Sodium and Chlorine Ions as Part of the DNA Solvation Shell

AbstractThe distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C5T5) · (A5G5) in explicit solvent with 0.8M additional NaCl salt. One simulation was carried out for 10ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12ns with the AMBER force field that preferentially stabilizes B-DNA conformations (Feig and Pettitt, 1998, Biophys. J. 75:134–149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B-DNA conformations are discussed