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Nucleic Acids Research Advance Access originally published online on August 26, 2006
Nucleic Acids Research 2006 34(16):4324-4334; doi:10.1093/nar/gkl088
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Nucleic Acids Research, 2006, Vol. 34, No. 16 4324-4334
© The Author 2006. 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@oxfordjournals.org

Chemistry

Synthesis of 2'-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties

Kohji Seio1,3, Takeshi Sasami2,3, Ryuya Tawarada2,3 and Mitsuo Sekine2,3,*

1 Frontier Collaborative Research Center, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan 2 Department of Life Science, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan 3 CREST, JST (Japan Science and Technology Agency) 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan

*To whom correspondence should be addressed. Tel: +81 45 924 5706; Fax: +81 45 924 5772; Email: msekine{at}bio.titech.ac.jp

Received January 19, 2006. Revised February 8, 2006. Accepted March 7, 2006.

2'-O-Methyl-RNAs incorporating 3-deazaguanine (c3G) were synthesized by use of N,N-diphenylcarbamoyl and N,N-dimethylaminomethylene as its base protecting groups to suppress sheared-type 5'-GA-3'/5'-GA-3' tandem mismatched base pairing which requires the N3 atom. These modified RNAs hybridized more weakly with the complementary and single mismatch-containing RNAs than the unmodified RNAs. The Tm experiments were performed to clarify the effects of replacement of the fifth G with c3G on stabilization of 2'-O-methyl-(5'-CGGCGAGGAG-3')/5'-CUCCGAGCCG-3' and 2'-O-methyl-(5'-CGGGGACGAG-3')/5'-CUCGGACCCG-3'duplexes, which form sheared-type and face-to-face type 5'-GA-3'/5'-GA-3' tandem mismatched base pairs, respectively. Consequently, this replacement led to more pronounced destabilization of the former duplex that needs the N3 atom for the sheared-type base pair than the latter that does not need it for the face-to-face type base pair. A similar tendency was observed for 2'-O-methyl-RNA/DNA duplexes. These results suggest that the N3 atom of G plays an important role in stabilization of the canonical G/C base pair as well as the base discrimination and its loss suppressed formation of the undesired sheared-type mismatched base pair. Computational studies based on ab initio calculations suggest that the weaker hydrogen bonding ability and larger dipole moment of c3G can be the origin of the lower Tm.


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