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RNA. Apr 2001; 7(4): 499–512.
PMCID: PMC1370104

Geometric nomenclature and classification of RNA base pairs.


Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition. An unambiguous and descriptive nomenclature with well-defined and nonoverlapping parameters is needed to communicate concisely structural information about RNA base pairs. The definitions should reflect underlying molecular structures and interactions and, thus, facilitate automated annotation, classification, and comparison of new RNA structures. We propose a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge (which includes the 2'-OH and which has also been referred to as the Shallow-groove edge). Bases can interact in either of two orientations with respect to the glycosidic bonds, cis or trans relative to the hydrogen bonds. This gives rise to 12 basic geometric types with at least two H bonds connecting the bases. For each geometric type, the relative orientations of the strands can be easily deduced. High-resolution examples of 11 of the 12 geometries are presently available. Bifurcated pairs, in which a single exocyclic carbonyl or amino group of one base directly contacts the edge of a second base, and water-inserted pairs, in which single functional groups on each base interact directly, are intermediate between two of the standard geometries. The nomenclature facilitates the recognition of isosteric relationships among base pairs within each geometry, and thus facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences. Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated.

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Selected References

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  • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905–920. [PubMed]
  • Batey RT, Rambo RP, Doudna JA. Tertiary Motifs in RNA Structure and Folding. Angew Chem Int Ed Engl. 1999 Aug;38(16):2326–2343. [PubMed]
  • Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science. 2000 Feb 18;287(5456):1232–1239. [PubMed]
  • Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. [PubMed]
  • Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF. X-ray crystal structures of 70S ribosome functional complexes. Science. 1999 Sep 24;285(5436):2095–2104. [PubMed]
  • Correll CC, Freeborn B, Moore PB, Steitz TA. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell. 1997 Nov 28;91(5):705–712. [PubMed]
  • Correll CC, Munishkin A, Chan YL, Ren Z, Wool IG, Steitz TA. Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13436–13441. [PMC free article] [PubMed]
  • Crick FH. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. [PubMed]
  • Damberger SH, Gutell RR. A comparative database of group I intron structures. Nucleic Acids Res. 1994 Sep;22(17):3508–3510. [PMC free article] [PubMed]
  • Ferré-D'Amaré AR, Doudna JA. RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct. 1999;28:57–73. [PubMed]
  • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997 Dec;18(15):2714–2723. [PubMed]
  • Hermann T, Patel DJ. Stitching together RNA tertiary architectures. J Mol Biol. 1999 Dec 10;294(4):829–849. [PubMed]
  • Jovine L, Hainzl T, Oubridge C, Scott WG, Li J, Sixma TK, Wonacott A, Skarzynski T, Nagai K. Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA. Structure. 2000 May 15;8(5):527–540. [PubMed]
  • Klinck R, Westhof E, Walker S, Afshar M, Collier A, Aboul-Ela F. A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. RNA. 2000 Oct;6(10):1423–1431. [PMC free article] [PubMed]
  • Lavery R, Zakrzewska K, Sun JS, Harvey SC. A comprehensive classification of nucleic acid structural families based on strand direction and base pairing. Nucleic Acids Res. 1992 Oct 11;20(19):5011–5016. [PMC free article] [PubMed]
  • Leontis NB, Westhof E. The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure. RNA. 1998 Sep;4(9):1134–1153. [PMC free article] [PubMed]
  • Leontis NB, Westhof E. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J Mol Biol. 1998 Oct 30;283(3):571–583. [PubMed]
  • Leontis NB, Westhof E. Conserved geometrical base-pairing patterns in RNA. Q Rev Biophys. 1998 Nov;31(4):399–455. [PubMed]
  • Masquida B, Westhof E. On the wobble GoU and related pairs. RNA. 2000 Jan;6(1):9–15. [PMC free article] [PubMed]
  • Michel F, Jacquier A, Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 1982 Oct;64(10):867–881. [PubMed]
  • Nagaswamy U, Voss N, Zhang Z, Fox GE. Database of non-canonical base pairs found in known RNA structures. Nucleic Acids Res. 2000 Jan 1;28(1):375–376. [PMC free article] [PubMed]
  • Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science. 2000 Aug 11;289(5481):920–930. [PubMed]
  • Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, et al. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell. 2000 Sep 1;102(5):615–623. [PubMed]
  • Su L, Chen L, Egli M, Berger JM, Rich A. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Biol. 1999 Mar;6(3):285–292. [PubMed]
  • Varani G, McClain WH. The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep. 2000 Jul;1(1):18–23. [PMC free article] [PubMed]
  • Westhof E. Westhof's rule. Nature. 1992 Aug 6;358(6386):459–460. [PubMed]
  • Westhof E, Dumas P, Moras D. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallogr A. 1988 Mar 1;44(Pt 2):112–123. [PubMed]
  • Westhof E, Fritsch V. RNA folding: beyond Watson-Crick pairs. Structure. 2000 Mar 15;8(3):R55–R65. [PubMed]
  • Wimberly BT, Brodersen DE, Clemons WM, Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327–339. [PubMed]

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