Equilibrium Fluctuations of DNA Plectonemes

TL;DR

This study investigates the fluctuations in the extension of supercoiled DNA molecules, revealing that phase-exchange dynamics between stretched and plectonemic regions dominate the variance, supported by simulations and a two-phase model.

Contribution

The paper introduces a two-phase model for supercoiled DNA fluctuations and validates it with Monte Carlo simulations, highlighting phase-exchange as the main source of extension variance.

Findings

Phase-exchange fluctuations dominate extension variance.

Monte Carlo simulations agree with the two-phase model.

High-force extension and variance are accurately captured by the model.

Abstract

Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from the experimental and modeling side. In this work, we investigate fluctuations of the end-point distance z of supercoiled linear DNA molecules subject to external stretching forces. Our analysis is based on a two-phase model, which describes the supercoiled DNA as composed of a stretched and of a plectonemic phase. Several different mechanisms are found to contribute to extension fluctuations, characterized by the extension variance. We find the dominant contribution to the variance to originate from phase-exchange fluctuations, the transient shrinking and expansion of plectonemes, which is accompanied by an exchange of molecular length between the two phases. We perform Monte Carlo simulations of the Twistable Wormlike Chain and analyze the fluctuation of various quantities, which are found to agree with the two-phase model predictions. Furthermore, we show that the extension and its variance at high forces are very well captured by the two-phase model, provided that one goes beyond quadratic approximations.