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Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules
We present a systematic structural and energetic characterization of phosphate(OP)–nucleobase anion…π stacking interactions in RNAs. We observed OP–nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from th...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9723503/ https://www.ncbi.nlm.nih.gov/pubmed/36416268 http://dx.doi.org/10.1093/nar/gkac1081 |
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author | Chawla, Mohit Kalra, Kanav Cao, Zhen Cavallo, Luigi Oliva, Romina |
author_facet | Chawla, Mohit Kalra, Kanav Cao, Zhen Cavallo, Luigi Oliva, Romina |
author_sort | Chawla, Mohit |
collection | PubMed |
description | We present a systematic structural and energetic characterization of phosphate(OP)–nucleobase anion…π stacking interactions in RNAs. We observed OP–nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol(−1), for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP–uracil and OP–guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations. |
format | Online Article Text |
id | pubmed-9723503 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-97235032022-12-07 Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules Chawla, Mohit Kalra, Kanav Cao, Zhen Cavallo, Luigi Oliva, Romina Nucleic Acids Res Computational Biology We present a systematic structural and energetic characterization of phosphate(OP)–nucleobase anion…π stacking interactions in RNAs. We observed OP–nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol(−1), for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP–uracil and OP–guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations. Oxford University Press 2022-11-23 /pmc/articles/PMC9723503/ /pubmed/36416268 http://dx.doi.org/10.1093/nar/gkac1081 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://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 |
spellingShingle | Computational Biology Chawla, Mohit Kalra, Kanav Cao, Zhen Cavallo, Luigi Oliva, Romina Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules |
title | Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules |
title_full | Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules |
title_fullStr | Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules |
title_full_unstemmed | Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules |
title_short | Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules |
title_sort | occurrence and stability of anion–π interactions between phosphate and nucleobases in functional rna molecules |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9723503/ https://www.ncbi.nlm.nih.gov/pubmed/36416268 http://dx.doi.org/10.1093/nar/gkac1081 |
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