Molecular Dynamics of the DNA Double Helix

Abstract

Molecular dynamics has been used to simulate the room temperature atomic motion of 12 and 24 base-pair DNA double helices for periods of up to 96 picoseconds. The hydrogen bonds between base-pairs are all found to be stable on this time-scale, and the motions of the torsion angles are found to be of small amplitude (<10°). Both DNA fragments show cooperative overall bending motions of large amplitude that do not involve any major pertubation of the DNA torsion angles. This smooth bending differs from that expected of an isotropic elastic rod in that (a) it is asymmetric always acting to close the major groove of DNA and (b) it consists predominantly of the normal-mode that has a wavelength close to the helical repeat length. The stack of base- pairs is also seen to kink into the minor groove. The extent of this global motion is consistent with nuclear magnetic resonance measurements and explains the observed sensitivity of DNA conformation to local environment.