Dynamical Transition of Water in the Grooves of DNA Duplex at Low Temperature

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dc.contributor.author Biswal, Debasmita
dc.contributor.author Jana, Biman
dc.contributor.author Pal, Subrata
dc.contributor.author Bagchi, Biman
dc.date.accessioned 2014-03-15T14:20:14Z
dc.date.available 2014-03-15T14:20:14Z
dc.date.issued 2009-03
dc.identifier.citation Pal, Subrata et al., “Dynamical transition of water in the grooves of DNA duplex at low temperature” The Journal of Physical Chemistry B, DOI: 10.1021/jp8078343, vol. 113, no. 13, pp. 4394–4399, March. 2009. en_US
dc.identifier.issn 1520-6106
dc.identifier.uri http://dx.doi.org/10.1021/jp8078343
dc.identifier.uri https://repository.iitgn.ac.in/handle/123456789/741
dc.description.abstract At low temperature (below its freezing/melting temperature), liquid water under confinement is known to exhibit anomalous dynamical features. Here we study structure and dynamics of water in the grooves of a long DNA duplex using molecular dynamics simulations with TIP5P potential at low temperature. 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 (TGL ≈ 255 K) than the temperature at which the bulk water is found to undergo a dynamical transition, which for the TIP5P potential is at 247 K. 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 ≈ 255 K can be characterized as a strong-to-strong dynamical transition. Confinement of water in the grooves of DNA favors the formation of a low density four-coordinated state (as a consequence of enthalpy−entropy balance) that makes the liquid−liquid transition stronger. The low temperature water is characterized by pronounced tetrahedral order, as manifested in the sharp rise near 109° in the O−O−O angle distribution. We find that the 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 weakly dependent on temperature. en_US
dc.description.statementofresponsibility by Subrata Pal et al.,
dc.format.extent Vol. 113, No. 13, pp. 4394–4399
dc.language.iso en en_US
dc.publisher American Chemical Society en_US
dc.subject Angle distributions en_US
dc.subject Bulk waters en_US
dc.subject Configurational entropies en_US
dc.subject DNA duplexes en_US
dc.subject Dynamical feature en_US
dc.subject Dynamical transitions en_US
dc.subject Entropy balances en_US
dc.subject Higher temperatures en_US
dc.subject Liquid waters en_US
dc.subject Minor grooves en_US
dc.title Dynamical Transition of Water in the Grooves of DNA Duplex at Low Temperature en_US
dc.type Article en_US
dc.relation.journal The Journal of Physical Chemistry B


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