Dynamical simulations of DNA supercoiling and compression | Zendy

David Swigon | Zendy; Sookkyung Lim | Zendy; Yongsam Kim | Zendy

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Dynamical simulations of DNA supercoiling and compression

Author(s) -

David Swigon,

Sookkyung Lim,

Yongsam Kim

Publication year - 2013

Publication title -

biochemical society transactions

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.562

H-Index - 144

eISSN - 1470-8752

pISSN - 0300-5127

DOI - 10.1042/bst20120316

Subject(s) - dna supercoil , radius of gyration , electric field , dna , periodic boundary conditions , molecular dynamics , ionic strength , electrostatics , persistence length , physics , radius , classical mechanics , molecule , chemical physics , chemistry , boundary value problem , polymer , computational chemistry , quantum mechanics , aqueous solution , dna replication , nuclear magnetic resonance , computer security , computer science , biochemistry

In the present article, we summarize our recent studies of DNA dynamics using the generalized immersed boundary method. Our analysis of the effects of electrostatic repulsion on the dynamics of DNA supercoiling revealed that, after perturbation, a pre-twisted DNA collapses into a compact supercoiled configuration that is sensitive to the initial excess link and ionic strength of the solvent. A stochastic extension of the generalized immersed boundary method shows that DNA in solution subjected to a constant electric field is compressed into a configuration with smaller radius of gyration and smaller ellipticity ratio than those expected for such a molecule in a thermodynamic equilibrium.

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