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Nucleic Acids Research Advance Access published online on February 24, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp011
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Frequency and isostericity of RNA base pairs

Jesse Stombaugh1,2, Craig L. Zirbel2,3, Eric Westhof4 and Neocles B. Leontis2,5,*

1Department of Biological Sciences, 2Center for Biomolecular Sciences, 3Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA, 4Architecture et réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France and 5Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA

*To whom correspondence should be addressed. Tel: +1 419 372 8663; Fax: +1 419 372 9809; Email: leontis{at}bgsu.edu

Received July 31, 2008. Revised December 31, 2008. Accepted January 7, 2009.

Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson–Crick base pairs play a central role. Non-Watson–Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can potentially occur in conserved motifs. We extract and classify base pairs from a reduced-redundancy set of RNA 3D structures from the Protein Data Bank (PDB) and calculate centroids (exemplars) for each base combination and geometric base pair type (family). We use the exemplars and IDI values to update our online Basepair Catalog and the Isostericity Matrices (IM) for each base pair family. From the database of base pairs observed in 3D structures we derive base pair occurrence frequencies for each of the 12 geometric base pair families. In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments.


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