Synthesis and properties of novel asymmetric monomethine cyanine dyes as non-covalent labels for nucleic acids

Sixteen, novel monomethine cyanine dyes with benzothiazolo-[3.2-a]-pyrimidinium, 4-methyl-(5H)-pyrido-[1,2-a]-pyrimidinium, 1-cyano-4-methyl-(3H)-benzothiazolo-[3,2-a]-pyridinium and 4-methyl-8-methoxy-(8H)-benzothiazolo-[3,2-a]-pyrimidinium end groups have been synthesized. Their chemical structures and purity were confirmed by 1H NMR and elemental analysis. The longest wavelength absorption maxima of the studied dyes are in the region 450–500 nm. Most of the dyes have very high molar absorptivities, usually over 100 000 l mol−1 cm−1. The investigated dyes have low fluorescence in their free form but some of them become strongly fluorescent after binding to DNA.