Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending
arXiv:2008.05686 · doi:10.1039/D0SM01812K
Abstract
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.
arXiv commentMain text: 5 pages and 3 figures. Supplementary material: 9 pages, 6 figures and 2 movies
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