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Cellular Analysis

SNAP- and CLIP-tag protein labeling systems enable the specific, covalent attachment of virtually any molecule to a protein of interest. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag® fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O6-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag substrates are dyes, fluorophores, biotin, or beads conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag™ is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells. 

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

Cellular Analysis includes these subcategories:

Starter Kits
SNAP-tag® Substrates
CLIP-tag™ Substrates
Blocking Agents
Cellular Analysis Vectors
Biotin/Vista Labels
Building Blocks

FAQs for Cellular Analysis

    Publications related to Cellular Analysis

  1. Damoiseaux, R. et al 2002. Towards the generation of artificial O6-alkylguanine-DNA alkyltransferases: in vitro selection of antibodies with reactive cysteine residues ChemBioChem . 3, PubMedID: 12325014, DOI:
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  3. Gendreizig, S. et al. 2003. Induced protein dimerizaton in vivo through covalent labeling JACS . 125, PubMedID: 14653715, DOI:
  4. Gendreizig S. et al. 2003. Covalent labeling of fusion proteins with chemical probes in living cells Chimia . 57, PubMedID: , DOI:
  5. Juillerat A. et al. 2003. Directed evolution of O6-alkylguanine-DNA alkyltransferase for efficient labeling of fusion proteins with small molecules in vivo Chem. Biol.  . 10, PubMedID: , DOI:
  6. Keppler A. et al. 2004. Labeling of fusion proteins with synthetic fluorophores in live cells PNAS . 101, PubMedID: , DOI:
  7. Keppler A. et al. 2004. Labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase with small molecules in vitro and in vivo Methods . 32, PubMedID: 15003606, DOI:
  8. Kindermann M. et al. 2004. Synthesis and characterization of bifunctional probes for the specific labeling of fusion proteins Bioorg. Med. Chem. Lett. . 14, PubMedID: , DOI:
  9. Hoskins, A. et al. 2011. Ordered and dynamic assembly of single spliceoseoms Science . 331 , PubMedID: 21393538, DOI:
  10. Eckhardt, M. et al. 2011. A SNAP-tagged detivative of HIV-1 - A versatile tool to study virus-cell interactions PLoS One . , PubMedID: 21799764, DOI: 10.137/journal. P One .0022007
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  12. Gronemeyer T. et al. 2006. Directed evolution of O6-alkylguanine-DNA alkyltransferase for applications in protein labeling Prot. Eng. Des. Sel. . 19, PubMedID: 12725859, DOI:
  13. Keppler A. et al. 2006. Fluorophores for live cell imaging of AGT fusion proteins across the visible spectrum BioTechniques . 41, PubMedID: 16925018, DOI:
  14. Krayl M. et al. 2006. Fluorescence-mediated analysis of mitochondrial preprotein import in vitro Anal. Biochem.  . 335, PubMedID: 16750157, DOI:
  15. Tirat A. et al. 2006. Evaluation of two novel tag-based labeling technologies for site-specific modification of proteins Int. J. Biol. Macromol.. 39, PubMedID: 16503347, DOI:
  16. Heinis C. et al. 2006. Evolving the substrate specificity of O6 alkylguanine DNA alkyltransferase through loop insertion for applications in molecular imaging ACS Chem Biol. . 1, PubMedID: 17168553, DOI:
  17. Johnsson N. et al. 2005. Protein chemistry on the surface of living cells Chembiochem. . 6 , PubMedID: 15558647, DOI:
