Thermal denaturation of an helicoidal DNA model

TL;DR

This paper investigates the static and dynamic behavior of a helicoidal DNA model near melting, revealing characteristics of a first-order transition influenced by stacking forces and suggesting an underlying continuous transition.

Contribution

It introduces a simple mechanical model of DNA with helicoidal geometry that enables exact numerical analysis of thermodynamics and dynamical properties near melting.

Findings

Long chains exhibit first-order transition features.

Simulation results suggest an underlying continuous transition.

Model captures both static and dynamic denaturation properties.

Abstract

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's ``universality class'' strongly suggests the presence of an ``underlying'' continuous transition.