Synthesis of novel monomeric asymmetric tri- and tetracationic monomethine cyanine dyes as fluorescent non-covalent nucleic acid labels

Several novel tricationic and one tetracationic monomethine cyanine dyes belonging to the Thiazole Orange family have been prepared via an improved synthetic procedure. The dyes, useful for nucleic acid detection, bear trimethylamonium, triethylamonium, 1-methylpyrrolidinium, 4-methylmorpholinium, pyridinium, N,N-dimethylpyridinium and 3-(dimethylamonio)propan-1-ol substituents. All derivatives absorb in the region 501–514 nm and have a molar absorptivity of 62 000–93 000 l mol−1 cm−1. The reaction products were characterized by 1H NMR spectroscopy and elemental analysis.