Occurrence and classification of T-shaped interactions between nucleobases in RNA structures

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 3262 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of high-resolution crystal structures deposited in the Protein Databank. These analyses add to the understanding of the physicochemical forces that are responsible for structure and dynamics of RNA.

Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA

“…The RNA crystal structures were retrieved from the PDBsum database, using the search window in the “Het Groups” class of the “Browse Option” menu, by searching the unique three-letter code corresponding to each modified base (Figure ). The retrieved list of PDBs, with a search date cut-off of 24 April 2022, was further filtered by elucidation technique (restricted to X-ray crystallography) and refinement resolution (≤3.5 Å), in accordance with previous studies. ,, This resulted in a dataset of 190 structures (Table S1).…”

“…2 The retrieved list of PDBs, with a search date cutoff of 24 April 2022, was further filtered by elucidation technique (restricted to X-ray crystallography) and refinement resolution (≤3.5 Å), in accordance with previous studies. 28,32,35 This resulted in a dataset of 190 structures (Table S1).…”