NCIR - Non-Canonical Interactions in RNA

NAR Molecular Biology Database Collection entry number 380
Nagaswamy, U., Huang, H-C., Larios-Sanz, M., Wang, J., Zhao, Q., Fox, G.E.
Dept. of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA

Database Description

The known occurrences of non-canonical base-base interactions in RNA are tabulated in the NCIR ( database. Currently, there are over 1700 entries including those from the crystal and NMR structures of RNAs published in the year 2003/2004. 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) has been incorporated into the database based on the three interacting edges: Watson-Crick (WC), Hoogsteen (HG), sugar edge (SE). To date, 46 different base pairs connected by at least two hydrogen bonds have been observed. Additionally, base pairs connected by single and bifurcated hydrogen bonds are also observed. Higher order base-base interactions including base triples, quadruples and quintuples have also been categorized. Frequently occurring non-canonical base pairs are the GA trans SE/HG, AU trans HG/WC, GA cis WC/WC, UU cis WC/SE 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. A recent addition to the entries includes RNA motif information for the associated base-base interactions.


This work was supported in part by grants from the Robert A. Welch Foundation (E-1451) and the National Aeronautics and Space Administration (NAG5-12366) to G.E.Fox.


1. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA,7,499-512.

Subcategory: Nucleic acid structure

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