title: Modeling DNA structure, elasticity, and deformations at the base-pair level.
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 the neighboring base pairs. The sugar-phosphate backbones are taken into account by semirigid harmonic springs with a nonzero spring length. The competition between these two interactions and the introduction of a simple geometrical constraint lead 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 which partially preserves the stacking of successive base pairs.
authors.affiliation: Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany. mergell@mpip-mainz.mpg.de
authors.forename: Boris
authors.initials: B
authors.lastname: Mergell
authors.forename: Mohammad R
authors.initials: MR
authors.lastname: Ejtehadi
authors.forename: Ralf
authors.initials: R
authors.lastname: Everaers
mesh_terms: D001482:Base Composition; D020029:Base Pairing; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D008962:Models, Theoretical; D008968:Molecular Conformation; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA