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Nucleic Acids Research 2004 32(22):6650-6659; doi:10.1093/nar/gkh1002
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Published online 17 December 2004

Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved

The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery

Leven M. Wadley and Anna Marie Pyle1,2,*

Department of Physics, Columbia University, New York, NY 10027, USA, 1 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA and 2 Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA

* To whom correspondence should be addressed. Tel: +1 203 432 5633; Fax: +1 203 432 5316; Email: anna.pyle{at}yale.edu

Received July 29, 2004; Revised November 2, 2004; Accepted November 27, 2004

Recurring RNA structural motifs are important sites of tertiary interaction and as such, are integral to RNA macromolecular structure. Although numerous RNA motifs have been classified and characterized, the identification of new motifs is of great interest. In this study, we discovered four new conformationally recurring motifs: the {pi}-turn, the {Omega}-turn, the {alpha}-loop and the C2'-endo mediated flipped adenosine motif. Not only do they have complex and interesting structures, but they participate in contacts of high biological significance. In a first for the RNA field, new motifs were discovered by a fully automated algorithm. This algorithm, COMPADRES, utilized a reduced representation of the RNA backbone and was highly successful at discerning unique structural relationships. This study also shows that recurring RNA substructures are not necessarily accompanied by consistent primary or secondary structure.


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