Anharmonic stacking in supercoiled DNA

TL;DR

This study uses a mesoscopic Hamiltonian model to show that anharmonic stacking interactions and DNA twisting significantly influence the stability and melting behavior of supercoiled DNA, highlighting the importance of nonlinear effects.

Contribution

It introduces a model that incorporates helicoidal geometry and anharmonic stacking to analyze DNA denaturation, emphasizing the role of twisting in thermodynamic stability.

Findings

Anharmonic stacking stabilizes the double helix against thermal disruption.

Twisting is crucial for capturing nonlinear thermodynamic effects.

Moderately untwisted helices resist strand separation better.

Abstract

Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.