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Nucleic Acids Research 2006 34(13):3609-3614; doi:10.1093/nar/gkl232
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Published online 26 July 2006

Nucleic Acids Research, 2006, Vol. 34, No. 13 3609-3614
© 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

Article

Nearest neighbor parameters for Watson–Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides

Elzbieta Kierzek1,2, David H. Mathews3,4, Anna Ciesielska2, Douglas H. Turner1,3,* and Ryszard Kierzek2

1 Department of Chemistry, University of Rochester RC Box 270216, Rochester, NY 14627, USA 2 Institute of Bioorganic Chemistry, Polish Academy of Sciences 60-714 Poznan, Noskowskiego 12/14, Poland 3 Center for Pediatric Biomedical Research, University of Rochester School of Medicine and Dentistry Rochester, NY 14642, USA 4 Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry Rochester, NY 14642, USA

*To whom correspondence should be addressed. Tel: +1 585 275 3207; Fax: +1 585 276 0205; Email: turner{at}chem.rochester.edu

Received January 20, 2006. Revised January 30, 2006. Accepted March 28, 2006.

Results from optical melting studies of Watson–Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides are used to determine nearest neighbor thermodynamic parameters for predicting the stabilities of such duplexes. The results are consistent with the physical model assumed by the individual nearest neighbor-hydrogen bonding model, which contains terms for helix initiation, base pair stacking and base pair composition. The sequence dependence is similar to that for Watson–Crick complementary RNA/RNA duplexes, which suggests that the sequence dependence may also be similar to that for other backbones that favor A-form RNA conformations.


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