A three-state model with loop entropy for the over-stretching transition of DNA

TL;DR

This paper presents a three-state DNA model incorporating loop entropy, enabling accurate force-extension curve predictions and phase diagram mapping, with implications for understanding DNA overstretching and denaturation.

Contribution

The authors develop a novel three-state DNA model that explicitly includes loop entropy and separates stacking energy effects, improving the understanding of DNA overstretching.

Findings

The model accurately fits experimental force-extension data.

The phase diagram in force-temperature space is established.

The loop exponent c is estimated to be small, indicating nicks dominate DNA behavior.

Abstract

We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the exponent c in the asymptotic expression S ~ - c ln n for the entropy of a loop of length n. Force extension curves are derived exactly employing a generalized Poland-Scheraga approach and compared to experimental data. Simultaneous fitting to force-extension data at room temperature and to the denaturation phase transition at zero force is possible and allows to establish a global phase diagram in the force-temperature plane. Under a stretching force, the effects of the stacking energy, entering as a domain-wall energy between paired and unpaired bases, and the loop entropy are separated. Therefore we can estimate the loop exponent c independently from the precise value of the stacking energy. The fitted value for c is small, suggesting that nicks dominate the experimental force extension traces of natural DNA.