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Nucleic Acids Research 2006 34(8):2340-2346; doi:10.1093/nar/gkl120
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Published online 5 May 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

Automated extraction and classification of RNA tertiary structure cyclic motifs

Sébastien Lemieux and François Major*

Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Université de Montréal PO Box 6128, Downtown station, Montreal, Quebec H3C 3J7, Canada

*To whom correspondence should be addressed. Tel: 514 343 6752; Fax: 514 343 5839; Email: francois.major{at}umontreal.ca

Received October 4, 2005. Revised November 12, 2005. Accepted March 13, 2006.

A minimum cycle basis of the tertiary structure of a large ribosomal subunit (LSU) X-ray crystal structure was analyzed. Most cycles are small, as they are composed of 3- to 5 nt, and repeated across the LSU tertiary structure. We used hierarchical clustering to quantify and classify the 4 nt cycles. One class is defined by the GNRA tetraloop motif. The inspection of the GNRA class revealed peculiar instances in sequence. First is the presence of UA, CA, UC and CC base pairs that substitute the usual sheared GA base pair. Second is the revelation of GNR(Xn)A tetraloops, where Xn is bulged out of the classical GNRA structure, and of GN/RA formed by the two strands of interior-loops. We were able to unambiguously characterize the cycle classes using base stacking and base pairing annotations. The cycles identified correspond to small and cyclic motifs that compose most of the LSU RNA tertiary structure and contribute to its thermodynamic stability. Consequently, the RNA minimum cycles could well be used as the basic elements of RNA tertiary structure prediction methods.


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