Generation and functional analysis of zinc finger nucleases

Methods in Molecular Biology

Volumn 434, Issue , 2008, Pages 277-290

  Cathomen, Toni ^a   Segal, David J ^a   Brondani, Vincent ^a   Müller Lerch, Felix ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

Artificial nuclease; Custom nuclease; DNA double strand break; DSB; Homologous recombination; HR; ZFN

Indexed keywords

EID: 84934444590     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-248-3_17     Document Type: Article

References (29)

1. Vasquez, K. M., Marburger, K., Intody, Z., and Wilson, J. H. (2001) Manipulating the mammalian genome by homologous recombination. Proc Natl Acad Sci USA 98:8403-8410.
2. Urnov, F. D., Miller, J. C., Lee, Y. L., Beausejour, C. M., Rock, J. M., Augustus, S., Jamieson, A. C., Porteus, M. H., Gregory, P. D., and Holmes, M. C. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646-651.
3. Porteus, M. H. (2006) Mammalian gene targeting with designed zinc finger nucleases. Mol Ther 13:438-446.
4. Porteus, M. H. and Baltimore, D. (2003) Chimeric nucleases stimulate gene targeting in human cells. Science 300:763.
5. Alwin, S., Gere, M. B., Guhl, E., Effertz, K., Barbas, C. F., 3rd, Segal, D. J., Weitzman, M. D., and Cathomen, T. (2005) Custom zinc-finger nucleases for use in human cells. Mol Ther 12:610-617.
6. Beumer, K., Bhattacharyya, G., Bibikova, M., Trautman, J. K., and Carroll, D. (2006) Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics 172:2391-2403.
7. Wright, D. A., Townsend, J. A., Winfrey, R. J., Jr., Irwin, P. A., Rajagopal, J., Lonosky, P. M., Hall, B. D., Jondle, M. D., and Voytas, D. F. (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J 44:693-705.
8. Kim, Y. G., Cha, J., and Chandrasegaran, S. (1996) Hybrid restriction enzymes: zinc finger fusions to FokI cleavage domain. Proc Natl Acad Sci USA 93: 1156-1160.
9. Durai, S., Mani, M., Kandavelou, K., Wu, J., Porteus, M. H., and Chandrasegaran, S. (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res 33:5978-5990.
10. Pavletich, N. P. and Pabo, C. O. (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252:809-817.
11. Rebar, E. J. and Pabo, C. O. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263:671-673.
12. 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.
13. Jamieson, A. C., Wang, H., and Kim, S. H. (1996) A zinc finger directory for high-affinity DNA recognition. Proc Natl Acad Sci USA 93:12834-12839.
14. Wu, H., Yang, W. P., and Barbas, C. F., 3rd. (1995) Building zinc fingers by selection: toward a therapeutic application. Proc Natl Acad Sci USA 92: 344-348.
15. Liu, Q., Xia, Z., Zhong, X., and Case, C. C. (2002) Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J Biol Chem 277: 3850-3856.
16. Segal, D. J., Dreier, B., Beerli, R. R., and Barbas, C. F., 3rd. (1999) Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. Proc Natl Acad Sci USA 96:2758-2763.
17. Dreier, B., Beerli, R. R., Segal, D. J., Flippin, J. D., and Barbas, C. F., 3rd. (2001) Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 276:29466-29478.
18. Dreier, B., Fuller, R. P., Segal, D. J., Lund, C. V., Biancafort, P., Huber, A., Koksch, B., and Barbas, C. F., 3rd. (2005) Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 280:35588-35597.
19. Biancafort, P., Magnenat, L., and Barbas, C. F., 3rd. (2003) Scanning the human genome with combinatorial transcription factor libraries. Nat Biotechnol 21: 269-274.
20. Smith, J., Bibikova, M., Whitby, F. G., Reddy, A. R., Chandrasegaran, S., and Carroll, D. (2000) Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 28: 3361-3369.
21. Bitinaite, J., Wah, D. A., Aggarwal, A. K., and Schildkraut, I. (1998) Fokl dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95:10570-10575.
22. Bibikova, M., Carroll, D., Segal, D. J., Trautman, J. K., Smith, J., Kim, Y. G., and Chandrasegaran, S. (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21:289-297.
23. Mandell, J. G. and Barbas, C. F., 3rd. (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res 34:W516-523.
24. 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.
25. 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.
26. Cheng, X., Boyer, J. L., and Juliano, R. L. (1997) Selection of peptides that functionally replace a zinc finger in the SpI transcription factor by using a yeast combinatorial library. Proc Natl Acad Sci USA 94:14120-14125.
27. Hughes, M. D., Zhang, Z. R., Sutherland, A. J., Santos, A. F., and Hine, A. V. (2005) Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins. Nucleic Acids Res 33:e32.
28. Hurt, J. A., Thibodeau, S. A., Hirsh, A. S., Pabo, C. O., and Joung, J. K. (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100:12271-12276.
29. Radecke, F., Peter, I., Radecke, S., Gellhaus, K., Schwarz, K., and Cathomen, T. (2006) Targeted chromosomal gene modification in human cells by single-stranded oligodeoxynucleotides in the presence of a DNA double-strand break. Mol Ther 14:798-808.