Synthesis and properties of YOYO-1-type homodimeric monomethine cyanine dyes as noncovalent nucleic acid labels

Several novel homodimeric asymmetric monomethine cyanine dyes based on the oxazole yellow (YO) chromophore were synthesized. The two YO chromophores [1-(omega-bromoalkyl)-4-[(3-methyl-2-(3H)-benzaxozolilydene)methyl]-quinolinium perchlorate with different chain lengths of the omega-bromoalkyl substituent were bisquaternized with N,N,N',N'-tetramethyl-1,3-propanediamine, N,N,N',N'-tetramethyl-1,6-hexanediamine, 1,4-diazabi-cyclo[2,2,2]octan and bipyridine. The homodimeric dyes have molar absorptivity 140,000-180,0000 1.mol(-1)cm(-1) at 479 nm upon binding to ds DNA. The fluorescence maxima of the complexes are around 505 nm and the fluorescence quantum yields (Q(F)) are between 0.2 and 0.7 (C) 2003 Elsevier Science Ltd. All rights reserved.