Dynamical transition in translational and rotational dynamics of water in the grooves of DNA duplex at low temperature

Details Dynamical transition in translational and rotational dynamics of water in the grooves of DNA duplex at low temperature Dynamical transition in translational and rotational dynamics of water in the grooves of DNA duplex at low temperature

2008-09-21

arxiv.org/abs/0809.3616v1

Physics

Condensed Matter

Soft Condensed Matter

14 pages, 7 figures

Scientific paper

We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both the major and the minor grooves of a DNA duplex. The transition occurs at a slightly higher temperature ($T_{GL} \approx $ 255 K) than the temperature ($T_L\approx$ 247 K) where the bulk water is conjectured to undergo a dynamical transition. Groove water, however, exhibits markedly different temperature dependence of its properties from the bulk. Entropy calculations reveal that the minor groove water is ordered even at room temperature and the transition at $T \approx$ 255 K can be characterized as a {\em strong-to-strong} dynamical transition. The low temperature water is characterized by pronounced tetrahedral order, as manifested in the sharp rise near $109^{\circ}$ in the O-O-O angle distribution. We find that Adams-Gibbs relation between configurational entropy and translational diffusion holds quite well when the two quantities are plotted together in a master plot for different region of aqueous DNA duplex (bulk, major and minor grooves) at different temperatures. The activation energy for the transfer of water molecules between different regions of DNA is found to be independent of temperature.

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