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Published online 30 April 2004

Nucleic Acids Research, 2004, Vol. 32, No. 8 2342-2352
© 2004 Oxford University Press

Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns

Peter S. Klosterman1, Donna K. Hendrix1, Makio Tamura2, Stephen R. Holbrook2 and Steven E. Brenner*,1,2

1 Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720-3102, USA and 2 Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

*To whom correspondence should be addressed. Tel: +1 510 643 9131; Fax: +1 208 279 8978; Email: brenner{at}compbio.berkeley.edu
Present address:
Peter S. Klosterman, Department of Pediatrics, University of California, San Francisco, 3333 California Street, Box 1245, San Francisco, CA 94118-1245, USA

Received as resubmission February 21, 2004; Accepted March 22, 2004

Release 2.0.1 of the Structural Classification of RNA (SCOR) database, http://scor.lbl.gov, contains a classification of the internal and hairpin loops in a comprehensive collection of 497 NMR and X-ray RNA structures. This report discusses findings of the classification that have not been reported previously. The SCOR database contains multiple examples of a newly described RNA motif, the extruded helical single strand. Internal loop base triples are classified in SCOR according to their three-dimensional context. These internal loop triples contain several examples of a frequently found motif, the minor groove AGC triple. SCOR also presents the predominant and alternate conformations of hairpin loops, as shown in the most well represented tetraloops, with consensus sequences GNRA, UNCG and ANYA. The ubiquity of the GNRA hairpin turn motif is illustrated by its presence in complex internal loops.


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