Bioorthogonal reactions for labeling proteins

ACS Chemical Biology

Volumn 9, Issue 1, 2014, Pages 16-20

  Lang, Kathrin ^a   Chin, Jason W ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE; AMINO ACID TRANSFER RNA LIGASE; BORONIC ACID DERIVATIVE; HYDRAZINE DERIVATIVE; KETONE; PALLADIUM; RUTHENIUM;

AQUEOUS SOLUTION; ARTICLE; BIOCOMPATIBILITY; CATALYSIS; CATALYST; CELL SURFACE; CHEMICAL LABELING; CHEMICAL REACTION; COVALENT BOND; CYCLOADDITION; DIELS ALDER REACTION; ENVIRONMENTAL TEMPERATURE; GENETIC CODE; IN VITRO STUDY; NONHUMAN; NUCLEAR REPROGRAMMING; PH; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN LABELING; RIBOSOME; THERMODYNAMICS;

ALDEHYDES; ANIMALS; AZIDES; CATALYSIS; CHEMISTRY TECHNIQUES, SYNTHETIC; COLORING AGENTS; HUMANS; HYDROCARBONS, ACYCLIC; INDICATORS AND REAGENTS; KETONES; PROTEINS; STAINING AND LABELING;

EID: 84898072114     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb4009292     Document Type: Article

References (85)

1. Prescher, J. A., and Bertozzi, C. R. (2005) Chemistry in living systems. Nat. Chem. Biol. 1 (1), 13-21.
2. Sletten, E. M., and Bertozzi, C. R. (2009) Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem., Int. Ed. 48 (38), 6974-98.
3. Lim R. K.Lin Q. 2010 Bioorthogonal chemistry: recent progress and future directions. Chem. Commun 46 (10), 1589-600
4. Liu, C. C., and Schultz, P. G. (2010) Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413-444.
5. Davis, L., and Chin, J. W. (2012) Designer proteins: applications of genetic code expansion in cell biology. Nat. Rev. Mol. Cell Biol. 13 (3), 168-182.
6. Prescher, J. A., and Bertozzi, C. R. (2006) Chemical technologies for probing glycans. Cell 126 (5), 851-854. (Pubitemid 44310782)
7. Laughlin, S. T., and Bertozzi, C. R. (2008) Imaging the glycome. Proc. Natl. Acad. Sci. U.S.A. 106, 12-17.
8. Lang, K.; Chin, J. W. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem. Rev. 2014, in press.
9. Chin, J. W. Expanding and reprogramming the genetic code of cells and animals. Ann. Rev. Biochem. 2014, in press.
10. Carrico, I. S., Carlson, B. L., and Bertozzi, C. R. (2007) Introducing genetically encoded aldehydes into proteins. Nat. Chem. Biol. 3 (6), 321-322. (Pubitemid 46789266)
11. Jing, C., and Cornish, V. W. (2011) Chemical tags for labeling proteins inside living cells. Acc. Chem. Res. 44 (9), 784-92.
12. Chen, I., Howarth, M., Lin, W., and Ting, A. Y. (2005) Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nat. Methods 2 (2), 99-104. (Pubitemid 41131030)
13. Liu, D. S., Tangpeerachaikul, A., Selvaraj, R., Taylor, M. T., Fox, J. M., and Ting, A. Y. (2012) Diels-Alder cycloaddition for fluorophore targeting to specific proteins inside living cells. J. Am. Chem. Soc. 134 (2), 792-795.
14. Mukai, T., Kobayashi, T., Hino, N., Yanagisawa, T., Sakamoto, K., and Yokoyama, S. (2008) Adding L-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyltRNA synthetases. Biochem. Biophys. Res. Commun. 371 (4), 818-822.
15. Gautier, A., Nguyen, D. P., Lusic, H., An, W., Deiters, A., and Chin, J. W. (2010) Genetically encoded photocontrol of protein localization in mammalian cells. J. Am. Chem. Soc. 132 (12), 4086-4088.
16. Lang, K., Davis, L., Torres-Kolbus, J., Chou, C., Deiters, A., and Chin, J. W. (2012) Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nat. Chem. 4, 298.
