Nucleation at the DNA supercoiling transition

TL;DR

This paper models the thermally activated nucleation of supercoiled structures in twisted DNA, predicting transition rates and highlighting the role of sequence disorder and experimental limitations.

Contribution

It introduces a combined analytical and numerical approach to predict DNA plectoneme nucleation rates, accounting for sequence disorder and experimental viscosity effects.

Findings

Predicted nucleation rate of ~10^4 Hz

Experimental hopping rates limited by bead viscosity

Sequence disorder influences free energy barriers

Abstract

Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of order 10^4 Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscosity of the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the base-pair sequence is important for understanding the free energy barrier that governs the transition. Both analytic and numerical methods are used in the calculations. We provide extensive details on the numerical methods for simulating the elastic rod model with and without disorder.