All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

Molecular dynamics simulations based on empirical force fields can greatly enhance knowledge of DNA and RNA structure and dynamics in solution. Presented are results on simulations of three DNA sequences and one RNA sequence using the new all-atom CHARMM27 force field for nucleic acids presented in the accompanying manuscript (Foloppe, MacKerell, J Comput Chem, this issue). Data are reported on structural, dynamic, and hydration properties including dihedral angle, sugar puckering, and helicoidal parameter probability distributions. Also presented are calculations of a DNA hexamer in 0 and 75% ethanol starting from both the canonical A and B forms. Analysis of RMS differences with respect to the canonical A and B forms of DNA show a highly anticorrelated behavior indicating that the force field samples the equilibrium between the A and B forms of DNA. Proper stabilization of B form DNA in aqueous solution and A form DNA in 75% ethanol show that this equilibrium can be perturbed by environmental contributions. Success of the force field in reproducing a variety of experimental data for duplex DNA and RNA indicates that it is of general use for computational investigations of nucleic acids as well as nucleic acids in complexes with proteins and lipids. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 105–120, 2000