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Published July 8, 2003 | Published
Journal Article Open

Water at DNA surfaces: Ultrafast dynamics in minor groove recognition


Water molecules at the surface of DNA are critical to its equilibrium structure, DNA–protein function, and DNA–ligand recognition. Here we report direct probing of the dynamics of hydration, with femtosecond resolution, at the surface of a DNA dodecamer duplex whose native structure remains unperturbed on recognition in minor groove binding with the bisbenzimide drug (Hoechst 33258). By following the temporal evolution of fluorescence, we observed two well separated hydration times, 1.4 and 19 ps, whereas in bulk water the same drug is hydrated with time constants of 0.2 and 1.2 ps. For comparison, we also studied calf thymus DNA for which the hydration exhibits similar time scales to that of dodecamer DNA. However, the time-resolved polarization anisotropy is very different for the two types of DNA and clearly elucidates the rigidity in drug binding and difference in DNA rotational motions. These results demonstrate that hydration at the surface of the groove is a dynamical process with two general types of trajectories; the slowest of them ({approx}20 ps) are those describing dynamically ordered water. Because of their ultrafast time scale, the "ordered" water molecules are the most weakly bound and are accordingly involved in the entropic (hydration/dehydration) process of recognition.

Additional Information

© 2003 National Academy of Sciences. Contributed by Ahmed H. Zewail, May 21, 2003. We thank Drs. Jorge Peon and Spencer Baskin for helpful discussion and Profs. Kenneth J. Breslauer and Peter B. Dervan for careful reading of the manuscript and helpful suggestions. This work was supported by the National Science Foundation.

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