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Nucleic Acids Research Advance Access originally published online on January 9, 2009
Nucleic Acids Research 2009 37(4):1225-1238; doi:10.1093/nar/gkn1062
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Nucleic Acids Research, 2009, Vol. 37, No. 4 1225-1238
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chemistry and Synthetic Biology

A bridged nucleic acid, 2',4'-BNACOC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNACOC monomers and RNA-selective nucleic-acid recognition

Yasunori Mitsuoka, Tetsuya Kodama, Ryo Ohnishi, Yoshiyuki Hari, Takeshi Imanishi and Satoshi Obika*

Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan

*To whom correspondence should be addressed. Tel: +81 6 6879 8200; Fax: +81 6 6879 8204; Email: obika{at}phs.osaka-u.ac.jp

Received September 19, 2008. Revised December 15, 2008. Accepted December 16, 2008.

Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNACOC) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNACOC) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNACOC consisting of 2',4'-BNACOC monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNACOC monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNACOC/BNACOC duplex possessed excellent thermal stability and that the BNACOC increased thermal stability with a complementary RNA strand. On the other hand, BNACOC/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNACOC generally improved the sequence selectivity with Watson–Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNACOC formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.


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