Journal
BIOPOLYMERS
Volume 73, Issue 3, Pages 327-339Publisher
WILEY-BLACKWELL
DOI: 10.1002/bip.10542
Keywords
DNA flexibility; elastic properties; persistence length; EcoRI dodecamer; AMBER
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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 EcoRI dodecamer are presented. (C) 2003 Wiley Periodicals, Inc.
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