DNA-enhanced CuAAC ligand enables live-cell detection of intracellular biomolecules

Of the various conjugation strategies for cellular biomolecules, Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is the preferred click chemistry approach due to its fast reaction rate and the commercial availability of a wide range of conjugates. While extracellular labeling of biomolecules using CuAAC has been widely adopted, intracellular labeling in live cells has been challenging; the high copper concentration required for CuAAC reaction can be toxic to biological systems. As a critical first step towards achieving intracellular labeling with CuAAC, an ultrasensitive CuAAC ligand is needed to reduce the required copper concentration while maintaining fast reaction kinetics. Here, we develop a new DNA oligomer-conjugated CuAAC ligand for click reaction biomolecular labeling. The DNA oligo attachment serves several purposes: 1. Increases availability of local copper atoms in proximity to the ligand, which drives up reaction rates, 2. Enables the ligation of azide tags with up to 10-fold lower copper concentrations as compared to commercially available CuAAC ligands, 3. Allows nucleic acid template-driven proximity ligation through the choice of the attached DNA sequence and 4. Allows the CuAAC ligand and copper to traverse the cell and nuclear membrane. We demonstrate that this ligand enhances the intracellular 5-ethynyl uridine labeling of nascent RNAs using fluorogenic dyes. We also show that our DNA-enhanced CuAAC ligand enables the ligation of fluorogenic dyes to label both sialylated glycans on the surface on live cells as well as the live-cell intracellular labeling of nascent RNAs. This new ligand advances our efforts toward the final goal of applying CuAAC for live-cell applications.