(Asterisks indicate publications with Consortium members as authors)

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.

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.

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