Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level

TL;DR

This paper introduces a generic, base-pair level DNA model that captures structural and elastic properties, reproduces experimental observables, and predicts the force-induced B-to-S DNA transition.

Contribution

A novel DNA model combining stacking and backbone interactions that accurately reproduces experimental data and predicts critical overstretching forces.

Findings

Reproduces experimentally known persistence lengths and base-pair step parameters.

Predicts the B-to-S DNA transition at approximately 140 pN.

Observes S-DNA conformation with inclined bases maintaining stacking.

Abstract

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid harmonic springs with a non-zero spring length. The competition of these two interactions and the introduction of a simple geometrical constraint leads to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean squared base-pair step parameters. For the optimized model parameters we measured the critical force where the transition from B- to S-DNA occurs to be approximately $140{pN}$. We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.