Twist-stretch profiles of DNA chains

TL;DR

This study models short DNA molecules to analyze how they twist and stretch under mechanical loads, revealing over-twisting behavior under tension and its relation to helix diameter and base pair fluctuations.

Contribution

The paper introduces a mesoscopic Hamiltonian model combined with finite temperature path integral techniques to simulate DNA twist-stretch behavior, capturing over-twisting and untwisting phenomena.

Findings

DNA over-twists when stretched, linked to helix diameter contraction.

Over-twisting occurs at weak forces, then untwisting at higher forces.

Results align qualitatively with experimental data for long DNA molecules.

Abstract

Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are applied to generate a large ensemble of possible configurations for the base pairs of the sequence. The model also accounts for the bending and twisting fluctuations between adjacent base pairs along the molecules stack. Simulating a broad range of twisting conformation, we compute the helix structural parameters by averaging over the ensemble of base pairs configurations. The method selects, for any applied force, the average twist angle which minimizes the molecule's free energy. It is found that the chains generally over-twist under an applied stretching and the over-twisting is physically associated to the contraction of the average helix diameter, i.e. to the damping of the base pair fluctuations. Instead, assuming that the maximum amplitude of the bending fluctuations may decrease against the external load, the DNA molecule first over-twists for weak applied forces and then untwists above a characteristic force value. Our results are discussed in relation to available experimental information albeit for kilo-base long molecules.