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Nucleic Acids Research 2005 33(22):7019-7028; doi:10.1093/nar/gki1003
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Published online 23 December 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

Synthesis and hybridization studies of oligonucleotides containing 1-(2-deoxy-2-{alpha}-C-hydroxymethyl-ß-D-ribofuranosyl)thymine (2'-{alpha}-hm-dT)

Chang Geng Peng and Masad J. Damha*

Department of Chemistry, McGill University 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6

*To whom correspondence should be addressed. Tel: +1 514 398 7552; Fax: +1 514 398 3797; Email: masad.damha{at}mcgill.ca

Received September 8, 2005. Revised November 17, 2005. Accepted November 17, 2005.

We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-{alpha}-C-hydroxymethyl-ß-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as ‘H’). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-RNA and RNA chains. The hybridization properties of the modified oligonucleotides have been studied via thermal denaturation and circular dichroism studies. While 3',5'-linked H was shown previously to significantly destabilize DNA:RNA hybrids and DNA:DNA duplexes (modification in the DNA strand; {Delta}Tm ~ –3°C/insert), we find that 2',5'-linked H have a smaller effect on 2',5'-RNA:RNA and RNA:RNA duplexes ({Delta}Tm = –0.3°C and –1.2°C, respectively). The incorporation of 3',5'-linked H into 2',5'-RNA:RNA and RNA:RNA duplexes was found to be more destabilizing (–0.7°C and –3.6°C, respectively). Significantly, however, the 2',5'-linked H units confer marked stability to RNA hairpins when they are incorporated into a 2',5'-linked tetraloop structure ({Delta}Tm = +1.5°C/insert). These results are rationalized in terms of the compact and extended conformations of nucleotides.


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