17. Greiss, S., and Chin, J. W. (2011) Expanding the genetic code of an animal. J. Am. Chem. Soc. 133 (36), 14196-14199.
18. Bianco, A., Townsley, F. M., Greiss, S., Lang, K., and Chin, J. W. (2012) Expanding the genetic code of Drosophila melanogaster. Nat. Chem. Biol. 8 (9), 748-750.
19. Neumann, H., Wang, K., Davis, L., Garcia-Alai, M., and Chin, J. W. (2010) Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464 (7287), 441-444.
20. Johnson, J. A., Lu, Y. Y., Van Deventer, J. A., and Tirrell, D. A. (2010) Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications. Curr. Opin. Chem. Biol. 14 (6), 774-780.
21. Ngo, J. T., and Tirrell, D. A. (2011) Noncanonical amino acids in the interrogation of cellular protein synthesis. Acc. Chem. Res. 44 (9), 677-685.
22. Shi, X., Jung, Y., Lin, L.-J., Liu, C., Wu, C., Cann, I. K. O., and Ha, T. (2012) Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging. Nat. Methods 9 (5), 499-503.
23. Rideout, D. (1986) Self-assembling cytotoxins. Science 233 (4763), 561-563. (Pubitemid 16019912)
24. Mahal, L. K. (1997) Engineering chemical reactivity on cell surfaces through oligosaccharide biosynthesis. Science 276 (5315), 1125-1128. (Pubitemid 27218123)
25. Jencks, W. P. (1959) Studies on the mechanism of oxime and semicarbazone formation1. J. Am. Chem. Soc. 81 (2), 475-481.
26. Sander, E. G., and Jencks, W. P. (1968) Equilibria for additions to the carbonyl group. J. Am. Chem. Soc. 90 (22), 6154-6162.
27. Nauman, D. A. D., and Bertozzi, C. R. C. (2001) Kinetic parameters for small-molecule drug delivery by covalent cell surface targeting. Biochim. Biophys. Acta, Bioenerg. 1568 (2), 147-154.
28. Griffin, R. J. (1994) The medicinal chemistry of the azido group. Prog. Med. Chem. 31, 121-232.
29. Tsao, M.-L., Tian, F., and Schultz, P. G. (2005) Selective Staudinger modification of proteins containing p-azidophenylalanine. ChemBioChem 6 (12), 2147-2149.
30. Yanagisawa, T., Ishii, R., Fukunaga, R., Kobayashi, T., Sakamoto, K., and Yokoyama, S. (2008) Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem. Biol. 15 (11), 1187-1197.
31. Ovaa, H., van Swieten, P. F., Kessler, B. M., Leeuwenburgh, M. A., Fiebiger, E., van den Nieuwendijk, A. M. C. H., Galardy, P. J., van der Marel, G. A., Ploegh, H. L., and Overkleeft, H. S. (2003) Chemistry in living cells: Detection of active proteasomes by a twostep labeling strategy. Angew. Chem., Int. Ed. 42 (31), 3626-3629. (Pubitemid 37010644)
32. Vocadlo, D. J., Hang, H. C., Kim, E.-J., Hanover, J. A., and Bertozzi, C. R. (2003) A chemical approach for identifying O-GlcNAcmodified proteins in cells. Proc. Natl. Acad. Sci. U.S.A. 100 (16), 9116-9121. (Pubitemid 37033892)
33. Hangauer, M. J., and Bertozzi, C. R. (2008) A FRET-based fluorogenic phosphine for live-cell imaging with the Staudinger ligation. Angew. Chem., Int. Ed. 47 (13), 2394-2397.
34. Saxon, E., and Bertozzi, C. R. (2000) Cell surface engineering by a modified Staudinger reaction. Science 287 (5460), 2007-2010. (Pubitemid 30158675)
35. Prescher, J. A. J., Dube, D. H. D., and Bertozzi, C. R. C. (2004) Chemical remodelling of cell surfaces in living animals. Nature 430 (7002), 873-877.
