Benzothiazole-based cyanines as fluorescent “light-up” probes for duplex and quadruplex DNA

Analogs of benzothiazole orange ( BO ) with one, two or three methylbenzothiazolylmethylidene substituents in the 1-methylpyridinium ring were obtained from the respective picolinium, lutidinium or collidinium salts. Fluorescence parameters of the known and new dyes in complexes with various DNA structures , including G-quadruplexes (G4s) and i-motifs (IMs), were analyzed. All dyes efficiently distinguished G4s and ss-DNA. The bi- and tri-substituted derivatives had basically similar distributions of relative fluorescence intensities. The mono-substituted derivatives exhibited enhanced sensitivity to parallel G4s. All dyes were particularly sensitive to a G4 structure with an additional duplex module (the thrombin-binding aptamer TBA31), presumably due to a distinctive binding mode (interaction with the junction between the two modules). In particular, BO showed a strong (160-fold) enhancement in fluorescence quantum yield in complex with TBA31 compared to the free dye. The fluorescence quantum yields of the 2,4-bisubstituted derivative in complex with well-characterized G4s from oncogene promoters were in the range of 0.04–0.28, i.e. comparable to those of ThT. The mono/bi-substituted derivatives should be considered as possible light-up probes for G4 formation. • Analogs of benzothiazole orange with 1, 2 or 3 substituents in the pyridinium ring were obtained. • Mono/bi-substituted dyes have the potential for use as light-up probes for G4 formation. • 2,4-substituted analog could be used in FID assays for profiling of G4 ligands. • 2,4-substituted analog enhances melting temperatures of hybrid and parallel G4s in the presence of dsDNA. • All dyes were particularly sensitive to a TBA31 (G4 structure with an additional duplex module).