INFLUENCE OF MAGNESIUM-IONS ON DUPLEX DNA STRUCTURAL, DYNAMIC, AND SOLVATION PROPERTIES

Molecular dynamics (MD) simulations were performed on the DNA dodecame r comprising the EcoRI recognition site in aqueous solution. Three sim ulations, 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 conf ormations of DNA. Certain aspects of the MD solution structures are si milar to the EcoRI dodecamer crystal structure. Interactions of the ph osphates with Mg2+ occur primarily with Mg+2 fully hydrated, although direct ion-phosphate contact pairs are observed. The presence of Mg2leads to decreased root mean square fluctuations of the DNA phosphate backbone and the waters hydrating the DNA major groove and phosphate b ackbone. Calculations also indicate a small increase in hydration of t he minor groove and phosphate backbone due to the presence of Mg2+. Th ese results suggest that decreased water mobility rather than decrease d hydration number is responsible for Mg2+-induced dehydration of DNA associated with decreased water activity.