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Nucleic Acids Research 2006 34(5):1481-1491; doi:10.1093/nar/gkj500
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Published online 10 March 2006

© 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

Single nucleotide RNA choreography

Chiaolong Hsiao, Srividya Mohan, Eli Hershkovitz1,2, Allen Tannenbaum1,2 and Loren Dean Williams*

School of Chemistry and Biochemistry, Georgia Institute of Technology Atlanta, GA 30332-0400, USA 1Departments of Electrical and Computer Engineering, Georgia Institute of Technology Atlanta, GA 30332-0400, USA 2Department of Biomedical Engineering, Georgia Institute of Technology Atlanta, GA 30332-0400, USA

*To whom correspondence should be addressed. Tel: +1 404 894 9752; Fax: +1 404 894 7452; Email: loren.williams{at}chemistry.gatech.edu

Received October 1, 2005. Revised December 9, 2005. Accepted January 25, 2006.

New structural analysis methods, and a tree formalism re-define and expand the RNA motif concept, unifying what previously appeared to be disparate groups of structures. We find RNA tetraloops at high frequencies, in new contexts, with unexpected lengths, and in novel topologies. The results, with broad implications for RNA structure in general, show that even at this most elementary level of organization, RNA tolerates astounding variation in conformation, length, sequence and context. However the variation is not random; it is well-described by four distinct modes, which are 3-2 switches (backbone topology variations), insertions, deletions and strand clips.


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