On the rupture of DNA molecule

TL;DR

This study uses Langevin Dynamic simulations to analyze how shear force affects DNA rupture, revealing that rupture force varies with application points and chain length, validated by analytical models.

Contribution

It introduces a detailed simulation and analytical comparison of DNA rupture mechanics considering different force application points and chain lengths.

Findings

Rupture force depends on whether force is applied at 3'-3' or 5'-5' ends.

Distribution of bond extensions varies significantly with rupture conditions.

Rupture force varies with chain length, consistent with experimental observations.

Abstract

Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of individual segments of the diblock copolymer are considered to be different. We showed that the magnitude of the rupture force depends on whether the force is applied at $3'-3'-$ends or $5'-5'-$ends. Distributions of extension in hydrogen bonds and covalent bonds along the chain show the striking differences. Motivated by recent experiments, we have also calculated the variation of rupture force for different chain lengths. Results obtained from simulations have been validated with the analytical calculation based on the ladder model of DNA.