNA.}, journal = {Biophysical journal}, year = {1998}, volume = {74}, number = {5}, pages = {2491-2500}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIOJAU} }
Martino, J. A. & Olson, W. K.	Modeling protein-induced configurational changes in DNA minicircles. [Abstract] [BibTeX]	1997	Biopolymers	article
Abstract: A method is offered for obtaining min. energy configurations of DNA minicircles constrained by one or more DNA-binding proteins. The minicircles are modeled as elastic rods, while the presence of bound protein is implied by rigidly fixing portions of these chains. The configurations of the geometrically constrained circular rods are sampled stochastically and optimized according to a simple elastic energy model of nicked DNA. The shapes of the min. energy structures identified after a simulated annealing process are analyzed in terms of relative protein orientation and writhing no. The procedure is applied to minicircles 500 base pairs in length, bound to two evenly spaced DNA-wrapping proteins. The presence of histone octamers is suggested by rigidly fixing the two protein-bound portions of each minicircle as small superhelices similar in dimension to nucleosomal DNA. The folded min. energy forms of sample chains with different degrees of protein wrapping are noteworthy in themselves in that they offer a new resoln. to the well-known minichromosome linking no. paradox and point to future minicircle simulations of possible import. [on SciFinder (R)]
BibTeX: @article{RefWorks:410, author = {Jennifer A. Martino and Wilma K. Olson}, title = {Modeling protein-induced configurational changes in DNA minicircles.}, journal = {Biopolymers}, year = {1997}, volume = {41}, number = {4}, pages = {419-430}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Matsumoto, A. & Olson, W. K.	Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level [Abstract] [BibTeX]	2002	Biophys J	article
Abstract: Computer simulation of the dynamic structure of DNA can be carried out at various levels of resolution. Detailed high resolution information about the motions of DNA is typically collected for the atoms in a few turns of double helix. At low resolution, by contrast, the sequence-dependence features of DNA are usually neglected and molecules with thousands of base pairs are treated as ideal elastic rods. The present normal mode analysis of DNA in terms of six base-pair "step" parameters per chain residue addresses the dynamic structure of the double helix at intermediate resolution, i.e., the mesoscopic level of a few hundred base pairs. Sequence-dependent effects are incorporated into the calculations by taking advantage of "knowledge-based" harmonic energy functions deduced from the mean values and dispersion of the base-pair "step" parameters in high-resolution DNA crystal structures. Spatial arrangements sampled along the dominant low frequency modes have end-to-end distances comparable to those of exact polymer models which incorporate all possible chain configurations. The normal mode analysis accounts for the overall bending, i.e., persistence length, of the double helix and shows how known discrepancies in the measured twisting constants of long DNA molecules could originate in the deformability of neighboring base-pair steps. The calculations also reveal how the natural coupling of local conformational variables affects the global motions of DNA. Successful correspondence of the computed stretching modulus with experimental data requires that the DNA base pairs be inclined with respect to the direction of stretching, with chain extension effected by low energy transverse motions that preserve the strong van der Waals' attractions of neighboring base-pair planes. The calculations further show how one can "engineer" the macroscopic properties of DNA in terms of dimer deformability so that polymers which are intrinsically straight in the equilibrium state exhibit the mesoscopic bending anisotropy essential to DNA curvature and loop formation. [on SciFinder (R)]
BibTeX: @article{RefWorks:435, author = {Atsushi Matsumoto and Wilma K. Olson}, title = {Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level}, journal = {Biophys J}, year = {2002}, volume = {83}, number = {1}, pages = {22-41}, note = {Journal Code: 0370626; CAS Registry Numbers: 9007-49-2 (DNA); Chemical Name: 0 (Ligands); 0 (Polymers)} }
Matsumoto, A., Tobias, I. & Olson, W. K.	Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 1. Comparison of Computed Motions with the Predicted Behavior of an Ideal Elastic Rod. [Abstract] [BibTeX]	2005	Journal of Chemical Theory and Computation	article
Abstract: We have extended a newly developed approach to study the low-frequency normal modes of mesoscopic fragments of linear DNA in order to investigate the dynamics of closed circular mols. of comparable size, i.e., a few hundred base pairs. We have added restraint energy terms and a global minimization step to treat the more complicated, spatially constrained duplex in terms of the intrinsic conformation and flexibility of the constituent base-pair tepparameters. Initial application of the methodol. to the normal modes of an ideal closed circular DNA mol.-which is naturally straight in its relaxed open linear state, inextensible, and capable of isotropic bending and independent twisting at the base-pair level-matches theor. predictions of elastic rod dynamics. The energy-optimized closed circular states and the types of low frequency motions follow expected behavior, with (1) uniform twist d. and uniform energy d. in the min. energy state; (2) a near-zero frequency torsional mode with reerotation about the global helical axis; (3) higher-order torsional modes accompanied by global rocking motions and pure in-plane and out-of-plane bending motions in the torsionally relaxed circle; and (4) mixed modes of bending when the chain is supercoiled (over- or undertwisted). Furthermore, the computed changes in normal-mode frequencies with imposed supercoiling or with variation of chain length are virtually identical to theor. predicted values. [on SciFinder (R)]
BibTeX: @article{RefWorks:373, author = {Atsushi Matsumoto and Irwin Tobias and Wilma K. Olson}, title = {Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 1. Comparison of Computed Motions with the Predicted Behavior of an Ideal Elastic Rod.}, journal = {Journal of Chemical Theory and Computation}, year = {2005}, volume = {1}, number = {1}, pages = {118-130}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JCTCCE} }
Matsumoto, A., Tobias, I. & Olson, W. K.	Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule. [Abstract] [BibTeX]	2005	Journal of Chemical Theory and Computation	article
Abstract: Fine structural and energetic details embedded in the DNA base sequence, such as intrinsic curvature, are important to the packaging and processing of the genetic material. Here we investigate the internal dynamics of a 200 bp closed circular mol. with natural curvature using a newly developed normal-mode treatment of DNA in terms of neighboring base-pair tepparameters. The intrinsic curvature of the DNA is described by a 10 bp repeating pattern of bending distortions at successive base-pair steps. We vary the degree of intrinsic curvature and the superhelical stress on the mol. and consider the normal-mode fluctuations of both the circle and the stable figure-8 configuration under conditions where the energies of the two states are similar. To ext. the properties due solely to curvature, we ignore other important features of the double helix, such as the extensibility of the chain, the anisotropy of local bending, and the coupling of step parameters. We compare the computed normal modes of the curved DNA model with the corresponding dynamical features of a covalently closed duplex of the same chain length constructed from naturally straight DNA and with the theor. predicted dynamical properties of a naturally circular, inextensible elastic rod, i.e., an O-ring. The cyclic mols. with intrinsic curvature are found to be more deformable under superhelical stress than rings formed from naturally straight DNA. As superhelical stress is accumulated in the DNA, the frequency, i.e., energy, of the dominant bending mode decreases in value, and if the imposed stress is sufficiently large, a global configurational rearrangement of the circle to the figure-8 form takes place. We combine energy minimization with normal-mode calcns. of the two states to decipher the configurational pathway between the two states. We also describe and make use of a general anal. treatment of the thermal fluctuations of an elastic rod to characterize the motions of the minicircle as a whole from knowledge of the full set of normal modes. The remarkable agreement between computed and theor. predicted values of the av. deviation and dispersion of the writhe of the circular configuration adds to the reliability in the computational approach. Application of the new formalism to the computed modes of the figure-8 provides insights into macromol. motions which are beyond the scope of current theor. treatments. [on SciFinder (R)]
BibTeX: @article{RefWorks:374, author = {Atsushi Matsumoto and Irwin Tobias and Wilma K. Olson}, title = {Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule.}, journal = {Journal of Chemical Theory and Computation}, year = {2005}, volume = {1}, number = {1}, pages = {131-143}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JCTCCE} }
Olson, W. K.	Simulating DNA at low resolution. [Abstract] [BibTeX]	1996	Current opinion in structural biology	article
Abstract: A review and discussion with 76 refs. This review begins with anal. of the virtual bond geometry of neighboring DNA base pairs, covering math. approaches recently developed to quantify the arrangements of base pairs as well as structural trends and sequence-dependent features revealed in the growing database of nucleic acid crystal structures. Recent computational advances in treating the polyelectrolyte nature of DNA and in incorporating other environmental factors that affect the global folding of the chain, new polymer statistical mech. methods and elastic rod models developed to incorporate the local base sequence dependent features of the double helix in linear and spatially constrained mols., a discussion of the equil. structures and the information gained in various simulations of DNA with bound proteins or natural curvature and finally a brief commentary on the complementary of different computational perspectives of DNA structure and some likely new developments in the coming years are included in this review. [on SciFinder (R)]
BibTeX: @article{RefWorks:414, author = {Wilma K. Olson}, title = {Simulating DNA at low resolution.}, journal = {Current opinion in structural biology}, year = {1996}, volume = {6}, number = {2}, pages = {242-256}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-0; CA Section Cross-references: 6; CODEN: COSBEF} }
Olson, W. K.	Theoretical probes of nucleic acid conformation. [Abstract] [BibTeX]	1983	Jerusalem Symposia on Quantum Chemistry and Biochemistry	article
Abstract: Computations which illustrate the interrelation between the local structure and macroscopic behavior of the DNA helix are discussed. Statistical mech. studies help to identify the most likely morphol. arrangements of the polynucleotide backbone and to understand the macroscopic flexibility of DNA as a whole. Model building and potential energy calcns. uncover the detailed local geometries of the chain and clarify the likely paths between the multitude of allowed spatial forms. [on SciFinder (R)]
BibTeX: @article{RefWorks:341, author = {Wilma K. Olson}, title = {Theoretical probes of nucleic acid conformation.}, journal = {Jerusalem Symposia on Quantum Chemistry and Biochemistry}, year = {1983}, volume = {16}, number = {Nucleic Acids}, pages = {217-227}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JSQCA7} }
Olson, W. K.	Configurational statistics of polynucleotide chains. [Abstract] [BibTeX]	1983	Fenzi Kexue Yu Huaxue Yanjiu	article
Abstract: The application of polymer chain statistics, or configurational statistics, to nucleic acids is discussed and summarized. The unique features of double-stranded DNA stem from the pronounced tendency of adjacent heterocyclic bases to stack like coins in parallel arrays. These preferred arrangements limit the local flexibility of the chain. The sugar-phosphate-sugar segments, however, can assume a large variety of stacked arrangements, thereby accounting for the unusual local mobility of this very stiff chain. [on SciFinder (R)]
BibTeX: @article{RefWorks:343, author = {Wilma K. Olson}, title = {Configurational statistics of polynucleotide chains.}, journal = {Fenzi Kexue Yu Huaxue Yanjiu}, year = {1983}, volume = {3}, number = {2}, pages = {117-138}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: FKYYDG} }
Olson, W. K.	The long-range stiffness and local mobility of double-stranded DNA. [Abstract] [BibTeX]	1982	Jerusalem Symposia on Quantum Chemistry and Biochemistry	article
Abstract: A theor. conformational anal. which provides a basis for understanding the unique features of double-stranded DNA in terms of its chem. architecture, e.g. base stacking and backbone conformation, is discussed. The well-known stiffness of the chain as a whole derives from the sequence of heterocyclic bases, whereas the local mobility of the constituent nucleotides reflects the structural complexity of the sugar-phosphate backbone. [on SciFinder (R)]
BibTeX: @article{RefWorks:345, author = {Wilma K. Olson}, title = {The long-range stiffness and local mobility of double-stranded DNA.}, journal = {Jerusalem Symposia on Quantum Chemistry and Biochemistry}, year = {1982}, volume = {15}, number = {Intramol. Dyn.}, pages = {525-536}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JSQCA7} }
Olson, W. K.	Computational studies of polynucleotide flexibility. [Abstract] [BibTeX]	1982	Nucleic acids research	article
Abstract: A review with 41 refs. on polynucleotide conformation based on potential energy calcns. and statistical mech. analyses. [on SciFinder (R)]
BibTeX: @article{RefWorks:348, author = {Wilma K. Olson}, title = {Computational studies of polynucleotide flexibility.}, journal = {Nucleic acids research}, year = {1982}, volume = {10}, number = {3}, pages = {777-787}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-0; CA Section Cross-references: 9; CODEN: NARHAD} }
Olson, W. K.	How flexible is the furanose ring? 2. An updated potential energy estimate. [Abstract] [BibTeX]	1982	Journal of the American Chemical Society	article
Abstract: A potential energy function is developed to est. the pseudorotational motions of ribose and 2'-deoxyribose sugars. In addn. to std. nonbonded, torsional, and valence angle strain contributions, an intrinsic gauche energy term is required to account for the puckering preferences and hindered ring flexibilities suggested by solid-state and soln. studies. The gauche effect is also an essential factor in reproducing the properties of 3'-deoxyribose and 2'-fluoro-2'-deoxyribose rings in soln. The extreme sensitivity of the potential energies to variations in ring geometry is helpful in understanding the disparities found in earlier theor. studies of furanose pseudorotation. Apparently minor deviations of valence bond angles from std. x-ray values perturb the normal motions of the furanose drastically. [on SciFinder (R)]
BibTeX: @article{RefWorks:350, author = {Wilma K. Olson}, title = {How flexible is the furanose ring? 2. An updated potential energy estimate.}, journal = {Journal of the American Chemical Society}, year = {1982}, volume = {104}, number = {1}, pages = {278-286}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-1; CA Section Cross-references: 22; CODEN: JACSAT; CAS Registry Numbers: 79681-15-5; 79681-16-6; 79681-17-7; 79681-18-8 Role: PRP (Properties) (potential energy of, furanose pseudorotation and)} }
Olson, W. K.	Three-state models of furanose pseudorotation. [Abstract] [BibTeX]	1981	Nucleic acids research	article
Abstract: A general procedure is described to treat the pseudorotation of the furanose ring in terms of a three-state conformational equil. In addn. to the principal n (C3'-endo) and s (C2'-endo) puckering domains, the unusual e (O1'-endo) intermediate is included in the anal. Each of these 3 conformational categories is represented by a blend of 5 closely related puckered forms rather than by a single rotational isomeric state. Using this model together with exptl. measured NMR coupling consts., the puckering populations of various nucleic acid analogs are estd. The conventional two-state n/s equil. is confirmed in ordinary ribose and deoxyribose systems. The e domain, however, is of major importance in several chem. modified furanoses including certain pyrimidine deoxynucleosides damaged by radiation and various nucleosides and nucleotides forced by bulky substituents on the base into unusual syn glycosyl arrangements. The ''free'' pseudorotation of these modified systems is not detected by conventional two-state puckering analyses. [on SciFinder (R)]
