Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model

TL;DR

This study uses a coarse-grained DNA model to systematically analyze supercoil formation, twist/writhe partitioning, and their dependence on chain length and linking number, aligning with experimental observations.

Contribution

It introduces a new coarse-grained DNA model derived from atomistic data to explore supercoiling behavior in long DNA minicircles.

Findings

Asymmetric supercoiling transition observed, consistent with experiments.

Fraction of linking number absorbed as twist and writhe depends on chain length.

Longer chains tend to absorb more linking number as writhe.

Abstract

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion, therefore our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.