Simulation of DNA in water/ethanol mixture

The study of B-DNA in mixed solvent comprised of water and ethanol with different concentrations at 298 K has been conducted by molecular dynamics simulation. We find that the structure of DNA is easily affected by the aqueous environment. Property and structure changes of the solvent will influence the local structure of DNA helix, induce the conformation transition between different forms, and even cause the degeneration of DNA. The addition of ethanol can reduce the activity of water, changes the solvent structure around DNA. DNA in the solvent with low concentration of ethanol changes little, when the ethanol increases in the solvent, large structure changes occur at the ends of the helix first, then show the characters of A-form, the minor groove becomes wider and shallower, and the length is shortened when in the solvent with the concentration of 0.88 g/cm3. The mechanism behind is discussed, and we find the competition between the solvent molecules and counterions coupling to the free oxygen atoms of the phosphate groups, and the breaking of the spin of water both contribute to the structure changes of DNA in the simulation.