DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

TL;DR

This study uses Monte Carlo simulations to reveal that DNA cruciform structures nucleate through a cooperative, non-synchronous mechanism involving bubble diffusion and arm formation, advancing understanding of DNA stress relief.

Contribution

The paper introduces a detailed simulation-based model showing the stepwise, cooperative nucleation process of DNA cruciforms, highlighting the non-synchronous growth pathway.

Findings

Cruciform nucleation involves bubble diffusion near IR sequence center.

Initial arm formation requires fewer bases than the final structure.

Growth often proceeds synchronously after initial nucleation.

Abstract

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.