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

TL;DR

This study combines analytical theory and molecular dynamics simulations to explore the relaxation dynamics, twist spreading, and buckling instability of ring DNA, highlighting the role of groove asymmetry and anisotropic bending.

Contribution

It introduces a detailed analysis of DNA relaxation stages and the impact of twist-bend coupling, providing new insights into DNA buckling behavior.

Findings

Identification of three distinct relaxation time scales

Effective diffusion equation for twist spreading influenced by twist-bend coupling

Mapping of realistic DNA to simplified models fails to predict buckling instability accurately

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.