Open Access
Nucleic Acids Research, volume 45, issue 19, pages 11019-11032
Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs
3
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
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4
Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy.
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Publication type: Journal Article
Publication date: 2017-08-28
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
PubMed ID:
28977572
Genetics
Abstract
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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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Chawla M. et al. Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs // Nucleic Acids Research. 2017. Vol. 45. No. 19. pp. 11019-11032.
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Chawla M., Chermak E., Zhang Q., Bujnicki J. M., Oliva R., Cavallo L. M. Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs // Nucleic Acids Research. 2017. Vol. 45. No. 19. pp. 11019-11032.
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TY - JOUR
DO - 10.1093/nar/gkx757
UR - https://doi.org/10.1093%2Fnar%2Fgkx757
TI - Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs
T2 - Nucleic Acids Research
AU - Chermak, Edrisse
AU - Zhang, Qingyun
AU - Chawla, Mohit
AU - Bujnicki, Janusz M.
AU - Oliva, Romina
AU - Cavallo, Luigi Maria
PY - 2017
DA - 2017/08/28 00:00:00
PB - Oxford University Press
SP - 11019-11032
IS - 19
VL - 45
PMID - 28977572
SN - 0305-1048
SN - 1362-4962
ER -
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@article{2017_Chawla,
author = {Edrisse Chermak and Qingyun Zhang and Mohit Chawla and Janusz M. Bujnicki and Romina Oliva and Luigi Maria Cavallo},
title = {Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs},
journal = {Nucleic Acids Research},
year = {2017},
volume = {45},
publisher = {Oxford University Press},
month = {aug},
url = {https://doi.org/10.1093%2Fnar%2Fgkx757},
number = {19},
pages = {11019--11032},
doi = {10.1093/nar/gkx757}
}
Cite this
MLA
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Chawla, Mohit, et al. “Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs.” Nucleic Acids Research, vol. 45, no. 19, Aug. 2017, pp. 11019-11032. https://doi.org/10.1093%2Fnar%2Fgkx757.