Occurrence and stability of lone pair-π and OH–π interactions between water and nucleobases in functional RNAs
Type
ArticleKAUST Department
Chemical ScienceChemical Science Program
KAUST Catalysis Center (KCC)
Physical Science and Engineering (PSE) Division
Date
2020-05-11Online Publication Date
2020-05-11Print Publication Date
2020-06-19Submitted Date
2019-07-17Permanent link to this record
http://hdl.handle.net/10754/662824
Metadata
Show full item recordAbstract
Abstract We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp–π) or the OH–π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1–3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp–π interaction as compared to the OH–π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp–π or the OH–π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.Citation
Kalra, K., Gorle, S., Cavallo, L., Oliva, R., & Chawla, M. (2020). Occurrence and stability of lone pair-π and OH–π interactions between water and nucleobases in functional RNAs. Nucleic Acids Research. doi:10.1093/nar/gkaa345Sponsors
L.C. and M.C. acknowledge King Abdullah University of Science and Technology (KAUST) for support and the KAUST Supercomputing Laboratory for providing computational resources of the supercomputer Shaheen II; R.O. thanks MIUR-FFABR (Fondo per il Finanziamento Attivita Base di Ricerca) for funding. Funding for open access charge: King Abdullah University of Science and Technology.Publisher
Oxford University Press (OUP)Journal
Nucleic Acids ResearchAdditional Links
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa345/5835811https://doi.org/10.1093/nar/gkaa345
ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkaa345