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

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• 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. Keywords: covalent RNA labeling; FLAP; fluorophore synthesis; HBC530; self-alkylating ribozymes; Introduction The discovery of fluorescent reporters, such as green

• fluorophores that provide the parent HBC530 ((4-((2-hydroxyethyl)(methyl)amino)benzylidene)cyanophenylacetonitrile) stilbene core [7] but offer an electrophilic alkyl handle on the amino group replacing the original N-hydroxyethyl residue. Three of them have been applied in the cellular applications (Brc3HBC