Stretching and twisting of the DNA duplexes in coarse grained dynamical models

TL;DR

This paper introduces three coarse-grained DNA models with varying bead representations, demonstrating their ability to replicate experimental and all-atom simulation results in mechanical manipulation scenarios like twisting and stretching.

Contribution

The paper proposes and compares three novel coarse-grained DNA models differing in bead count, showing they produce consistent qualitative behavior with experimental data.

Findings

Models exhibit similar behavior in torque-force phase diagrams.

All models align qualitatively with experimental and all-atom simulation results.

Models effectively capture DNA mechanical responses to twisting and stretching.

Abstract

Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behavior and, in particular, lead to a torque-force phase diagrams qualitatively consistent with experiments and all-atom simulations.