Specific labeling of zinc finger proteins using noncanonical amino acids and copper-free click chemistry

Bioconjugate Chemistry

Volumn 23, Issue 9, 2012, Pages 1891-1901

  Kim, Younghoon ^a   Kim, Sung Hoon ^b   Ferracane, Dean ^a   Katzenellenbogen, John A ^b   Schroeder, Charles M ^a,c  

^a University of Illinois at Urbana Champaign   (United States)

^b Department of Chemistry ^*  (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOCHIPS; COPPER; CYCLOADDITION; ELECTROPHORETIC MOBILITY; ENERGY TRANSFER; METABOLISM; PROTEINS; SYNTHESIS (CHEMICAL); ZINC;

CLICK CHEMISTRY; COPPER-FREE CLICKS; DNA BINDING ACTIVITY; GENE MODIFICATION; LABELINGS; METALLO-PROTEINS; NON-CANONICAL AMINO ACIDS; TRANSCRIPTIONAL REGULATION; UNNATURAL AMINO ACIDS; ZINC FINGER PROTEIN;

AMINO ACIDS;

AMINO ACID; AZIDE; AZIDOHOMOALANINE; COPPER; CYSTEINE; HISTIDINE; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ARTICLE; CHEMICAL LABELING; CLICK CHEMISTRY; CONTROLLED STUDY; CYCLOADDITION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GEL MOBILITY SHIFT ASSAY; MASS SPECTROMETRY; NONHUMAN; PROTEIN DNA BINDING; PROTEIN MICROARRAY;

EID: 84866370271     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc300262h     Document Type: Article

References (53)

