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DNA sequence‐dependent deformability—insights from computer simulations
Author(s) -
Lankaš Filip
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10542
Subject(s) - sequence (biology) , molecular dynamics , dodecameric protein , chemistry , force field (fiction) , statistical physics , focus (optics) , resolution (logic) , field (mathematics) , dna , nanotechnology , computational chemistry , physics , computer science , artificial intelligence , quantum mechanics , optics , materials science , biochemistry , mathematics , pure mathematics
The article reviews some recent developments in studying DNA sequence‐dependent deformability, with emphasis on computer modeling. After a brief outline of available experimental techniques, we proceed to computational methods and focus on atomic‐resolution molecular dynamics (MD) simulations. A sequence‐dependent local (base‐pair step) force field inferred from MD is compared with force fields obtained by other techniques. Various methods for establishing global (flexible‐rod) DNA elastic constants are reviewed, including an approach based on atomic resolution MD. The problem of defining the global deformation variables, as well as the question of anisotropy and nonlocal effects, are discussed. As an example, both local and global deformability calculations from atomic‐resolution MD of Eco RI dodecamer are presented. © 2003 Wiley Periodicals, Inc. Biopolymers 73:327–339, 2004