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Zinc Finger Engineering

Bae, K. H., Do Kwon, Y., Shin, H. C., Hwang, M. S., Ryu, E. H., Park, K. S., Yang, H. Y., Lee, D. K., Lee, Y., Park, J., Sun Kwon, H., Kim, H. W., Yeh, B. I., Lee, H. W., Hyung Sohn, S., Yoon, J., Seol, W. & Kim, J. S. (2003) Human zinc fingers as building blocks in the construction of artificial transcription factors Nat Biotechnol 21, 275-80.

Bae, K.H. & Kim, J. S. (2006) One-step selection of artificial transcription factors using an in vivo screening system Mol Cells 21: 376-380.

Beerli, R. R. & Barbas, C. F., 3rd (2002) Engineering polydactyl zinc-finger transcription factors Nat Biotechnol 20, 135-41.

Beerli, R. R., Segal, D. J., Dreier, B. & Barbas, C. F., 3rd (1998) Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks Proc Natl Acad Sci U S A 95, 14628-33.

Carroll D., Morton, J. J., Beumer, K. J. & Segal, D. J. (2006) Design, construction and in vitro testing of zinc finger nucleases Nature Protocols 1: 1329-1341.

Choo, Y. & Klug, A. (1994) Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions Proc Natl Acad Sci U S A 91, 11168-72.

Choo, Y. & 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 U S A 91, 11163-7.

Dreier, B., Beerli, R. R., Segal, D. J., Flippin, J. D. & 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, 29466-78.

Dreier, B., Fuller, R. P., Segal, D. J., Lund, C., Blancafort, P., Huber, A., Koksch, B. & 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.

Dreier, B., Segal, D. J. & Barbas, C. F., 3rd (2000) Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains J Mol Biol 303, 489-502.

Elrod-Erickson, M., Benson, T. E. & Pabo, C. O. (1998) High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition Structure 6, 451-64.

Elrod-Erickson, M. & Pabo, C. O. (1999) Binding studies with mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the Zif268 zinc finger-DNA complex J Biol Chem 274, 19281-5.

Elrod-Erickson, M., Rould, M. A., Nekludova, L. & Pabo, C. O. (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions Structure 4, 1171-80.

Greisman, H. A. & Pabo, C. O. (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites Science 275, 657-61.

Hurt, J. A., Thibodeau, S. A., Hirsh, A. S., Pabo, C. O. & Joung, J. K. (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection Proc Natl Acad Sci U S A 100, 12271-6.

Isalan, M., Choo, Y. & Klug, A. (1997) Synergy between adjacent zinc fingers in sequence-specific DNA recognition Proc Natl Acad Sci U S A 94, 5617-21.

Isalan, M., Klug, A. & Choo, Y. (2001) A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter Nat Biotechnol 19, 656-60.

Isalan, M., Klug, A. & Choo, Y. (1998) Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers Biochemistry 37, 12026-33.

Jamieson, A. C., Miller, J. C. & Pabo, C. O. (2003) Drug Discovery with Engineered Zinc-Finger Proteins Nature Reviews Drug Discovery 2, 361-368.

Jantz, D., Amann, B. T., Gatto, G. J., Jr. & Berg, J. M. (2004) The design of functional DNA-binding proteins based on zinc finger domains Chem Rev 104, 789-99.

Joung, J. K., Ramm, E. I. & Pabo, C. O. (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions Proc Natl Acad Sci U S A 97, 7382-7.

Lee, D. K., Seol, W. & Kim, J. S. (2003) Custom DNA-Binding Proteins and Artificial Transcription Factors Curr Top Med Chem 3, 645-57.

Liu, Q., Segal, D. J., Ghiara, J. B. & Barbas, C. F., 3rd (1997) Design of polydactyl zinc-finger proteins for unique addressing within complex genomes Proc Natl Acad Sci U S A 94, 5525-30.

Liu, Q., Xia, Z., Zhong, X. & Case, C. C. (2002) Validated zinc finger protein designs for all 16 GNN DNA triplet targets J Biol Chem 277, 3850-6.

