Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs
Type
ArticleAuthors
Chawla, Mohit
Chermak, Edrisse

Zhang, Qingyun
Bujnicki, Janusz M.
Oliva, Romina

Cavallo, Luigi

KAUST Department
Chemical Science ProgramComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
KAUST Catalysis Center (KCC)
Physical Science and Engineering (PSE) Division
Date
2017-08-18Permanent link to this record
http://hdl.handle.net/10754/625519
Metadata
Show full item recordAbstract
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.Citation
Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, et al. (2017) Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs. Nucleic Acids Research. Available: http://dx.doi.org/10.1093/nar/gkx757.Sponsors
King Abdullah University of Science and Technology (KAUST) [to L.C.]; Polish National Science Center (NCN) [2012/04/A/NZ2/00455 to J.M.B.]. Funding for open access charge: King Abdullah University of Science and Technology. For computer time, this research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.Publisher
Oxford University Press (OUP)Journal
Nucleic Acids ResearchAdditional Links
https://academic.oup.com/nar/article/doi/10.1093/nar/gkx757/4096351/Occurrence-and-stability-of-lone-pair%CF%80-stacking#95774552ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkx757
Scopus Count
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com