BibTeX: @article{RefWorks:351, author = {Wilma K. Olson}, title = {Three-state models of furanose pseudorotation.}, journal = {Nucleic acids research}, year = {1981}, volume = {9}, number = {5}, pages = {1251-1262}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 22; CODEN: NARHAD} }
Olson, W. K.	Theoretical estimates of helical structure in polynucleotides. [Abstract] [BibTeX]	1980	ACS Symposium Series	article
Abstract: A computational method is offered to identify the double-helical structures of polynucleotides compatible with given base pairing schemes. The feasibility of a duplex is estd. on the basis of semi-empirical energy ests. of base stacking and H bonding in a miniature double-helix of specified conformation. The method allows the extrapolation of exptl. studies on the conformation of small models to the polynucleotide level and to test the relevance of the data in a helical complex. It also allows the potential energy anal. of double-helical conformation and stability. [on SciFinder (R)]
BibTeX: @article{RefWorks:352, author = {Wilma K. Olson}, title = {Theoretical estimates of helical structure in polynucleotides.}, journal = {ACS Symposium Series}, year = {1980}, volume = {141}, number = {Fiber Diffr. Methods}, pages = {251-265}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 9; CODEN: ACSMC8} }
Olson, W. K.	Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking. [Abstract] [BibTeX]	1980	Macromolecules	article
Abstract: A virtual bond method for treatment of polynucleotide conformations including long-range effects of base stacking was developed. The relative rigidity of rotation about the C-O bonds of the sugar-phosphate backbone enables representation of the 6 chem. bonds constituting each nucleotide in terms of 2 bonds of comparable magnitude spanning C-C-O-P chain segments. Helix-coil transitions of poly(riboadenylic acid) [24937-83-5] at -12 Deg to +60 Deg were modeled on the basis of conformational anal. and Karplus treatment of NMR coupling consts. At low temps., the mol. is a flexible helix similar to RNA. At higher temps., as the nucleotides fluctuate over 12 conformational domains the chain dimensions decrease in agreement with expt. [on SciFinder (R)]
BibTeX: @article{RefWorks:353, author = {Wilma K. Olson}, title = {Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking.}, journal = {Macromolecules}, year = {1980}, volume = {13}, number = {3}, pages = {721-728}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 35-5; CA Section Cross-references: 33; CODEN: MAMOBX; CAS Registry Numbers: 24937-83-5 Role: PRP (Properties) (helix-coil transition of, base stacking in modeling of)} }
Olson, W. K.	The flexible DNA double helix. II. Superhelix formation. [Abstract] [BibTeX]	1979	Biopolymers	article
Abstract: A simple super or s-virtual bond scheme was developed for the treatment of tertiary or superhelical structure in polynucleotide chains. The various spatial configurations accessible to the flexible double helix were rendered more readily intelligible by the introduction of these hypothetical bonds to replace real sequences of regular secondary structure. The scheme was utilized to exam. the variety of tertiary structure that can be generated by regularly bending a B-DNA ref. helix at the phosphodiester linkages. Of particular interest were the large families of bends that generate superhelixes of identical macroscopic dimensions. Various modes of folding the B-type helix into superhelixes that fit the exptl. measured dimensions of chromatin nucleosomes are illustrated. [on SciFinder (R)]
BibTeX: @article{RefWorks:354, author = {Wilma K. Olson}, title = {The flexible DNA double helix. II. Superhelix formation.}, journal = {Biopolymers}, year = {1979}, volume = {18}, number = {5}, pages = {1235-1260}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 68878-00-2 Role: PRP (Properties) (mol. structure of, DNA superhelix in relation to)} }
Olson, W. K.	The flexible DNA double helix. I. Average dimensions and distribution functions. [Abstract] [BibTeX]	1979	Biopolymers	article
Abstract: A scheme was developed to treat the spatial arrangements and properties of double-helical DNA in terms of the constituent atoms and bonds of the system. The flexibility of the double helix was taken to arise from minor perturbations of the rotation angles along the polynucleotide backbone. The rotational motions of the chain were limited to conformations within the B-DNA family of helixes that permit base stacking. The disruptions of H bonding assocd. with these angular fluctuations may explain the breathing of double-stranded DNA. Radii of gyration computed on the basis of this model agreed with exptl. measurements on B-DNA helixes spanning a wide range of mol. wts. Moreover, the 3-dimensional spatial distribution functions Wa(r) generated by these limited internal rotations was compatible with various macroscopic descriptions (i.e., rigid rod, wormlike coil, ideal Gaussian) previously ascribed to DNA of different chain lengths. Based on the Wa(r),the rigid B-DNA backbone modeled here, if long enough, can bend into compact conformations. Thus, it is not necessary to invoke sharp bends or kinks to account for the condensed forms of DNA in naturally occurring systems. [on SciFinder (R)]
BibTeX: @article{RefWorks:355, author = {Wilma K. Olson}, title = {The flexible DNA double helix. I. Average dimensions and distribution functions.}, journal = {Biopolymers}, year = {1979}, volume = {18}, number = {5}, pages = {1213-1233}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Olson, W. K.	Spatial configuration of ordered polynucleotide chains. V. Conformational energy estimates of helical structure. [Abstract] [BibTeX]	1978	Biopolymers	article
Abstract: Semiempirical potential energy functions used previously to account successfully for the mean-square unperturbed dimensions and NMR coupling consts. of randomly coiling polynucleotides are used, after modifications, to account for base stacking and interstrand H bonding, and to evaluate the conformational energies of single- and double-stranded polynucleotide helices. Attention is focused upon the variety of A-genus helices with local backbone conformations resembling the known double-helical structures of RNA. Distinct structural differences between single- and double-stranded helices are predicted from the energy calcns. A 2nd point of interest is the apparent failure of 2 conformationally identical left-handed polynucleotide chains to form a left-handed duplex. The 3rd major observation is the wide morphol. variety of theor. allowed right-handed polynucleotide duplexes. In addn. to the familiar double helix stabilized by horizontal base stacking and hydrogen bonding, an unusual vertical double helix is predicted to form between complementary bases fixed in the unusual but not energetically forbidden high anti glycosyl conformation. Exptl. results bearing upon the theor. predictions are discussed. [on SciFinder (R)]
BibTeX: @article{RefWorks:357, author = {Wilma K. Olson}, title = {Spatial configuration of ordered polynucleotide chains. V. Conformational energy estimates of helical structure.}, journal = {Biopolymers}, year = {1978}, volume = {17}, number = {4}, pages = {1015-1040}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 22; CODEN: BIPMAA} }
Olson, W. K.	The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking. [Abstract] [BibTeX]	1976	Biopolymers	article
Abstract: A single virtual bond scheme for the treatment of average properties of randomly coiling polynucleotides is applied to the calcn. of helical parameters which characterize a regularly repeating polynucleotide molecule. Only a fraction of the enormous no. of conformationally feasible helixes fulfill the geometric criteria of vertical base stacking usually assocd. with ordered polynucleotide chains. Detailed examn. of the nature and mode of base stacking feasible in a single helical backbone structure indicates that the handedness of a base stacking arrangement does not correlate either quant. or qual. with the handedness of the polymer backbone. A no. of polynucleotide chains which exhibit lefthanded base stacking patterns in NMR and CD studies may, in fact, be righthanded helixes. [on SciFinder (R)]
BibTeX: @article{RefWorks:360, author = {Wilma K. Olson}, title = {The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking.}, journal = {Biopolymers}, year = {1976}, volume = {15}, number = {5}, pages = {859-878}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Olson, W. K.	The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix. [Abstract] [BibTeX]	1975	Nucleic acids research	article
Abstract: Approx. details of the spatial configuration of the ordered single-stranded poly(A) mol. in dil. soln. were obtained in a combined theor. anal. of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based on all available exptl. and theor. evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern obsd. in NMR investigations of poly(A) are deemed suitable single-stranded helixes. In addn., the helical geometry of the stacked structures is required to be consistent with the exptl. obsd. dimensions of both completely ordered and partially ordered poly(A) chains. Only a single category of poly(A) helixes (very similar in all conformational details to the individual chains of the poly(A) double-stranded x-ray structure) is thus obtained. Other conformational feasible polynucleotide helixes characterized simply by a parallel and overlapping base stacking arrangement are also discussed. [on SciFinder (R)]
BibTeX: @article{RefWorks:361, author = {Wilma K. Olson}, title = {The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.}, journal = {Nucleic acids research}, year = {1975}, volume = {2}, number = {11}, pages = {2055-2068}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: NARHAD; CAS Registry Numbers: 24937-83-5 Role: PRP (Properties) (conformation of)} }
Olson, W. K.	Configuration-dependent properties of randomly coiling polynucleotide chains. II. Role of the phosphodiester linkage. [Abstract] [BibTeX]	1975	Biopolymers	article
Abstract: The dependence of the unperturbed dimensions of randomly coiling polynucleotides on the rotations about the phosphodiester linkages of the chain was examd. Large values for the characteristic ratio (r2)0/nz2, which agree with the exptl. behavior of the chain, are obtained only if a sizeable proportion of the polymer residues have trans- w' values (angle of the phosphodiester bond) values. The asymmetric torsional potential that is believed to arise from gauche effects assocd. with the P-O bonds was approximated using a hard core model. The calcd. characteristic ratio exhibits a strong dependence upon the magnitude of this torsional barrier (sepg. trans and gauche conformations) and shows agreement with exptl. values for polyribonucleotides only if this energy difference is 1 kcal/mole or less. [on SciFinder (R)]
BibTeX: @article{RefWorks:362, author = {Wilma K. Olson}, title = {Configuration-dependent properties of randomly coiling polynucleotide chains. II. Role of the phosphodiester linkage.}, journal = {Biopolymers}, year = {1975}, volume = {14}, number = {9}, pages = {1797-1810}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 22, 28, 35; CODEN: BIPMAA} }
Olson, W. K.	Configuration-dependent properties of randomly coiling polynucleotide chains. I. Comparison of theoretical energy estimates. [Abstract] [BibTeX]	1975	Biopolymers	article
Abstract: Theor. estimates of the conformational energy assocd. with polynucleotides in soln. were compared with each other and also with exptl. obsd. conformations found in x-ray crystallog. investigations of low-mol.-wt. nucleic acid analogs. Certain configuration-dependent properties (i.e., the mean-square unperturbed end-to-end distance and the av. vicinal NMR coupling const. appropriate to randomly coiling polynucleotides described by either the energy estimates or by the crystallog. preferred conformations were calcd. and compared with the known soln. behavior of polynucleotide chains. Both the theor. energy surfaces and the x-ray data show good agreement with the NMR coupling const. indications of the preferred rotations about the O-C and C-C bonds of the chain backbone. The principal discrepancies between the theor. methods and x-ray data arise in their ability to predict successfully the preferred rotations about the two phosphodiester bonds of the chain backbone and the unperturbed dimensions of randomly coiling polynucleotide chains. [on SciFinder (R)]
BibTeX: @article{RefWorks:363, author = {Wilma K. Olson}, title = {Configuration-dependent properties of randomly coiling polynucleotide chains. I. Comparison of theoretical energy estimates.}, journal = {Biopolymers}, year = {1975}, volume = {14}, number = {9}, pages = {1775-1795}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 22, 28; CODEN: BIPMAA} }
Olson, W. K.	Configurational statistics of polynucleotide chains. Single virtual bond treatment. [Abstract] [BibTeX]	1975	Macromolecules	article
Abstract: A single virtual bond scheme was developed for calcn. of the mean-square unperturbed dimensions in polynucleotide chains. Computed values of chain dimension based on the single virtual bond scheme are comparable to those obtained by the 2 virtual bond model which permits rotational flexibility in the sugar moieties of the chain. [on SciFinder (R)]
BibTeX: @article{RefWorks:364, author = {Wilma K. Olson}, title = {Configurational statistics of polynucleotide chains. Single virtual bond treatment.}, journal = {Macromolecules}, year = {1975}, volume = {8}, number = {3}, pages = {272-275}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 22; CODEN: MAMOBX} }
Olson, W. K.	Syn-anti effects on the spatial configuration of polynucleotide chains. [Abstract] [BibTeX]	1973	Biopolymers	article
Abstract: Semiempirical energy calcns. were performed on model nucleic acid systems to assess the preferred conformation of the rotation c about the glycosidic linkage and also the effect of this rotation on the spatial configuration of the sugar-phosphate chain backbone. The rotation angle F' about bond C5'-C4' in purine polyribonucleotides and 5'-monoribonucleotides depended on whether the conformational range of c was syn or anti. The preferred conformation of c in these mols. also depended upon the nature of the attached base. The orientation of c in poly(adenylic acid) chains was predicted to be predominantly anti, whereas in poly(guanylic acid) the syn conformer was expected to occur in significant proportions. The syn conformer was preferred almost exclusively in certain unusual purine polynucleotides, such as poly(8-bromoadenylic acid). The preferred conformation of c in polynucleotides was not necessarily the same as that calcd. for 5'-mononucleotides and nucleosides. On the basis of these calcns., the influence of the orientation and nature of a purine base on the spatial configuration of a polynucleotide chain as a whole was examd. The random coil dimensions of a syn polynucleotide chain were larger than those of an anti chain as a consequence of the effect of a syn base on the local conformation of the chain skeleton. The occurrence of a syn base in an ordered polynucleotide chain may prevent the formation of normal stacking with the preceeding base. [on SciFinder (R)]
BibTeX: @article{RefWorks:365, author = {Wilma K. Olson}, title = {Syn-anti effects on the spatial configuration of polynucleotide chains.}, journal = {Biopolymers}, year = {1973}, volume = {12}, number = {8}, pages = {1787-1814}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 61-19-8; 73-24-5; 73-40-5; 85-32-5; 24937-83-5; 25191-14-4; 30475-28-6; 50828-34-7 Role: PRP (Properties) (conformation of)} }
Olson, Wilma K., Babcock, Marla S., Gorin, Andrey, Liu, Guohua, Marky, Nancy L., Martino, Jennifer A., Pedersen, Scott C., Srinivasan, A. R., Tobias, Irwin & et al	Erratum to: Flexing and folding double helical DNA (Biophys. Chem., 55 (1995) 7-29) (BIOCHE1986) 1. [BibTeX]	1996	Biophysical chemistry	article
