Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

Handle URI:
http://hdl.handle.net/10754/325456
Title:
Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs
Authors:
Chawla, Mohit; Abdel-Azeim, Safwat ( 0000-0001-8611-1251 ) ; Oliva, Romina; Cavallo, Luigi ( 0000-0002-1398-338X )
Abstract:
The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).
KAUST Department:
KAUST Catalysis Center (KCC); Physical Sciences and Engineering (PSE) Division
Citation:
Chawla M, Abdel-Azeim S, Oliva R, Cavallo L (2014) Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Research 42: 714-726. doi:10.1093/nar/gkt800.
Publisher:
Oxford University Press
Journal:
Nucleic Acids Research
Issue Date:
10-Oct-2013
DOI:
10.1093/nar/gkt800
PubMed ID:
24121683
PubMed Central ID:
PMC3902895
Type:
Article
ISSN:
03051048
Appears in Collections:
Articles; Physical Sciences and Engineering (PSE) Division; KAUST Catalysis Center (KCC)

Full metadata record

DC FieldValue Language
dc.contributor.authorChawla, Mohiten
dc.contributor.authorAbdel-Azeim, Safwaten
dc.contributor.authorOliva, Rominaen
dc.contributor.authorCavallo, Luigien
dc.date.accessioned2014-08-27T09:52:06Z-
dc.date.available2014-08-27T09:52:06Z-
dc.date.issued2013-10-10en
dc.identifier.citationChawla M, Abdel-Azeim S, Oliva R, Cavallo L (2014) Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Research 42: 714-726. doi:10.1093/nar/gkt800.en
dc.identifier.issn03051048en
dc.identifier.pmid24121683en
dc.identifier.doi10.1093/nar/gkt800en
dc.identifier.urihttp://hdl.handle.net/10754/325456en
dc.description.abstractThe G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en
dc.subjectBase Pairingen
dc.subjectComputational Biologyen
dc.subjectCytosineen
dc.subjectGuanineen
dc.subjectHydrogen Bondingen
dc.subjectModels, Molecularen
dc.subjectNucleic Acid Conformationen
dc.subjectNucleotide Motifsen
dc.subjectQuantum Theoryen
dc.subjectRiboswitchen
dc.subjectRNAen
dc.subjectWateren
dc.titleHigher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAsen
dc.typeArticleen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.identifier.journalNucleic Acids Researchen
dc.identifier.pmcidPMC3902895en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Sciences and Technologies, University of Naples 'Parthenope', Centro Direzionale Isola C4, I-80143, Naples, Italyen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorAbdel-Azeim, Safwaten
kaust.authorCavallo, Luigien
kaust.authorChawla, Mohiten
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