Comparison of SNAP-tag®/CLIP-tag™ Technologies to GFP

While SNAP-tag®/CLIP-tag™ technologies are complementary to GFP, there are several applications for which SNAP- and CLIP-self-labeling technologies are advantageous.

Application SNAP-tag/CLIP-tag GFP and other fluorescent proteins
Time-resolved fluorescence Fluorescence can be initiated upon addition of label Color is genetically encoded and always expressed. Also, photoactivatable fluorescent proteins require high-intensity laser light, which may activate undesired cellular pathways (e.g., apoptosis)
Pulse-chase analysis Labeling of newly synthesized proteins can be turned off using available blocking reagents (e.g., SNAP-Cell® Block) Fluorescence of newly synthesized proteins cannot be quenched to investigate dynamic processes
Ability to change colors A single construct can be used with different dye substrates to label with multiple colors Requires separate cloning and expression for each color
Surface-specific labeling Can specifically label subpopulation of target protein expressed on cell surface using non-cell permeable substrates Surface subpopulation cannot be specifically visualized
 Single molecule detection  Conjugation with high quantum yield and photostable fluorophores  Fluorescent proteins are generally less bright and photobleach quicker than most organic fluorophores.
Visualizing fixed cells Resistant to fixation; strong labeling Labile to fixation; weak labeling
Pull-down studies "Bait" proteins can be covalently captured on BG beads Requires anti-GFP antibody to non-covalently capture “bait" protein, complicating downstream analysis
Live animal imaging  Cell Permeable Farred dye available, permitting deep tissue visualization Signal is easily quenched by fixation ( whole-mount specimens or thick sections); Limited spectral flexibility and weaker fluorescence.

SNAP-tag® and SNAP-Cell® are registered trademarks of New England Biolabs, Inc.
CLIP-tag™ is a trademark of New England Biolabs, Inc.