Supercoil formation in DNA denaturation

TL;DR

This paper extends the Poland-Scheraga model to circular DNA, incorporating supercoiling effects and predicting how torsional stress influences denaturation transitions based on entropy parameters.

Contribution

It introduces a generalized model accounting for supercoils in circular DNA, highlighting the role of writhe in denaturation and contrasting with previous twist-based assumptions.

Findings

Denaturation transition is suppressed for entropy parameter c ≤ 2.

A first-order denaturation transition occurs for c > 2, consistent with some experimental observations.

Supercoiling and writhe absorption are key factors in DNA denaturation behavior.

Abstract

We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces formation of supercoils whose writhe absorbs the linking number expelled by the loops. Our model predicts that, when the entropy parameter of a loop satisfies $c \le 2$, denaturation transition does not take place. On the other hand for $c>2$ a first-order denaturation transition is consistent with our model and may take place in the actual system, as in the case with no supercoils. These results are in contrast with other treatments of circular DNA melting where denaturation is assumed to be accompanied by an increase in twist rather than writhe on the bound segments.