An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

Handle URI:
http://hdl.handle.net/10754/558768
Title:
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies
Authors:
Chawla, Mohit; Oliva, R.; Bujnicki, J. M.; Cavallo, Luigi ( 0000-0002-1398-338X )
Abstract:
Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.
KAUST Department:
Physical Sciences and Engineering (PSE) Division; KAUST Catalysis Center (KCC)
Citation:
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies 2015 Nucleic Acids Research
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
Issue Date:
27-Jun-2015
DOI:
10.1093/nar/gkv606
Type:
Article
ISSN:
0305-1048; 1362-4962
Additional Links:
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv606
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.authorOliva, R.en
dc.contributor.authorBujnicki, J. M.en
dc.contributor.authorCavallo, Luigien
dc.date.accessioned2015-07-02T07:54:34Zen
dc.date.available2015-07-02T07:54:34Zen
dc.date.issued2015-06-27en
dc.identifier.citationAn atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies 2015 Nucleic Acids Researchen
dc.identifier.issn0305-1048en
dc.identifier.issn1362-4962en
dc.identifier.doi10.1093/nar/gkv606en
dc.identifier.urihttp://hdl.handle.net/10754/558768en
dc.description.abstractPosttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttp://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv606en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.titleAn atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energiesen
dc.typeArticleen
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italyen
dc.contributor.institutionLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Polanden
dc.contributor.institutionLaboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Polanden
kaust.authorChawla, Mohiten
kaust.authorCavallo, Luigien
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