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

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-(omega-bromoalkyl)-4-[(3-methyl-2-(3 H)-benzothiazolilyden)methyl] quinolinium iodide], with different chain len gths of the methylene linker between the quinolinium ring and the quaternar y ammonium nitrogen, were connected by bisquaternization with N,N,N',N'-tet ramethyl-1,3-propanediamine, N,N,N',N'-tetramethyl-1,6-hexanediamine, 1,4-d iazabicyclo- [2,2,2]octane and 1,4'-bipyridine. The homodimeric;dyes have l arge molar absorptivity (epsilon 130 000-180 000 l mol(-1) cm(-1)) at 505-5 06 Mn. 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. (C) 1999 Elsevier Science Ltd. All rights reserved.