NCIR: a database of non-canonical interactions in known RNA structures

Abstract

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 1400, which is an increase of >700% since the database was first published. This dramatic increase reflects the addition of data from the recently published crystal structures of the 50S (2.4 A) and 30S (3.0 A) 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, glycosidic angle conformation, melting temperature, chemical shift and free energy, are also reported when available. Out of the 29 anticipated pairs with at least two hydrogen bonds, 28 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 an A with the amino of a G that is also involved in a standard Watson-Crick pair.

Structural basis of UGUA recognition by the Nudix protein CFI m 25 and implications for a regulatory role in mRNA 3′ processing

“…To date, only six examples of sugar-edge/Watson-Crick base pairs have been reported in the Noncanonical Base Pair Database, out of 1,860 base pairs (29). In each case, the base pair is located within a double-stranded segment of the ribosome or ribonuclease P (30)(31)(32).…”

Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs

“…We have developed a database that summarizes all the known occurrences of noncanonical base-base interactions (Nagaswamy et al+, 2002)+ In particular, examples of the UA trans WC/HG base pair were examined+ It was found that a number of the occurrences in the large (Ban et al+, 2000) and the small (Wimberly et al+, 2000) subunit ribosomal RNAs were in very similar structural contexts (Fig+ 2)+ In all the examples, the key UA pair is always stacked on a Watson-Crick pair and the nucleotides 39 to the adenine base are bulged out+ Examination of additional interactions in the loops revealed the similarity of these structures to the tRNA T-loop+ Two distinct families of these T-loop motifs were identified in ribosomal RNAs+…”

Identification of potential conserved RNA secondary structure throughout influenza A coding regions

“…There are many examples where noncanonical base pairs play important roles in RNA secondary structure (Nagaswamy et al 2002). In particular, AC pairs can induce little perturbation to the A-form helix and can play a role in protein recognition (Jang et al 1998;Lima et al 2002).…”