Proceedings PaperMolecular dynamics simulations of fast conformational changes in double-helix DNA in solution
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Fast conformational changes in B-DNA and Z-DNA have been studied using MD simulation techniques. The double helix right-handed B-DNA is simulated in a high-salt aqueous NaCl (2.5 M) solution, while the double helix left-handed Z-DNA is put in a non-salt solution with only potassium ions, enough to electro-neutralize the phosphates. The fast conformational changes are followed by studying the changes in the backbone and sugar torsional angles, as well as, the glycosidic bond angle. The B-DNA goes over to A form during the simulation of 30 pico seconds and the Z-DNA exhibits a Z(I) yields Z(II) transition within 70 pico seconds.