Show simple item record

dc.contributor.authorKalra, Kanav
dc.contributor.authorGorle, Suresh
dc.contributor.authorCavallo, Luigi
dc.contributor.authorOliva, Romina
dc.contributor.authorChawla, Mohit
dc.date.accessioned2020-05-13T12:19:44Z
dc.date.available2020-05-13T12:19:44Z
dc.date.issued2020-05-11
dc.date.submitted2019-07-17
dc.identifier.citationKalra, 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/gkaa345
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.doi10.1093/nar/gkaa345
dc.identifier.urihttp://hdl.handle.net/10754/662824
dc.description.abstractAbstract 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.
dc.description.sponsorshipL.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.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa345/5835811
dc.relation.urlhttps://doi.org/10.1093/nar/gkaa345
dc.rightsThis is an open access article.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.titleOccurrence and stability of lone pair-π and OH–π interactions between water and nucleobases in functional RNAs
dc.typeArticle
dc.contributor.departmentChemical Science
dc.contributor.departmentChemical Science Program
dc.contributor.departmentKAUST Catalysis Center (KCC)
dc.contributor.departmentPhysical Science and Engineering (PSE) Division
dc.identifier.journalNucleic Acids Research
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
dc.contributor.institutionDepartment of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
kaust.personKalra, Kanav
kaust.personCavallo, Luigi
kaust.personChawla, Mohit
dc.date.accepted2020-05-07
refterms.dateFOA2020-05-13T12:20:24Z
kaust.acknowledged.supportUnitKAUST Supercomputing Laboratory
kaust.acknowledged.supportUnitsupercomputer Shaheen II
dc.date.published-online2020-05-11
dc.date.published-print2020-06-19


Files in this item

Thumbnail
Name:
occurance and stability.pdf
Size:
5.235Mb
Format:
PDF
Description:
Published version

This item appears in the following Collection(s)

Show simple item record

This is an open access article.
Except where otherwise noted, this item's license is described as This is an open access article.