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Nucleic Acids Research 2005 33(18):5887-5895; doi:10.1093/nar/gki889
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Published online 19 October 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}oxfordjournals.org

Article

Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference

Mitsunobu Nakamura, Yudai Fukunaga, Kazuhiro Sasa, Yukinori Ohtoshi, Kenji Kanaori1, Haruhisa Hayashi, Hidehiko Nakano and Kazushige Yamana*

Department of Materials Science and Chemistry, University of Hyogo 2167 Shosha, Himeji, Hyogo 671-2201, Japan 1Department of Applied Biology, Kyoto Institute of Technology Matsugasaki, Sakyo-ku, Kyoto 605-8585, Japan

*To whom correspondence should be addressed. Tel: +81 792 67 4895; Fax: +81 792 67 4895; Email: yamana{at}eng.u-hyogo.ac.jp

Received August 30, 2005. Revised September 16, 2005. Accepted September 26, 2005.

Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene–DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. 1H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene–RNA/RNA and the pyrene–DNA/DNA duplexes.


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