BibTeX: @article{RefWorks:412, author = {Wilma K. Olson and Marla S. Babcock and Andrey Gorin and Guohua Liu and Nancy L. Marky and Jennifer A. Martino and Scott C. Pedersen and A. R. Srinivasan and Irwin Tobias and et al}, title = {Erratum to: Flexing and folding double helical DNA (Biophys. Chem., 55 (1995) 7-29) (BIOCHE1986) 1.}, journal = {Biophysical chemistry}, year = {1996}, volume = {60}, number = {3}, pages = {155-155}, note = {Copyright (C) 2007 ACS on SciFinder (R)); CODEN: BICIAZ} }
Olson, Wilma K., Babcock, Marla S., Gorin, Andrey, Liu, Guohua, Marky, Nancy L., Martino, Jennifer A., Pedersen, Scott C., Srinivasan, A. R., Tobias, Irwin & et al	Flexing and folding double helical DNA. [Abstract] [BibTeX]	1995	Biophysical chemistry	article
Abstract: A review with 85 refs. DNA base sequence, once thought to be interesting only as a carrier of the genetic blueprint, is now recognized as playing a structural role in modulating the biol. activity of genes. Primary sequences of nucleic acid bases describe real three-dimensional structures with properties reflecting those structures. Moreover, the structures are base sequence dependent with individual residues adopting characteristic spatial forms. As a consequence, the double helix can fold into tertiary arrangements, although the deformation is much more gradual and spread over a larger mol. scale than in proteins. As part of an effort to understand how local structural irregularities are translated at the macromol. level in DNA and recognized by proteins, a series of calcns. probing the structure and properties of the double helix have been performed. By combining several computational techniques, complementary information as well as a series of built-in checks and balances for assessing the significance of the findings are obtained. The known sequence dependent bending, twisting, and translation of simple dimeric fragments have been incorporated into computer models of long open DNAs of varying length and chem. compn. as well as in closed double helical circles and loops. The extent to which the double helix can be forced to bend and twist is monitored with newly parameterized base sequence dependent elastic energy potentials based on the obsd. configurations of adjacent base pairs in the B-DNA crystallog. literature. [on SciFinder (R)]
BibTeX: @article{RefWorks:422, author = {Wilma K. Olson and Marla S. Babcock and Andrey Gorin and Guohua Liu and Nancy L. Marky and Jennifer A. Martino and Scott C. Pedersen and A. R. Srinivasan and Irwin Tobias and et al}, title = {Flexing and folding double helical DNA.}, journal = {Biophysical chemistry}, year = {1995}, volume = {55}, number = {1-2}, pages = {7-29}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-0; CODEN: BICIAZ} }
Olson, W. K., Bansal, M., Burley, S. K., Dickerson, R. E., Gerstein, M., Harvey, S. C., Heinemann, U., Lu, X., Neidle, S., Shakked, Z., Sklenar, H., Suzuki, M., Tung, C., Westhof, E., Wolberger, C. & Berman, H. M.	A standard reference frame for the description of nucleic acid base-pair geometry. [Abstract] [BibTeX]	2001	Journal of Molecular Biology	article
Abstract: To address the need for a common point of ref. to describe the 3D arrangements of bases and base pairs in nucleic acid structures, a std. base ref. frame for nucleic acid conformational anal. is proposed. The definitions build upon qual. guidelines established previously to specify the arrangements of bases and base pairs in DNA and RNA structures. Base coordinates are derived from a survey of high resoln. crystal structures of nucleic acid analogs stored in the Cambridge Structural Database. Conformational analyses using this ref. frame lead to interpretations of local helical structure that are essentially independent of computational scheme. (c) 2001 Academic Press. [on SciFinder (R)]
BibTeX: @article{RefWorks:381, author = {Wilma K. Olson and Manju Bansal and Stephen K. Burley and Richard E. Dickerson and Mark Gerstein and Stephen C. Harvey and Udo Heinemann and Xiang-Jun Lu and Stephen Neidle and Zippora Shakked and Heinz Sklenar and Masashi Suzuki and Chang-Shung Tung and Eric Westhof and Cynthia Wolberger and Helen M. Berman}, title = {A standard reference frame for the description of nucleic acid base-pair geometry.}, journal = {Journal of Molecular Biology}, year = {2001}, volume = {313}, number = {1}, pages = {229-237}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK; CAS Registry Numbers: 65-71-4 (Thymine); 66-22-8 (Uracil); 71-30-7 (Cytosine); 73-24-5 (Adenine); 73-40-5 (Guanine) Role: MSC (Miscellaneous), PRP (Properties) (std. ref. frame for the description of nucleic acid base-pair geometry)} }
Olson, W. K. & Cicariello, J.	Computer simulation of DNA supercoiling. [Abstract] [BibTeX]	1986	Annals of the New York Academy of Sciences	article
Abstract: A differential geometric approach is set fourth which provides a convenient way to generate detailed structural models of DNA supercoiling. Structural details assocd. with macroscopic changes are monitored by simple potential energy functions. The electrostatic interactions between neg. charged phosphate groups are esp. sensitive to the formation of cyclic structures from linear pieces and to the different 3-dimensional ways of accommodating a given level of supercoiling. [on SciFinder (R)]
BibTeX: @article{RefWorks:338, author = {Wilma K. Olson and Janet Cicariello}, title = {Computer simulation of DNA supercoiling.}, journal = {Annals of the New York Academy of Sciences}, year = {1986}, volume = {482}, number = {Comput. Simul. Chem. Biomol. Syst.}, pages = {69-81}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: ANYAA9} }
Olson, W. K. & Dasika, R. D.	Spatial configuration of ordered polynucleotide chains. 3. Polycyclonucleotides. [Abstract] [BibTeX]	1976	Journal of the American Chemical Society	article
Abstract: Approx. details of the spatial configuration of the ordered 8,2'-purine polycyclonucleotide chain in dil. soln. are reported from a combined theor. anal. of chain flexibility and base stacking. Only a fraction of the wide variety of regular polycyclonucleotide helices accommodates the array of stacked bases that characterizes the ordered form of the mol. The bases comprising these stacked helices are arranged almost exclusively in left-handed stacking patterns. The backbone structures to which the stacked polycyclonucleotide bases attach are right-handed helices. The sugar-phosphate units of these polycyclonucleotide helices are identical with backbone conformations deduced in x-ray fiber diffraction analyses of ordered double-stranded polynucleotides. Unlike the bases aligned in planes approx. perpendicular to the long axes of ordered polynucleotide chains, the polycyclonucleotide bases attached to the same backbone frameworks are stacked in planes that approx. parallel the helix axis. This parallel alignment permits the bases of the polycyclonucleotide simultaneously both to exhibit left-handed stacking and to conform to right-handed helical organization. [on SciFinder (R)]
BibTeX: @article{RefWorks:359, author = {Wilma K. Olson and Rama D. Dasika}, title = {Spatial configuration of ordered polynucleotide chains. 3. Polycyclonucleotides.}, journal = {Journal of the American Chemical Society}, year = {1976}, volume = {98}, number = {17}, pages = {5371-5380}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 28, 35; CODEN: JACSAT; CAS Registry Numbers: 60828-43-5 Role: PRP (Properties) (spatial configuration of)} }
Olson, W. K. & Flory, P. J.	Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides. Virtual bond model. [Abstract] [BibTeX]	1972	Biopolymers	article
Abstract: A simplified scheme for treating the spatial configurations of polynucleotide chains is developed using the rotational isomeric state approxn. and statistical methods applicable to linear systems of interacting subunits. As a consequence of geometry constraints imposed by the skeletal structure and of the severity of certain steric interactions, it is possible to represent the repeat unit comprising 6-skeletal bonds by 2 virtual bonds of fixed length. The configuration of the polynucleotide chain as a whole is described by an alternating succession of these 2 virtual bonds. Anal. of steric interactions suggests that bond rotations governing the mutual orientation of a given pair of successive virtual bonds should be sensibly independent of the rotations affecting the mutual orientation of other pairs. The statistical mechanical treatment of configuration-dependent properties is much simplified in consequence of this mutual independence. Mean-square dimensions calcd. by giving equal wts. to all sterically allowed conformations are smaller than values detd. by Felsenfeld and co-workers. The calcd. dimensions are increased by placing arbitrary restrictions on the rotations about selected pairs of skeletal bonds. It is demonstrated that steric interactions alone are insufficient to account for the spatial characteristics of polynucleotide chains. The dimensions are also sensitive to the conformation of the ribose ring of each nucleotide unit; insofar as the influences of steric interactions are concerned, the dimensions do not depend on the heterocyclic base attached to the ribose ring. [on SciFinder (R)]
BibTeX: @article{RefWorks:366, author = {Wilma K. Olson and Paul J. Flory}, title = {Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides. Virtual bond model.}, journal = {Biopolymers}, year = {1972}, volume = {11}, number = {1}, pages = {1-23}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33; CA Section Cross-references: 22, 35; CODEN: BIPMAA; CAS Registry Numbers: 24937-83-5 Role: PRP (Properties) (configuration of, virtual bond model)} }
Olson, W. K. & Flory, P. J.	Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides. [Abstract] [BibTeX]	1972	Biopolymers	article
Abstract: Conformational energies are calcd. for pairs of successive bond rotations within an internal residue of a polyribonucleotide chain. Contributions to these energies include bond torsional strain, van der Waals repulsions, London attractions, electrostatic interactions, and inductive interactions between nonbonded atoms in the nucleotide repeat unit. The av. dimensions of unperturbed random-coil polyribonucleotide chains are then evaluated on the basis of estd. energies, using for this purpose the virtual bond treatment. The characteristic ratio C... = n->... lim (r20/nl.hivin.2) of the mean-square end-to-end distance calcd. for polyribonucleotide chains in which all pentose rings are fixed in a C-3'-endo conformation is 9; for chains consisting exclusively of C-2'-endo units it is ~25. These values are greater than those obtained by giving equal wt. to all conformations judged to be sterically allowed. Satisfactory agreement between the calcns. here and exptl. values from viscosity and light-scattering studies is achieved by treating the chain as a random copolymer of C-3'-endo and C-2'-endo conformational isomers. The critical dependence of the characteristic ratio on the rotation about bond C-3'-O-3' in the C-2'-endo chain, however, obscures the interpretation of chain dimensions. The chain is also treated in higher approxn. as a sequence of independent repeat units, each of which consists of six chem. bonds. The characteristic ratio obtained in this manner is 6.5 for the C-3'-endo chain and 18.5 for the C-2'-endo chain. Finally, the effects of partially stacked conformations in polyribonucleotides are investigated using the virtual bond treatment. Chain dimensions are calcd. for random coil poly rA chains in which stacking is introduced by both noncooperative and cooperative processes. [on SciFinder (R)]
BibTeX: @article{RefWorks:367, author = {Wilma K. Olson and Paul J. Flory}, title = {Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides.}, journal = {Biopolymers}, year = {1972}, volume = {11}, number = {1}, pages = {25-56}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33; CA Section Cross-references: 22, 35; CODEN: BIPMAA} }
Olson, W. K. & Flory, P. J.	Spatial configurations of polynucleotide chains. III. Polydeoxyribonucleotides. [Abstract] [BibTeX]	1972	Biopolymers	article
Abstract: The virtual bond scheme for treating the av. properties of polyriboadenylic acid (poly rA) is applied to the calcn. of the unperturbed mean-square end-to-end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the HO group at C-2' in the ribose residue by H in deoxyribose produce only minor modifications in the conformational energies assocd. with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy assocd. with rotations about the C-3'-O-3' bond of the deoxyribose residue in the C-2' endo conformation; accessible rotations are confined to the range between 0 Deg and 30 Deg relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approx. 35 Deg and 85 Deg. The characteristic ratio r20/nl.hivin.2 calcd. on the basis of the conformational energy estimates is ~9 for the poly dA chain with all deoxyribose residues in the C-3'-endo conformation and ~21 with all residues in the C-2'-endo form. Satisfactory agreement is achieved between the theoretical values and exptl. results on apurinic acid by treating the poly dA chain as a random copolymer of C-3'-endo and C-2'-endo conformational isomers present in a ratio of .apprx.1 to 9. [on SciFinder (R)]
BibTeX: @article{RefWorks:368, author = {Wilma K. Olson and Paul J. Flory}, title = {Spatial configurations of polynucleotide chains. III. Polydeoxyribonucleotides.}, journal = {Biopolymers}, year = {1972}, volume = {11}, number = {1}, pages = {57-66}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33; CA Section Cross-references: 22, 35; CODEN: BIPMAA; CAS Registry Numbers: 25191-20-2 Role: PRP (Properties) (spatial configuration of, kinetics of)} }
Olson, W. K., Gorin, A. A., Lu, X., Hock, L. M. & Zhurkin, V. B.	DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. [Abstract] [BibTeX]	1998	Proceedings of the National Academy of Sciences of the United States of America	article
Abstract: The deformability of double helical DNA is crit. for its packaging in the cell, recognition by other mols., and transient opening during biochem. important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extd. from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochem. measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as flexible ingesfitting the duplex to the protein surface. In addn. to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The obsd. correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences. [on SciFinder (R)]
BibTeX: @article{RefWorks:399, author = {Wilma K. Olson and Andrey A. Gorin and Xiang-Jun Lu and Lynette M. Hock and Victor B. Zhurkin}, title = {DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {1998}, volume = {95}, number = {19}, pages = {11163-11168}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-7; CA Section Cross-references: 3; CODEN: PNASA6} }
Olson, W. K., Kosikov, K. M., Colasanti, A., Gorin, A. A. & Zhurkin, V. B.	Pulling and pushing the DNA double helix. [Abstract] [BibTeX]	1999	AIP Conference Proceedings	article
Abstract: Systematic, computer-simulated elongation of A- and B-DNA double helixes beyond the range of normal room temp. fluctuations provides new insights into recent phys. manipulations of single DNA mols. The calcns. include unusual states that are energetically disfavored under equil. conditions but that become favored as the DNA is highly stretched or compressed. The variation of potential energy vs. stretching provides a detailed picture of cooperative conformational change that points to the possible role played by the non-canonical states. Dramatic structural changes take place as the energies of different conformers approach one another. In particular, large-scale, concerted changes in base pair inclination, brought about by changes in backbone and glycosyl torsions, offer a model of the obsd. sharp increase in force required to stretch single DNA mols. more than 1.6 times their canonical extension. Small degees of over- and under-twisting have limited effects on the over-stretching transition, but influence local eltingof the double helix. The energy landscapes of the systems evaluated here reveal the energetically economical pathways for mol. deformations operative in DNA processing, such as recombination and transcription. [on SciFinder (R)]
BibTeX: @article{RefWorks:392, author = {Wilma K. Olson and Konstantin M. Kosikov and Andrew Colasanti and Andrey A. Gorin and Victor B. Zhurkin}, title = {Pulling and pushing the DNA double helix.}, journal = {AIP Conference Proceedings}, year = {1999}, volume = {487}, number = {Biological Physics}, pages = {14-36}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: APCPCS} }
Olson, W. K. & Manning, G. S.	A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils. [Abstract] [BibTeX]	1976	Biopolymers	article
