Computational investigation of the conformation transitions of DNA in modified water models

Modified water models with different bond length are used to investigate solvent activity effects on DNA structure. The dodecamer d(CGCGAATTCGCG) DNA segment is merged into the different model solvents and its conformation transition is studied with molecular dynamics (MD) simulations in detail. We find that DNA undergos B→A-DNA transition when the solvent activity is reduced with decreasing bond length, while the DNA is restrained in B form by over activity solvent with strong hydrogen bonding when bond length is increased. Under conditions of over activity solvent, the solvent molecules are highly occupied around oxygen atoms of phosphate group leading to the lower interphosphate repulsion on DNA backbone. With decreasing solvent activity, the hydration shell around DNA becomes weak and the counterions are given the chance to interact with DNA's negative charge sites. When rO−H = 0.7 Å, the counterions are strongly coordinated to free phosphate oxygen atoms and bases. Its arrangement around DNA major groove is more compact, leading to the electrostatic repulsion on the backbones be restrained. Hence, the DNA favours A form conformation.