Synthetic zinc finger nuclease design and rapid assembly

Human Gene Therapy

Volumn 22, Issue 9, 2011, Pages 1155-1165

  Osborn, Mark J ^a   Defeo, Anthony P ^a   Blazar, Bruce R ^a   Tolar, Jakub ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEVO IDURONIDASE; OLIGONUCLEOTIDE; ZINC FINGER PROTEIN;

ARTICLE; CHROMOSOME 4; COMPUTER MODEL; CONTROLLED STUDY; DRUG DESIGN; ENZYME ACTIVITY; GENE EXPRESSION SYSTEM; GENE LOCUS; GENE MUTATION; GENE TARGETING; HUMAN; HUMAN CELL; HURLER SYNDROME; SEQUENCE ANALYSIS;

BASE SEQUENCE; ENDONUCLEASES; ENZYME ACTIVATION; GENE TARGETING; HEK293 CELLS; HUMANS; IDURONIDASE; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; PROTEIN ENGINEERING; ZINC FINGERS;

EID: 80053032008     PISSN: 10430342     EISSN: 15577422     Source Type: Journal    
DOI: 10.1089/hum.2011.072     Document Type: Article

References (32)

1. Alwin, S., Gere, M.B., Guhl, E., et al. (2005). Custom zinc-finger nucleases for use in human cells. Mol. Ther. 12, 610-617. (Pubitemid 41350142)
2. Bhakta, M.S., and Segal, D.J. (2010). The generation of zinc finger proteins by modular assembly. Methods Mol. Biol. 649, 3-30.
3. Carroll, D., Morton, J.J., Beumer, K.J., and Segal, D.J. (2006). Design, construction and in vitro testing of zinc finger nucle-ases. Nat. Protoc. 1, 1329-1341.
4. Cermak, T., Doyle, E.L., Christian, M., et al. (2011). Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82.
5. Christian, M., Cermak, T., Doyle, E.L., et al. (2010). Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186, 757-761.
6. Cleary, M.A., and Wraith, J.E. (1995). The presenting features of mucopolysaccharidosis type IH (Hurler syndrome). Acta Paediatr. 84, 337-339.
7. Doyon, Y., Vo, T.D., Mendel, M.C., et al. (2011). Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat. Methods 8, 74-79.
8. Gibson, D.G., Smith, H.O., Hutchison, C.A., III, et al. (2011). Chemical synthesis of the mouse mitochondrial genome. Nat. Methods 7, 901-903.
9. Gibson, D.G., Young, L., Chuang, R.Y., et al. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345.
10. Guschin, D.Y., Waite, A.J., Katibah, G.E., et al. (2010). A rapid and general assay for monitoring endogenous gene modification. Methods Mol. Biol. 649, 247-256.
11. Handel, E.M., Alwin, S., and Cathomen, T. (2009). Expanding or restricting the target site repertoire of zinc-finger nucleases: The inter-domain linker as a major determinant of target site selectivity. Mol. Ther. 17, 104-111.
12. Kim, H.J., Lee, H.J., Kim, H., et al. (2009). Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res. 19, 1279-1288.
13. Kim, S., Lee, M.J., Kim, H., et al. (2011). Preassembled zinc-finger arrays for rapid construction of ZFNs. Nat. Methods 8, 7.
14. Maeder, M.L., Thibodeau-Beganny, S., Osiak, A., et al. (2008). Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol. Cell 31, 294-301. (Pubitemid 352001401)
15. Meng, X., Noyes, M.B., Zhu, L.J., et al. (2008). Targeted gene inactivation in zebrafish using engineered zinc-finger nucle-ases. Nat. Biotechnol. 26, 695-701. (Pubitemid 351809594)
16. Miller, J.C., Holmes, M.C., Wang, J., et al. (2007). An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778-785. (Pubitemid 47052191)
17. Miller, J.C., Tan, S., Qiao, G., et al. (2011). A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29, 143-148.
18. Muenzer, J., Wraith, J.E., and Clarke, L.A. (2009). Mucopoly- saccharidosis I: Management and treatment guidelines. Pediatrics 123, 19-29.
19. Orlando, S.J., Santiago, Y., Dekelver, R.C., et al. (2010). Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res. 38, e152.
20. Osborn, M.J., Panoskaltsis-Mortari, A., McElmurry, R.T., et al. (2005). A picornaviral 2A-like sequence-based tricistronic vector allowing for high-level therapeutic gene expression coupled to a dual-reporter system. Mol. Ther. 12, 569-574. (Pubitemid 41150144)
21. Porteus, M. (2010). Creating zinc finger nucleases using a modular-assembly approach. Cold Spring Harbor Protoc. 2010, pdb.prot5530.
22. Porteus, M.H., and Carroll, D. (2005). Gene targeting using zinc finger nucleases. Nat. Biotechnol. 23, 967-973. (Pubitemid 41114030)
23. Pruett-Miller, S.M., Connelly, J.P., Maeder, M.L., et al. (2008). Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol. Ther. 16, 707-717. (Pubitemid 351426172)
24. Ramirez, C.L., Foley, J.E., Wright, D.A., et al. (2008). Unexpected failure rates for modular assembly of engineered zinc fingers. Nat. Methods 5, 374-375. (Pubitemid 351619087)
25. Rasband, W.S. (1997-2011). ImageJ (U.S. National Institutes of Health, Bethesda, MD). Available at http://imagej.nih.gov/ij/(accessed June 2011).
26. Remy, S., Tesson, L., Menoret, S., et al. (2010). Zinc-finger nu-cleases: A powerful tool for genetic engineering of animals. Transgenic Res. 19, 363-371.
27. Sander, J.D., Dahlborg, E.J., Goodwin, M.J., et al. (2011). Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat. Methods 8, 67-69.
28. Sander, J.D., Zaback, P., Joung, J.K., et al. (2007). Zinc Finger Targeter (ZiFiT): An engineered zinc finger/target site design tool. Nucleic Acids Res. 35, W599-W605.
29. Voskarides, K., and Deltas, C. (2009). Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches. J. Mol. Diagn. 11, 311-318.
30. Xiong, A.S., Peng, R.H., Zhuang, J., et al. (2008). Chemical gene synthesis: Strategies, softwares, error corrections, and applications. FEMS Microbiol. Rev. 32, 522-540. (Pubitemid 351538748)
31. Zhang, F., Maeder, M.L., Unger-Wallace, E., et al. (2010). High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc. Natl. Acad. Sci. U.S.A. 107, 12028-12033.
32. Zou, J., Maeder, M.L., Mali, P., et al. (2009). Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 5, 97-110.