ArticleRNA (New York, N.Y.)2008
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers.
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150 citing papers in PubMed.
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- Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA.Journal of molecular biology · 2025Article
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- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- The structural basis for RNA slicing by human Argonaute2.bioRxiv : the preprint server for biology · 2024Article
- The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex.Molecular cell · 2024Article
- Synthesis and properties of RNA constrained by a 2'-O-disulfide bridge.ChemistryOpen · 2024Article
- The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex.bioRxiv : the preprint server for biology · 2024Article
- Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning.Biophysical journal · 2024Article
- CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.Proteins · 2023Article
90 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
Abstract
A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.
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