The Influence of solvent condition on DNA structures studied by molecular dynamics simulations

Fujii, Satoshi*; Kono, Hidetoshi; Sarai, Akinori*

The conformational properties of DNA play important roles in various biological processes. For example, interactions of proteins with DNA sequences are known to be affected by the conformational properties of DNA. It has also been known that the transitions among various conformational states are induced by the change in environments: Variations in ionic strength and identity, sequence, water activity, and ligand/protein binding all can modulate DNA structure. In this study, we analyzed how the sequence and the environments such as water activity influence the DNA conformations. We have carried out a series of molecular dynamics (MD) simulations to explore the conformational preferences and dynamical behavior of DNA duplex. We prepared the initial structure models with two different sequences in two kinds of conformations; d(CGCGTATACGCG)2 and d(CGCGTATACGCG)2 in Band A-forms. The MD simulations were carried out in four different environments: in only water solvent and in 75, 85 and 95 % (v/v) ethanol / water mixture solvent. We analyzed the differences of the DNA backbone conformation, the base-pair step parameter and the localization of water molecules in the groove on each structure. The variability of the conformation was different depending on the solvation condition. The DNA conformation seemed to be influenced by the localization of the water molecules in the groove.