Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

TL;DR

This study models the coalescence of DNA bubbles as a problem of two vicious walkers in opposite potentials, revealing temperature-dependent behaviors and providing distributions for coalescence times and positions.

Contribution

It introduces a novel mapping of DNA bubble coalescence dynamics to vicious walkers in opposite potentials, offering analytical insights into the process.

Findings

Barrier crossing behavior below melting temperature

Drift-diffusion dynamics at high temperatures

Distribution of coalescence times and positions

Abstract

We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.