Temperature dependence of circular DNA topological states

TL;DR

This paper uses Monte Carlo simulations to explore how temperature affects the distribution of topological states in small circular DNA, highlighting the roles of local melting, unstacking, and defects in altering DNA rigidity and unwinding.

Contribution

It introduces a model predicting temperature-dependent changes in DNA topological states based on defect excitations, providing a new approach to study DNA micromechanics and stability.

Findings

Reduced bending rigidity affects linking number variance.

Local unwinding amplifies the effect of defects.

Predictions are experimentally testable and relevant for DNA-protein interactions.

Abstract

Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of small circular DNAs. Our predictions are based on flexible defect excitations resulted from local melting or unstacking of DNA base pairs. We found that the reduced bending rigidity alone can lead to measurable changes of the variance of linking number distribution of short circular DNAs. If the defect is accompanied by local unwinding, the effect becomes much more prominent. The predictions can be easily investigated in experiments, providing a new method to study the micromechanics of sharply bent DNAs and the thermal stability of specific DNA sequences. Furthermore, the predictions are directly applicable to the studies of binding of DNA distorting proteins that can locally reduce DNA rigidity, form DNA kinks, or introduce local unwinding.