Cell-free selection of DNA-binding proteins for future gene therapy applications

Gene Therapy and Regulation

Volumn 3, Issue 1, 2007, Pages 51-63

  Sepp, Armin ^a   Ghadessy, Farid ^b   Choo, Yen ^c  

^a Institute of Molecular and Cell Biology ^*  (United Kingdom)

^b INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^c Plasticell Limited   (United Kingdom)

Author keywords

DNA polymerase; Emulsion; Expression; In vitro; Methyltransferase; Selection; Zinc finger

Indexed keywords

DNA BINDING PROTEIN; DNA POLYMERASE; METHYLTRANSFERASE; VASCULOTROPIN; VIRUS VECTOR; ZINC FINGER PROTEIN;

ANGIOGENESIS; CELL COMPARTMENTALIZATION; DNA BINDING; DNA RECOMBINATION; EMULSION; ENZYME ACTIVITY; GENE EXPRESSION; GENE SEGREGATION; GENE SEQUENCE; GENE SWITCHING; GENE THERAPY; GENETIC SELECTION; GENETIC TRANSCRIPTION; IN VITRO STUDY; PROTEIN ENGINEERING; PROTEIN EXPRESSION; REVIEW; RNA TRANSLATION; TRANSGENE;

EID: 33750282015     PISSN: 13889532     EISSN: 15685586     Source Type: Journal    
DOI: 10.1142/S156855860700006X     Document Type: Review

References (65)