Maeder, M. L., Thibodeau-Beganny, S., Osiak, A., Wright, D. A., Anthony, R. M., Eichtinger, M., Jiang, T., Foley, J. E., Winfrey, R. J., Townsend, J. A., Unger-Wallace, E., Sander, J. D., Müller-Lerch, F., Fu, F., Pearlberg, J., Göbel, C., Dassie, J. P., Pruett-Miller, S. M., Porteus, M. H., Sgroi, D. C., Iafrate, A. J., Dobbs, D., McCray, P. B., Cathomen, T., Voytas, D. F., and Joung, J. K. (2008). Rapid "Open-Source" Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification. Mol. Cell. 2008; 31: 294-301.

Meng, X., Thibodeau-Beganny, S., Jiang, T., Joung, J.K., & Wolfe, S.A. (2007) Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method Nucleic Acids Res 35, e81.

Moore, M., Klug, A. & Choo, Y. (2001) Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units Proc Natl Acad Sci U S A 98, 1437-41.

Pabo, C. O., Peisach, E. & Grant, R. A. (2001) Design and selection of novel Cys2His2 zinc finger proteins Annu Rev Biochem 70, 313-40.

Pavletich, N. P. & Pabo, C. O. (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A Science 252, 809-17.

Rebar, E. J., Greisman, H. A. & Pabo, C. O. (1996) Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities Methods Enzymol 267, 129-49.

Rebar, E. J. & Pabo, C. O. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities Science 263, 671-3.

Segal, D. J., Crotty, J. W., Bhakta, M. S., Barbas, C. F., 3rd & Horton, N. C. (2006) Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA J Mol Biol. 363, 405-421.

Segal, D. J., Dreier, B., Beerli, R. R. & 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 U S A 96, 2758-63.

Thibodeau-Beganny, S., and Joung, J. K. (2007). Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system. Methods Mol Biol 408, 317-334.

Wolfe, S. A., Grant, R. A., Elrod-Erickson, M. & Pabo, C. O. (2001) Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes Structure (Camb) 9, 717-23.

Wolfe, S. A., Greisman, H. A., Ramm, E. I. & Pabo, C. O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code J Mol Biol 285, 1917-34.

Wolfe, S. A., Nekludova, L. & Pabo, C. O. (2000) DNA recognition by Cys2His2 zinc finger proteins Annu Rev Biophys Biomol Struct 29, 183-212.

Wright, D. A., Thibodeau-Beganny, S., Sander, J. D., Winfrey, R. J., Hirsh, A. S., Eichtinger, M., Fu, F., Porteus, M. H., Dobbs, D., Voytas, D. F. & Joung, J. K. (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly Nature Protocols 1, 1637-1652.

Wu, H., Yang, W. P. & Barbas, C. F., 3rd (1995) Building zinc fingers by selection: toward a therapeutic application Proc Natl Acad Sci U S A 92, 344-8.

Zinc Finger Nucleases

Alwin, S., Gere, M. B., Guhl, E., Effertz, K., Barbas, C. F., 3rd, Segal, D. J., Weitzman, M. D. & Cathomen, T. (2005) Custom Zinc-Finger Nucleases for Use in Human Cells Mol Ther, 12, 610-617.

Beumer, K., Bhattacharyya, G., Bibikova, M., Trautman, J.K. & Carroll, D. (2006) Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics 172, 2391-2403.

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

Bibikova, M., Carroll, D., Segal, D. J., Trautman, J. K., Smith, J., Kim, Y. G. & Chandrasegaran, S. (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases Mol Cell Biol 21, 289-97.

Bibikova, M., Golic, M., Golic, K. G. & Carroll, D. (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases Genetics 161, 1169-75.

Carroll, D. (2004) Using nucleases to stimulate homologous recombination Methods Mol Biol 262, 195-207.

Cathomen, T., and Joung, J. K. (2008). Zinc-finger nucleases: the next generation emerges. Mol Ther 16, 1200-1207.

Chandrasegaran, S. & Smith, J. (1999) Chimeric restriction enzymes: what is next? Biol Chem 380, 841-8.

Cornu, T.I., Thibodeau-Beganny, S., Guhl, E., Alwin, S., Eichtinger, M., Joung, J.K., & Cathomen, T. (2008)DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases. Mol Ther 16, 352-358.

