Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending

By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation of local bending, (II) the slow twist spreading, and (III)...

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Bibliographic Details
Published in:arXiv.org 2020-08
Main Authors: Yair Augusto Gutierrez Fosado, Landuzzi, Fabio, Sakaue, Takahiro
Format: Article
Language:English
Subjects:
Asymmetry
Bending
Buckling
Computer simulation
Coupling (molecular)
Deoxyribonucleic acid
Diffusion coefficient
DNA
Dynamic stability
Grooves
Mapping
Molecular dynamics
Perturbation
Time
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Summary:By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation of local bending, (II) the slow twist spreading, and (III) the buckling transition taking place in a much longer time scale. In all of these stages, the twist-bend coupling arising from the groove asymmetry in DNA double helix clearly manifests. In particular, the separation of time scales allows to deduce an effective diffusion equation in stage (II), with a diffusion coefficient influenced by the twist-bend coupling. We also discuss the mapping of the realistic DNA model to the simplest isotropic twistable worm-like chain using the renormalized bending and twist moduli; although useful in many cases, it fails to make a quantitative prediction on the instability mode of buckling transition.
ISSN:2331-8422