Identification of conserved G-quadruplex motifs in the genome of bovine immunodeficiency virus

Guanine rich DNA and RNA fragments tend to form stable noncanonical secondary structures ― G quadruplexes (G4) ― which can be of different topologies (monomolecular, interstranded bimolecular, interstranded tetramolecular). Canonical G4s contain 2 4 G tetrads, which are stabilized by stacking interactions, Hoogsteen hydrogen bonds and connected by a loop of 1 12 nucleotides. Based on the analysis of the nucleotide sequence, conservative G quadruplexes that can be formed in genomic RNA and proviral DNA of the bovine immunodeficiency virus (BIV) were determined. In addition to the known potential G4 in the 3'LTR of BIV RNA, 20 stable conservative motifs of G quadruplexes were identified for the «+» strand of the RNA, as well as for the «–» strand sequence of the proviral DNA, which G score value (a relative parameter that characterizes stability G4) varies from 33 to 36. Two fragments with potential G4 previously identified only for the 3'U5 LTR were shown to be direct repeats and localized also in the 5'R5 LTR. A localization map of potentially stable conservative intramolecular G quadruplexes formed by two G tetrads was created on the BIV genome. G4 is unevenly distributed throughout the genome: for the env gene, the density was 2.6 G4 per 1000 nt., for the tat rev gene ― 2.7 G4 per 1000 nt., the highest density values were determined for the tmx (5.4 G4 per 1000 nt.) and pol genes (2.8 G4 per 1000 nt.), the lowest for gag gene (1.4 G4 per 1000 nt.). The importance of G4 search in the sequence of the minus strand of proviral DNA, in which one G4 was identified, was proved