Covalent live-cell labeling of proteins using a photoreactive fluorogen

Fluorescence microscopy has dramatically advanced our understanding of the processes that drive biological systems by enabling the imaging and tracking of biomolecules of interest inside of living cells. In particular, proteins of interest can be genetically tagged with fluorescent proteins or labeled with small molecule fluorophore probes to enable visualization. However, both of these methods are generally limited in signal-to-background resolution and options are limited for achieving temporal control over labeling. Photoreactive "fluorogenic" dyes can overcome these limitations and enable user-defined crosslinking with low background fluorescence. In this chapter, we discuss current approaches for live cell protein labeling with particular emphasis on the novel use of photoreactive fluorogenic dyes for protein imaging. We further describe in detail the synthesis and characterization of a fluorogenic malachite green probe functionalized with a photoreactive diazirine crosslinker and illustrate how to apply this probe toward covalent photoaffinity labeling and imaging of target proteins in live cells.