Parametric Molecular Dynamics Study of dsDNA Stretching

The most common computational technique used to obtain mechanical properties of DNA is molecular dynamics (MD) simulation. The effects of several key parameters of MD calculations expected to have an important role in the overstretching simulations of DNAare investigated. Steered MD simulations are carried out on a 12-base pairs d(ACTG)3 oligomer, which were constructed in a canonical B-DNA conformation. The MD simulations revealed that although overstretching of DNA in silico is essentially a non-equilibrium process,integrating with 1-fs and 2-fs time steps result in the force-extension curves without any significant difference, for pulling velocity that are not larger than 3 m/s in explicit solvent environment. The DNA pulling simulation with cutoff of 15 Å can increases over threefoldcompared to the case of simulation with 9-Å cutoff, while the measured force-extension curves do not show considerably differences in the two cases. Also, using small periodic box leads to incorrect prediction of the DNA behavior by MD simulations. This issue affectsthe results more significantly when the overstretching of DNA is simulated. It was observed that the long axis of DNA rotates such that the long axis becomes nearly along the short box dimension which will bring the ends of the DNA near its periodic image, especially underlow pulling velocities