Abstract: The structural implications arising from the observation that the charge d. of a single-stranded randomly coiling polynucleotide chain is approx. equal to that of 1 strand of the double helix are examd. A computational scheme is described to obtain (using bond lengths, valence bond angles, and internal rotation angles) the mean phosphate-phosphate spacing parameter b along the chain axes of any single-stranded polynucleotide mol. Attention was then focused on the computed interphosphate spacing assocd. with both the theor. randomly coiling polynucleotide that reproduces the obsd. exptl. nonperturbed dimensions and the familiar single-stranded helix. The calcns. clearly demonstrated that the parameter b only weakly reflects the spatial configuration of the chain. The approx. equivalence of the b values assocd. with the single-stranded helix and the nonperturbed randomly coiling polynucleotide was not indicative of strong configurational similarities between the 2 forms. The familiar helix is composed of a sequence of identically conformed compact structural residues, whereas the random coil is characterized by a variety of chain-repeating residues of which a large proportion are extended units. [on SciFinder (R)]
BibTeX: @article{RefWorks:358, author = {Wilma K. Olson and Gerald S. Manning}, title = {A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils.}, journal = {Biopolymers}, year = {1976}, volume = {15}, number = {12}, pages = {2391-2405}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Olson, W. K., Marky, N. L., Jernigan, R. L. & Zhurkin, V. B.	Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. [Abstract] [BibTeX]	1993	Journal of Molecular Biology	article
Abstract: Matrix-generator and Monte Carlo methods have been employed to study the influence of thermal fluctuations on the overall sizes and shapes of curved pieces of DNA. The DNA model involves the independent angular parameters relating successive base-pair steps: the sequence-dependent equil. values and fluctuations of the twist, tilt, and roll angles. The curved sequence under study is the (A5X5)n repeating polymer, the AA and XX steps having different equil. roll and twist values. Both planar circles and superhelices are analyzed. Detailed comparison is made between the rigorous statistical mech. representation of the DNA and simplified static models currently used in the literature. I.e., a more realistic lexible wedgemodel is contrasted with the existing tatic wedgemodel of DNA curvature, which is demonstrated to be inadequate. The size of the coils is described by the unperturbed root-mean-square end-to-end distance and the shape by a ratio of the principal moments of the radius of gyration. The moment ratios indicate that when DNA is relatively short (e.g. its length is shorter than half a turn of the static superhelix), the flexible chains are more hort and thickthan the static structure. The end-to-end distances, however, are practically the same in the two models. For longer DNA fragments, the flexible chain is more extended in terms of the end-to-end distance and more globular in terms of the moment ratio. Thus, fluctuations lurthe curvature of longer DNA fragments compared with static models. Furthermore, the overall av. shape of slightly curved DNA subject to natural bending and twisting fluctuations is essentially indistinguishable from that of the corresponding traightDNA. Such configurational similarities are apparently responsible for the relative insensitivity of the polyacrylamide gel matrix to small degrees of DNA curvature. These findings raise serious questions regarding the quant. estn. of wedge angles in DNA from electrophoretic expts., based on static models. Comparison between planar circles and superhelices shows that when fluctuations are considered, the flexible circles are more spherical than the superhelices. The results imply that when DNA bending is exactly ïn phasewith the helical repeat (i.e. when the DNA loop is exactly planar at 0 K), the DNA coil is packed more tightly than when bending and twisting are öut of phase(and a superhelix is formed at 0 K). This finding is consistent with polyacrylamide gel electrophoresis data testifying to an increase in DNA retardation when twisting is more precisely uned. Finally, it is found that asymmetry of bending in the roll coordinate can produce significant macroscopic curvature of DNA. Skewed bending of AA steps in the A5X5 polymer is indistinguishable from sym. bending with the same mean value and fluctuation of roll. Asym. rolling in the AA dimer thus can introduce substantial curvature in DNAs contg. An.Tn blocks, even if the lowest energy stacked arrangement of AA base pair steps is nearly flat, thereby resolving apparent contradictions between the crystallog. and soln. structures of chains contg. An.Tn tracts. [on SciFinder (R)]
BibTeX: @article{RefWorks:311, author = {Wilma K. Olson and Nancy L. Marky and Robert L. Jernigan and Victor B. Zhurkin}, title = {Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.}, journal = {Journal of Molecular Biology}, year = {1993}, volume = {232}, number = {2}, pages = {530-554}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 9; CODEN: JMOBAK; CAS Registry Numbers: 65-71-4 (Thymine) Role: PRP (Properties) (base pair with adenine, in DNA, curvature of tracts of, mol. modeling of); 73-24-5 (Adenine) Role: BIOL (Biological study) (base pair with thymine, in DNA, curvature induced by tracts of, mol. modeling of)} }
Olson, W. K., Marky, N. L., Srinivasan, A. R., Do, K. D. & Cicariello, J.	Theoretical studies of perturbed nucleic acid structures. [Abstract] [BibTeX]	1985	Progress in clinical and biological research	article
Abstract: The probability of perturbing DNA in A or B helixes into 3-dimensional conformations able to bind bulky intercalating or base-binding agents was calcd. by an elaborated form of the Jacobson-Stockmayer cyclization theory (Jacobson, H.; Stockmayer, W. H., 1950). Likely conformational routes linking intact duplexes to bulged forms were identified. Bases in one type of structure distorted to accept bulky ligands were estd. to be free to rotate about the glycosyl linkage as if they were in isolated nucleosides. Single bases in the bulge appeared to rotate out of the helix; rotation out of the duplex was predicted to cause alternation in sugar ring orientation, which is a characteristic of Z-DNA, suggesting a role for such a conformational intermediate in the B->Z transition. A 2nd type of bulge was characterized; it appeared to cause local winding and unwinding of the DNA, with features reminiscent of transitions between right- and left-handed helixes of the same morphol. sense. The influence the local deformations considered on superhelical d. was also examd. with respect to the interactions between secondary and higher-order structures. [on SciFinder (R)]
BibTeX: @article{RefWorks:340, author = {Wilma K. Olson and Nancy L. Marky and Annankoil R. Srinivasan and Khang D. Do and Janet Cicariello}, title = {Theoretical studies of perturbed nucleic acid structures.}, journal = {Progress in clinical and biological research}, year = {1985}, volume = {172}, number = {Mol. Basis Cancer, Pt. A}, pages = {109-121}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 4; CODEN: PCBRD2} }
Olson, W. K. & Srinivasan, A. R.	The translation of DNA primary base sequence into three-dimensional structure. [Abstract] [BibTeX]	1988	CABIOS, Computer Applications in the Biosciences	article
Abstract: A procedure is described for obtaining a reliable computer-generated representation of the DNA duplex from its primary sequence of base pairs. The calcns. are based on the potential energies of interaction of adjacent side groups. The methods are, however, completely general and can be adapted to any set of base sequence dependent conformation rules. Static representations of the DNA are compared with the distributions of conformations obtained from Monte Carlo simulation studies. Direct matrix generator calcns. of the av. (equil.) extension and orientation of various sequences and numerical ests. of the flexibility of the chains as a whole are also reported. The methods are applied to 3 short fragments of kinetoplast DNA from Crithidia fasciculata which exhibit dramatically different behavior on non-denaturing polyacrylamide gels. [on SciFinder (R)]
BibTeX: @article{RefWorks:333, author = {Wilma K. Olson and A. R. Srinivasan}, title = {The translation of DNA primary base sequence into three-dimensional structure.}, journal = {CABIOS, Computer Applications in the Biosciences}, year = {1988}, volume = {4}, number = {1}, pages = {133-142}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 3-5; CA Section Cross-references: 6; CODEN: COABER} }
Olson, W. K., Srinivasan, A. R., Marky, N. L. & Balaji, V. N.	Theoretical probes of DNA conformation examining the B -> Z conformational transition. [Abstract] [BibTeX]	1983	Cold Spring Harbor symposia on quantitative biology	article
Abstract: Theor. studies on the B -> Z transition of DNA, with focus on the variations of the glycosyl torsion, showed that the bases interconvert between syn and anti arrangements without substantial increase in potential energy, provided >=1 parallel, nonadjacent torsions in the sugar-phosphate backbone simultaneously vary in the opposite rotational sense. If coupled with rotational changes in the acyclic bonds that immediately precede and follow them in the chain sequence, the mobile bases also maintain their parallel alignment in the helical structure and their capacity to H bond with complementary residues in the opposite strand. The correlated glycosyl backbone changes displace the bases in question with respect to their immediate neighbors, creating sharp U-turns in the double helix and providing topol. direct connections between B and Z DNA. The reversals of direction, however, condense the polynucleotide structure during the right-to-left transition, the effect being more pronounced at greater chain lengths. The macroscopic dimensions at the 2 ends of the transition, nevertheless, approach the extremely high values typical of stiff, rodlike chains. [on SciFinder (R)]
BibTeX: @article{RefWorks:344, author = {Wilma K. Olson and A. R. Srinivasan and N. L. Marky and V. N. Balaji}, title = {Theoretical probes of DNA conformation examining the B -> Z conformational transition.}, journal = {Cold Spring Harbor symposia on quantitative biology}, year = {1983}, volume = {47}, number = {1}, pages = {229-241}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: CSHSAZ} }
Olson, W. K. & Sussman, J. L.	How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies. [Abstract] [BibTeX]	1982	Journal of the American Chemical Society	article
Abstract: A series of statistical computations have been carried out to test various theor. potential energy ests. of furanose pseudorotation. Energy surfaces describing the flexibility of both ribose and deoxyribose have been compared through a Boltzmann anal. with each other and also with published x-ray and NMR measurements of pseudorotation (i.e., with distributions of solid state puckerings, std. valence angle geometries, and mean vicinal coupling consts. in RNA and DNA analog. No single theor. approach is able to account simultaneously for the exptl. properties of both ribose and deoxyribose. Methods generally satisfactory for ribose pseudorotation are unsuitable for deoxyribose and vice versa. In the commonly occurring mononucleosides and -nucleotides the pseudorotational motions are decidedly tiffwith the potential energy barrier somewhat higher for ribose than for deoxyribose. When incorporated into a polynucleotide backbone, this local stiffness is a major determinant of chain flexibility and a characteristic difference between RNA and DNA systems. [on SciFinder (R)]
BibTeX: @article{RefWorks:349, author = {Wilma K. Olson and Joel L. Sussman}, title = {How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies.}, journal = {Journal of the American Chemical Society}, year = {1982}, volume = {104}, number = {1}, pages = {270-278}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 6, 22; CODEN: JACSAT; CAS Registry Numbers: 79681-15-5; 79681-16-6 Role: RCT (Reactant), RACT (Reactant or reagent) (pseudorotation in)} }
Olson, W. K., Swigon, D. & Coleman, B. D.	Implications of the dependence of the elastic properties of DNA on nucleotide sequence [Abstract] [BibTeX]	2004	Philos Transact A Math Phys Eng Sci	article
Abstract: Recent advances in structural biochemistry have provided evidence that not only the geometric properties but also the elastic moduli of duplex DNA are strongly dependent on nucleotide sequence in a way that is not accounted for by classical rod models of the Kirchhoff type. A theory of sequence-dependent DNA elasticity is employed here to calculate the dependence of the equilibrium configurations of circular DNA on the binding of ligands that can induce changes in intrinsic twist at a single base-pair step. Calculations are presented of the influence on configurations of the assumed values and distribution along the DNA of intrinsic roll and twist and a modulus coupling roll to twist. Among the results obtained are the following. For minicircles formed from intrinsically straight DNA, the distribution of roll-twist coupling strongly affects the dependence of the total elastic energy Psi on the amount alpha of imposed untwisting, and that dependence can be far from quadratic. (In fact, for a periodic distribution of roll-twist coupling with a period equal to the intrinsic helical repeat length, Psi can be essentially independent of alpha for -90 degrees < alpha <90 degrees.) When the minicircle is homogeneous and without roll-twist coupling, but with uniform positive intrinsic roll, the point at which Psi attains its minimum value shifts towards negative values of alpha. It is remarked that there are cases in which one can relate graphs of Psi versus alpha to the 'effective values' of bending and twisting moduli and helical repeat length obtained from measurements of equilibrium distributions of topoisomers and probabilities of ring closure. For a minicircle formed from DNA that has an 'S' shape when stress-free, the graphs of Psi versus alpha have maxima at alpha = 0. As the binding of a twisting agent to such a minicircle results in a net decrease in Psi, the affinity of the twisting agent for binding to the minicircle is greater than its affinity for binding to unconstrained DNA with the same sequence. [on SciFinder (R)]
BibTeX: @article{RefWorks:434, author = {Wilma K. Olson and David Swigon and Bernard D. Coleman}, title = {Implications of the dependence of the elastic properties of DNA on nucleotide sequence}, journal = {Philos Transact A Math Phys Eng Sci}, year = {2004}, volume = {362}, number = {1820}, pages = {1403-1422}, note = {Journal Code: 101133385; CAS Registry Numbers: 9007-49-2 (DNA); Chemical Name: 0 (DNA-Binding Proteins); 0 (Nucleotides)} }
Olson, W. K., Westcott, T. P., Martino, J. A. & Liu, G.	Computational studies of spatially constrained DNA. [Abstract] [BibTeX]	1996	IMA Volumes in Mathematics and Its Applications	article
Abstract: A review, with 51 refs., on various elastic energy models and computer simulation techniques that are in studying protein-induced folding of DNA. [on SciFinder (R)]
BibTeX: @article{RefWorks:409, author = {Wilma K. Olson and Timothy P. Westcott and Jennifer A. Martino and Guo-Hua Liu}, title = {Computational studies of spatially constrained DNA.}, journal = {IMA Volumes in Mathematics and Its Applications}, year = {1996}, volume = {82}, number = {Mathematical Approaches to Biomolecular Structure and Dynamics}, pages = {195-217}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-0; CODEN: IVMAFU} }
Olson, W. K. & Zhang, P.	Computer simulation of DNA supercoiling. [Abstract] [BibTeX]	1991	Methods in enzymology	article
Abstract: The simulation and modeling of DNA supercoiling is described. The procedure for the computer anal. of this process is discussed. [on SciFinder (R)]
BibTeX: @article{RefWorks:321, author = {Wilma K. Olson and Peisen Zhang}, title = {Computer simulation of DNA supercoiling.}, journal = {Methods in enzymology}, year = {1991}, volume = {203}, number = {Mol. Des. Model.: Concepts Appl., Pt. B.}, pages = {403-432}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: MENZAU} }
Olson, W. K. & Zhurkin, V. B.	Modeling DNA deformations. [Abstract] [BibTeX]	2000	Current opinion in structural biology	article
