title: Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
abstract: 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.
authors.affiliation: Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720-3102, USA.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Klosterman
authors.forename: Donna K
authors.initials: DK
authors.lastname: Hendrix
authors.forename: Makio
authors.initials: M
authors.lastname: Tamura
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Holbrook
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D016384:Consensus Sequence; D030561:Databases, Nucleic Acid; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000145:classification
chemical_list: D012313:RNA