1. Urnov, F., Miller, J., Lee, Y., Beausejour, C., Rock, J., Augustus, S., Jamieson, A., Porteus, M., Gregory, P., and Holmes, M. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases Nature 435, 646-651 (Pubitemid 40825505)
2. Hockemeyer, D., Soldner, F., Beard, C., Gao, Q., Mitalipova, M., DeKelver, R., Katibah, G., Amora, R., Boydston, E., and Zeitler, B. (2009) Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases Nat. Biotechnol. 27, 851-857
3. Rebar, E. and Pabo, C. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities Science 263, 671
4. Bibikova, M., Beumer, K., Trautman, J., and Carroll, D. (2003) Enhancing gene targeting with designed zinc finger nucleases Science 300, 764 (Pubitemid 36532104)
5. Hockemeyer, D., Soldner, F., Beard, C., Gao, Q., Mitalipova, M., DeKelver, R., Katibah, G., Amora, R., Boydston, E., and Zeitler, B. (2009) Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases Nat. Biotechnol. 27, 851-857
6. Kim, H., Lee, H., Kim, H., Cho, S., and Kim, J. (2009) Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly Genome Res. 19, 1279
7. Wright, D., Thibodeau-Beganny, S., Sander, J., Winfrey, R., Hirsh, A., Eichtinger, M., Fu, F., Porteus, M., Dobbs, D., and Voytas, D. (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly Nat. Protocols 1, 1637-1652
8. Maeder, M. L., Thibodeau-Beganny, S., Sander, J. D., Voytas, D. F., and Joung, J. K. (2009) Oligomerized pool engineering (OPEN): anopen-sourceprotocol for making customized zinc-finger arrays Nat. Protocols 4, 1471-1501
9. Sander, J. D., Dahlborg, E. J., Goodwin, M. J., Cade, L., Zhang, F., Cifuentes, D., Curtin, S. J., Blackburn, J. S., Thibodeau-Beganny, S., and Qi, Y. (2010) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA) Nat. Methods 8, 67-69
10. Joung, J., Ramm, E., and Pabo, C. (2000) A bacterial two-hybrid selection system for studying protein DNA and protein-protein interactions Proc. Natl. Acad. Sci. U.S.A. 97, 7382
11. Wang, Y., Guo, L., Golding, I., Cox, E. C., and Ong, N. (2009) Quantitative transcription factor binding kinetics at the single-molecule level Biophys. J. 96, 609-620
12. Carroll, D., Morton, J., Beumer, K., and Segal, D. (2006) Design, construction and in vitro testing of zinc finger nucleases Nat. Protocols 1, 1329-1341
13. Chen, I. and Ting, A. Y. (2005) Site-specific labeling of proteins with small molecules in live cells Curr. Opin. Biotechnol. 16, 35-40 (Pubitemid 40249757)
14. Lee, Y. M. and Lim, C. Factors controlling the reactivity of zinc finger cores. J. Am. Chem. Soc. 2011, not supplied.
15. Ahel, I., Ahel, D., Matsusaka, T., Clark, A. J., Pines, J., Boulton, S. J., and West, S. C. (2008) Poly (ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins Nature 451, 81-85
16. Aldovini, A. and Young, R. A. (1990) Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus J. Virol. 64, 1920-1926 (Pubitemid 20148432)
17. Link, A. and Tirrell, D. (2003) Cell surface labeling of Escherichia coli via copper (I)-catalyzed [3+ 2] cycloaddition J. Am. Chem. Soc. 125, 11164-11165 (Pubitemid 37108030)
18. Kolb, H., Finn, M., and Sharpless, K. (2001) Click chemistry: diverse chemical function from a few good reactions Angew. Chem., Int. Ed. 40, 2004-2021
19. Meldal, M. and Tornoee, C. (2008) Cu-Catalyzed azide- alkyne cycloaddition Chem. Rev. 108, 2952-3015
20. Kolb, H., Finn, M., and Sharpless, K. (2001) Click chemistry: diverse chemical function from a few good reactions Angew. Chem., Int. Ed. 40, 2004-2021
21. Natarajan, A., Du, W., Xiong, C., DeNardo, G., DeNardo, S., and Gervay-Hague, J. (2007) Construction of di-scFv through a trivalent alkyne azide 1, 3-dipolar cycloaddition Chem. Commun. 2007, 695-697 (Pubitemid 46233533)
22. 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, 16793
23. Chang, P. V., Prescher, J. A., Sletten, E. M., Baskin, J. M., Miller, I. A., Agard, N. J., Lo, A., and Bertozzi, C. R. (2010) Copper-free click chemistry in living animals Proc. Natl. Acad. Sci. U.S.A. 107, 1821-1826
24. Ausubel, F. M., Brent, R., Kingston, R., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K. (2011) Current Protocols in Molecular Biology, Wiley.
25. Wright, D., Thibodeau-Beganny, S., Sander, J., Winfrey, R., Hirsh, A., Eichtinger, M., Fu, F., Porteus, M., Dobbs, D., and Voytas, D. (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly Nat. Protocols 1, 1637-1652
26. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: visual molecular dynamics J. Mol. Graphics 14, 33-38 (Pubitemid 26152973)
27. Lakowicz, J. R. (2006) Principles of Fluorescence Spectroscopy, 3 rd ed., Springer, New York.
28. Barbara, A. L. and Owen, C. T. M. Rapid method for measuring DNA binding to protein using fluorescence anisotropy. Nat. Protocols 2009, not supplied.
29. Hellman, L. M. and Fried, M. G. (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions Nat. Protocols 2, 1849-1861 (Pubitemid 47308124)
30. Selvin, P. and Ha, T. (2008) Single-molecule techniques: a laboratory manual, Cold Spring Harbor Laboratory Press.
31. Kim, S. H., Tamrazi, A., Carlson, K. E., Daniels, J. R., Lee, I. Y., and Katzenellenbogen, J. A. (2004) Estrogen receptor microarrays: subtype-selective ligand binding J. Am. Chem. Soc. 126, 4754-5 (Pubitemid 38490123)
32. Lee, Y. M. and Lim, C. Factors controlling the reactivity of zinc finger cores. J. Am. Chem. Soc. 2011, not supplied.
33. Kiick, K., Saxon, E., Tirrell, D., and Bertozzi, C. (2002) Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation Proc. Natl. Acad. Sci. U.S.A. 99, 19
34. Kiick, K., Saxon, E., Tirrell, D., and Bertozzi, C. (2002) Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation Proc. Natl. Acad. Sci. U.S.A. 99, 19
35. Chin, J. W., Cropp, T. A., Anderson, J. C., Mukherji, M., Zhang, Z., and Schultz, P. G. (2003) An expanded eukaryotic genetic code Science 301, 964-967 (Pubitemid 36994808)
36. Wang, L., Brock, A., Herberich, B., and Schultz, P. G. (2001) Expanding the genetic code of Escherichia coli Science 292, 498-500 (Pubitemid 32335951)
37. Wang, A., Winblade Nairn, N., Johnson, R. S., Tirrell, D. A., and Grabstein, K. (2008) Processing of N-Terminal Unnatural Amino Acids in Recombinant Human Interferon-β in Escherichia coli ChemBioChem 9, 324-330 (Pubitemid 351196801)
38. Rauscher, F. J., Morris, J. F., Tournay, O. E., Cook, D. M., and Curran, T. (1990) Binding of the Wilms tumor locus zinc finger protein to the EGR-1 consensus sequence Science 250, 1259
39. Kim, M. S., Stybayeva, G., Lee, J. Y., Revzin, A., and Segal, D. J. (2011) A zinc finger protein array for the visual detection of specific DNA sequences for diagnostic applications Nucleic Acids Res. 39, e29-e29
40. Sander, J., Zaback, P., Joung, J., Voytas, D., and Dobbs, D. (2009) An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins Nucleic Acids Res. 37, 506
41. Ben-Bassat, A., Bauer, K., Chang, S. Y., Myambo, K., Boosman, A., and Chang, S. (1987) Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure J. Bacteriol. 169, 751
42. Pabo, C. O., Peisach, E., and Grant, R. A. (2001) Design and selection of novel Cys2His2 zinc finger proteins Annu. Rev. Biochem. 70, 313-340 (Pubitemid 32662213)
43. Michael, S. F., Kilfoil, V. J., Schmidt, M. H., Amann, B. T., and Berg, J. M. (1992) Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide Proc. Natl. Acad. Sci. U.S.A. 89, 4796
44. Nyborg, J. K. and Peersen, O. B. (2004) That zincing feeling: the effects of EDTA on the behaviour of zinc-binding transcriptional regulators. Biochem. J. 381.
45. Hutchens, T. W., Allen, M. H., Li, C. M., and Yip, T. T. (1992) Occupancy of a C2-C2 type Zinc-fingerprotein domain by copper Direct observation by electrospray ionization mass spectrometry FEBS Lett. 309, 170-174
46. Predki, P. F. and Sarkar, B. (1994) Metal replacement in zinc finger and its effect on DNA binding Environ. Health Perspect. 102, 195
47. Carroll, D., Morton, J., Beumer, K., and Segal, D. (2006) Design, construction and in vitro testing of zinc finger nucleases Nat. Protocols 1, 1329-1341
48. Nurmemmedov, E. and Thunnissen, M. (2006) Expression, purification, and characterization of the 4 zinc finger region of human tumor suppressor WT1 Protein Express. Purif. 46, 379-389
49. 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, 16793
50. Lutz, J. F. (2008) Copper free azide-alkyne cycloadditions: new insights and perspectives Angew. Chem., Int. Ed. 47, 2182-2184
51. Ning, X., Guo, J., Wolfert, M., and Boons, G. (2008) Visualizing metabolically labeled glycoconjugates of living cells by copper free and fast huisgen cycloadditions Angew. Chem. 120, 2285-2287
52. Szabo, A., Stolz, L., and Granzow, R. (1995) Surface plasmon resonance and its use in biomolecular interaction analysis (BIA) Curr. Opin. Struct. Biol. 5, 699-705
53. Elf, J., Li, G. W., and Xie, X. S. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell Science 316, 1191