Screening of G-quadruplex DNA ligands by fluorescence detection of peptide displacement

G-quadruplexes (G4s) are noncanonical DNA/RNA structures involved in key cellular processes, and their interactions with proteins are emerging as therapeutic targets. However, strategies to identify ligands that bind G4s and potentially modulate these interactions remain limited. Here, we describe a fluorescence-based assay for rapid, quantitative evaluation of small molecules that bind G4s and potentially interfere with protein recognition. The method employs a fluorophore-labeled peptide derived from a conserved G4-binding protein motif, and a G4-forming sequence labeled with a fluorescence acceptor. Ligand-induced peptide displacement is detected via fluorescence increase. A panel of known G4 ligands was tested, and results correlated with binding affinities. A duplex DNA competition assay further assessed ligand selectivity. This method provides a scalable tool for screening G4 ligands with ability to compete with G4-recognition motifs, supporting drug discovery efforts.