36. Lin, F. L., Hoyt, H. M., van Halbeek, H., Bergman, R. G., and Bertozzi, C. R. (2005) Mechanistic investigation of the Staudinger ligation. J. Am. Chem. Soc. 127 (8), 2686-2695. (Pubitemid 40327832)
37. Rostovtsev, V. V., Green, L. G., Fokin, V. V., and Sharpless, K. B. (2002) A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective ligation of azides and terminal alkynes. Angew. Chem., Int. Ed. 41 (14), 2596-2599. (Pubitemid 34803480)
38. Torne, C. W., Christensen, C., and Meldal, M. (2002) Peptidotriazoles on solid phase: [1,2,3]-Triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67 (9), 3057-3064. (Pubitemid 34457265)
39. Speers, A. E., and Cravatt, B. F. (2004) Profiling enzyme activities in vivo using click chemistry methods. Chem, Biol, 11 (4), 535-546. (Pubitemid 38511759)
40. Agard, N. J., Baskin, J. M., Prescher, J. A., Lo, A., and Bertozzi, C. R. (2006) A comparative study of bioorthogonal reactions with azides. ACS Chem. Biol. 1 (10), 644-8.
41. Wolbers, F., ter Braak, P., Le Gac, S., Luttge, R., Andersson, H., Vermes, I., and van den Berg, A. (2006) Viability study of HL60 cells in contact with commonly used microchip materials. Electrophoresis 27 (24), 5073-5080. (Pubitemid 46040720)
42. Hong, V., Steinmetz, N. F., Manchester, M., and Finn, M. G. (2010) Labeling live cells by coppercatalyzed alkyne-azide click chemistry. Bioconjugate Chem. 21 (10), 1912-1916.
43. Rodionov, V. O., Presolski, S. I., Díaz Díaz, D., Fokin, V. V., and Finn, M. G. (2007) Ligand-accelerated Cu-catalyzed azide-alkyne cycloaddition: A mechanistic report. J. Am. Chem. Soc. 129 (42), 12705-12712. (Pubitemid 350004482)
44. Presolski, S. I., Hong, V., Cho, S.-H., and Finn, M. G. (2010) Tailored ligand acceleration of the Cu-catalyzed azide-alkyne cycloaddition reaction: Practical and mechanistic implications. J. Am. Chem. Soc. 132 (41), 14570-14576.
45. Besanceney-Webler C. Jiang H. Zheng T. Feng L. Soriano del Amo D. Wang W. Klivansky L. M. Marlow F. L. Liu Y.Wu P. 2011 Increasing the efficacy of bioorthogonal click reactions for bioconjugation: A comparative study. Angew. Chem., Int. Ed 50 (35), 8051-8056.
46. Soriano del Amo, D., Wang, W., Jiang, H., Besanceney, C., Yan, A. C., Levy, M., Liu, Y., Marlow, F. L., and Wu, P. (2010) Biocompatible copper(I) catalysts for in vivo imaging of glycans. J. Am. Chem. Soc. 132 (47), 16893-16899.
47. Hong, V., Presolski, S. I., Ma, C., and Finn, M. G. (2009) Analysis and optimization of coppercatalyzed azide-alkyne cycloaddition for bioconjugation. Angew. Chem., Int. Ed. 48 (52), 9879-9883.
48. Kennedy D. C McKay C. S., Legault, M. C. B., Danielson, D. C., Blake, J. A., Pegoraro, A. F., Stolow, A., Mester, Z., and Pezacki, J. P. (2011) Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions. J. Am. Chem. Soc 133 (44), 17993-18001.
49. Brotherton, W. S., Michaels, H. A., Simmons, J. T., Clark, R. J., Dalal, N. S., and Zhu, L. (2009) Apparent copper(II)-accelerated azide-alkyne cycloaddition. Org. Lett. 11 (21), 4954-4957.
50. Kuang G.-C. Michaels H. A. Simmons J. T. Clark R. J. Zhu L. 2010 Chelation-assisted, copper(II)-acetate-accelerated azide-alkyne cycloaddition. J. Org. Chem 75 (19), 6540-6548
51. Uttamapinant, C., Tangpeerachaikul, A., Grecian, S., Clarke, S., Singh, U., Slade, P., Gee, K. R., and Ting, A. Y. (2012) Fast, cellcompatible click chemistry with copper-chelating azides for biomolecular labeling. Angew. Chem., Int. Ed. 51 (24), 5852-5856.
52. Alder, K., Stein, G., and Finzenhagen, H. (1931) Uber das abgestufte Additionsvermogen von ungesattigten Ringsystemen. Justus Liebigs Ann. Chem. 485, 211-222.
