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Nucleic Acids Research, 2003, Vol. 31, No. 12 3267-3273
© 2003 Oxford University Press

Triplex formation with 2'-O,4'-C-ethylene-bridged nucleic acids (ENA) having C3'-endo conformation at physiological pH

Makoto Koizumi, Koji Morita, Makiko Daigo, Shinya Tsutsumi1, Koji Abe2, Satoshi Obika3 and Takeshi Imanishi3

Exploratory Chemistry Research Laboratories, 1 Biomedical Research Laboratories and 2 Pharmacokinetics and Drug Delivery Research Laboratories, Sankyo Co. Ltd, Tokyo 140-8710, Japan and 3 Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan

*To whom correspondence should be addressed. Tel: +81 3 3492 3131; Fax: +81 3 5436 8570; Email: koizum{at}shina.sankyo.co.jp
This paper is dedicated to the memory of the late Professor Claude Hélène.

Antigenes, which are substances that inhibit gene expression by binding to double-stranded DNA (dsDNA) in a sequence-specific manner, are currently sought for the treatment of various gene-related diseases. As such antigenes, we developed new nuclease-resistant oligopyrimidine nucleotides that are partially modified with 2'-O,4'-C-ethylene nucleic acids (ENA), which are constrained in the C3'-endo conformation and can form a triplex with dsDNA at physiological pH. It was found that these oligonucleotides formed triplexes similarly to those partially modified with 2'-O,4'-C-methylene nucleic acids (2',4'-BNA or LNA), as determined by UV melting analyses, electromobility shift assays, CD spectral analyses and restriction enzyme inhibition assays. In our studies, oligonucleotides fully modified with ENA have {delta} torsion angle values that are marginally higher than those of 2',4'-BNA/LNA. ENA oligonucleotides present in 10-fold the amount of dsDNA were found to be favorable in forming triplexes. These results provide useful information for the future design of triplex-forming oligonucleotides fully modified with such nucleic acids constrained in the C3'-endo conformation considering that oligonucleotides fully modified with 2',4'-BNA/LNA do not form triplexes.


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