  18. Regoes A. et al. 2005. SNAP-tag mediated live cell labeling as an alternative to GFP in anaerobic organisms BioTechniques . 39, PubMedID: , DOI:
  19. Juillerat A. et al. 2005. Engineering substrate specificity of O6-alkylguanine-DNA alkyltransferase for specific protein labeling in living cells ChemBioChem . 6, PubMedID: 15934048, DOI:
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  24. Campos, C. et al. 2010. Labeling cell structures and tracking cell lineage in zebrafish using SNAP-Tag Dev. Dynamics . 240 , PubMedID: 21360787, DOI:
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  29. Hein B. et al. 2010. Stimulated emission depletion nanoscopy of living cells using SNAP-Tag fusion proteins Biophys. J.  . 98 , PubMedID: 20074516, DOI:
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  40. Stein, V. et al. 2007. A covalent chemical genotype-phenotype linkage for in vitro protein evolution ChemBioChem. . 8, PubMedID: 17948318, DOI:
  41. Pick H. et al. 2007. Distribution plasticity of the human estrogen receptor alpha in live cells: distinct imaging of consecutively expressed receptors J. Mol. Biol. . 14, PubMedID: 17991486, DOI:
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  47. Böhme I and Beck-Sickinger A. G. 2009. Illuminating the life of GPCRs Cell Commun. Signal . 7 , PubMedID: 19602276, DOI:
  48. Farr G. A. et al. 2009. Membrane proteins follow multiple pathways to the basolateral cell surface in polarized epithelial cells J. Cell Biol. . 186 , PubMedID: 19620635, DOI:
  49. Johnsson K. 2009. Visualizing biochemical activities in living cells Nat Chem Biol . 5 , PubMedID: 19148167, DOI:
  50. Uano Y. and Matsuzaki K. 2009. Tag-probe labeling methods for live-cell imaging of membrane proteins Biochim. Biophys. Acta. . 1788 , PubMedID: 19646952, DOI:
  51. Kapmeier F. et al. 2009. Site-Specific, covalent labeling of recombinant antibody fragments via fusion to an engineered version of 6-O-alkylguanine DNA alkyltransferase Bioconjug Chem. . 23-Apr , PubMedID: 19388673, DOI:
  52. Stein V. and Hollfeder F. 2009. An efficient method to assemble linear DNA templates for in vitro screening and selection systems Nuc. Acids Res . 37, PubMedID: 19617373, DOI:
  53. Donovan C. et al. 2009. Characterization and subcellular localization of bacterial flotillin homologue Microbiology . 155 , PubMedID: 19383680, DOI:
  54. Sletten E. and Bertozzi C. 2009. Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality Angew. Chem. Int. Ed. . 48 , PubMedID: 19714693, DOI:
  55. Carroll C.W. et al. 2009. Centromere assembly requires the direct recognition of CENP-A nucleosomes by CENP-N Nat. Cell Biol. . 11 , PubMedID: 19543270, DOI:
  56. Foltz D.R. et al. 2009. Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP Cell . 137 , PubMedID: 19410544, DOI:
  57. Ahier A. et al. 2009. A new family of receptor tyrosine kinases with a venus flytrap binding domain in insects and other invertebrates activated by aminoacids PLoS One . 4, PubMedID: 19461966, DOI:
  58. Cornish, V. W. 2009. Fluorescence in living systems: applications in chemical biology Wiley Encyc. of Chem. Biol. . 2 , PubMedID: , DOI:
  59. Chattopadhaya S. et al. 2009. Expanding the chemical Biologist's tool kit: chemical labelling strategies and its applications Curr. Med. Chem.  . 16 , PubMedID: 19903152, DOI:
  60. Degorce F. et al. 2009. HTRF: A technology tailored for drug discovery - a review of theoretical aspects and recent applications Curr. Chem. Genomics .  3 , PubMedID: 20161833, DOI:
  61. Samoshkin A. et al. 2009. Human condensin function is essential for centromeric chromatin assembly and proper sister kinetochore orientation PLoS One . 4 , PubMedID: 19714251, DOI:
  62. Keppler A. et al. 2009. Chromophore-assisted laser inactivation of α- and γ-tubulin SNAP-tag fusion proteins inside living cells ACS Chem. Biol. . 4 , PubMedID: 19191588, DOI:
  63. McMurray, M.A. and Thorner, J. 2008. Septin stability and recycling during dynamic structural transitions in cell division and development Current Biology . 18 , PubMedID: 18701287, DOI:
  64. Lin M.Z. and Wang L. 2008. Selective labeling of proteins with chemical probes in living cells Physiology . 23 , PubMedID: 18556466, DOI:
  65. Mao S. et al. 2008. Optical lock-in detection of FRET using synthetic and genetically encoded optical switches Biophys. J. . 94, PubMedID: 18281383, DOI:
  66. Tomat, E. et al. 2008. Organelle-specific zinc detection using zinpyr-labeled fusion proteins in live cells J. Am. Chem. Soc. . 130 , PubMedID: 18973293, DOI:
  67. Adams D. G. et al. 2008. Cellular Ser/Thr-kinase assays using generic peptide substrates Curr. Chem. Gen. . 1 , PubMedID: 20161828, DOI:
  68. Banala J. et al. 2008. Caged substrates for protein labeling and immobilization Chembiochem . 4, PubMedID: 18033718, DOI:
  69. Maurel D. et al. 2008. Cell-surface protein-protein interaction analysis with time-resolved FRET and SNAP-tag technologies: application to GPCR oligomerization Nature Methods . 5, PubMedID: 18488035, DOI:
  70. Chidley C. et al. 2008. A designed protein for the specific and covalent heteroconjugation of biomolecules Bioconj. Chem. . 19 , PubMedID: 18754573, DOI:
  71. Gautier A. et al. 2008. AGT/SNAP-Tag: A versatile tag for covalent protein labeling from probes and tags to study biomolecular function Ed. Edited by Miller, L. W. . , PubMedID: , DOI:
  72. Erhardt, S. et al. 2008. Genome-wide analysis reveals a cell cycle-dependent mechanism controling centromere propagation J. Cell Biol.. 183 , PubMedID: 19047461, DOI:
  73. Howland S.W. et al. 2008. Inducing efficient cross-priming using antigen-coated yeast particles J. Immunother.. 31 , PubMedID: 18600183, DOI:
  74. Southwell, A.L. et al. 2008. Intrabodies binding the proline-rich domains of mutant huntingtin increase its turnover and reduce neurotoxicity J. Neurosci. . 28, PubMedID: 18768695, DOI:
  75. Fururta, K. et al. 2008. Diffusion and directed movement: in vitro motile properties of fission yeast kinesin-14 Plk1 J. Biol. Chem.  . 283 , PubMedID: 18984586, DOI:
  76. Johnson K. 2008. SNAP-tag Technologies: Novel tools to study protein function NEB Expressions . 3.3 , PubMedID: , DOI:
  77. Kindermann M. et al. 2003. Covalent and selective immobilization of fusion proteins JACS . 125, PubMedID: 12822993, DOI:
  78. La Clair, J.J. et al. 2004. Manipulation of carrier proteins in antibiotic biosynthesis Chem. Biol. . 11, PubMedID: 15123281, DOI:
  79. George N. et al. 2004. Specific labeling of cell surface proteins with chemically diverse compounds J .Am. Chem. Soc.  . 126, PubMedID: 15264811, DOI:
  80. Huber W. et al. 2004. SPR-based interaction studies with small molecular weight ligands using hAGT fusion proteins Anal. Biochem. . 333, PubMedID: 15450803, DOI:
  81. Sielaff I. et al. 2006. Protein function microarrays based on self-immobilizing and self-labeling fusion proteins ChemBioChem.. 7, PubMedID: 16342318, DOI:
  82. Prummer M. et al. 2006. Post-translational covalent labeling reveals heterogeneous mobility of individual G protein-coupled receptors in living cells ChemBioChem . 7, PubMedID: 16607667, DOI:
