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 water molecule or sodium ion to study their influence on DMP conformational energetics. The presence of sodium had only minimal effect on the energetics of DMP. In the presence of a single water significant changes versus anhydrous DMP were calculated including a lowering of the energies of the g,t and t,t conformers relative to the g,g conformer. Analysis of results from surveys of DNA crystal structures indicate that the calculated differences in DMP energetics, when applied to the phosphodiester backbone in DNA, may contribute to experimentally observed structural differences between the A and B forms of duplex DNA. Molecular dynamics simulations using three phosphodiester backbone parameter sets further suggest that ab initio calculated changes in the conformational properties of DMP may indeed influence DNA structure. These results suggest that changes in the conformational energetics of the phosphodiester backbone due to interactions with water or counterions may contribute to experimentally observed changes in DNA structure associated with alterations in the DNA environment.