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Bipartite Selection of Zinc Fingers by Phage Display for Any 9-bp DNA Target Site

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Engineered Zinc Finger Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 649))

Abstract

Phage display has been used to engineer DNA-binding proteins with new sequence specificities, which has allowed applications in the blockage or enhancement of gene expression as well as targeting specific sites on DNA for methylation, recombination, and cleavage. To effectively and quickly conduct selections that consider the synergistic mode of DNA binding by zinc fingers, Isalan and Choo in Aaron Klug’s lab devised a bipartite phage display approach that enables selection and recombination of variants of zinc finger DNA-binding domains from a pair of premade complementary phage libraries for any given 9-bp DNA sequence. The bipartite phage display has the advantage of rapid, high-throughput selection of sequence-specific zinc finger DNA-binding domains for use in diverse applications of expression control and gene targeting.

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References

  1. 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.

    Article  PubMed  CAS  Google Scholar 

  2. Rebar, E.J. and Pabo, C.O. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science. 263, 671–673.

    Article  PubMed  CAS  Google Scholar 

  3. 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.

    Article  PubMed  CAS  Google Scholar 

  4. Choo, Y. and Klug, A. (1995) Designing DNA-binding proteins on the surface of filamentous phage. Curr Opin Biotechnol. 6, 431–436.

    Article  PubMed  CAS  Google Scholar 

  5. Choo, Y. and Klug, A. (1994) Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA. 91, 11168–11172.

    Article  PubMed  CAS  Google Scholar 

  6. Rebar, E.J., Greisman, H.A., and Pabo, C.O. (1996) Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities. Methods Enzymol. 267, 129–149.

    Article  PubMed  CAS  Google Scholar 

  7. Wu, H., Yang, W.P., and Barbas, C.F., III (1995) Building zinc fingers by selection: toward a therapeutic application. Proc Natl Acad Sci USA. 92, 344–348.

    Article  PubMed  CAS  Google Scholar 

  8. Klug, A. (1999) Zinc finger peptides for the regulation of gene expression. J Mol Biol. 293, 215–218.

    Article  PubMed  CAS  Google Scholar 

  9. Greisman, H.A. and Pabo, C.O. (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science. 275, 657–661.

    Article  PubMed  CAS  Google Scholar 

  10. Bartsevich, V.V., Miller, J.C., Case, C.C., and Pabo, C.O. (2003) Engineered zinc finger proteins for controlling stem cell fate. Stem Cells. 21, 632–637.

    Article  PubMed  CAS  Google Scholar 

  11. Bibikova, M., Beumer, K., Trautman, J.K., and Carroll, D. (2003) Enhancing gene targeting with designed zinc finger nucleases. Science. 300, 764.

    Article  PubMed  CAS  Google Scholar 

  12. Dai, Q., Huang, J., Klitzman, B., Dong, C., Goldschmidt-Clermont, P.J., March, K.L., Rokovich, J., Johnstone, B., Rebar, E.J., Spratt, S.K., Case, C.C., Kontos, C.D., and Annex, B.H. (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.

    Article  PubMed  CAS  Google Scholar 

  13. Papworth, M., Moore, M., Isalan, M., Minczuk, M., Choo, Y., and Klug, A. (2003) Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors. Proc Natl Acad Sci USA. 100, 1621–1626.

    Article  PubMed  CAS  Google Scholar 

  14. Reynolds, L., Ullman, C., Moore, M., Isalan, M., West, M.J., Clapham, P., Klug, A., and Choo, Y. (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.

    Article  PubMed  CAS  Google Scholar 

  15. Shieh, J.C., Cheng, Y.C., Su, M.C., Moore, M., Choo, Y., and Klug, A. (2007) Tailor-made zinc-finger transcription factors activate FLO11 gene expression with phenotypic consequences in the yeast Saccharomyces cerevisiae. PLoS ONE. 2(8), e746.

    Article  PubMed  Google Scholar 

  16. Tan, W., Zhu, K., Segal, D.J., Barbas, C.F., III, and Chow, S.A. (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.

    Article  PubMed  CAS  Google Scholar 

  17. Li, F., Papworth, M., Minczuk, M., Rohde, C., Zhang, Y., Ragozin, S., and Jeltsch, A. (2007) Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res. 35, 100–112.

    Article  PubMed  Google Scholar 

  18. McCafferty, J., Griffiths, A.D., Winter, G., and Chiswell, D.J. (1990) Phage antibodies: filamentous phage displaying antibody variable domains. Nature. 348, 552–554.

    Article  PubMed  CAS  Google Scholar 

  19. Smith, G.P. (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 228, 1315–1317.

    Article  PubMed  CAS  Google Scholar 

  20. 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, 656–660.

    Article  PubMed  CAS  Google Scholar 

  21. Beerli, R.R. and Barbas, C.F., III (2002) Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol. 20, 135–141.

    Article  PubMed  CAS  Google Scholar 

  22. Segal, D.J. and Barbas, C.F., III (2000) Design of novel sequence-specific DNA-binding proteins. Curr Opin Chem Biol. 4, 34–39.

    Article  PubMed  CAS  Google Scholar 

  23. Wolfe, S.A., Greisman, H.A., Ramm, E.I., and Pabo, C.O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol. 285, 1917–1934.

    Article  PubMed  CAS  Google Scholar 

  24. Minczuk, M., Papworth, M.A., Kolasinska, P., Murphy, M.P., and Klug, A. (2006) Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase. Proc Natl Acad Sci USA. 103, 19689–19694.

    Article  PubMed  CAS  Google Scholar 

  25. Minczuk, M., Papworth, M.A., Miller, J.C., Murphy, M.P., and Klug, A. (2008) Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA. Nucleic Acids Res. 36, 3926–3938.

    Article  PubMed  CAS  Google Scholar 

  26. Isalan, M., Klug, A., and Choo, Y. (1998) Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry. 37, 12026–12033.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The author thanks Professor Aaron Klug for giving me the opportunity to work on zinc fingers with the yeast model of my choice and for his advice. The author is also indebted to colleagues in Aaron’s lab at the MRC-Laboratory of Molecular Biology, particularly Yen Choo and Mark Isalan who have originally developed the method of bipartite phage display, and most of materials and methods are directly derived from their work. This work is supported by the Medical Research Council of the United Kingdom and a grant from National Science Council (NSC92-2311-B-040-007) of the Republic of China.

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Authors and Affiliations

  1. Department of Biomedical Sciences, Chung Shan Medical University, Taichung City, Taiwan

    Jia-Ching Shieh

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  1. Jia-Ching Shieh
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Editors and Affiliations

  1. School of Molecular &, Microbial Biosciences, University of Sydney, Cnr. Butlin Ave. & Maze Cres., Sydney, 2006, New South Wales, Australia

    Joel P. Mackay

  2. Dept. Pharmacology & Genome Center, University of California, Davis, E. Health Sciences Drive 451, Davis, 95616, California, USA

    David J. Segal

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Shieh, JC. (2010). Bipartite Selection of Zinc Fingers by Phage Display for Any 9-bp DNA Target Site. In: Mackay, J., Segal, D. (eds) Engineered Zinc Finger Proteins. Methods in Molecular Biology, vol 649. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-753-2_3

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  • DOI: https://doi.org/10.1007/978-1-60761-753-2_3

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-752-5

  • Online ISBN: 978-1-60761-753-2

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