Journal
NUCLEIC ACIDS RESEARCH
Volume 32, Issue 8, Pages 2342-2352Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkh537
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Funding
- NHGRI NIH HHS [K22 HG000056, 1 K22 HG00056] Funding Source: Medline
- NIGMS NIH HHS [1 R01 GM066199, R01 GM066199] Funding Source: Medline
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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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