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

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.

Main text: 5 pages and 3 figures. Supplementary material: 9 pages, 6 figures and 2 movies

References in corpus (1)

• Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops

Cited by in corpus (3)

• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Mechanical properties of Nucleic Acids and the non-local Twistable Wormlike Chain model
• Coarse-graining DNA: Symmetry, non-local elasticity and persistence length