title: An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.
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.
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
authors.forename: Mohit
authors.initials: M
authors.lastname: Chawla
authors.affiliation: Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy oliva@uniparthenope.it.
authors.forename: Romina
authors.initials: R
authors.lastname: Oliva
authors.affiliation: 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.
authors.forename: Janusz M
authors.identifier: http://orcid.org/0000-0002-6633-165X
authors.initials: JM
authors.lastname: Bujnicki
authors.affiliation: 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.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cavallo
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives; D020029:Base Pairing; D003596:Cytosine / Q000031:analogs & derivatives; D006147:Guanine / Q000031:analogs & derivatives; D015394:Molecular Structure; D012313:RNA / Q000737:chemistry*; D014498:Uracil / Q000031:analogs & derivatives
chemical_list: D014498:Uracil; D006147:Guanine; D012313:RNA; D003596:Cytosine; D000225:Adenine