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Site- and sequence-selective ultrafast hydration of DNA

Pal, Samir Kumar and Zhao, Liang and Xia, Tianbing and Zewail, Ahmed H. (2003) Site- and sequence-selective ultrafast hydration of DNA. Proceedings of the National Academy of Sciences of the United States of America, 100 (24). pp. 13746-13751. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:PALpnas03b

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Abstract

Water molecules in the DNA grooves are critical for maintaining structural integrity, conformational changes, and molecular recognition. Here we report studies of site- and sequence-specific hydration dynamics, using 2-aminopurine (Ap) as the intrinsic fluorescence probe and with femtosecond resolution. The dodecamer d[CGCA(Ap)ATTTGCG]2 was investigated, and we also examined the effect of a specific minor groove-binding drug, pentamidine, on hydration dynamics. Two time scales were observed: {approx}1 ps (bulk-like) and 10–12 ps (weakly bound type), consistent with layer hydration observed in proteins and DNA. However, for denatured DNA, the cosolvent condition of 40% formamide hydration is very different: it becomes that of bulk (in the presence of formamide). Well known electron transfer between Ap and nearby bases in stacked assemblies becomes inefficient in the single-stranded state. The rigidity of Ap in the single strands is significantly higher than that in bulk water and that attached to deoxyribose, suggesting a unique role for the dynamics of the phosphate-sugar-base in helix formation. The disparity in minor and major groove hydration is evident because of the site selection of Ap and in the time scale observed here (in the presence and absence of the drug), which is different by a factor of 2 from that observed in the minor groove–drug recognition.


Item Type:Article
Additional Information:Contributed by Ahmed H. Zewail, September 26, 2003. This work was supported by the National Science Foundation.
Record Number:CaltechAUTHORS:PALpnas03b
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:PALpnas03b
Alternative URL:http://dx.doi.org/10.1073/pnas.2336222100
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:496
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:11 Jul 2005
Last Modified:14 Nov 2014 19:18

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