The non-Watson-Crick base pairs and their associated isostericity matrices
Open accessAbstract
RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
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Non-Watson-Crick pairings are relatively common in RNA structures.
“Such non-Watson-Crick pairings are relatively common in RNA structures (Leontis et al. 2002)”
From The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability (2013) · cites this paper as Leontis et al. 2002
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- Authors
- Leontis, N. B.
- Affiliations
- Bowling Green State University (US)
- Corresponding author
- Leontis, N. B.
- ORCID
- Leontis, N. B.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-08-15
- Volume
- 30
- Issue
- 16
- Pages
- 3497-3531
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC134247
- OpenAlex
- W2115729502
- Cited by
- 796
- References
- 62
- Citations by year
- 2026: 21 · 2025: 28 · 2024: 23 · 2023: 35 · 2022: 39 · 2021: 31 · 2020: 38 · 2019: 36 · 2018: 36 · 2017: 40 · 2016: 27 · 2015: 52 · 2014: 32 · 2013: 45 · 2012: 42
- FWCI
- 8.13
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ScholarWorks@BGSU (Bowling Green State University) (submittedVersion)
- Funders
- National Science Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (R15GM055898, 2R15 GM 55898)
- Division of Chemistry
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- non-Watson-Crick base pairing, Hoogsteen base pairing, RNA-RNA interactions, crystal structure, sequence conservation
- MeSH terms
- Algorithms, Base Sequence, Hydrogen Bonding, Models, Molecular, Terminology as Topic, RNA, Sequence Homology, Base Pairing
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