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Nucleic Acids Research Advance Access originally published online on September 2, 2008
Nucleic Acids Research 2008 36(17):5652-5659; doi:10.1093/nar/gkn525
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Nucleic Acids Research, 2008, Vol. 36, No. 17 5652-5659
© 2008 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.

RNA

Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs

Stacy Miller, Laura E. Jones, Karen Giovannitti, Dan Piper and Martin J. Serra*

Department of Chemistry, Allegheny College, 520 N. Main St, 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 June 12, 2008. Revised July 30, 2008. Accepted July 31, 2008.

Thermodynamic parameters are reported for duplex formation of 40 self-complementary RNA duplexes containing wobble terminal base pairs with all possible 3' single and double-nucleotide overhangs, mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest neighbor analysis, the addition of a single 3' dangling nucleotide increases the stability of duplex formation up to 1 kcal/mol in a sequence-dependent manner. The addition of a second dangling nucleotide increases the stability of duplexes closed with wobble base pairs in an idiosyncratic manner. The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3' single or double-nucleotide overhangs. Phylogenetic analysis of naturally occurring miRNAs was performed. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3' double-nucleotide overhang. Thermodynamic parameters for the 5' single terminal overhangs adjacent to wobble closing base pairs are also presented.


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