ArticleNucleic acids research2017
Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 62 citations in OpenAlex.
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- Occurrence and classification of T-shaped interactions between nucleobases in RNA structures.RNA (New York, N.Y.) · 2023Article
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- Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.Nucleic acids research · 2022Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
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- Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of theMolecules (Basel, Switzerland) · 2021Article
- Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes.Nucleic acids research · 2021Article
- Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study.Computational and structural biotechnology journal · 2021Article
- Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes.Nucleic acids research · 2020Article
- Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs.Nucleic acids research · 2020Article
- Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides.Antimicrobial agents and chemotherapy · 2019Article
- The structure of the SAM/SAH-binding riboswitch.Nucleic acids research · 2019Article
- Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA.Nucleic acids research · 2018Article
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.
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