DNA sequence-dependent deformability-insights from computer simulations

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 seq...

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Bibliographic Details
Published in:Biopolymers 2004-02, Vol.73 (3), p.327-339
Main Author: Lankas, Filip
Format: Article
Language:English
Subjects:
AMBER
Base Sequence
Binding Sites
Computer Simulation
Deoxyribonuclease EcoRI - metabolism
DNA - chemistry
DNA - metabolism
DNA flexibility
EcoRI dodecamer
elastic properties
Models, Molecular
Nucleic Acid Conformation
persistence length
Thermodynamics
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Summary: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. © 2003 Wiley Periodicals, Inc. Biopolymers 73:327–339, 2004
ISSN:0006-3525
1097-0282
DOI:10.1002/bip.10542