53. Alder, K., and Stein, G. (1933) Uber das abgestufte Additionsvermogen von ungesattigten Ringsystemen. II. Justus Liebigs Ann. Chem. 501, 1-48.
54. Wittig, G., and Krebs, A. (1961) Zur Existenz niedergliedriger Cycloalkine, I. Chem. Ber. 94 (12), 3260-3275.
55. Agard, N. J., Prescher, J. A., and Bertozzi, C. R. (2004) A strainpromoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. J. Am. Chem. Soc. 126 (46), 15046-15047. (Pubitemid 39557262)
56. Baskin, J. M., Prescher, J. A., Laughlin, S. T., Agard, N. J., Chang, P. V., Miller, I. A., Lo, A., Codelli, J. A., and Bertozzi, C. R. (2007) Copper-free click chemistry for dynamic in vivo imaging. Proc. Natl. Acad. Sci. U.S.A. 104 (43), 16793-16797. (Pubitemid 350210944)
57. Laughlin, S. T., Baskin, J. M., Amacher, S. L., and Bertozzi, C. R. (2008) In vivo imaging of membrane-associated glycans in developing zebrafish. Science 320 (5876), 664-667. (Pubitemid 351928348)
58. Codelli, J. A., Baskin, J. M., Agard, N. J., and Bertozzi, C. R. (2008) Second-generation difluorinated cyclooctynes for copper-free click chemistry. J. Am. Chem. Soc. 130 (34), 11486-11493.
59. Ning, X., Guo, J., Wolfert, M. A., and Boons, G.-J. (2008) Visualizing metabolically labeled glycoconjugates of living cells by copper-free and fast Huisgen cycloadditions. Angew. Chem., Int. Ed. 47 (12), 2253-2255.
60. Gordon, C. G., Mackey, J. L., Jewett, J. C., Sletten, E. M., Houk, K. N., and Bertozzi, C. R. (2012) Reactivity of biarylazacyclooctynones in copper-free click chemistry. J. Am. Chem. Soc. 134 (22), 9199-9208.
61. Ning, X., Temming, R. P., Dommerholt, J., Guo, J., Ania, D. B., Debets, M. F., Wolfert, M. A., Boons, G.-J., and van Delft, F. L. (2010) Protein modification by strain-promoted alkyne-nitrone cycloaddition. Angew. Chem., Int. Ed. 49 (17), 3065-3068.
62. McKay C. S.Moran, J.Pezacki, J. P. (2010) Nitrones as dipoles for rapid strain-promoted 1,3-dipolar cycloadditions with cyclooctynes. Chem. Commun. 46 (6) 931
63. Debets M. F.van Berkel S. S. Dommerholt J. Dirks A. T. J. Rutjes F. P. J. T. van Delft F L. (2011) Bioconjugation with strained alkenes and alkynes. Acc. Chem. Res 44 9), 805-815
64. Lin, Y. A., Chalker, J. M., Floyd, N., Bernardes, G. a. J. L., and Davis, B. G. (2008) Allyl sulfides are privileged substrates in aqueous cross-metathesis: application to site-selective protein modification. J. Am. Chem. Soc. 130 (30), 9642-9643.
65. Lin, Y. A., Chalker, J. M., and Davis, B. G. (2010) Olefin cross-metathesis on proteins: investigation of allylic chalcogen effects and guiding principles in metathesis partner selection. J. Am. Chem. Soc. 132 (47), 16805-16811.
66. Lin, Y. A., Boutureira, O., Lercher, L., Bhushan, B., Paton, R. S., and Davis, B. G. (2013) Rapid cross-metathesis for reversible protein modifications via chemical access to Se-allyl-selenocysteine in proteins. J. Am. Chem. Soc. 135 (33), 12156-12159.
67. Chalker, J. M., Wood, C. S. C., and Davis, B. G. (2009) A convenient catalyst for aqueous and protein Suzuki-Miyaura crosscoupling. J. Am. Chem. Soc. 131 (45), 16346-16347.
68. Spicer, C. D., Triemer, T., and Davis, B. G. (2012) Palladium-mediated cell-surface labeling. J. Am. Chem. Soc. 134 (2), 800-803.
