Abstract

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Water dynamics at the interface of DNA

I-26

Water dynamics at the interface of DNA


E. Duboué-Dijon1, A.C. Fogarty1, J.T. Hynes1,2, D. Laage1*

1Ecole Normale Supérieure, Department of Chemistry, UMR ENS-CNRS-UPMC8640, rue Lhomond, Paris, France

2University of Colorado, Department of Chemistry and Biochemistry, Boulder, CO 80309-0215, USA

The hydration layer encasing DNA is of major importance for its biomolecular function and plays a role in a great variety of processes including DNA-ligand binding, drug intercalation and in the protection of the delicate DNA structure against heat denaturation. The dynamics of water in the vicinity of DNA has thus been actively studied with a broad range of techniques, most prominently by time-dependent Stokes’ shift measurements[1], ultrafast infrared spectroscopy[2], NMR[3] and numerical simulations[4]. Here we combine molecular dynamics simulations and an analytic jump model [5] to map the water reorientation and hydrogen-bond dynamics at the DNA interface. We show that the water reorientation dynamics is governed by hydrogen-bond exchanges towards a new water acceptor and we confirm that water dynamics is particularly retarded in the minor groove. For these strongly confined water molecules, a pronounced dynamical heterogeneity is found and we establish that water dynamics changes sensitively with the DNA groove width fluctuations.

Map of the water reorientation time at the interface of a DNA dodecamer.

Map of the water reorientation time at the interface of a DNA dodecamer.

References:

[1] S.K. Pal, L. Zhao, T. Xia, A.H. Zewail Proc. Natl. Acad. Sci. USA 100, 13746 (2003).

[2] L; Szyc, M. Yang, E.T.J. Nibbering, T. Elsaesser, Angew. Chem. 49, 3598 (2010).

[3] V.P. Denisov, G. Carlström, K. Venu, B. Halle J. Mol. Biol. 268, 118 (1997).

[4] K.E. Furse, S.A. Corcelli, J. Phys. Chem. Lett. 1, 1813 (2010).

[5] A.C. Fogarty, E. Duboué-Dijon, F. Sterpone, J.T. Hynes, D. Laage, Chem. Soc. Rev. 42, 5672 (2013).