Protein-mediated Loops and Phase Transition in Nonthermal Denaturation of DNA

TL;DR

This paper presents a statistical mechanical model demonstrating how protein-mediated loops can induce a first-order phase transition in DNA denaturation, with implications for understanding cellular processes.

Contribution

It introduces a novel model linking protein-mediated looping to phase transition behavior in DNA denaturation, supported by transition time estimates.

Findings

Looping proteins can cause a first-order phase transition in DNA.

The model estimates denaturation transition times near the phase transition.

Multiple loop formation via dynamical linking is crucial in cellular processes.

Abstract

We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a first-order phase transition. We estimate the denaturation transition time near the phase transition, which can be compared with experimental data. The model describes the formation of multiple loops via dynamical (fluctuational) linking between looping proteins, that is essential in many cellular biological processes.