Effect of Sequence-Dependent Rigidity on Plectoneme Localization in dsDNA

TL;DR

This study uses Monte-Carlo simulations to explore how sequence-dependent rigidity influences plectoneme formation and localization in supercoiled dsDNA, revealing that softer sequences attract plectoneme edges and potentially affect transcription factor targeting.

Contribution

The paper demonstrates how variable DNA rigidity affects plectoneme localization, providing a new understanding of DNA supercoiling behavior and proposing experimental validation methods.

Findings

Soft sequences increase plectoneme branches

Plectoneme edges tend to localize at softer sequences

Potential role in transcription factor search processes

Abstract

We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled dsDNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences. We propose an experimental approach to test our results in vitro, and discuss the possible role played by plectoneme localization in the search process of transcription factors for their targets (promoter regions) on the bacterial genome.