Occurrence and classification of T-shaped interactions between nucleobases in RNA structures
Open Access
- 15 May 2023
- journal article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 29 (8), 1215-1229
- https://doi.org/10.1261/rna.079486.122
Abstract
Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid–protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of <= 3.5 Å resolution crystal structures deposited in the Protein Data Bank.Keywords
Funding Information
- Department of Science and Technology
- University Grants Commission
- Department of Science and Technology (DST) and University Grants Commission (UGC), New Delhi
- DST Inspire (IFA14-CH162)
- UGC FRP (F.4−5(176-FRP/2015)
- Natural Sciences and Engineering Research Council of Canada
- UGC for a Senior Research Fellowship
This publication has 54 references indexed in Scilit:
- Comprehensive survey and geometric classification of base triples in RNA structuresNucleic Acids Research, 2011
- RNA structural motifs that entail hydrogen bonds involving sugar–phosphate backbone atoms of RNANew Journal of Chemistry, 2010
- CD-HIT Suite: a web server for clustering and comparing biological sequencesBioinformatics, 2010
- Classification and energetics of the base-phosphate interactions in RNANucleic Acids Research, 2009
- Frequency and isostericity of RNA base pairsNucleic Acids Research, 2009
- FR3D: finding local and composite recurrent structural motifs in RNA 3D structuresJournal of Mathematical Biology, 2007
- Modeling RNA tertiary structure motifs by graph-grammarsNucleic Acids Research, 2007
- RNA Tertiary Structure PredictionPublished by Wiley ,2007
- How RNA foldsJournal of Molecular Biology, 1999
- Floppy structure of the benzene dimer: Ab initio calculation on the structure and dipole momentThe Journal of Chemical Physics, 1990