Local elasticity of strained DNA studied by all-atom simulations

TL;DR

This study uses all-atom simulations to explore how local mechanical properties of DNA, such as rigidity and elasticity, change under torsional and tensile stresses, revealing sequence-dependent effects with biological implications.

Contribution

It provides detailed insights into how DNA's local elastic properties vary under mechanical stresses, highlighting sequence-dependent differences and biological relevance.

Findings

Stretching rigidity increases with tension and twisting.

Torsional rigidity is unaffected by stretching but varies with twisting.

AT-alternating DNA shows a minimum in twist near experimental values.

Abstract

Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light upon earlier experimental observations.