Year: 2026
Type: article
Abstract: Background. G-quadruplexes (G4s) are non-canonical secondary structures consisting of two or more planar G-tetrads formed by four guanidines and stabilized by Hoogsteen hydrogen bonds, stacking and coordination ion interactions. Currently, the formation of G-pentaplexes (G5s) has only been determined for structures in which guanidine is replaced by its isomer, isoguanidine [1]. The aim was the determination of putative G4s from two tetrads in the genome of bovine mycobacteria. Methods. QGRS Mapper software was used for search of G-rich motifs in DNA sense and antisense strands of M. bovis AF2122/97 reference strain [2]. 3D models G4s and G5 were generated by AlphaFold 3 AI (AF3) with 10 K+ ions [3]. Results. 4345 putative G4s in sense strand and 4649 G4s from two tetrads were identified in antisense DNA strand of the AF2122/97 M. bovis reference strain which were characterized by typical parameters for such G4s with loop from 1 to 3 nt, namely, a G-score was varied from 19 to 21, length from 11 to 17 nt. During the analysis of mentioned G4s, attention was drawn to a G-rich palindrome with length of 14 nt, for which 16 repeats in the sense and 6 repeats in the antisense strand were found. 3D model of this aptamer represents G5 which is formed by two planar G-pentads stabilized by 11 and 7 hydrogen bonds, respectively, as well as stacking and two coordination ions K+, unlike G4, in which one K+ ion is localized between two tetrads. Putative G5 was identified in the sense and antisense DNA strands of CDC1551 of M. tuberculosis, 1331 Danish M. bovis BCG applied for vaccination in Ukraine, PA14 Pseudomonas aeruginosa strains. Conclusions. Putative G5 formed by two pentads was identified in the sense and antisense strands of M. bovis and predicted by AF3 with high reliability (pLDDT>90). It is localized in the genes encoding pe-pgrs and ppe families proteins which are crucial for the host-pathogen interactions, immune modulation, suppression host’s immune defense. Grant. 35.00.03.02 from NAAS of Ukraine. Keywords: G-pentaplex, G-quadruplex, Mycobacterium bovis, AlphaFold 3, Pseudomonas aeruginosa, Mycobacterium tuberculosis. REFERENCES: 1. Lin S et al. A G-pentaplex-based assay for Cs(+) ions in aqueous solution using a luminescent Ir(III) complex. Biosens Bioelectron. 2016; 77:609—12. 2. Kikin O et al. QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 2006; 34(2):W676–W82. 3. Abramson J et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. 2024; 630(8016):493— 500.
Source: Biopolymers and Cell
DOI: 10.7124/bc.000b5e
Authors: Olga Limanskaya, Oleksij Balak, Alex Limanskii
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: diamond
OpenAlex ID: W7214744858