Molecular dynamics study of DNA oligomers under angled pulling

Abstract

Extensive 13-microsecond steered molecular dynamics simulations (SMD) were performed to study the mechanical properties of short double-stranded DNA under tensile loads at the atomistic level. We elucidate the influence of the pulling rate and the pulling angle on stretching behavior of the DNA duplex. Generalized Born implicit solvent methodology and Langevin dynamics were employed to represent the effects of aqueous solvation under physiological conditions. Our simulations show that for all pulling angles, within the range of pulling rates studied here, the DNA force-extension curves consist of three different regimes: elastic, strain softening and strain hardening phases. Angled pulling can, however, alter the mechanical properties unpredictably, especially in the overstretched regime. In addition, these properties may depend on the velocity at which the DNA is pulled making the problem even more complex. A detailed analysis of the base-pairing and base-stacking interactions during stretching is carried out to investigate the origin of the different DNA behaviors under various pulling angles and velocities.