Abstract: A review, with .apprx.84 refs. Recent developments have been made in modeling double-helical DNA at four levels of three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is surrounded by a shroud of solvent mols.; the base-pair level, with explicit backbone atoms; the mesoscopic level, i.e., a few hundred base pairs, with the local duplex conformation described by knowledge-based harmonic energy functions; and the scale of several thousand nucleotides, with the duplex described as an ideal elastic rod. Predictions of the sequence-dependent bending and twisting of the double helix, as well as solvent- and force-induced B->A and over-stretching conformational transitions, are compared with exptl. data. These subtle conformational changes are crit. to the functioning of the double helix, including its packaging in the close confines of the cell, the mutual fit of DNA and protein in nucleoprotein complexes, and the effective recognition of base pairs in recombination and transcription. [on SciFinder (R)]
BibTeX: @article{RefWorks:384, author = {Wilma K. Olson and Victor B. Zhurkin}, title = {Modeling DNA deformations.}, journal = {Current opinion in structural biology}, year = {2000}, volume = {10}, number = {3}, pages = {286-297}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-0; CODEN: COSBEF} }
Pilch, D. S., Yu, C., Makhey, D., LaVoie, E. J., Srinivasan, A. R., Olson, W. K., Sauers, R. R., Breslauer, K. J., Geacintov, N. E. & Liu, L. F.	Minor Groove-Directed and Intercalative Ligand-DNA Interactions in the Poisoning of Human DNA Topoisomerase I by Protoberberine Analogs. [Abstract] [BibTeX]	1997	Biochemistry	article
Abstract: Spectroscopic, calorimetric, DNA cleavage, electrophoretic, and computer modeling techniques have been employed to characterize the DNA binding and topoisomerase poisoning properties of three protoberberine analogs, 8-demethylcoralyne (DMC), 5,6-dihydro-8-demethylcoralyne (DHDMC), and palmatine, which differ in the chem. structures of their B- and/or D-rings. DNA topoisomerase-mediated cleavage assays revealed that these compds. were unable to poison mammalian type II topoisomerase. By contrast, the three protoberberine analogs poisoned human topoisomerase I according to the following hierarchy: DHDMC > DMC > palmatine. DNA binding by all three protoberberine analogs induced neg. flow linear dichroism signals as well as unwinding of the host duplex. These two observations are consistent with an intercalative mode of protoberberine binding to duplex DNA. However, a comparison of the DNA binding properties for DMC and DHDMC, which differ only by the state of satn. at the 5,6 positions of the B-ring, revealed that the protoberberine analogs do not ehavelike classic DNA intercalators. Specifically, satn. of the 5-6 double bond in the B-ring of DMC, thereby converting it to the DHDMC mol., was assocd. with enhanced DNA unwinding as well as a reversal of DNA binding preference from a DNA duplex with an inaccessible or occluded minor groove poly[d(G-C)]2 to DNA duplexes with accessible or unobstructed minor grooves poly[d(A-T)]2 and poly[d(I-C)]2. In addn., a comparison of the DNA binding properties for DHDMC and palmatine revealed that transferring the 11-methoxy moiety on the D-ring of DHDMC to the 9 position, thereby converting it to palmatine, was assocd. with a redn. in binding affinity for both duplexes with unobstructed minor grooves as well as for duplexes with occluded minor grooves. These DNA binding properties are consistent with a ixed-modeDNA binding model for protoberberines in which a portion of the ligand mol. (rings C and D) intercalates into the double helix, while the nonintercalated portion of the ligand mol. (ring A) protrudes into the minor groove of the host duplex, where it is thereby available for interactions with atoms lining the floor and/or walls of the minor groove. Furthermore, satn. at the 5,6 positions of the B-ring, which causes the A-ring to be tilted relative to the plane formed by rings C and D, appears to stabilize the interaction between the host duplex and the minor groove-directed portion of the protoberberine ligand. Computer modeling studies on the DHDMC-poly[d(A-T)]2 complex suggest that this interaction may involve van der Waals contacts between the ligand A-ring and backbone sugar atoms lining the minor groove of the host duplex. The hierarchy of topoisomerase I poisoning noted above suggests that this minor groove-directed interaction may play an important role in topoisomerase I poisoning by protoberberine analogs. In the aggregate, our results presented here, coupled with the recent demonstration of topoisomerase I poisoning by minor groove-binding terbenzimidazoles [Sun, Q., Gatto, B., Yu, C., Liu, A., Liu, L. F., & LaVoie, E. J. (1995) J. Med. Chem. 38, 3638-3644], suggest that minor groove-directed ligand-DNA interactions may be of general importance in the poisoning of topoisomerase I. [on SciFinder (R)]
BibTeX: @article{RefWorks:405, author = {Daniel S. Pilch and Chiang Yu and Darshan Makhey and Edmond J. LaVoie and A. R. Srinivasan and Wilma K. Olson and Ronald R. Sauers and Kenneth J. Breslauer and Nicholas E. Geacintov and Leroy F. Liu}, title = {Minor Groove-Directed and Intercalative Ligand-DNA Interactions in the Poisoning of Human DNA Topoisomerase I by Protoberberine Analogs.}, journal = {Biochemistry}, year = {1997}, volume = {36}, number = {41}, pages = {12542-12553}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 1-6; CODEN: BICHAW; CAS Registry Numbers: 3486-67-7 (Palmatine); 6872-81-7 (8-Demethylcoralyne); 19716-66-6 (5,6-Dihydro-8-demethylcoralyne); 19716-69-9D (Protoberberine) Role: BAC (Biological activity or effector, except adverse), BSU (Biological study, unclassified), BIOL (Biological study) (minor groove-directed and intercalative ligand-DNA interactions in poisoning of human DNA topoisomerase I by protoberberine analogs); 143180-75-0 (DNA Topoisomerase I) Role: BAC (Biological activity or effector, except adverse), BSU (Biological study, unclassified), BIOL (Biological study) (poisoning of; minor groove-directed and intercalative ligand-DNA interactions in poisoning of human DNA topoisomerase I by protoberberine analogs)} }
Ruan, Q., Zhuang, P., Li, S., Perlow, R., Srinivasan, A. R., Lu, X., Broyde, S., Olson, W. K. & Geacintov, N. E.	Base Sequence Effects in Bending Induced by Bulky Carcinogen-DNA Adducts: Experimental and Computational Analysis. [Abstract] [BibTeX]	2001	Biochemistry	article
Abstract: The covalent binding of bulky mutagenic or carcinogenic compds. to DNA can lead to bending, which could significantly alter the interactions of DNA with crit. replication and transcription proteins. The impact of adducts derived from the highly reactive bay region enantiomeric (+)- and (-)-anti-7,8-diol-9,10-epoxide derivs. of benzo[a]pyrene (BPDE) are of interest because the (+)-7R,8S,9S,10R-anti-BPDE enantiomer is highly tumorigenic in rodents, while the (-)-7S,8R,9R,10S-anti-BPDE enantiomer is not. Both (+)- and (-)-anti-BPDE bind covalently with DNA predominantly by trans addn. at the exocyclic amino group of guanine to yield 10S (+)- and 10R (-)-trans-anti-[BP]-N2-dG adducts. The authors have synthesized a no. of different oligonucleotides with single (+)- and (-)-trans-anti-[BP]-N2-dG adducts (G) in the base sequence context XGY, where X and Y are different DNA bases. The G* residues were positioned at or close to the center of 11 base pair (.apprx.1 helical turn) or 16 base pair (.apprx.1.5 turns) duplexes. All bases, except for X and Y and their partners, were identical. These sequences were self-ligated with T4 ligase to form multimers that yield a ladder of bands upon electrophoresis in native polyacrylamide gels. The extent of bending in each oligonucleotide was assessed by monitoring the decrease in gel mobilities of these linear, self-ligated oligomers, relative to unmodified oligonucleotides of the same base sequence. The extent of global bending was then estd. using a sequence-specific three-dimensional model from which the values of the base-pair step parameter roll adjacent to the lesion site could be extd. The authors find that (+)-trans-anti-[BP]-N2-dG adducts are considerably more bent than the (-) isomers regardless of sequence and that A-T base pairs flanking the [BP]-N2-dG lesion site allow for local flexibility consistent with adduct conformational heterogeneity. Interestingly, the fit of computed vs. obsd. gel mobilities using classical reptation treatments requires enhancement of unmodified DNA flexibility in gels, compared to aq. salt soln. The differences in bending between the two stereoisomeric adduct duplexes and the obsd. base sequence context effects may play a significant role in the differential processing of these lesions by cellular replication, transcription, and repair enzymes. [on SciFinder (R)]
BibTeX: @article{RefWorks:382, author = {Qian Ruan and Ping Zhuang and Sheng Li and Rebecca Perlow and A. R. Srinivasan and Xiang-Jun Lu and Suse Broyde and Wilma K. Olson and Nicholas E. Geacintov}, title = {Base Sequence Effects in Bending Induced by Bulky Carcinogen-DNA Adducts: Experimental and Computational Analysis.}, journal = {Biochemistry}, year = {2001}, volume = {40}, number = {35}, pages = {10458-10472}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 4-6; CODEN: BICHAW; CAS Registry Numbers: 63323-30-8D; 63323-31-9D Role: ADV (Adverse effect, including toxicity), PRP (Properties), BIOL (Biological study) (base sequence effects in bending induced by bulky carcinogen-DNA adducts: exptl. and computational anal.); 65437-20-9P; 85026-87-5P; 366850-05-7P; 366850-06-8P; 366850-07-9P; 366850-08-0P; 366850-09-1P; 366850-10-4P; 366850-11-5P; 366850-12-6P; 367317-58-6P; 367317-59-7P; 367317-60-0P; 367317-61-1P; 367317-62-2P; 367317-63-3P; 367317-64-4P; 367317-65-5P Role: PRP (Properties), SPN (Synthetic preparation), PREP (Preparation) (base sequence effects in bending induced by bulky carcinogen-DNA adducts: exptl. and computational anal.)} }
Schlick, T., Li, B. & Olson, W. K.	The influence of salt on the structure and energetics of supercoiled DNA. [Abstract] [BibTeX]	1994	Biophysical journal	article
Abstract: The authors present a detailed computation study of the influence of salt on the configurations, energies, and dynamics of supercoiled DNA. A potential function that includes both elastic and electrostatic energy components is employed. Specifically, the electrostatic term, with salt-dependent coeffs., is modeled after Stigter's pioneering work on the effective diam. of DNA as a function of salt concn. Because an effective charge per unit length is used, the electrostatic formulation does not require explicit modeling of phosphates and can be used to study long DNAs at any desired resoln. of charge. With explicit consideration of the electrostatic energy, an elastic bending const. corresponding to the nonelectrostatic part of the bending contribution to the persistence length is used. The authors show, for a series of salt concns. ranging from 0.005 to 1.0 M sodium, how configurations and energies of supercoiled DNA (1000 and 3000 base pairs) change dramatically with the simulated salt environment. At high salt, the DNA adopts highly compact and bent interwound states, with the bending energy dominating over the other components, and the electrostatic energy playing a minor role in comparison to the bending energy dominating over low salt, the DNA supercoils are much more open and loosely interwound, and the electrostatic components are dominant. Over the range of three decades of salt examd., the electrostatic energy changes by a factor of 10. The buckling transition between the circle and figure-8 is highly sensitive to salt concn.: this transition is delayed as salt concn. decreases, with a particularly sharp increase below 0.1 M. For example, for a bending-to-twisting force const. ratio of A/C = 1.5, the linking no. difference (DLK) corresponding to equal energies for the circle and figure-8 increases from 2.1 to 3.25 as salt decreases from 0.1 to 0.005 M. The authors also present in detail a family of three-lobed supercoiled DNA configurations that are predicted by elasticity theory to be stable at low DLK. To the authors' knowledge, such three-dimensional structures have not been previously presented in connection with DNA supercoiling. These branched forms have a higher bending energy than the corresponding interwound configurations at the same DLK but, esp. at low salt, this bending energy difference is relatively small in comparison with the total energy, which is dominated by the electrostatic contributions. Significantly, the electrostatic energies of the three-lobed and (straight) interwound forms are comparable at each salt environment. The authors show how the three-lobed configurations change slowly with DLK, resulting in branched interwound forms at higher salt. In longer chains, the branched forms are highly interwound, with bent arms. At low salt, the branched supercoils are asym., with a longer interwound stem and two shorter arms. From mol. dynamics simulations the authors observe differences in the motions of the DNA as a function of salt. At high salt, the supercoiled chain is quite compact but fairly rigid, whereas at low salt the DNA is loosely coiled but more dynamic. Esp. notable at low salt are the large-scale opening and closing of the chain as a whole and the rapid litheringof individual residues past one another. Toroidal forms are not detected under these conditions. However, the overall features of the open, loose supercoils found at low salt are more similar to those of toroidal than interwound configurations. Indeed, simulated x-ray scattering profiles reveal the same trends obsd. exptl. and are consistent with a change from closed to open forms as salt is decreased. Like the minimization studies, the dynamics reveal a crit. point near 0.1 M assocd. with the collapse of loose to tight supercoils. Near this physiol. concn., enhanced flexibility of the DNA is noted. The collective observations suggest a potential regulatory role for salt on supercoiled DNA function, not only for closed circular DNA, but also for linear DNA with small looped regions. [on SciFinder (R)]
BibTeX: @article{RefWorks:425, author = {Tamar Schlick and Bin Li and Wilma K. Olson}, title = {The influence of salt on the structure and energetics of supercoiled DNA.}, journal = {Biophysical journal}, year = {1994}, volume = {67}, number = {6}, pages = {2146-2166}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 3; CODEN: BIOJAU; CAS Registry Numbers: 7647-14-5 (Sodium chloride) Role: BSU (Biological study, unclassified), PRP (Properties), BIOL (Biological study) (influence of salt on structure and energetics of supercoiled DNA)} }
Schlick, T. & Olson, W. K.	Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA. [Abstract] [BibTeX]	1992	Science (Washington, DC, United States)	article
Abstract: Computer simulations of the supercoiling of DNA, largely limited to stochastic search techniques, can offer important information to complement anal. models and exptl. data. Through assocn. of an energy function, min.-energy supercoiled conformations, fluctuations about these states, and interconversions among forms may be sought,. In theory, the observation of such large-scale conformational changes is possible, but modeling and numerical considerations limit the picture obtained in practice. A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and mol. dynamics algorithms. A trefoil knotting result, made possible by a large time-step dynamics scheme, is described. The simulated strand passage supports and details a supercoiled-directed knotting mechanism. This process may be assocd. with collective bending and twisting motions involved in supercoiling propagation and interwound branching. The results also demonstrate the potential effectiveness of the Langevin/implicit-Euler dynamics scheme for studying biomol. folding and reactions over biol. interesting time scales. [on SciFinder (R)]
BibTeX: @article{RefWorks:316, author = {Tamar Schlick and Wilma K. Olson}, title = {Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA.}, journal = {Science (Washington, DC, United States)}, year = {1992}, volume = {257}, number = {5073}, pages = {1110-1115}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CA Section Cross-references: 9; CODEN: SCIEAS} }
Schlick, T. & Olson, W. K.	Supercoiled DNA energetics and dynamics by computer simulation. [Abstract] [BibTeX]	1992	Journal of Molecular Biology	article