  83. Jacquier V. et al. 2006. Visualizing receptor trafficking in living PNAS . 103, PubMedID: 16980412, DOI:
  84. Jongsma M.A., Litjens R. H. 2006. Self-assembling protein arrays on DNA chips by auto-labeling fusion proteins with a single DNA address  Proteomics . 6, PubMedID: 16596705, DOI:
  85. Meyer B.H. et al. 2006. Covalent labeling of cell-surface proteins for in vivo FRET studies FEBS Letters . 580, PubMedID: 16497304, DOI:
  86. Meyer B.H. et al. 2006. FRET imaging reveals that functional neurokinin-1 receptors are monomeric and reside in membrane microdomains of live cells Proc. Natl. Acad. Sci. USA . 103, PubMedID: 16461466, DOI:
  87. Tugulu S. et al. 2005. Protein-functionalized polymer brushes Biomacromolecules . 6, PubMedID: 15877383, DOI:
  88. Cravatt B.F. 2005. Live chemical reports from the cell surface Chem. Biol. . 12, PubMedID: 16183017, DOI:
  89. Vivero-Pol L. et al. 2005. Multicolor imaging of cell surface proteins J. Am. Chem. Soc. . 127, PubMedID: 16159249, DOI:
  90. Yin J. et al. 2005. Single-cell FRET imaging of transferrin receptor trafficking dynamics by Sfp-catalyzed, site-specific protein labeling Chem. Biol . 12, PubMedID: 16183024, DOI:
  91. Yin J. et al. 2005. Labeling proteins with small molecules by site-specific posttranslational modification J Am Chem Soc. 126 , PubMedID: 15212504, DOI:
  92. Kufer S.K. et al. 2005. Covalent immobilization of recombinant fusion proteins with hAGT for single molecule force spectroscopy Eur. Biophys. J . 35, PubMedID: 16160825, DOI:
  93. Mosiewicz, K. A. et al. 2010. Phosphopantetheinyl Transferase-Catalyzed Formation of Bioactive Hydrogels for Tissue Engineering J. Am. Chem. Soc. . 132, PubMedID: 20373804, DOI:
  94. Engin S. et al. 2010. Benzylguanine Thiol self-assembled monolayers for the immobilization of SNAP-tag proteins on microcontact-printed surface structures Langmuir . ASAP, PubMedID: 20369837, DOI:
  95. Waichman S. et al. 2010. Functional Immobilization and Patterning of Proteins by an Enzymatic Transfer Reaction Anal. Chem. . 82 , PubMedID: 20092261, DOI:
  96. Zelman-Femiak, M. et al. 2010. Covalent quantum dot receptor linkage via the acyl carrier protein for single-molecule tracking, internalization, and trafficking studies BioTechniques . 49, PubMedID: 20701592, DOI:
  97. Liu E and Bruner S. D. 2007. Rational manipulation of carrier-domain geometry in nonribosomal peptide synthetases ChemBioChem. . 8, PubMedID: 17335097, DOI:
  98. Zhou Z. et al. 2007. Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases ACS Chemical Biology . 2, PubMedID: 17465518, DOI:
  99. Gautier A. et al. 2009. Selective cross-linking of interacting proteins using self-labeling tags J. Am. Chem. Soc. . 131, PubMedID: 19916541, DOI:
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  103. Generosi J. et al. 2008. Photobleaching-free infrared near-field microscopy localizes molecules in neurons J. App. Phys. . 104, PubMedID: , DOI:
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  • Simultaneous dual protein labeling inside live cells
  • Protein localization and translocation
  • Pulse-chase experiments
  • Receptor internalization studies
  • Selective cell surface labeling
  • Protein pull-down assays
  • Protein detection in SDS-PAGE
  • Flow cytometry
  • High throughput binding assays in microtiter plates
  • Biosensor interaction experiments
  • FRET-based binding assays
  • Single molecule labeling
  • Super-resolution microscopy

