Go to the abstract in the NAR 2002 Database Issue.
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http://prion.bchs.uh.edu/bp_type/
Nagaswamy, U., Larios-Sanz, M., Hury, J., Wang, J., Kalaimani, K., Zhao, Q., Fox, G. E.
Dept. Biology and Biochemistry University of Houston Houston, TX 77204-
Contact fox@uh.edu
The known occurrences of non-canonical base-base interactions in RNA are tabulated in the NCIR (http://prion.bchs.uh.edu/bp_type/) database. Currently, there are over 1400 entries including those from the crystal and NMR structures of RNAs published in the year 2002. The database summarizes the important structural properties of these interactions such as the sequence context, the sugar pucker, glycosidic conformation, melting temperature, chemical shift and free energy, when the information is available. The recent nomenclature proposed by Leontis and Westhof (1) have been incorporated into the database based on the three interacting edges: Watson-Crick (WC), Hoogsteen (HG), sugar edge (SE). Frequently occurring non-canonical base pairs are the GA trans SE/HG, GA cis WC/WC, AU trans HG/WC, and the GU and the AC cis wobble pairs. The most common base triple is an AGC trans SE/SE • cis WC/WC interaction, often stabilizing long range tertiary interaction in RNA. Additionally, quadruple and quintuple interactions are also observed.
This work was supported in part by grants from the Robert A. Welch Foundation (E-1451) and the National Aeronautics and Space Administration to (NAG5-12366) G.E.Fox.
1. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs.
RNA,7,499-512.
Category RNA Sequences
Go to the abstract in the NAR 2002 Database Issue.