Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

The fluorescent light-up aptamer (FLAP) Pepper can utilize fluorophores that are equipped with an electrophilic handle for the covalent attachment of the surrogate to the RNA. The resulting irreversibly tethered dye-RNA complexes have opened up new avenues for RNA imaging in live cells. Here, we report the syntheses of such modified HBC530 ((4-((2-hydroxyethyl)(methyl)amino)benzylidene)cyanophenylacetonitrile) fluorophores for easy access, which will contribute to the rapid dissemination of the RNA imaging approaches associated therewith.