Occurrence and classification of T-shaped interactions between nucleobases in RNA structures
- 1Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- 2Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
- 3Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana, 500032, India
- Corresponding authors: j.trant{at}uwindsor.ca, psharma{at}pu.ac.in
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 data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.
Keywords
- Received October 22, 2022.
- Accepted April 25, 2023.
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