Indirect identification of genomic G-quadruplexes via a small protein probe that specifically recognizes C-rich single-stranded DNA

Detecting intracellular genomic G-quadruplexes (G4s) is crucial for understanding their biological functions. Although various G4 recognition probes have been developed, there remains a need for new G4 detection technologies to create detailed and reliable genomic G4 maps. In this study, we developed a small protein (CK13) that specifically recognizes the complementary C-rich single-stranded DNA (ssDNA) released during the formation of G4. Based on CK13 and CUT&Tag technology, we identified tens of thousands of C-rich ssDNA sites within human genomic DNA. These sites contain the vast majority of G4 sites detected by G4 probes, indicating that CK13 can well confirm the results of traditional G4 probes. Since CK13’s binding to C-rich ssDNA is minimally influenced by G4-binding proteins, it produces strong signals at the sites where intracellular G4-binding proteins are present. This indicates that, beyond free G4 structures, CK13 can also detect G4s occupied by G4-binding proteins within cells. Our findings demonstrate that C-rich ssDNA complementary to G4 can serve as an indirect marker for G4 formation, offering a promising approach to further explore the regulatory roles of G4s and their interacting proteins.