Synthesis of New Fluorogenic Cyanine Dyes and Incorporation into RNA Fluoromodules

A new fluorogenic cyanine dye was synthesized and found to have low fluorescence quantum yield in fluid solution and in the presence of double-stranded DNA but 80-fold enhanced fluorescence in viscous glycerol solution. An RNA aptamer selected for binding to the new dye exhibits K_d = 87 nM and 60-fold fluorescence enhancement. The dye−aptamer pair is a fluoromodule that can be incorporated into fluorescent sensors and labels.