DNA sequence-dependent deformability--insights from computer simulations.

Filip Lankas

doi:10.1002/bip.10542

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DNA sequence-dependent deformability--insights from computer simulations.

Filip Lankas

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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 EcoRI dodecamer are presented.

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Base Sequence Binding Sites Computer Simulation DNA Deoxyribonuclease EcoRI Models, Molecular Nucleic Acid Conformation Thermodynamics Journal Article Research Support, Non-U.S. Gov't Review

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Filip Lankas. 2004-02-15. DNA sequence-dependent deformability--insights from computer simulations.. https://doi.org/10.1002/bip.10542

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