1. Aharoni, A., Amitai, G., Bernath, K., et al. (2005). High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. Chem Biol, 12: 1281-1289.
2. Astatke, M., Ng, K., Grindley, N. D., et al. (1998). A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc Natl Acad Sci USA, 95: 3402-3407.
3. Beerli, R. R., Dreier, B. and Barbas, C. F., 3rd (2000a). Positive and negative regulation of endogenous genes by designed transcription factors. Proc Natl Acad Sci USA, 97: 1495-1500.
4. Beerli, R. R., Schopfer, U., Dreier, B., et al. (2000b). Chemically regulated zinc finger transcription factors. J Biol Chem, 275: 32617-32627.
5. Bernath, K., Hai, M., Mastrobattista, E., et al. (2004). In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Anal Biochem, 325: 151-157.
6. Bernath, K., Magdassi, S. and Tawfik, D. S. (2005). Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery. J Mol Biol, 345: 1015-1026.
7. Bertschinger, J. and Neri, D. (2004). Covalent DNA display as a novel tool for directed evolution of proteins in vitro. Protein Eng Des Sel, 17: 699-707.
8. Bushman, F. D. and Miller, M. D. (1997). Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites. J Virol, 71: 458-464.
9. Choo, Y. and Klug, A. (1994). Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc Natl Acad Sci USA, 91: 11163-11167.
10. Choo, Y. and Klug, A. (1995). Designing DNA-binding proteins on the surface of filamentous phage. Curr Opin Biotechnol, 6: 431-436.
11. Choo, Y. and Klug, A. (1997). Physical basis of a protein-DNA recognition code. Curr Opin Struct Biol, 7: 117-125.
12. Choo, Y., Sanchez-Garcia, I. and Klug, A. (1994). In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence. Nature, 372: 642-645.
13. Choo, Y., Castellanos, A., Garcia-Hernandez, B., et al. (1997). Promoter-specific activation of gene expression directed by bacteriophage- selected zinc fingers. J Mol Biol, 273: 525-532.
14. Cohen, H. M., Tawfik, D. S. and Griffiths, A. D. (2004). Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization. Protein Eng Des Sel, 17: 3-11.
15. Dai, Q., Huang, J., Klitzman, B., et al. (2004). Engineered zinc finger-activating vascular endothelial growth factor transcription factor plasmid DNA induces therapeutic angiogenesis in rabbits with hindlimb ischemia. Circulation, 110: 2467-2475.
16. Ghadessy, F. J. and Holliger, P. (2004). A novel emulsion mixture for in vitro compartmentalisation of transcription and translation in the rabbit reticulocyte system. Protein Eng Des Sel, 17: 201-204.
17. Ghadessy, F. J., Ong, J. L. and Holliger, P. (2001). Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA, 98: 4552-4557.
18. Ghadessy, F. J., Ramsay, N., Boudsocq, F., et al. (2004). Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol, 22: 755-759.
19. Goldsby, R. E., Lawrence, N. A., Hays, L. E., et al. (2001). Defective DNA polymerase-delta proofreading causes cancer susceptibility in mice. Nat Med, 7: 638-639.
20. Goodman, M. F. (2002). Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem, 71: 17-50.
21. Irving, R. A., Coia, G., Roberts, A., et al. (2001). Ribosome display and affinity maturation: from antibodies to single V-domains and steps towards cancer therapeutics. J Immunol Methods, 248: 31-45.
22. Isalan, M., Klug, A. and Choo, Y. (2001). A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat Biotechnol, 19: 656-560.
23. Jamieson, A. C., Kim, S. H. and Wells, J. A. (1994). In vitro selection of zinc fingers with altered DNA-binding specificity. Biochemistry, 33: 5689-5695.
24. Jamieson, A. C., Miller, J. C. and Pabo, C. O. (2003). Drug discovery with engineered zinc-finger proteins. Nat Rev Drug Discov, 2: 361-368.
25. Jestin, J. L., Kristensen, P. and Winter, G. (1999). A method for the selection of catalytic activity using phage display and proximity coupling. Angew. Chem. Int. Ed, 38: 1124-1127.
26. Joung, J. K., Ramm, E. I. and Pabo, C. O. (2000). A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci USA, 97: 7382-7387.
27. Kim, J. S. and Pabo, C. O. (1998). Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants. Proc Natl Acad Sci USA, 95: 2812-2817.
28. Kim, Y. G., Cha, J. and Chandrasegaran, S. (1996). Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain, Proc Natl Acad Sci USA, 93: 1156-1160.
29. Kim, Y. G., Shi, Y., Berg, J. M., et al. (1997). Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions. Gene, 203: 43-49.
30. Klug, A. (1995). Gene regulatory proteins and their interaction with DNA. Ann NY Acad Sci, 758: 143-160.
31. Kumar, R. (2004). 5-(1-Substituted) alkyl pyrimidine nucleosides as antiviral (herpes) agents. Curr Med Chem, 11: 2749-2766.
32. Lee, Y. F., Tawfik, D. S. and Griffiths, A. D. (2002). Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalisation. Nucleic Acids Res, 30: 4937-4944.
33. Li, Y., Mitaxov, V. and Waksman, G. (1999). Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc Natl Acad Sci USA, 96: 9491-9496.
