A model for melting of confined DNA

TL;DR

This paper introduces a model to study how nanochannel confinement influences DNA melting transitions, revealing that narrower channels lead to smoother melting behavior, with simulations confirming the effect's strength.

Contribution

The paper presents a new model predicting the impact of confinement on DNA melting, including effects of self-avoidance through Monte Carlo simulations.

Findings

Narrower channels cause smoother melting transitions.

Self-avoidance amplifies the effect of confinement.

Model aligns qualitatively with simulation results.

Abstract

When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.