Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions

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dc.contributor.author Pal, Subrata
dc.contributor.author Jana, Biman
dc.contributor.author Bagchi, Biman
dc.date.accessioned 2014-03-15T08:55:17Z
dc.date.available 2014-03-15T08:55:17Z
dc.date.issued 2010-03
dc.identifier.citation Jana, Biman; Pal, Subrata and Bagchi, Biman, “Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions”, The Journal of Physical Chemistry B, DOI: 10.1021/jp907513w, vol. 114, no. 10, pp. 3633–3638, Mar. 2010. en_US
dc.identifier.issn 1520-6106
dc.identifier.uri http://dx.doi.org/10.1021/jp907513w
dc.identifier.uri https://repository.iitgn.ac.in/handle/123456789/709
dc.description.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). © 2010 American Chemical Society. en_US
dc.description.statementofresponsibility by Biman Jana, Subrata Pal and Biman Bagchi
dc.format.extent Vol. 114, No. 10, pp. 3633-3638
dc.language.iso en en_US
dc.publisher American Chemical Society en_US
dc.subject Atomistic molecular dynamics simulations en_US
dc.subject Configurational entropy en_US
dc.subject DNA duplexes en_US
dc.subject Molecular Dynamics Simulation en_US
dc.subject Moleculesc en_US
dc.subject Specific interaction en_US
dc.subject Tetrahedral ordering en_US
dc.subject Thermoanalysis en_US
dc.title Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions en_US
dc.type Article en_US
dc.relation.journal The Journal of Physical Chemistry B


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