34. Mastrobattista, E., Taly, V., Chanudet, E., et al. (2005). High-throughput screening of enzyme libraries: in vitro evolution of a beta-galactosidase by fluorescence-activated sorting of double emulsions. Chem Biol, 12: 1291-1300.
35. McNamara, A. R., Hurd, P. J., Smith, A. E., et al. (2002). Characterisation of site-biased DNA methyltransferases: specificity, affinity and subsite relationships. Nucleic Acids Res, 30: 3818-3830.
36. Miller, J., McLachlan, A. D. and Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Embo J, 4: 1609-1614.
37. Mitsuya, H., Yarchoan, R. and Broder, S. (1990). Molecular targets for AIDS therapy. Science, 249: 1533-1544.
38. Moore, M., Choo, Y. and Klug, A. (2001a). Design of polyzinc finger peptides with structured linkers. Proc Natl Acad Sci USA, 98: 1432-1436.
39. Moore, M., Klug, A. and Choo, Y. (2001b). Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proc Natl Acad Sci USA, 98: 1437-1441.
40. Munakata, T., Nakamura, M., Liang, Y., et al. (2005). Down-regulation of the retinoblastoma tumor suppressor by the hepatitis C virus NS5B RNA-dependent RNA polymerase. Proc Natl Acad Sci USA, 102: 18159-18164.
41. Nahon, E. and Raveh, D. (1998). Targeting a truncated Ho-endonuclease of yeast to novel DNA sites with foreign zinc fingers. Nucleic Acids Res, 26: 1233-1239.
42. Nardelli, J., Gibson, T. J., Vesque, C. and Charnay, P. (1991). Base sequence discrimination by zinc-finger DNA-binding domains. Nature, 349: 175-178.
43. Nishikura, K. (2001). A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst. Cell, 107: 415-418.
44. Papworth, M., Moore, M., Isalan, M., et al. (2003). Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors. Proc Natl Acad Sci USA, 100: 1621-1626.
45. Pollock, R., Giel, M., Linher, K., et al. (2002). Regulation of endogenous gene expression with a small-molecule dimerizer. Nat Biotechnol, 20: 729-733.
46. Pomerantz, J. L., Wolfe, S. A. and Pabo, C. O. (1998). Structure-based design of a dimeric zinc finger protein. Biochemistry, 37: 965-970.
47. Porteus, M. H. and Carroll, D. (2005). Gene targeting using zinc finger nucleases. Nature Biotechnol, 23: 967-973.
48. Rebar, E. J. and Pabo, C. O. (1994). Zinc finger phage: affinity selection of fingers with new DNA-binding specificities, Science, 263: 671-673.
49. Rebar, E. J., Huang, Y., Hickey, R., et al. (2002). Induction of angiogenesis in a mouse model using engineered transcription factors. Nat Med, 8: 1427-1432.
50. Reynolds, L., Ullman, C., Moore, M., et al. (2003). Repression of the HIV-1 5′ LTR promoter and inhibition of HIV-1 replication by using engineered zinc-finger transcription factors. Proc Natl Acad Sci USA, 100: 1615-1620.
51. Ryabova, L. A., Desplancq, D., Spirin, A. S., et al. (1997). Functional antibody production using cell-free translation: effects of protein disulfide isomerase and chaperones. Nat Biotechnol, 15: 79-84.
52. Sepp, A. and Choo, Y. (2005). Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization. J Mol Biol, 354: 212-219.
53. Sepp, A., Tawfik, D. S. and Griffiths, A. D. (2002). Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS Lett, 532: 455-458.
54. Sweasy, J. B. and Loeb, L. A. (1993). Detection and characterization of mammalian DNA polymerase beta mutants by functional complementation in Escherichia coli. Proc Natl Acad Sci USA, 90: 4626-4630.
55. Tan, S., Guschin, D., Davalos, A., et al. (2003). Zinc-finger protein-targeted gene regulation: genomewide single-gene specificity. Proc Natl Acad Sci USA, 100: 11997-12002.
56. Tan, W., Zhu, K., Segal, D. J., et al. (2004). Fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc finger protein E2C direct integration of viral DNA into specific sites. J Virol, 78: 1301-1313.
57. Tawfik, D. S. and Griffiths, A. D. (1998). Man-made cell-like compartments for molecular evolution. Nat Biotechnol, 16: 652-656.
58. Urnov, F. D., Miller, J. C., Lee, Y. L., et al. (2005). Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature, 435: 646-651.
59. Wang, B. S. and Pabo, C. O. (1999). Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences. Proc Natl Acad Sci USA, 96: 9568-9573.
60. Wolfe, S. A., Ramm, E. I. and Pabo, C. O. (2000). Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers. Structure, 8: 739-750.
61. Xia, G., Chen, L., Sera, T., et al. (2002). Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc Natl Acad Sci USA, 99: 6597-6602.
62. Xu, Z., Fulop, Z., Zhong, Y., et al. (2005). DNA lesions and repair in immunoglobulin class switch recombination and somatic hypermutation. Ann NY Acad Sci, 1050: 146-162.
63. Yonezawa, M., Doi, N., Kawahashi, Y., et al. (2003). DNA display for in vitro selection of diverse peptide libraries. Nucleic Acids Res, 31: E118.
64. Yu, J., Lei, L., Liang, Y., et al. (2006). An engineered VEGF-activating zinc finger protein transcription factor improves blood flow and limb salvage in advanced-age mice. Faseb J, 20: 479-481.
65. Zhang, L., Spratt, S. K., Liu, Q., et al. (2000). Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene. J Biol Chem, 275: 33850-33860.