Selected Publications by Application


Lukinavičius, G. et al. (2015) "Fluorescent labeling of SNAP-tagged proteins in cells" Methods Mol. Biol. 1266, 107-118.
Corrêa Jr., I. R. (2015) "Considerations and protocols for the synthesis of custom protein labeling probes" Methods Mol. Biol. 1266, 55-79.
Corrêa Jr., I. R. (2014) "Live-cell reporters for fluorescence imaging" Curr. Opin. Chem. Biol. 20, 36-45.

Single-Molecule Imaging

Bosch, P. J. et al. (2014) "Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells" Biophys. J. 107, 803-814.
Smith, B. A. et al. (2013) "Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation" eLife 2, e01008.
Jaiswal, R. et al. (2013) "The Formin Daam1 and Fascin Directly Collaborate to Promote Filopodia Formation" Curr. Biol. 23, 1373-1379.
Breitsprecher, D. et al. (2012) "Rocket Launcher Mechanism of Collaborative Actin Assembly Defined by Single-Molecule Imaging" Science 336, 1164-1168.
Hoskins, A. A. et al. (2011) "Ordered and dynamic assembly of single spliceosomes." Science 331 (6022), 1289-1295.

Super-Resolution Imaging

Zhao, Z. W. et al. (2014) "Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy" Proc. Natl. Acad. Sci. USA 111, 681-686.
Lukinavičius, G. et al. (2013) "A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins" Nat. Chem. 5, 132-139.
Jones, S. A. et al. (2011) "Fast, three-dimensional super-resolution imaging of live cells." Nat. Methods 8, 499-505.
Klein, T. et al. (2011) "Live-cell dSTORM with SNAP-tag fusion proteins." Nat. Methods 8, 7-9.
Pellett, P. A. et al. (2011) "Two-color STED microscopy in living cells." Biomed. Opt. Expr. 2, 2364-2371
Hein, B. et al. (2010) "Stimulated Emission Depletion Nanoscopy of Living Cells Using SNAP-Tag Fusion Proteins." Biophys. J. 98, 158-163.

Tissue and Animal Imaging:

Yang, G. et al. (2015) "Genetic targeting of chemical indicators in vivo" Nat. Methods 12, 137-139.
Kohl, J. et al. (2014) "Ultrafast tissue staining with chemical tags" Proc. Natl. Acad. Sci. USA 111, E3805-E3814.
Ivanova, A. et al. (2013) "Age-dependent labeling and imaging of insulin secretory granules" Diabetes 62, 3687-3696.
Gong, H. et al. (2012) "Near-Infrared Fluorescence Imaging of Mammalian Cells and Xenograft Tumors with SNAP-Tag" PLoS ONE 7(3): e34003.
Bojkowska K. et al. (2011) "Measuring in vivo protein half-life." Chem. Biol. 18, 805-815.

Cell-Surface Protein Labeling and Internalization Analysis:

Bitsikas, V. et al. (2014) "Clathrin-independent pathways do not contribute significantly to endocytic flux" eLife 3, e03970.
Jaensch, N. et al. (2014) "Stable Cell Surface Expression of GPI-Anchored Proteins, but not Intracellular Transport, Depends on their Fatty Acid Structure" Traffic 15, 1305-1329.
Cole, N. B. and Donaldson, J. G. (2012) "Releasable SNAP-tag Probes for Studying Endocytosis and Recycling" ACS Chem. Biol. 7, 464-469.

Pulse-Chase Analysis:

Rošić, S. et al. (2014) "Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division" J. Cell Biol. 207, 335-349.
Stoops, E. H. et al. (2014) "SNAP-Tag to Monitor Trafficking of Membrane Proteins in Polarized Epithelial Cells" Methods Mol. Biol. 1174, 171-182.
Bordor, D. L. et al. (2012) "Analysis of Protein Turnover by Quantitative SNAP-Based Pulse-Chase Imaging" Curr. Protoc. Cell Biol. 55, 8.8.1-8.8.34.

Pull-Down Studies:

Register, A. C. et al. (2014) "SH2-Catalytic Domain Linker Heterogeneity Influences Allosteric Coupling across the SFK Family" Biochemistry 53, 6910-6923.
Shi, G. et al. (2012) "SNAP-tag based proteomics approach for the study of the retrograde route" Traffic 13, 914-925.
Bieling, P. et al. (2010) "A minimal midzone protein module controls formation and length of antiparallel microtubule overlaps" Cell 142, 420-432.

Protein-Protein and Protein-Ligand Interactions:

Griss, R. et al. (2014) "Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring" Nat. Chem. Biol. 10, 598-603.
Chidley, C. et al. (2011) "A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis." Nat. Chem. Biol. 7, 375-383.
Gautier A. et al. (2009) "Selective Cross-Linking of Interacting Proteins using Self-Labeling Tags" J. Am. Chem. Soc. 131, 17954-17962.
Maurel D. et al. (2008) "Cell-surface protein-protein interaction analysis with time-resolved FRET and SNAP-tag technologies: application to GPCR oligomerization." Nat. Methods 5, 561-567.


  • Clone and express once, then use with a variety of substrates
  • Non-toxic to living cells
  • Wide selection of fluorescent substrates
  • Highly specific covalent labeling
  • Simultaneous dual labeling

Protein Labeling with SNAP-tag and CLIP-tag

The SNAP- (gold) or CLIP-tag (purple) is fused to the protein of interest (blue). Labeling occurs through covalent attachment to the tag, releasing either a guanine or a cytosine moiety.

SNAP-tag®, CLIP-tag™ and ACP/MCP-tag Substrate Selection Chart

NEB offers a large selection of fluorescent labels (substrates) for SNAP-, CLIP-, ACP- and MCP-tag fusion proteins.

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This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.