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

Raphael Bereiter¹, Ronald Micura¹

¹Institute of Organic Chemistry, Center for Molecular Biosciences, Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.

Beilstein Journal of Organic Chemistry

|April 15, 2025

Abstract:

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.

Keywords:

FLAP HBC530 covalent RNA labeling fluorophore synthesis self-alkylating ribozymes

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