Enhanced tetrahedral ordering of water molecules in minor grooves of DNA: relative role of DNA rigidity, nanoconfinement, and surface specific interactions

Jana, Biman ; Pal, Subrata ; Bagchi, Biman (2010) Enhanced tetrahedral ordering of water molecules in minor grooves of DNA: relative role of DNA rigidity, nanoconfinement, and surface specific interactions Journal of Physical Chemistry B, 114 (10). pp. 3633-3638. ISSN 1089-5647

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Official URL: http://pubs.acs.org/doi/abs/10.1021/jp907513w

Related URL: http://dx.doi.org/10.1021/jp907513w

Abstract

Confinement and surface specific interactions can induce structures otherwise unstable at that temperature and pressure. Here we study the groove specific water dynamics in the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) can be attributed to an enhanced tetrahedral ordering (th) of water. The largest value of th in the AT minor groove is related to the spine of hydration found in X-ray structure. The calculated configurational entropy (SC) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TSC), and also with th.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:4593
Deposited On:18 Oct 2010 07:25
Last Modified:07 Jan 2011 04:44

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