Synthesis of homodimeric monomethine cyanine dyes as noncovalent nucleic acid labels and their absorption and fluorescence spectral characteristics

Abstract Several novel homodimeric asymmetric monomethine cyanine dyes based on the thiazole orange (TO) chromophore were synthesised via an improved synthetic procedure. The two TO chromophores [1-(ω-bromoalkyl)-4-[(3-methyl-2-(3H)-benzothiazolilyden)methyl] quinolinium iodide], with different chain lengths of the methylene linker between the quinolinium ring and the quaternary ammonium nitrogen, were connected by bisquaternization with N,N,N′,N′-tetramethyl-1,3-propanediamine, N,N,N′,N′-tetramethyl-1,6-hexanediamine, 1,4-diazabicyclo- [2,2,2]octane and 1,4′-bipyridine. The homodimeric dyes have large molar absorptivity (e 130 000–180 000 l mol−1 cm−1) at 505–506 nm. In the presence of ds DNA, their fluorescence maxima were located at 530–534 nm and the fluorescence quantum yields were in the range 0.48–0.96. Fluorescence maxima between 560–650 nm and fluorescence quantum yields of 0.3–0.8 were observed in the presence of ss DNA.