Repeatable Construction Method for Engineered Zinc Finger Nuclease Based on Overlap Extension PCR and TA-Cloning

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Fujii, Wataru ^a   Kano, Kiyoshi ^b   Sugiura, Koji ^a   Naito, Kunihiko ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b YAMAGUCHI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 1B; DNA BINDING PROTEIN; GENOMIC DNA; INTERLEUKIN 2 RECEPTOR GAMMA; MESSENGER RNA; TRANSCRIPTION FACTOR GLI3; ZINC FINGER NUCLEASE; ZINC FINGER PROTEIN;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; CYCLIN DEPENDENT KINASE INHIBITOR 1B GENE; DNA HELIX; DNA SEQUENCE; EMBRYO; ENZYME ACTIVITY; ENZYME ENGINEERING; ENZYME STRUCTURE; FEMALE; GENE; GLI3 GENE; IN VITRO STUDY; INTERLEUKIN 2 RECEPTOR GAMMA GENE; MALE; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OVERLAP EXTENSION POLYMERASE CHAIN REACTION AND TA CLONING; PROTEIN DOMAIN; PROTEIN SYNTHESIS; ROSA26 GENE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS;

ANIMALS; CLONING, MOLECULAR; ENDONUCLEASES; FEMALE; GENE EXPRESSION; GENE ORDER; GENETIC VECTORS; MALE; MICE; MICE, TRANSGENIC; MUTAGENESIS, SITE-DIRECTED; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; ZINC FINGERS;

MUS;

EID: 84875409094     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059801     Document Type: Article

References (39)

1. Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, et al. (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res 33: 5978-5990.
2. Porteus MH, Carroll D, (2005) Gene targeting using zinc finger nucleases. Nat Biotechnol 23: 967-973.
3. Perez-Pinera P, Ousterout DG, Gersbach CA, (2012) Advances in targeted genome editing. Curr Opin Chem Biol 16: 268-277.
4. Meyer M, de Angelis MH, Wurst W, Kühn R, (2010) Gene targeting by homologous recombination in mouse zygotes mediated by zinc-finger nucleases. Proc Natl Acad Sci U S A 107: 15022-15026.
5. Hermann M, Maeder ML, Rector K, Ruiz J, Becher B, et al. (2012) Evaluation of OPEN zinc finger nucleases for direct gene targeting of the ROSA26 locus in mouse embryos. PLoS One 7: e41796.
6. Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, et al. (2009) Knockout rats via embryo microinjection of zinc-finger nucleases. Science 325: 433.
7. Hauschild J, Petersen B, Santiago Y, Queisser AL, Carnwath JW, et al. (2011) Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases. Proc Natl Acad Sci U S A 108: 12013-12017.
8. Young JJ, Cherone JM, Doyon Y, Ankoudinova I, Faraji FM, et al. (2011) Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases. Proc Natl Acad Sci U S A 108: 7052-7057.
9. Yu S, Luo J, Song Z, Ding F, Dai Y, et al. (2011) Highly efficient modification of beta-lactoglobulin (BLG) gene via zinc-finger nucleases in cattle. Cell Res 21: 1638-1640.
10. Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA, (2008) Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 26: 695-701.
11. Cai CQ, Doyon Y, Ainley WM, Miller JC, Dekelver RC, et al. (2008) Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol 69: 699-709.
12. Wood AJ, Lo TW, Zeitler B, Pickle CS, Ralston EJ, et al. (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333: 307.
13. Bibikova M, Beumer K, Trautman J, Carroll D, (2003) Enhancing Gene Targeting with Designed Zinc Finger Nucleases. Science 300: 764.
14. Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, et al. (2008) Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31: 294-301.
15. Miller JC, Holmes MC, Wang J, Guschin DY, Lee YL, et al. (2007) An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25: 778-785.
16. Carroll D, Morton JJ, Beumer KJ, Segal DJ, (2006) Design, construction and in vitro testing of zinc finger nucleases. Nat Protoc 1: 1329-1341.
17. Mackay JP, Segal DJ (2010) Engineered Zinc Finger Proteins. Humana Press: New York.
18. Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, et al. (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8: 67-69.
19. Gupta A, Christensen RG, Rayla AL, Lakshmanan A, Stormo GD, et al. (2012) An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 9: 588-590.
20. Mandell JG, Barbas CF 3rd (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res 34: W516-523.
21. Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, et al. (2009) Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res 37: D279-283.
22. Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, et al. (2010) ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res 38: W462-268.
23. Cradick TJ, Ambrosini G, Iseli C, Bucher P, McCaffrey AP, (2011) ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics 12: 152.
24. Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, et al. (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc 1: 1637-1652.
25. Gonzalez B, Schwimmer LJ, Fuller RP, Ye Y, Asawapornmongkol L, Barbas CF 3rd (2010) Modular system for the construction of zinc-finger libraries and proteins. Nat Protoc 5: 791-810.
26. Osborn MJ, DeFeo AP, Blazar BR, Tolar J, (2011) Synthetic zinc finger nuclease design and rapid assembly. Hum Gene Ther 22: 1155-1165.
27. Defrancesco L, (2011) Move over ZFNs. Nat Biotechnol 29: 681-684.
28. Perez-Pinera P, Ousterout DG, Brown MT, Gersbach CA, (2012) Gene targeting to the ROSA26 locus directed by engineered zinc finger nucleases. Nucleic Acids Res 240: 3741-3752.
29. Mashimo T, Takizawa A, Voigt B, Yoshimi K, Hiai H, et al. (2010) Generation of knockout rats with X-linked severe combined immunodeficiency (X-SCID) using zinc-finger nucleases. PLoS One 5: e8870.
30. Guo J, Gaj T, Barbas CF 3rd (2010) Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J Mol Biol 400: 96-107.
31. Sallés FJ, Strickland S, (1999) Analysis of poly(A) tail lengths by PCR: the PAT assay. Methods Mol Biol 118: 441-448.
32. Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO, (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure 4: 1171-1180.
33. Wolfe SA, Greisman HA, Ramm EI, Pabo CO, (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol 285: 1917-1934.
34. Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO, (2001) Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure 9: 717-723.
35. Naito K, Kagii H, Iwamori N, Sugiura K, Yamanouchi K, et al. (1999) Establishment of a small-scale Western blotting system named as "micro-Western blotting" for mammalian ova analysis. J Mamm Ova Res 16: 154-157.
36. Shimizu Y, Şöllü C, Meckler JF, Adriaenssens A, Zykovich A, et al. (2011) Adding fingers to an engineered zinc finger nuclease can reduce activity. Biochemistry 50: 5033-5041.
37. Bhakta MS, Henry IM, Ousterout DG, Das KT, Lockwood SH, et al. (2013) Highly active zinc-finger nucleases by extended modular assembly. Genome Res In press.
38. Radecke S, Radecke F, Cathomen T, Schwarz K, (2010) Zinc-finger nuclease-induced gene repair with oligodeoxynucleotides: wanted and unwanted target locus modifications. Mol Ther 18: 743-753.
39. Pattanayak V, Ramirez CL, Joung JK, Liu DR, (2011) Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods 8: 765-770.