INFLUENCE OF WATER AND SODIUM ON THE ENERGETICS OF DIMETHYLPHOSPHATE AND ITS IMPLICATIONS FOR DNA-STRUCTURE

Ab initio calculations, including electron correlation, were performed on dimethylphosphate (DMP) in the presence and absence of a single wa ter molecule or sodium ion to study their influence on DMP conformatio nal energetics. The presence of sodium had only minimal effect on the energetics of DMP. In the presence of a single water significant chang es versus anhydrous DMP were calculated including a lowering of the en ergies of the g,t and t,t conformers relative to the g,g conformer. An alysis of results from surveys of DNA crystal structures indicate that the calculated differences in DMP energetics, when applied to the pho sphodiester backbone in DNA, may contribute to experimentally observed structural differences between the A and B forms of duplex DNA. Molec ular dynamics simulations using three phosphodiester backbone paramete r sets further suggest that ab initio calculated changes in the confor mational properties of DMP may indeed influence DNA structure. These r esults suggest that changes in the conformational energetics of the ph osphodiester backbone due to interactions with water or counterions ma y contribute to experimentally observed changes in DNA structure assoc iated with alterations in the DNA environment.