Doyon, Y., McCammon, J. M., Miller, J. C., Faraji, F., Ngo, C., Katibah, G. E., Amora, R., Hocking, T. D., Zhang, L., Rebar, E. J., et al. (2008). Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat Biotechnol 26, 702-708.

Durai, S., Mani, M., Kandavelou, K., Wu, J., Porteus, M. H. & Chandrasegaran, S. (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells Nucleic Acids Res 33, 5978-90.

Hirsh AS, Joung JK Designer zinc finger proteins for gene therapy: progress and challenges. Gene Therapy and Regulation, 2004, 2: 191-206.

Kim, Y. G., Cha, J. & Chandrasegaran, S. (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain Proc Natl Acad Sci U S A 93, 1156-60.

Lloyd, A., Plaisier, C.L., Carroll, D., Drews, G.N. (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci U S A 102, 2232-2237.

Lombardo, A. et al. (2007) Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 25, 1298-1306.

Meng, X., Noyes, M. B., Zhu, L. J., Lawson, N. D., and Wolfe, S. A. (2008). Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 26, 695-701.

Miller, J.C., Holmes, M.C., Wang, J., Guschin, D.Y., Lee, Y.L., Rupniewski, I., Beausejour, C.M., Waite, A.J., Wang, N.S., Kim, K.A., Gregory, P.D., Pabo, C.O., & Rebar, E.J. (2007) An improved zinc-finger nuclease architecture for highly specific genome editing, Nat Biotechnol 25, 778-785.

Moehle, E.A. et al. (2007) Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci U S A 104, 3055-3060.

Morton, J., Davis, M.W., Jorgensen, E.M., Carroll, D. (2006) Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc Natl Acad Sci U S A 103, 16370-16375.

Perez, E. E., Wang, J., Miller, J. C., Jouvenot, Y., Kim, K. A., Liu, O., Wang, N., Lee, G., Bartsevich, V. V., Lee, Y. L., et al. (2008). Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26, 808-816.

Porteus, M. H. & Baltimore, D. (2003) Chimeric nucleases stimulate gene targeting in human cells Science 300, 763.

Porteus, M. H., Cathomen, T., Weitzman, M. D. & Baltimore, D. (2003) Efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks Mol Cell Biol 23, 3558-65.

Porteus, M. H. (2006) Mammalian gene targeting with designed zinc finger nucleases Mol Ther, 13, 438-446.

Porteus, M. H. & Carroll, D. (2005) Gene targeting using zinc finger nucleases Nat Biotechnol 23, 967-73.

Pruett-Miller, S.M., Connelly, J.P., Maeder, M.L., Joung, J.K. & Porteus, M.H. (2008) Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol Ther 16, 707-717.

Ramirez, C.L., Foley, J.E., Wright, D.A., Müller-Lerch, F., Rahman, S.H., Cornu, T.I., Winfrey, R.J., Sander, J.D., Fu, F., Townsend, J.A., Cathomen, T., Voytas, D.F., & Joung, J.K. (2008) Unexpected failure rates for modular assembly of engineered zinc-fingers. Nat Methods 5, 374-375.

Sander, J.D., Zaback, P., Joung, J.K., Voytas, D.F. & Dobbs, D. (2007) Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res 35, W599-605.

Santiago, Y. et al. (2008) Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci U S A 105, 5809-5814.

Scott, C. T. (2005) The zinc finger nuclease monopoly Nat Biotechnol 23, 915-8

Smith, J., Berg, J. M. & Chandrasegaran, S. (1999) A detailed study of the substrate specificity of a chimeric restriction enzyme Nucleic Acids Res 27, 674-81.

Smith, J., Bibikova, M., Whitby, F. G., Reddy, A. R., Chandrasegaran, S. & Carroll, D. (2000) Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains Nucleic Acids Res 28, 3361-9.

Szczepek, M., Brondani, V., Büchel, J., Serrano, L., Segal, D.J., & Cathomen, T. (2007) Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases Nat Biotechnol 25: 786-793.

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. & Holmes, M. C. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases Nature 435, 646-51.

Wright, D. A., Townsend, J. A., Winfrey, R. J., Jr., Irwin, P. A., Rajagopal, J., Lonosky, P. M., Hall, B. D., Jondle, M. D. & Voytas, D. F. (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases Plant J 44, 693-705.