How do SNAP-tag and CLIP-tag work?

SNAP-tag and CLIP-tag are two self-labeling proteins derived from human O6-alkylguanine-DNA-alkyltransferase. SNAP-tag is engineered to react covalently with O6-benzylguanine derivatives while CLIP-tag reacts with benzylcytosine derivatives.

The SNAP-tagged or CLIP-tagged protein is expressed in the cell line or organism after transfection with a plasmid encoding the SNAP-tagged or CLIP-tagged fusion protein.  

By incubating with specific ligands, the SNAP-tag or CLIP-tag fusion protein can become fluorescent by binding to a fluorescent dye. It can also bind to a biotin ligand, allowing for immobilization or other streptavidin modifications.

Once the SNAP-tag or CLIP-tag covalently binds to a ligand, they cannot bind to any other ligands as the catalytic center is blocked, preventing further ligand-based applications. However, the tagged protein can still be immunoprecipitated or detected using antibodies or Nanobodies that bind outside the blocked catalytic center.