Deciphering the mechanical properties of B-DNA duplex

Structure and deformability of the DNA double helix play a key role in protein and small ligand binding, in genome regulation via looping, or in nanotechnology applications. Here we review some of the recent developments in modeling mechanical properties of DNA in its most common B-form. We proceed from atomic-resolution molecular dynamics (MD) simulations through rigid base and base-pair models, both harmonic and multistate, to rod-like descriptions in terms of persistence length and elastic constants. The reviewed models are illustrated and critically examined using MD data for which the two current Amber force fields, bsc1 and OL15, were employed. This article is categorized under: Structure and Mechanism > Molecular Structures Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods