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., Collins, S., Zhang, Z., Zhao, Q., Fox, G. E.
Dept. Biology and Biochemistry University of Houston Houston, TX 77204-5001
Contact fox@uh.edu
The secondary and tertiary structure of an RNA molecule typically includes a number of non-canonical base-base interactions. The known occurrences of these interactions are tabulated in the NCIR database, which can be accessed from http://prion.bchs.uh.edu/bp_type/ . The number of examples is now over 1200, which is an increase of over 400% since we first published this database. This dramatic increase reflects the addition of data from the recently published crystal structures of the 50S (2.4 =) and 30S (3.0 =) ribosomal subunits. In addition, non-canonical interactions observed in published crystal and NMR structures of tRNAs, group I introns, ribozymes, RNA aptamers and synthetic oligonucleotides are included. Properties associated with these interactions, such as sequence context, sugar pucker conformation, glycosydic angle conformation, melting temperature, chemical shift and free energy, are also reported when available. 28 of the 29 anticipated pairs with at least two hydrogen bonds have been observed to date. In addition, several novel examples, not generally predicted, have also been encountered, bringing the total of such pairs to 36. Added to this list are a variety of single, bifurcated, triple and quadruple interactions. The most common non-canonical pairs are the sheared GA, GA imino, AU reverse Hoogsteen, and the GU and AC wobble pairs. The most frequent triple interaction connects N3 of A with the amino of a G that is also involved in a standard Watson-Crick pair.
This work was supported in part by grants from the Robert A. Welch Foundation (E-1451) and the National Aeronautics and Space Administration to G.E. Fox.
Category RNA Sequences
Go to the abstract in the NAR 2002 Database Issue.