Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties

Molecular dynamics (MD) simulations were performed on the DNA dodecamer comprising the EcoRI recognition site in aqueous solution. Three simulations, each of 1 ns duration, were performed that included no salt, 0.26 M Mg+2, and 0.50 M Mg2+ and 0.59 M Cl-. The simulations yielded stable structures that were intermediate to the canonical A and B conformations of DNA. Certain aspects of the MD solution structures are similar to the EcoRI dodecamer crystal structure. Interactions of the phosphates with Mg2+ occur primarily with Mg+2 fully hydrated, although direct ion-phosphate contact pairs are observed. The presence of Mg2+ leads to decreased root mean square fluctuations of the DNA phosphate backbone and the waters hydrating the DNA major groove and phosphate backbone. Calculations also indicate a small increase in hydration of the minor groove and phosphate backbone due to the presence of Mg2+. These results suggest that decreased water mobility rather than decreased hydration number is responsible for Mg2+-induced dehydration of DNA associated with decreased water activity.