Interfacial instability and DNA fork reversal by repair proteins

TL;DR

This paper proposes a physical model explaining how repair proteins like RecG induce DNA fork reversal by softening the interface between zipped and unzipped DNA, leading to fork propagation or stalling.

Contribution

It introduces a novel physical mechanism linking aromatic interactions to DNA fork dynamics and provides a numerical analysis of the process.

Findings

Softening of the DNA interface facilitates fork propagation.

Aromatic interactions between RecG and DNA influence fork stability.

Numerical analysis shows possible stop-and-go motion of the fork.

Abstract

A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating towards the unzipped side. In this scenario, an ordinary helicase destabilizes the zipped state locally near the interface and the fork propagates towards the zipped side. The softening of the interface can be produced by the aromatic interaction, predicted from crystal structure, between RecG and the nascent broken base pairs at the Y-fork. A numerical analysis of the model also reveals the possibility of a stop and go type motion.