A benzothiazolium salt fluorophore for topology-specific discrimination of non-B DNA structures

Accurate detection of non-B DNA structures remains challenging yet critical for understanding their roles in gene regulation, genome stability, and disease mechanisms. To address this need, we synthesized a benzothiazolium salt-based fluorescent probe (BTPA) and characterized its topology-specific responses to non-B DNA. BTPA exhibited up to 56-fold fluorescence enhancement with AATT-rich hairpin DNA and successfully discriminated 16 distinct non-B DNA structures, including left-handed parallel, right-handed hybrid/antiparallel/parallel G-quadruplexes (G4s), and i-motifs, through conformation-dependent emission changes. BTPA thus serves as a versatile fluorescent tool for probing non-B DNA topology with near-zero background in biomedical applications, offering new opportunities for disease research and drug development. • A novel benzothiazolium fluorophore BTPA was synthesized for DNA sensing. • BTPA shows a 56-fold fluorescence enhancement with AATT-rich hairpin DNA. • The probe distinguishes 16 non-B DNA topologies via non-specific interactions.