Oxidative Probing of the G4 DNA Structure by Znp1 Porphyrin within Sequences of MYC and TERT Promotors

The formation of G4 structures in a DNA double helix competes with the complementary strand interaction. The local environment in DNA can change equilibrium of G4 structures, which are studied on single-stranded (ss) models by classical structural methods. A relevant task is to develop methods for detecting and localizing G4 structures in extended native double-stranded (ds) DNA in the promoter regions of the genome. The ZnP1 porphyrin derivative selectively binds to G4 structures and leads to photo-induced oxidation of guanine in ssDNA and dsDNA model systems. We have shown the oxidative effect of ZnP1 on native sequences of MYC and TERT oncogene promoters, which can form G4 structures. Single-strand breaks in the guanine-rich sequence because of ZnP1 oxidation and subsequent cleavage of the DNA strand with Fpg glycosylase have been identified and assigned to the nucleotide sequence. The detected break sites have been shown to correspond to sequences capable of forming G4 structures. Thus, we have demonstrated the possibility of using porphyrin ZnP1 for the identification and localization of G4 quadruplexes in extended regions of the genome. Here we have shown the novel data on a possibility of folding G4 structures in the presence of complementary strand in native DNA double helix.