paper

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

arXiv:cond-mat/0306015 · doi:10.1103/PhysRevE.68.021911

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 . We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.

15 pages, 25 figures. submitted to PRE

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