Length scale dependence of DNA mechanical properties

TL;DR

This study systematically investigates how DNA's mechanical properties vary with length scale, revealing increased flexibility at shorter lengths and elucidating the underlying modes and modulations through atomistic simulations.

Contribution

It provides the first detailed analysis of DNA elasticity from single base-pair to four helical turns, highlighting scale-dependent softening and mode contributions.

Findings

Evidence of cooperative softening of the stretch modulus at short scales

Helical periodicity influences bend correlation modulations

Twist modulus transitions smoothly from small to bulk values

Abstract

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for cellular processes such as DNA packaging and gene regulation. Here, we perform a systematic study of the effective elastic properties of DNA at different length scales by probing the conformation and fluctuations of DNA from single base-pair level up to four helical turns, using trajectories from atomistic simulation. We find evidence that supports cooperative softening of the stretch modulus and identify the essential modes that give rise to this effect. The bend correlation exhibits modulations that reflect the helical periodicity, while it yields a reasonable value for the effective persistence length, and the twist modulus undergoes a smooth crossover---from a relatively smaller value at the single base-pair level to the bulk value---over half a DNA-turn.