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Nucleic Acids Research 2005 33(22):7111-7119; doi:10.1093/nar/gki1018
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Published online 15 December 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

DNA base flipping by a base pair-mimic nucleoside

Shu-ichi Nakano1, Yuuki Uotani2, Kazuya Uenishi3, Masayuki Fujii3,4 and Naoki Sugimoto1,2,*

1Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan 2Department of Chemistry, Faculty of Science and Engineering, Konan University 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan 3Molecular Engineering Institute, Kinki University 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan 4Department of Environmental and Biological Chemistry, Kinki University 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan

*To whom correspondence should be addressed. Tel: +81 78 435 2497; Fax: +81 78 435 2539; Email: sugimoto{at}konan-u.ac.jp

Received October 27, 2005. Revised November 29, 2005. Accepted November 29, 2005.

On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson–Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol–1 while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol–1, respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.


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