Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2

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Abstract
Here we report constant pressure molecular dynamics simulations of the B‐DNA dodecamer d(GCGCGCGCGCGC)2 and the A‐RNA dodecamer r(GCGCGCGCGCGC)2 in aqueous solution. The molecular dynamics simulations were performed at reference pressures of 1 and 6000 atm. We obtained stable trajectories, especially for the A‐RNA dodecamer, using the standard atom based truncation cutoff method. For the B‐DNA dodecamer, a tendency to transform to the A‐DNA form was obtained. The atomic mean square fluctuations were lower for the A‐RNA dodecamer than for the B‐DNA, and were further reduced by increased pressure for the A‐RNA dodecamer. The backbone and glycosidic torsion angles were well preserved for the A‐RNA dodecamer and only small changes were observed for the B‐DNA dodecamer. In both dodecamers the Watson–Crick hydrogen bonds were preserved without any constraints. The differences in the exposed surface area between the dodecamers were mainly due to the 2′OH group and to the cytosine base being more exposed in the B‐DNA.