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PMID: 26117545 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 43 ·No. 14 ·2015-08-18 ·Pages 6714-29

Chawla M, Oliva R, Bujnicki JM, Cavallo L

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.

MeSH Terms
Adenine/analogs & derivatives Base Pairing Cytosine/analogs & derivatives Guanine/analogs & derivatives Molecular Structure RNA/chemistry Uracil/analogs & derivatives
Chemicals
Uracil Guanine RNA Cytosine Adenine
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Chawla Mohit
King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
Oliva Romina
Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy oliva@uniparthenope.it.
Bujnicki Janusz M ORCID
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
Cavallo Luigi
King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia luigi.cavallo@kaust.edu.sa.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkv606
Email
oliva@uniparthenope.it
luigi.cavallo@kaust.edu.sa
Published
2015-08-18
Epub
2015-00-27
Pages
6714-29
Language
English
Region
England
NLM ID
0411011
PMCID
PMC4538814
Subset
IM
Corrections
ErratumIn
PMID: 26358813
External Links
PubMed source DOI: 10.1093/nar/gkv606 PMC Full Text View journal details
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