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DNA sequence-dependent deformability—insights from computer simulations

✍ Scribed by Filip Lankaš

Publisher
Wiley (John Wiley & Sons)
Year
2004
Tongue
English
Weight
250 KB
Volume
73
Category
Article
ISSN
0006-3525

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✦ Synopsis

Abstract

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

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