ArticleNucleic acids research2002
NCIR: a database of non-canonical interactions in known RNA structures.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans.Journal of computational chemistry · 2025Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- Review of machine learning methods for RNA secondary structure prediction.PLoS computational biology · 2021Review
- Article
- Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.Biochemistry · 2019Article
- Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.RNA (New York, N.Y.) · 2019Article
- InterRNA: a database of base interactions in RNA structures.Nucleic acids research · 2016Article
- RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications.Nano today · 2015Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- NMR structure of the 5' splice site in the group IIB intron Sc.ai5γ--conformational requirements for exon-intron recognition.RNA (New York, N.Y.) · 2014Article
- Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.BMC research notes · 2014Article
- Computational approaches to predicting the impact of novel bases on RNA structure and stability.ACS chemical biology · 2013Review
- An innate twist between Crick's wobble and Watson-Crick base pairs.RNA (New York, N.Y.) · 2013Review
- Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site.Biochemistry · 2013Article
- NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.Nucleic acids research · 2012Article
- RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts.Journal of biomolecular NMR · 2012Article
- Charged nucleobases and their potential for RNA catalysis.Accounts of chemical research · 2011Article
- Identification of potential conserved RNA secondary structure throughout influenza A coding regions.RNA (New York, N.Y.) · 2011Article
- Structural characterization of naturally occurring RNA single mismatches.Nucleic acids research · 2011Article
- Novel base triples in RNA structures revealed by graph theoretical searching methods.BMC bioinformatics · 2011Article
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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