69. Nguyen, D. P., Elliott, T., Holt, M., Muir, T. W., and Chin, J. W. (2011) Genetically encoded 1,2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation. J. Am. Chem. Soc. 133 (30), 11418-11421.
70. Liang, G., Ren, H., and Rao, J. (2010) A biocompatible condensation reaction for controlled assembly of nanostructures in living cells. Nat. Chem. 2 (1), 54-60.
71. Song, W., Wang, Y., Qu, J., Madden, M. M., and Lin, Q. (2008) A photoinducible 1,3-dipolar cycloaddition reaction for rapid, selective modification of tetrazole-containing proteins. Angew. Chem., Int. Ed. 47 (15), 2832-2835.
72. Song, W., Wang, Y., Yu, Z., Vera, C. I. R., Qu, J., and Lin, Q. (2010) A metabolic alkene reporter for spatiotemporally controlled imaging of newly synthesized proteins in mammalian cells. ACS Chem Biol 5 (9), 875-885.
73. Yu, Z., Pan, Y., Wang, Z., Wang, J., and Lin, Q. (2012) Genetically encoded cyclopropene directs rapid, photoclick-chemistry-mediated protein labeling in mammalian cells. Angew. Chem., Int. Ed. 51 (42), 10600-10604.
74. Song, W., Wang, Y., Qu, J., and Lin, Q. (2008) Selective functionalization of a genetically encoded alkene-containing protein via photoclick chemistry in bacterial cells. J. Am. Chem. Soc. 130 (30), 9654-9655.
75. Yu, Z., Ohulchanskyy, T. Y., An, P., Prasad, P. N., and Lin, Q. (2013) Fluorogenic, two-photon-triggered photoclick chemistry in live mammalian cells. J. Am. Chem. Soc. 135 (45), 16766-16769.
76. Boger, D. L. (1986) Diels-Alder reactions of heterocyclic azadienes: Scope and applications. Chem. Rev. 86, 781-793.
77. Blackman, M. L., Royzen, M., and Fox, J. M. (2008) Tetrazine ligation: Fast bioconjugation based on inverse-electrondemand Diels-Alder reactivity. J. Am. Chem. Soc. 130 (41), 13518-13519.
78. Devaraj, N. K., Weissleder, R., and Hilderbrand, S. A. (2008) Tetrazine-based cycloadditions: Application to pretargeted live cell imaging. Bioconjugate Chem. 19 (12), 2297-2299.
79. Lang, K., Davis, L., Wallace, S., Mahesh, M., Cox, D. J., Blackman, M. L., Fox, J. M., and Chin, J. W. (2012) Genetic encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions. J. Am. Chem. Soc. 134 (25), 10317-10320.
80. Elliott, T.; Chin, J. W. (unpublished results)
81. Taylor, M. T., Blackman, M. L., Dmitrenko, O., and Fox, J. M. (2011) Design and synthesis of highly reactive dienophiles for the tetrazine-trans- cyclooctene ligation. J. Am. Chem. Soc. 133 (25), 9646-9649.
82. Devaraj, N. K., Hilderbrand, S., Upadhyay, R., Mazitschek, R., and Weissleder, R. (2010) Bioorthogonal turn-on probes for imaging small molecules inside living cells. Angew. Chem., Int. Ed. 49 (16), 2869-2872.
83. Plass, T., Milles, S., Koehler, C., Szymanski, J., Mueller, R., Wieler, M., Schultz, C., and Lemke, E. A. (2012) Amino acids for Diels-Alder reactions in living cells. Angew. Chem., Int. Ed. 51 (17), 4166-4170.
84. Borrmann, A., Milles, S., Plass, T., Dommerholt, J., Verkade, J. M. M., Wieler, M., Schultz, C., van Hest, J. C. M., van Delft, F. L., and Lemke, E. A. (2012) Genetic encoding of a bicyclo[6.1.0]nonynecharged amino acid enables fast cellular protein imaging by metal-free ligation. ChemBioChem 13 (14), 2094-2099.
85. Kaya, E., Vrabel, M., Deiml, C., Prill, S., Fluxa, V. S., and Carell, T. (2012) A genetically encoded norbornene amino acid for the mild and selective modification of proteins in a copper-free click reaction. Angew. Chem., Int. Ed. 51 (18), 4466-4469.