A Caltech Library Service

Water at DNA surfaces: Ultrafast dynamics in minor groove recognition

Pal, Samir Kumar and Zhao, Liang and Zewail, Ahmed H. (2003) Water at DNA surfaces: Ultrafast dynamics in minor groove recognition. Proceedings of the National Academy of Sciences of the United States of America, 100 (14). pp. 8113-8118. ISSN 0027-8424. PMCID PMC166191.

PDF - Published Version
See Usage Policy.


Use this Persistent URL to link to this item:


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.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
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.
Funding AgencyGrant Number
Subject Keywords:calf thymus DNA, time-resolved emission spectra
Issue or Number:14
PubMed Central ID:PMC166191
Record Number:CaltechAUTHORS:PALpnas03a
Persistent URL:
Official Citation:Samir Kumar Pal, Liang Zhao, and Ahmed H. Zewail Water at DNA surfaces: Ultrafast dynamics in minor groove recognition PNAS 2003 100 (14) 8113-8118; published ahead of print June 18, 2003, doi:10.1073/pnas.1433066100
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:498
Deposited By: Archive Administrator
Deposited On:11 Jul 2005
Last Modified:02 Oct 2019 22:34

Repository Staff Only: item control page