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Nucleic Acids Research 2005 33(9):3017-3024; doi:10.1093/nar/gki616
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Published online 24 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements

Shigeki Arai, Toshiyuki Chatake, Takashi Ohhara, Kazuo Kurihara, Ichiro Tanaka, Nobuhiro Suzuki1,2, Zui Fujimoto1, Hiroshi Mizuno1 and Nobuo Niimura*

Neutron Science Research Center, Japan Atomic Energy Research Institute 2-4 Shirakatashirane, Tokai, Ibaraki 319-1195, Japan 1Department of Biochemistry, National Institute of Agrobiological Sciences 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan 2Institute of Applied Biochemistry, University of Tsukuba Tsukuba, Ibaraki 305-8572, Japan

*To whom correspondence should be addressed. Tel: +81 294 38 5254; Fax: +81 294 38 5272; Email: niimura{at}mx.ibaraki.ac.jp

Received May 5, 2005. Accepted May 6, 2005.

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 Å resolution X-ray and 3.0 Å resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

Present addresses: Toshiyuki Chatake, Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 3 Shiomi-cho, Choshi, Chiba 288-0025, Japan

Ichiro Tanaka, Department of Biomolecular Functional Engineering, the College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan

Nobuo Niimura, Institute of Applied Beam Science, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan

Protein Data Bank ID 1WQY, 1WQZ


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