ArticleNucleic acids research2009
Frequency and isostericity of RNA base pairs.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed.
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- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- An information-theoretic argument for the restriction of the current biological alphabets to 4 nucleotides and 20 amino acids.Scientific reports · 2026Article
- Genomic variation of human microRNAs and its association with functional features.Cellular and molecular life sciences : CMLS · 2025Article
- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution.The New phytologist · 2025Article
- Doublet decoding of tRNANature communications · 2025Article
- RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.NAR genomics and bioinformatics · 2024Article
- Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent.Biophysical reviews · 2024Review
- Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.Bioinformatics (Oxford, England) · 2024Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- In vivo structure probing of RNA inRNA (New York, N.Y.) · 2023Article
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- Occurrence and classification of T-shaped interactions between nucleobases in RNA structures.RNA (New York, N.Y.) · 2023Article
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Seriation Using Tree-penalized Path Length.European journal of operational research · 2023Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
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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