Flexibility of short DNA helices under mechanical stretching

TL;DR

This study models the mechanical flexibility of short DNA helices, revealing significant bendability due to thermal effects and highlighting limitations of traditional models at short lengths.

Contribution

It introduces a Hamiltonian model that accurately captures the elastic response of short DNA segments, emphasizing the importance of base pair fluctuations and kinks.

Findings

Short DNA sequences remain flexible with significant bending.

Thermal fluctuations and kinks contribute to bendability.

Worm-like-chain model is inadequate for short DNA segments.

Abstract

The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces is obtained by computing the average bending angles between adjacent base pairs along the molecule axis. The ensemble averages are performed over a room temperature equilibrium distribution of base pair separations and bending fluctuations. The analysis of the end-to-end distances and persistence lengths shows that even short sequences with less than $100$ base pairs maintain a significant bendability ascribed to thermal fluctuational effects and kinks with large bending angles. The discrepancies between the outcomes of the discrete model and those of the worm-like-chain model are examined pointing out the inadequacy of the latter on short length scales.