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Issue 10, 2011
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Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration

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Abstract

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car–Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB–water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. colicell.

Graphical abstract: Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration

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Publication details

The article was received on 16 Oct 2010, accepted on 22 Dec 2010 and first published on 21 Jan 2011


Article type: Paper
DOI: 10.1039/C0CP02177F
Citation: Phys. Chem. Chem. Phys., 2011,13, 4311-4317
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    Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration

    A. Furmanchuk, O. Isayev, L. Gorb, O. V. Shishkin, D. M. Hovorun and J. Leszczynski, Phys. Chem. Chem. Phys., 2011, 13, 4311
    DOI: 10.1039/C0CP02177F

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