Role of Non-Canonical Stacking Interactions of Heterocyclic RNA Bases in Ribosome Function

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Valeriy G. Metelev¹, Eugene F. Baulin^2,5, Alexey A. Bogdanov^1,3,4,a*

¹Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia

²Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Moscow Region, Russia

³Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia

⁴Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia

⁵Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, 02-109, Poland

^* To whom correspondence should be addressed.

Received: October 21, 2024; Revised: October 21, 2024; Accepted: November 4, 2024

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Identification and analysis of repetitive elements (motifs) in DNA, RNA, and protein macromolecules is an important step in studying structure and functions of these biopolymers. Functional role of NA-BSE (non-adjacent base-stacking element, a widespread tertiary structure motif in various RNAs) in RNA–RNA interactions at various stages of the ribosome function during translation has been investigated in this work. Motifs of this type have been described to date that are reversibly formed during mRNA decoding, moving of the ribosome subunits relative to each other, and moving mRNA and tRNA along the ribosome during translocation. The EF-G-dependent NA-BSE formation involving 5S rRNA and 23S rRNA nucleotide residues is considered separately.

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KEY WORDS: stacking interactions, tertiary RNA structure, ribosomal RNA, A-, P-, E-site of tRNA, RNA motifs

DOI: 10.1134/S0006297924120137

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