Rational design of a photo-crosslinking BODIPY for in situ protein labeling

Photo-crosslinking agents have emerged as critical tools to investigate protein-protein interactions in complex proteomes, but there are few photocrosslinkers available at the moment. Here, we report the first rational design of a photo-crosslinking BODIPY fluorophore (pcBD) and its biological application for biomolecule labeling. As a photosensitizing functional motif, an aryl ketone group was incorporated into the BODIPY fluorophore, and a series of proteins were labeled by pcBD compounds upon UV irradiation. In order to investigate protein-protein interactions in a protein mixture, amino-functionalized pcBD was prepared and covalently attached to a ubiquitin ligase binding peptide. Upon UV irradiation, we could successfully visualize the substrates in the total lysate. These results provided a proof of concept for spatially controllable tagging via photo-activation of the pcBD scaffold, and demonstrated its potential usage for in situ labeling applications.