Abstract: The construction and application are described of a new supercoiled DNA model for investigating DNA energetics and dynamics by deterministic techniques. Minimizations of small DNA rings at low imposed linking no. differences produce a series of supercoiled interwound structures consistent with available electron microscopy data. Results are also in very good agreement with available anal. results and confirm early computational analyses by stochastic methods. [on SciFinder (R)]
BibTeX: @article{RefWorks:322, author = {Tamar Schlick and Wilma K. Olson}, title = {Supercoiled DNA energetics and dynamics by computer simulation.}, journal = {Journal of Molecular Biology}, year = {1992}, volume = {223}, number = {4}, pages = {1089-1119}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: JMOBAK} }
Schlick, T., Olson, W. K., Westcott, T. & Greenberg, J. P.	On higher buckling transitions in supercoiled DNA. [Abstract] [BibTeX]	1994	Biopolymers	article
Abstract: A combination of detailed energy minimization and mol. dynamics studies of closed circular DNA offers here new information that may be be relevant to the dynamics of short DNA chains and/or low superhelical densities. The authors find a complex dependence of supercoiled DNA energies and geometries on the linking no. difference DLk as physiol. superhelical densities (\|s\| .apprx. 0.006) are approached. The energy minimization results confirm and extend predictions of classical elasticity theory for the equil. of elastic rods. The mol. dynamics results suggest how these findings may affect the dynamics of supercoiled DNA. The minimization reveals sudden higher order configurational transitions in addn. to the well-known catastrophic buckling from the circle to the figure-8. The competition among the bending, twisting, and self-contact forces leads to different families of supercoiled forms. Some of those families begin with configurations of near-zero twist. This offers the intriguing possibility that nicked DNA may relax to low-twist forms to other than the circle, as generally assumed. Furthermore, for certain values of DLk, more than one interwound DNA min. exists. The writhing no. as a function of DLk is discontinuous in some ranges; it exhibits pronounced jumps as DLk is increased from zero, and it appears to level off to a characteristic slope only at higher values of DLk. These findings suggest that supercoiled DNA may undergo systematic rapid interconversions between different min. that are both close in energy and geometry. The authors' mol. dynamics simulations reveal such transitional behavior. The authors observe the macroscopic bending and twisting fluctuations of interwound forms about the global helix axis as well as the end-over-end tumbling of the DNA as a rigid body. The overall mobility can be related to \|s\| and to the bending, twisting, and van der Waals energy fluctuations. The general character of mol. motions is thus detd. by the types of energy min. found at a given DLk. Different time scales may be attributed to each type of motion: the overall chain folding occurs on a time scale almost an order of magnitude faster than the end-over-end tumbling. The local bending and twisting of individual chain residues occur at an even faster rate, which in turn correspond to several cycles of local variations for each large-scale bending and straightening motion of the DNA. [on SciFinder (R)]
BibTeX: @article{RefWorks:428, author = {Tamar Schlick and Wilma K. Olson and Timothy Westcott and Jerry P. Greenberg}, title = {On higher buckling transitions in supercoiled DNA.}, journal = {Biopolymers}, year = {1994}, volume = {34}, number = {5}, pages = {565-597}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Schneider, B., Cohen, D. M., Schleifer, L., Srinivasan, A. R., Olson, W. K. & Berman, H. M.	A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. [Abstract] [BibTeX]	1993	Biophysical journal	article
Abstract: A new method to analyze the distribution of water mols. around the bases in DNA is presented. This method relies on the notion of a ydrated building block,which represents the joint obsd. hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using at. coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calcd. for water mols. in each hydrated building block using std. crystallog. procedures. The electron densities were fitted to obtain äv. building blocks,which represent bases with waters only at av. or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced. [on SciFinder (R)]
BibTeX: @article{RefWorks:308, author = {Bohdan Schneider and Dawn M. Cohen and Leah Schleifer and A. R. Srinivasan and Wilma K. Olson and Helen M. Berman}, title = {A systematic method for studying the spatial distribution of water molecules around nucleic acid bases.}, journal = {Biophysical journal}, year = {1993}, volume = {65}, number = {6}, pages = {2291-2303}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-16; CA Section Cross-references: 6; CODEN: BIOJAU; CAS Registry Numbers: 58927-26-7 (d(CGCGCG) Role: ANST (Analytical study) (double-stranded, hydration of, mol. modeling of); 77889-82-8 (d(CGCGAATTCGCG) Role: ANST (Analytical study) (hydration of, mol. modeling of); 65-71-4 (Thymine); 71-30-7 (Cytosine); 73-24-5 (Adenine); 73-40-5 (Guanine) Role: PRP (Properties) (hydration sites of, DNA conformation effect on, mol. modeling study of)} }
Srinivasan, A. R. & Olson, W. K.	Molecular Models of Nucleic Acid Triple Helixes. II. PNA and 2'-5' Backbone Complexes. [Abstract] [BibTeX]	1998	Journal of the American Chemical Society	article
Abstract: We describe nucleic acid triple-helical structures contg. either amide or 2'-5' linkages, the former backbone describing the chem. of certain peptide nucleic acids (PNA). The methodol. and the starting ref. frame are the same as those described in the preceding article. Apart from evaluating the possible combinations of chain conformations that connect adjacent bases on each of the three strands, we have examd. the feasibility of triplex formation when neighboring Watson-Crick+Hoogsteen hydrogen-bonded base triples are displaced by small amts. along their short and long axes. The predicted triple-helical complexes are examd. in terms of relevant crystallog., spectroscopic, and calorimetric data. The computed models clarify why PNA cannot form B-like structures and also reveal principles useful for the design of other triplex-forming DNA mimics. [on SciFinder (R)]
BibTeX: @article{RefWorks:402, author = {A. R. Srinivasan and Wilma K. Olson}, title = {Molecular Models of Nucleic Acid Triple Helixes. II. PNA and 2'-5' Backbone Complexes.}, journal = {Journal of the American Chemical Society}, year = {1998}, volume = {120}, number = {3}, pages = {492-508}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JACSAT} }
Srinivasan, A. R. & Olson, W. K.	Molecular Models of Nucleic Acid Triple Helixes. I. DNA and RNA Backbone Complexes. [Abstract] [BibTeX]	1998	Journal of the American Chemical Society	article
Abstract: Using a constrained mol. modeling method, we have generated DNA (D), RNA (R), and hybrid DNA/RNA triple-helical structures. Starting with the ref. frame defined by the X-ray fiber diffraction model of the poly(dT).poly(dA)+poly(dT) triple helix, where denotes Watson-Crick pairing and indicates Hoogsteen pairing, we have exhaustively sampled the arrangements of the sugar-phosphate backbone that connect adjacent bases on each of the three strands. We focus attention on regular polymer models constructed from conformationally identical repeating units. Structures free of local steric constraints are combined in all possible ways to build short triplexes, and overall triple helix energies are computed under several different dielec. environments. The predicted ordering of Pyr.Pu+Pyr triplex stabilities, D.D+D > D.D+R > D.R+D > D.R+R > R.D+D > R.D+R > R.R+D > R.R+R, agrees qual. with measured stabilities of triplexes contg. DNA and/or RNA single strands in gel electrophoresis, NMR, X-ray, and thermodn. studies. The relevance of the computed data to other triple helical simulations is also discussed. [on SciFinder (R)]
BibTeX: @article{RefWorks:403, author = {A. R. Srinivasan and Wilma K. Olson}, title = {Molecular Models of Nucleic Acid Triple Helixes. I. DNA and RNA Backbone Complexes.}, journal = {Journal of the American Chemical Society}, year = {1998}, volume = {120}, number = {3}, pages = {484-491}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JACSAT} }
Srinivasan, A. R. & Olson, W. K.	Computer Models of DNA Four-Way Junctions. [Abstract] [BibTeX]	1994	Biochemistry	article
Abstract: A modeling scheme that combines a constrained backbone generating algorithm with simple hard-sphere packing calcns. is offered to build the four-stranded structures of DNA found in Holliday junctions. Two std. B-DNA duplexes are oriented side by side with helix axes at different relative inclinations and then systematically rotated and translated to identify closely spaced contact-free states. Attempts are subsequently made to introduce a low-energy sugar-phosphate linkage that serves as the site of strand exchange between the two duplexes. The chem. connection is sought using an algorithm which identifies the possible arrangements of the intervening backbone torsions between arbitrarily positioned bases. The goal is to identify the multiple conformational solns. assocd. with a particular arrangement of neighboring DNA helixes in the four-way junction rather than a single optimum structure. The methodol. is general, in terms of accommodating four-way junctions with arms of variable conformation and chain length and of dimensions much greater than treated heretofore. The only deformation in the four-way structures relative to B-DNA occurs at the site of backbone exchange, with base stacking and Watson-Crick pairing completely preserved in all models. The arrangements of neighboring bases at these sites resemble the unusual conformational steps found in a no. of small mol. nucleic acid crystal structures. An interesting outcome of the calcns. is the formation of sterically acceptable four-arm Holliday junctions over a wide range of angles at the cross. The potential mobility of the Holliday junctions is inferred from visualization and energetic anal. of the various models. Long-range electrostatic energies based on different currently available treatments of the dielec. const. are used to est. the conformational preferences and flexibility of the four-stranded structures. The various dielec. schemes, however, are not in complete agreement on the likely conformational variability of the four-way junctions. The structures suggest a possible mechanism for branch migration and detail a pathway linking the antiparallel uncrossed Holliday structure inferred from soln. measurements and the parallel cross-packed helical arrangements obsd. in single-crystal X-ray studies. [on SciFinder (R)]
BibTeX: @article{RefWorks:429, author = {A. R. Srinivasan and Wilma K. Olson}, title = {Computer Models of DNA Four-Way Junctions.}, journal = {Biochemistry}, year = {1994}, volume = {33}, number = {32}, pages = {9389-9404}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 3-1; CA Section Cross-references: 9; CODEN: BICHAW} }
Srinivasan, A. R. & Olson, W. K.	DNA associations: packing calculations in A-, B-, and Z-DNA structures. [Abstract] [BibTeX]	1992	Biophysical chemistry	article
Abstract: A detailed theor. study has been carried out to examine the modes of DNA-DNA interactions on the basis of hard-sphere contact criteria. Two helixes of identical structure and length are oriented side-by-side and their relative positions are controlled by translations along and rotations about specific axes. Short at. contacts between pairs of atoms in the structures are assessed and contact-free configurations are compiled. The computed contact-free arrangements of A, B, and Z double helixes are found to be remarkably similar to the packing motifs obsd. in DNA crystals and stretched fibers. Equally interesting in the study are the broad ranges of sterically acceptable arrangements that preserve the overall packing morphol. of neighboring duplexes: among the most notable morphol. features in the helical complexes are extended super major and minor grooves which might facilitate the wrapping and packaging of DNA chains in supramol. assemblies. The hard-sphere computations, however, are insufficient for quant. interpretation of the packing of DNA helixes in the solid state. The results are, nevertheless, a useful starting point for energy based studies as well as relevant to the anal. of long-range interactions in DNA supercoils and cruciforms. [on SciFinder (R)]
BibTeX: @article{RefWorks:319, author = {A. R. Srinivasan and Wilma K. Olson}, title = {DNA associations: packing calculations in A-, B-, and Z-DNA structures.}, journal = {Biophysical chemistry}, year = {1992}, volume = {43}, number = {3}, pages = {279-310}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BICIAZ} }
Srinivasan, A. R. & Olson, W. K.	Viewing stereo drawings. [Abstract] [BibTeX]	1989	Journal of chemical education	article
Abstract: An inherent error is described when viewing stereograms with the unaided cross-eyed stereopsis. Such stereo pairs in the literature are in general designed to provide the correct 3-dimensional appearance when viewed with a stereo viewer, and a mirror image of the true object is perceived with the unaided eye. This problem is avoided if stereo triptych representations are used in place of conventional stereo diagrams. [on SciFinder (R)]
BibTeX: @article{RefWorks:328, author = {A. R. Srinivasan and Wilma K. Olson}, title = {Viewing stereo drawings.}, journal = {Journal of chemical education}, year = {1989}, volume = {66}, number = {8}, pages = {664-665}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 20-4; CODEN: JCEDA8} }
Srinivasan, A. R. & Olson, W. K.	Spatial density distributions for illustrating the base sequence dependent features of double helical DNA: computer graphic visualization of Monte Carlo chain simulations. [Abstract] [BibTeX]	1988	Journal of Molecular Graphics	article
Abstract: The sequence-directed flexibility of double helical DNA is examd. with color-coded representations of the spatial probability d. distributions of the chain ends. The distributions are derived from Monte Carlo simulations that incorporate local sequence-dependent bending of neighboring Watson-Crick base pairs. The d. functions are compared with typical rigid representations of the double helix and with sample Monte Carlo trajectories. Applications are presented for three short fragments of kinetoplast DNA from Crithidia fasciculata, which exhibit dramatically different behavior on nondenaturing polyacrylamide gels. The distributions (based on 106 configurations per chain) are useful descriptors of overall chain flexibility, illustrating the effects of chain length and base sequence on macromol. configuration and revealing characteristic differences between curbed and rodlike DNA. [on SciFinder (R)]
BibTeX: @article{RefWorks:331, author = {A. R. Srinivasan and Wilma K. Olson}, title = {Spatial density distributions for illustrating the base sequence dependent features of double helical DNA: computer graphic visualization of Monte Carlo chain simulations.}, journal = {Journal of Molecular Graphics}, year = {1988}, volume = {6}, number = {3}, pages = {126-34, 141}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-15; CA Section Cross-references: 6; CODEN: JMGRDV; CAS Registry Numbers: 118389-74-5; 118389-75-6; 118389-78-9 Role: ANST (Analytical study) (spatial d. distribution of, color-coded representation of)} }
Srinivasan, A. R. & Olson, W. K.	Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. [Abstract] [BibTeX]	1987	Journal of Biomolecular Structure & Dynamics	article
Abstract: A constrained model building procedure is used to generate nucleic acid structures of the familiar A-, B-, and Z-DNA duplexes. Attention is focused upon the multiple structural solns. assocd. with the arrangements of nucleic acid base pairs rather than the optimum sugar-phosphate structure. The glycosyl (X) and sugar torsions (both the ring puckering and the exocyclic C5'-C4' (y) torsion) are treated as independent variables and the resulting O3'...O5' distances are used as closure determinants. When such distances conform to the known geometry of phosphate chem. bonding an intervening P atom with correct C-O-P valence angles can be located. Four sequential torsion angles-f', w', w and f-about the C3'-O3'-P-O5'-C5' bonds are then obtained as dependent variables. The resulting structures are categorized in terms of conformation, ranked in potential energy, and analyzed for torsional correlations. The numerical results are quite interesting with implications regarding nucleic acid models constructed to fit less than ideal exptl. data. The multiple solns. to the problem are useful for comprehending the conformational complexities of the local sugar-phosphate backbone and for understanding the transitions between different helical forms. According to these studies, unique characterization of a nucleic acid duplex involves more than the detn. of its base pair morphol., its sugar puckering preferences, or its groove binding features. [on SciFinder (R)]
