Used primarily as a photoactivatable crosslinking agent in biochemical and proteomic research. Its main application lies in studying protein-protein interactions, protein-ligand binding, and molecular interactions in complex biological systems. Upon exposure to UV light, the diazirine group generates highly reactive carbenes that form covalent bonds with nearby molecules, effectively "capturing" transient or weak interactions that are difficult to study with traditional methods.

Commonly incorporated into peptides, proteins, or small molecules via the lysine side chain, it enables targeted crosslinking within active sites or binding pockets. This allows researchers to map interaction domains, identify binding partners in cell lysates, or stabilize complexes for downstream analysis such as mass spectrometry or gel electrophoresis.

Due to its cell permeability and relatively small size, it is also used in live-cell crosslinking experiments, offering insights into native cellular environments. The hydrochloride salt form improves solubility and stability in aqueous buffers, making it suitable for a wide range of biological assays.