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Nucleic Acids Research 2006 34(11):3338-3344; doi:10.1093/nar/gkl428
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Published online 4 July 2006

© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson–Crick terminal base pairs

Amanda S. O'Toole, Stacy Miller, Nathan Haines, M. Coleen Zink and Martin J. Serra*

Department of Chemistry, Allegheny College 520 N. Main Street, Meadville, PA 16335, USA

*To whom correspondence should be addressed. Tel: +1 814 332 5356; Fax: +1 814 332 2789; Email: mserra{at}allegheny.edu

Received April 17, 2006. Revised May 30, 2006. Accepted May 30, 2006.

Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson–Crick terminal base pairs (GC, AU and UA) with all 16 possible 3' double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3' dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner. Results from this study in conjunction with data from a previous study [A. S. O'Toole, S. Miller and M. J. Serra (2005) RNA, 11, 512.] allows for the development of a refined nearest-neighbor model to predict the influence of 3' double-nucleotide overhangs on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against five oligomers with various core duplex sequences. Phylogenetic analysis of naturally occurring miRNAs was performed to support our results. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent upon the identity of the 3' double-nucleotide overhang. Thermodynamic parameters for 3' single terminal overhangs adjacent to a UA pair are also presented.


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