BibTeX: @article{RefWorks:337, author = {A. R. Srinivasan and Wilma K. Olson}, title = {Nucleic acid model building: the multiple backbone solutions associated with a given base morphology.}, journal = {Journal of Biomolecular Structure & Dynamics}, year = {1987}, volume = {4}, number = {6}, pages = {895-938}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JBSDD6} }
Srinivasan, A. R., Torres, R., Clark, W. & Olson, W. K.	Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. [Abstract] [BibTeX]	1987	Journal of Biomolecular Structure & Dynamics	article
Abstract: A series of potential energy calcns. were carried out to est. base sequence dependent structural differences in B-DNA. Attention has been focused on the simplest dimeric fragments that can be used to build long chains, computing the energy as a function of the orientation and displacement of the 16 possible base pair combinations within the double helix. Calcns. were performed, for simplicity, on free base pairs rather than complete nucleotide units. Conformational preferences and relative flexibilities are reported for various combinations of the roll, tilt, twist, lateral displacement, and propeller twist of individual residues. The predictions are compared with relevant exptl. measures of conformation and flexibility, where available. The energy surfaces fit into 2 distinct categories, some dimer duplexes preferring to bend in a sym. fashion and others in a skewed manner. The effects of common chem. substitutions (uracil for thymine, 5-Me cytosine for cytosine, and hypoxanthine for guanine) on the preferred arrangements of neighboring residues are also examd., and the interactions of the sugar-phosphate backbone are included in selected cases. As a 1st approxn., long range interactions between more distant neighbors, which may affect the local chain configuration, are ignored. A rotational isomeric state scheme is developed to describe the av. configurations of individual dimers and is used to develop a static picture of overall double helical structure. The ability of the energetic scheme to account for documented examples of intrinsic B-DNA curvature is presented, and some new predictions of sequence directed chain bending are offered. [on SciFinder (R)]
BibTeX: @article{RefWorks:336, author = {A. R. Srinivasan and Ramon Torres and William Clark and Wilma K. Olson}, title = {Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology.}, journal = {Journal of Biomolecular Structure & Dynamics}, year = {1987}, volume = {5}, number = {3}, pages = {459-96, 2 plates}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JBSDD6; CAS Registry Numbers: 65-71-4 (Thymine); 66-22-8 (Uracil); 68-94-0 (Hypoxanthine); 71-30-7 (Cytosine); 73-24-5 (Adenine); 73-40-5 (Guanine); 554-01-8 (5-Methylcytosine) Role: BIOL (Biological study) (base pairing of, conformational energy of, nearest neighbor effect on); 58495-66-2 Role: PRP (Properties) (conformational energy of); 114989-41-2 Role: BIOL (Biological study) (double-stranded, structure of, nucleotide nearest neighbor influence on); 24939-09-1; 30730-10-0; 114440-02-7; 114989-43-4 Role: PRP (Properties) (structure of, nucleotide nearest neighbor influence on)} }
Srinivasan, A. R., Westbrook, J. D. & Olson, W. K.	An interactive FORTRAN program for three-dimensional molecular visualization. [Abstract] [BibTeX]	1992	Computers & Chemistry (Oxford, United Kingdom)	article
Abstract: An interactive FORTRAN program executable in the VAX/VMS computer environment has been developed for three-dimensional mol. visualization on the Evans & Sutherland Picture System 390. The essential features of this program are described and the FORTRAN source code is available upon request. [on SciFinder (R)]
BibTeX: @article{RefWorks:318, author = {A. R. Srinivasan and John D. Westbrook and Wilma K. Olson}, title = {An interactive FORTRAN program for three-dimensional molecular visualization.}, journal = {Computers & Chemistry (Oxford, United Kingdom)}, year = {1992}, volume = {16}, number = {3}, pages = {265-266}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 20-5; CODEN: COCHDK} }
Sroud, R. M., Olson, W. K., Sheetz, M. P. & Editors	Annual Review of Biophysics and Biomolecular Structure, Volume 31. [BibTeX]	2002		article
BibTeX: @article{RefWorks:379, author = {Robert M. Sroud and Wilma K. Olson and Michael P. Sheetz and Editors}, title = {Annual Review of Biophysics and Biomolecular Structure, Volume 31.}, year = {2002}, pages = {559}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-7} }
Stroud, R. M., Olson, W. K., Sheetz, M. P. & Editors	Annual Review of Biophysics and Biomolecular Structure, Volume 32. [BibTeX]	2003		article
BibTeX: @article{RefWorks:375, author = {Robert M. Stroud and Wilma K. Olson and Michael P. Sheetz and Editors}, title = {Annual Review of Biophysics and Biomolecular Structure, Volume 32.}, year = {2003}, pages = {533}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-7} }
Swigon, D., Coleman, B. D. & Olson, W. K.	Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. [Abstract] [BibTeX]	2006	Proceedings of the National Academy of Sciences of the United States of America	article
Abstract: Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR-DNA complex to a wide range of heretofore-unconnected exptl. observations. Here, that theory is used to calc. the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking no., and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is obsd. in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published exptl. observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50-180 bp) give rise to loops with the extended form of LacR, and that loops formed within neg. supercoiled plasmids induce the V-shaped structure. [on SciFinder (R)]
BibTeX: @article{RefWorks:369, author = {David Swigon and Bernard D. Coleman and Wilma K. Olson}, title = {Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2006}, volume = {103}, number = {26}, pages = {9879-9884}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-7; CA Section Cross-references: 10; CODEN: PNASA6; CAS Registry Numbers: 9003-98-9 (DNase I) Role: BSU (Biological study, unclassified), BIOL (Biological study) (cutting patterns for; modeling the Lac repressor-operator assembly)} }
Taylor, E. R. & Olson, W. K.	Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains. [Abstract] [BibTeX]	1983	Biopolymers	article
Abstract: A combined geometric and potential energy anal. has been carried out to identify the torsional arrangements of the nucleic acid chain that can accommodate the intercalation of small planar moieties. In contrast to previous theor. efforts, which detail local conformations after adjacent bases are positioned in space, the likely geometries are found here on the basis of the base orientations that result from all feasible combinations of the 9 torsional variables of the basic dinucleotide intercalation unit. The relatively mobile nature of the sugar-phosphate backbone, together with the fairly long stretches of chem. bonds between adjacent units, is apparently responsible for the large no. of feasible binding geometries. Some previously overlooked conformations with unusual sugar puckering combinations and various phosphodiester arrangements are found in the survey. A large proportion of the energetically favored intercalation states are closely related to the backbone conformations of familiar double-helical models such as A-, B-, and Z-DNAs, as well as the Watson-Crick model. Moreover, the intercalated forms are found to interconvert smoothly along a continuous conformational path. The intercalation structures derived from x-ray crystallog. analyses of drug-oligonucleotide complexes, in contrast, are stiff 3-dimensional forms essentially frozen in a single domain of conformation space. Specific ligand-nucleic acid interactions that may be responsible for the exptl. observations are not included in this study. The classical intramol. potential energies reported here are highly approx., providing only rough gauges of the relative importance of the many competing conformations. [on SciFinder (R)]
BibTeX: @article{RefWorks:342, author = {Eric R. Taylor and Wilma K. Olson}, title = {Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains.}, journal = {Biopolymers}, year = {1983}, volume = {22}, number = {12}, pages = {2667-2702}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA; CAS Registry Numbers: 2391-46-0; 23339-45-9 Role: BIOL (Biological study) (ligand binding by, conformational forms in)} }
Tobias, I., Coleman, B. D. & Olson, W. K.	The dependence of DNA tertiary structure on end conditions: theory and implications for topological transitions. [Abstract] [BibTeX]	1994	Journal of Chemical Physics	article
Abstract: Explicit expressions are derived for the equil. configurations of long segments of a DNA double helix subject to boundary conditions of the type imposed by DNA-bending proteins at the ends of otherwise free segments. The expressions, which are exact within the framework of Kirchhoff's theory of elastic rods, show that, in appropriate ranges of parameters, small changes in end conditions can result in large changes in tertiary structure. A discussion is given of the implications of this observation for understanding the action of bending proteins and of proteins that induce topol. transitions that change the linking no. of closed loops of DNA. [on SciFinder (R)]
BibTeX: @article{RefWorks:424, author = {Irwin Tobias and Bernard D. Coleman and Wilma K. Olson}, title = {The dependence of DNA tertiary structure on end conditions: theory and implications for topological transitions.}, journal = {Journal of Chemical Physics}, year = {1994}, volume = {101}, number = {12}, pages = {10990-10996}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JCPSA6} }
Tobias, I. & Olson, W. K.	The effect of intrinsic curvature on supercoiling: predictions of elasticity theory. [Abstract] [BibTeX]	1993	Biopolymers	article
Abstract: Elasticity theory of naturally curved rods is employed to study the effects of intrinsic curvature on the properties of the equil. conformations of supercoiled DNA. The results stand in sharp contrast to those obtained when the mol. is viewed as being straight in its relaxed form. Starting from very fundamental principles of the theory, it is shown that the torsion of an open segment with a curved duplex axis can vary when the temp., and along with it, the intrinsic twist is changed. Conversely, an imposed helicity, such as might be assocd. with binding to a histone, can change the intrinsic twist. It is also shown that another consequence of the presence of naturally curved sequences is that the twist d. will, in general, vary with position along the chain in all equil. states. Then portions of the mol. will be more or less susceptible to interaction with other agents sensitive to such a variation. Finally, some closed equil. global structures uniquely assocd. with intrinsic curvature are discussed. [on SciFinder (R)]
BibTeX: @article{RefWorks:312, author = {Irwin Tobias and Wilma K. Olson}, title = {The effect of intrinsic curvature on supercoiling: predictions of elasticity theory.}, journal = {Biopolymers}, year = {1993}, volume = {33}, number = {4}, pages = {639-646}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIPMAA} }
Wang, L., Hingerty, B. E., Srinivasan, A. R., Olson, W. K. & Broyde, S.	Accurate representation of B-DNA double helical structure with implicit solvent and counterions. [Abstract] [BibTeX]	2002	Biophysical journal	article
Abstract: High-resoln. NMR and crystallog. data have been taken to refine the force field used in the torsion angle space nucleic acids mol. mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equil. was used to fine tune a sigmoidal, distance-dependent dielec. function so that reasonable relative energies could be obtained. In addn., the base-pair and backbone geometry from high-resoln. crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielec. function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo min., and a shift of the Lennard-Jones potential energy min. to a distance .apprx.0.4 .ANG. greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aq. liq. cryst. phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of mols. modified by carcinogens and other ligands. [on SciFinder (R)]
BibTeX: @article{RefWorks:378, author = {Lihua Wang and Brian E. Hingerty and A. R. Srinivasan and Wilma K. Olson and Suse Broyde}, title = {Accurate representation of B-DNA double helical structure with implicit solvent and counterions.}, journal = {Biophysical journal}, year = {2002}, volume = {83}, number = {1}, pages = {382-406}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: BIOJAU; CAS Registry Numbers: 471298-48-3; 471939-47-6; 471939-48-7 Role: PRP (Properties) (revised DUPLEX force field permits accurate representation of B-DNA double helical structure with implicit solvent and counterions)} }
Weller, D. D., Daly, D. T., Olson, W. K. & Summerton, J. E.	Molecular modeling of acyclic polyamide oligonucleotide analogs. [Abstract] [BibTeX]	1991	Journal of Organic Chemistry	article
Abstract: The feasibility of replacing the sugar-phosphate backbone of nucleic acids with a polyamide-type backbone was investigated by using mol. modeling techniques that exam. the ability of the acyclic backbone to adopt low energy conformations that conform to the nucleic acid A- and B-form helixes. Of the several backbone possibilities examd. (nylons, polyurethanes, polypeptides), the most favorable appear to be those derived from a polypeptide. For most of the cases studied, the models predict a preference for binding of a given backbone type to either A- or B-form targets and, in some cases, suggest an orientational bias for direction along the helical axis, or a preferred stereochem. at stereogenic atoms in the backbone. [on SciFinder (R)]
BibTeX: @article{RefWorks:323, author = {Dwight D. Weller and Daniel T. Daly and Wilma K. Olson and James E. Summerton}, title = {Molecular modeling of acyclic polyamide oligonucleotide analogs.}, journal = {Journal of Organic Chemistry}, year = {1991}, volume = {56}, number = {21}, pages = {6000-6006}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 9-14; CA Section Cross-references: 6, 33; CODEN: JOCEAH; CAS Registry Numbers: 136277-55-9; 136277-56-0; 136301-88-7; 136301-89-8; 136301-90-1; 136376-53-9 Role: PRP (Properties) (energy of, mol. modeling in relation to); 136277-48-0; 136277-49-1; 136277-50-4; 136277-51-5; 136277-52-6; 136277-53-7; 136277-54-8; 136301-87-6 Role: ANST (Analytical study) (mol. modeling of, nucleic acid binding in relation to); 136277-57-1P; 136277-58-2P; 136277-59-3P; 136277-60-6P; 136277-61-7P; 136277-62-8P; 136327-73-6P; 136375-16-1P; 136376-54-0P Role: PREP (Preparation) (prepn. of)} }
Westcott, T. P., Tobias, I. & Olson, W. K.	Modeling self-contact forces in the elastic theory of DNA supercoiling. [Abstract] [BibTeX]	1997	Journal of Chemical Physics	article
Abstract: A DNA polymer with thousands of base pairs is modeled as an elastic rod with the capability of treating each base pair independently. Elastic theory is used to develop a model of the double helix which incorporates intrinsic curvature as well as inhomogeneities in the bending, twisting, and stretching along the length of the polymer. Inhomogeneities in the elastic consts. can also be dealt with; thus, sequence-dependent structure and deformability can be taken into account. Addnl., external forces have been included in the formalism, and since these forces can contain a repulsive force, DNA self-contact can be explicitly treated. Here, the repulsive term takes the form of a modified Debye-Huckel force where screening can be varied to account for the effect of added salt. The supercoiling of a naturally straight, isotropic rod in 0.1M NaCl is investigated and compared with earlier treatments of supercoiled DNA modeled by a line of point charges subject to electrostatic interactions and an elastic potential. [on SciFinder (R)]
