Preparation of monomethine cyanine dyes as noncovalent labels for nucleic acids

By condensation of quaternary benzothiazolium, quinolinium and acridinium salts having an active methyl group with 1-(3-bromopropyl)-4-chloroquinolinium or 1-(3-bromo-2-hydroxypropyl)-4-chloroquinolinium salts in the presence of a basic agent such as triethylamine, 8 asymmetric and symmetric monomethine cyanine dyes bearing omega-bromopropyl substituent with one or two positive charges, were synthesized. Additionally, two of the dyes were quaternized with pyridine, and monomethine cyanines with two and three positive charges are prepared. Most of the dyes showed high molar absorptivity (70 000-100 0001 mol(-1) cm(-1)). The acridinium dyes showed broad peaks with lower intensity of 30 0001 mol(-1) cm(-1). In the presence of nucleic acid in aqueous solutions, a strong enhancement of the fluorescence of these new dyes was observed. (C) 1998 Elsevier Science Ltd. All rights reserved.