Molecular dynamics simulation of single DNA stretching reveals a novel structure

MD simulation, to closely mimic a torsionally unconstrained single-molecule stretching experiment of dsDNA, uncovers three distinct force regimes, characterized by fast and slow elongation regions with a transition regime in between, where the alpha and gamma backbone torsion angles of the elongated double-stranded DNA find rapidly new stationary values. In the slow elongation regime DNA gradually looses its twist, collectively breaks all base-pair H-bonds and develops a remarkable base-stacked structure with the bases strongly tilted, forming a zipper-like stack on the major groove side, stabilized by the narrowing distance between the elongated strands, and by specific water interactions. (c) 2005 Elsevier B.V. All rights reserved.