Solvent-induced DNA conformational transition

Modified water models with scaled charges are used to investigate solvent polarity effects on DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI dodecamer d(CGCGAATTCGCG) in different model solvents are performed. When the polarity of the solvent molecule decreases, from overpolarized to less polarized, DNA experiences the conformational transitions of constrained -> B form ->(A-B)mix -> A form. We demonstrate that one important cause of these structure changes is the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups on DNA backbones.