Biopolym. Cell. 2026; 42(Special Issue):37.
Computational biology, bioinformatics, and AI-driven research
Putative G-pentaplex in DNA of pathogens is predicted with AlphaFold 3 AI
1Limanskaya O. Yu., 2Balak O. K., 3Limanskii A. P.
  1. NSC “Institute of Experimental and Clinical Veterinary Medicine�
    83, Hryhoriia Skovorody Str., Kharkiv, Ukraine, 61023
  2. Kharkiv National Medical University
    4, Nauky Ave., Kharkiv, Ukraine, 61022
  3. LLC “Institute of Physiological Active Compounds�
    58, Nauky Ave., Kharkiv, Ukraine, 61072

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 em>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 em>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 em>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