Journal ArticleDOI
Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.
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TLDR
Comparisons are made between the rigorous statistical mechanical representation of the DNA and simplified static models currently used in the literature and the results imply that when DNA bending is exactly "in phase" with the helical repeat, the DNA coil is packed more tightly than when bending and twisting are "out of phase".About:
This article is published in Journal of Molecular Biology.The article was published on 1993-07-20. It has received 128 citations till now. The article focuses on the topics: Molecular models of DNA & Curvature.read more
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Journal ArticleDOI
DNA sequence-dependent deformability deduced from protein–DNA crystal complexes
TL;DR: A complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes, providing useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations.
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A standard reference frame for the description of nucleic acid base-pair geometry
Wilma K. Olson,Manju Bansal,Stephen K. Burley,Richard E. Dickerson,Mark Gerstein,Stephen C. Harvey,Udo Heinemann,Xiang-Jun Lu,Stephen Neidle,Zippora Shakked,Heinz Sklenar,Masashi Suzuki,Chang-Shung Tung,Eric Westhof,Cynthia Wolberger,Helen M. Berman +15 more
TL;DR: A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures and to pinpoint unique conformational features in individual structures.
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Structure and interactions of biological helices
TL;DR: The present article focuses on the most important and interesting aspects of the physics of structured macromolecules, highlighting various manifestations of the helical motif in their structure, elasticity, interactions with counterions, aggregation, and polyand mesomorphic transitions.
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Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility
TL;DR: The worm-like chain model has been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA, to polymers containing bends or sections of different flexibility and has been used to investigate DNA molecules with sequence-induced bending (A-tracts).
Journal ArticleDOI
DNA bending by asymmetric phosphate neutralization.
TL;DR: A series of experiments was devised to test the hypothesis that proteins with cationic surfaces can induce substantial DNA bending by neutralizing phosphates on one DNA face, and demonstrates that modified DNAs are deformed toward the neutralized surface, as predicted.