BibTeX: @article{RefWorks:406, author = {Timothy P. Westcott and Irwin Tobias and Wilma K. Olson}, title = {Modeling self-contact forces in the elastic theory of DNA supercoiling.}, journal = {Journal of Chemical Physics}, year = {1997}, volume = {107}, number = {10}, pages = {3967-3980}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JCPSA6; CAS Registry Numbers: 7647-14-5 (Sodium chloride) Role: BAC (Biological activity or effector, except adverse), BSU (Biological study, unclassified), BIOL (Biological study) (effect on supercoiling; modeling self-contact forces in elastic theory of DNA supercoiling)} }
Westcott, T. P., Tobias, I. & Olson, W. K.	Elasticity Theory and Numerical Analysis of DNA Supercoiling: An Application to DNA Looping. [Abstract] [BibTeX]	1995	Journal of Physical Chemistry	article
Abstract: A DNA polymer with 1000 base pairs (bp's) is modeled as an elastic rod at the base pair level. The elastic theory of rods is used to express the free energy of a double helix that has been deformed by stresses. After including a Lagrange multiplier in the energy expression to constrain the ends of the rod, an expression for the equil. configuration of the rod is obtained through the use of the appropriate Euler-Lagrange equations. The resulting set of differential equations is simplified to a set of nonlinear algebraic equations by discretizing the rod into individual elements. Because each element can have its own phys. characteristics, base sequence effects can be taken into account. The methods developed are applied to DNA loops that are either nicked (i.e., torsionally relaxed) or unnicked (i.e., supercoiled). Small changes in the orientations and displacements of the ends of the loops can cause large changes in the overall configuration of the DNA. The nicked DNA shows a greater propensity to change configuration than the same unnicked DNA. DNA loops that contain regions of intrinsic curvature require less elastic energy for loop formation and facilitate conversion between different looped configurations. [on SciFinder (R)]
BibTeX: @article{RefWorks:418, author = {Timothy P. Westcott and Irwin Tobias and Wilma K. Olson}, title = {Elasticity Theory and Numerical Analysis of DNA Supercoiling: An Application to DNA Looping.}, journal = {Journal of Physical Chemistry}, year = {1995}, volume = {99}, number = {51}, pages = {17926-17935}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 3-6; CODEN: JPCHAX} }
Xu, Z., Pilch, D. S., Srinivasan, A. R., Olson, W. K., Geacintov, N. E. & Breslauer, K. J.	Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation. [Abstract] [BibTeX]	1997	Bioorganic & medicinal chemistry	article
Abstract: The arom. diamidine, DAPI (4',6-diamidino-2-phenylindole), is used as an important biol. and cytol. tool since it forms highly fluorescent complexes with nucleic acid duplexes via minor groove-directed/intercalative modes of interaction. In this study, we find that DAPI binding can induce the formation of an RNA-DNA hybrid triplex that would not otherwise form. More specifically, through application of a broad range of spectroscopic, viscometric, and mol. modeling techniques, we demonstrate that DAPI intercalation induces the formation of the poly(dT).poly(rA).poly(dT) hybrid triple helix, a structure which does not form in the absence of the ligand. Using UV mixing studies, we demonstrate that, in the presence of DAPI, the poly(rA).poly(dT) duplex and the poly(dT) single strand form a 1:1 complex (a triplex) that does not form in the absence of DAPI. Through temp.-dependent absorbance measurements, we show that the poly(dT).poly(rA).poly(dT) triplex melts via two distinct transitions: initial conversion of the triplex to the duplex state, with the DAPI remaining bound, followed by denaturation of the duplex-DAPI complex to its component single strands and free DAPI. Using optical melting profiles, we show that DAPI binding enhances the thermal stability of the poly(dT).poly(rA).poly(dT) triplex, an observation consistent with the preferential binding of the ligand to the triplex vs. the duplex and single-stranded states. Our differential scanning calorimetric measurements reveal melting of the DAPI-satd. poly(dT).poly(rA).poly(dT) triplex to be assocd. with a lower enthalpy but greater cooperativity than melting of the corresponding DAPI-satd. poly(rA).poly(dT) duplex. Our flow linear dichroism and viscometric data are consistent with an intercalative mode of binding when DAPI interacts with both the poly(dT).poly(rA).poly(dT) triplex and the poly(rA).poly(dT) duplex. Finally, computer modeling studies suggest that a combination of both stacking and electrostatic interactions between the intercalated ligand and the host nucleic acid play important roles in the DAPI-induced stabilization of the poly(dT).poly(rA).poly(dT) triplex. In the aggregate, our results demonstrate that ligand binding can be used to induce the formation of triplex structures that do not form in the absence of the ligand. This triplex-inducing capacity has potentially important implications in the design of novel antisense, antigene, antiviral, and diagnostic strategies. [on SciFinder (R)]
BibTeX: @article{RefWorks:408, author = {Zhitao Xu and Daniel S. Pilch and A. R. Srinivasan and Wilma K. Olson and Nicholas E. Geacintov and Kenneth J. Breslauer}, title = {Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation.}, journal = {Bioorganic & medicinal chemistry}, year = {1997}, volume = {5}, number = {6}, pages = {1137-1147}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 3-1; CA Section Cross-references: 1, 6, 9; CODEN: BMECEP; CAS Registry Numbers: 25086-81-1 Role: BPR (Biological process), BSU (Biological study, unclassified), BIOL (Biological study), PROC (Process) (hybridization with poly(dA).poly(dT) in DAPI presence; modulation of nucleic acid structure by ligand binding: induction of DNA.RNA.DNA hybrid triplex by DAPI intercalation); 27156-07-6 (Poly(rA).poly(dT) Role: BPR (Biological process), BSU (Biological study, unclassified), BIOL (Biological study), PROC (Process) (hybridization with poly(dT) in DAPI presence; modulation of nucleic acid structure by ligand binding: induction of DNA.RNA.DNA hybrid triplex by DAPI intercalation); 47165-04-8 (DAPI) Role: BUU (Biological use, unclassified), THU (Therapeutic use), BIOL (Biological study), USES (Uses) (modulation of nucleic acid structure by ligand binding: induction of DNA.RNA.DNA hybrid triplex by DAPI intercalation); 108334-81-2 Role: PRP (Properties) (modulation of nucleic acid structure by ligand binding: induction of DNA.RNA.DNA hybrid triplex by DAPI intercalation)} }
Yang, Y., Tobias, I. & Olson, W. K.	Finite-element analysis of DNA supercoiling. [Abstract] [BibTeX]	1993	Journal of Chemical Physics	article
Abstract: A DNA polymer with hundreds or thousands of base pairs is modeled as a thin elastic rod. To find the equil. configurations and assocd. elastic energies as a function of linking no. difference (DLk), a finite element scheme based on Kirchhoff's rod theory is newly formulated so as to be able to treat self-contact. The numerical results obtained here agree well with those already published, both anal. and numerical, but a much more detailed picture emerges of the several equil. states which can exist for a given DLk. Of particular interest is the discovery of interwound states having odd integral values of the writhing no. and very small twist energy. The existence of a noncircular cross section, inhomogeneous elastic consts., intrinsic curvature, and sequence-dependent bending and twisting can all be readily incorporated into the new formalism. [on SciFinder (R)]
BibTeX: @article{RefWorks:314, author = {Yang Yang and Irwin Tobias and Wilma K. Olson}, title = {Finite-element analysis of DNA supercoiling.}, journal = {Journal of Chemical Physics}, year = {1993}, volume = {98}, number = {2}, pages = {1673-1686}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JCPSA6} }
Yang, Y., Westcott, T. P., Pedersen, S. C., Tobias, I. & Olson, W. K.	Effects of localized bending on DNA supercoiling. [Abstract] [BibTeX]	1995	Trends in biochemical sciences	article
Abstract: A review with 44 refs. The DNA double helix is straight only in the idealized case. In reality, it bends, twists and stretches in response to local base sequence and to specific interactions with proteins and other bound ligands. Naturally occurring bends appear to promote the assembly of nucleosomes, and in some cases can effectively replace regulatory DNA-binding proteins in vivo. Recently, a computational method known as finite element anal., which is used routinely by engineers to analyze the stability of buildings and bridges, has been applied to the quant. assessment of natural curvature in supercoiled DNA structures, providing new insight into the relation between local, sequence-dependent features and the overall topol. of these chains. [on SciFinder (R)]
BibTeX: @article{RefWorks:420, author = {Yang Yang and Timothy P. Westcott and Scott C. Pedersen and Irwin Tobias and Wilma K. Olson}, title = {Effects of localized bending on DNA supercoiling.}, journal = {Trends in biochemical sciences}, year = {1995}, volume = {20}, number = {8}, pages = {313-319}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-0; CODEN: TBSCDB} }
Yevich, R. & Olson, W. K.	The spatial distributions of randomly coiling polynucleotides. [Abstract] [BibTeX]	1979	Biopolymers	article
Abstract: Statistical mech. avs. of vectors and tensors characterizing the allowed configurations of randomly coiling polynucleotides have been calcd. for chains of 20-210 repeating units. Specifically, the persistence vector p = (r) has been obtained as a function of chain length. Configurational avs. of the Cartesian tensors formed from the displacement vector sho = r-p have been computed up to and including the tensor of seventh rank. From these tensors the three-dimensional spatial distributions of end-to-end vectors have been constructed to provide comprehensive pictures of the directional tendencies of the randomly coiling polynucleotide. The elements of the third and fourth moment tensors, however, give sufficient information to represent accurately the qual. features of the spatial distributions. For long chains, more than 64 repeating units, the spatial distributions assume spherically sym. shapes that can be adequately characterized by one-dimensional radial distribution functions. These radial distribution functions agree well with the radial distributions calcd. from Monte Carlo samples contg. more than 5000 chains. The constraints of fixed bond lengths, fixed bond angles, and hindered internal rotations severely distort the spatial distributions of short polynucleotide chains to mushroom-shaped vols. These skewed distributions provide information useful to the anal. of small, single-stranded loops, bulges, and circles. The formation of these structures requires the termini of the polynucleotides to lie within specifically delineated vols. with respect to coordinate systems affixed to the first bonds of the chains. The extent to which these loop closure vols. overlap the three-dimensional spatial distributions provides ests. of loop formation that are much more reliable than earlier studies based upon the radial distribution function. [on SciFinder (R)]
BibTeX: @article{RefWorks:356, author = {Rosemarie Yevich and Wilma K. Olson}, title = {The spatial distributions of randomly coiling polynucleotides.}, journal = {Biopolymers}, year = {1979}, volume = {18}, number = {1}, pages = {113-145}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 33-7; CA Section Cross-references: 6, 65; CODEN: BIPMAA} }
Zhang, P., Olson, W. K. & Tobias, I.	Accelerated record-keeping Fourier series Monte Carlo simulations of an isotropic elastic rod model of DNA. [Abstract] [BibTeX]	1991	Computational Polymer Science	article
Abstract: This paper investigates the phys. and geometric properties of supercoiled DNA with a new algorithm, namely accelerated record-keeping Fourier series Monte Carlo simulations. The configurational energy of the closed double helix is described by an isotropic elastic rod model characterized by bending and torsional stiffness consts. The axis of the closed double-helical trajectory of the polymer is represented by a finite Fourier series. The global equil. configurations with imposed linking no. differences are obtained by record-keeping Monte Carlo simulations. Various phys. and geometric properties, including the potential energy, the writhing no., and the radius of gyration are reported. The computer simulation data are compared with predictions of elasticity theory and exptl. measurements of DNA supercoiling when available. The record-keeping Monte Carlo simulation is carried out at several levels of acceleration and the procedure is compared with conventional simulated annealing of the DNA chain model. [on SciFinder (R)]
BibTeX: @article{RefWorks:324, author = {Peisen Zhang and Wilma K. Olson and Irwin Tobias}, title = {Accelerated record-keeping Fourier series Monte Carlo simulations of an isotropic elastic rod model of DNA.}, journal = {Computational Polymer Science}, year = {1991}, volume = {1}, number = {1}, pages = {3-17}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: CPOSEJ} }
Zhang, P., Tobias, I. & Olson, W. K.	Computer simulation of protein-induced structural changes in closed circular DNA. [Erratum to document cited in CA122:3762]. [Abstract] [BibTeX]	1995	Journal of Molecular Biology	article
Abstract: The errors were not reflected in the abstr. or the index entries. [on SciFinder (R)]
BibTeX: @article{RefWorks:419, author = {Peisen Zhang and Irwin Tobias and Wilma K. Olson}, title = {Computer simulation of protein-induced structural changes in closed circular DNA. [Erratum to document cited in CA122:3762].}, journal = {Journal of Molecular Biology}, year = {1995}, volume = {251}, number = {5}, pages = {721}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK} }
Zhang, P., Tobias, I. & Olson, W. K.	Computer simulation of protein-induced structural changes in closed circular DNA. [Abstract] [BibTeX]	1994	Journal of Molecular Biology	article
Abstract: The effect of protein-induced wrapping on overall DNA folding is studied using Monte Carlo computer simulation techniques. A new modeling scheme is devised to represent configurations of closed circular DNA contg. fragments of the double helix partially wrapped around a core of proteins. The DNA consists of two regions, a fragment wrapped in a left handed superhelical path around a phantom protein core and a free connecting loop. The loop has at least one single-stranded scission so that it can assume a torsionally relaxed state. The configuration of the loop is varied during the course of the computer simulations and the three-dimensional spatial arrangements of lowest total energy are identified. The axis of the DNA loop is represented by a finite three-dimensional Fourier series perturbation of an initial Bezier curve, making it possible to fix the position and orientation of the chain ends as well as the contour length of the free loop. The energy is approximated by elastic terms for the bending and twisting of the DNA and an excluded vol. contribution that prevents the self-intersection of sequentially distant chain segments. The proportions of the protein-DNA complex, the no. of superhelical turns, the chain length and the imposed linking no. difference of the closed DNA are varied in the calcns. The resulting min. energy structures are consistent with phys. models and suggest new ways to think about how proteins add and remove supercoils from DNA. Of special note in this regard is the sudden collapse of three-dimensional structure that accompanies small incremental wrapping of the DNA around the idealized protein core. These observations offer new structural insight into the mechanisms of action of proteins which add or remove supercoils from DNA and provide a first step in thinking about the activity of such systems at the chem. level whereby small fluctuations in local mol. structure are translated into large-scale macromol. changes. The configurations identified in the simulations can also be examd. in the context of the well known linking no. paradox assocd. with nucleosome formation on closed circular plasmids. The findings bear relevance to DNA with natural curvature as well as to protein-induced bending and deformations of the double helix. [on SciFinder (R)]
BibTeX: @article{RefWorks:426, author = {Peisen Zhang and Irwin Tobias and Wilma K. Olson}, title = {Computer simulation of protein-induced structural changes in closed circular DNA.}, journal = {Journal of Molecular Biology}, year = {1994}, volume = {242}, number = {3}, pages = {271-290}, note = {Copyright (C) 2007 ACS on SciFinder (R)); Section Code: 6-2; CODEN: JMOBAK} }

Created by JabRef on 27/07/2007.