Zinc finger nucleases

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Zinc finger nucleases (ZFN) are artificially produced restriction enzymes . They contain a zinc finger domain that binds to DNA and a nuclease domain that cuts the DNA. The zinc finger domain can be built to recognize a specific sequence of DNA. This means that with ZFN you can cut a complex genome at a very specific point and thus enable the targeted incorporation of foreign DNA.

Nuclease domain

Zinc finger nucleases usually contain the unspecifically cutting nuclease domain of the type IIS restriction enzyme FokI . This restriction domain is only active when it is dimerized, which is why two differently constructed ZFN monomers are required to cut the target DNA sequence. In the case of standard ZFN, the restriction domain is bound to the DNA-binding zinc finger domain via its N-terminal end. In order for the nuclease domains to dimerize and cut, the two different ZFN monomers have to bind to the two different strands of the DNA, with their C-termini having to be at a certain distance from one another.

Several different protein engineering techniques are used to increase enzyme activity on the one hand and the affinity and specificity of the zinc finger domain on the other . For example, “ Directed Evolution ” was used to generate FokI variants that have increased nuclease activity. In addition, structural design was used to generate so-called "obligate-heterodimeric" FokI variants by exchanging charged amino acids in the dimerization interface of the nuclease domain, which have a significantly increased restriction specificity.

DNA binding domain

The DNA binding domain typically contains between three and six different zinc finger motifs , each individual zinc finger motif recognizing 3 bp. If the zinc finger domains bind perfectly to their recognition sequence, three zinc fingers per ZFN monomer are sufficient to specifically recognize a certain locus in a complex genome. Several different strategies have been developed to produce Cys 2 His 2 zinc fingers that bind to desired sequences. These methods include both the modular assembly (see below) and selection strategies, such as the phage display , the yeast-1 hybrid system , the bacterial one-hybrid system , the bacterial two-hybrid system or cellular selection systems.

The easiest way to create new zinc finger arrays is to combine zinc fingers with known specificity. The most popular modular assembly process is combining three different zinc fingers that each recognize 3 bp into a new zinc finger array that recognizes 9 bp. The main disadvantage of this method is that the specificity of a zinc finger can change depending on the neighboring zinc finger in the array, which is why "context-dependent" selection strategies usually produce zinc finger arrays with a higher specificity.

Applications

Zinc fingernucleases are useful for targeting the genomes of many plant and animal species , including the genomes of Arabidopsis , tobacco , soy , corn , fruit fly , roundworm , Platynereis dumerilii , sea ​​urchin , silkworm , zebrafish , frog , mouse , rat , rabbit , pig , Bovine and various types of mammalian cells. In addition, ZFN has been used in vivo in a mouse model of hemophilia , and a clinical study has shown that autologous CD4 -positive T cells with the CCR5 gene knocked out by zinc finger nucleases are safe to serve as a treatment for HIV / AIDS . As an alternative to zinc finger nucleases, Transcription Activator-like Effector Nucleases and the CRISPR / Cas method can be used.

Individual evidence

  1. ↑ T. Cathomen, JK Joung: Zinc-finger nucleases: the next generation emerges . In: Mol. Ther. . 16, No. 7, July 2008, pp. 1200-7. doi : 10.1038 / mt.2008.114 . PMID 18545224 .
  2. ↑ YG Kim, J. Cha, S. Chandrasegaran: Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain . In: Proc Natl Acad Sci USA . 93, No. 3, 1996, pp. 1156-60. doi : 10.1073 / pnas.93.3.1156 . PMID 8577732 . PMC 40048 (free full text).
  3. ↑ J. Bitinaite, DA Wah, AK Aggarwal, I. Schildkraut: FokI dimerization is required for DNA cleavage . In: Proc Natl Acad Sci USA . 95, No. 18, 1998, pp. 10570-5. doi : 10.1073 / pnas.95.18.10570 . PMID 9724744 . PMC 27935 (free full text).
  4. ↑ Eva-Maria Handel, Stephen Alwin, Toni Cathomen: Expanding or Restricting the Target Site Repertoire of Zinc-finger Nucleases: The Inter-domain Linker as a Major Determinant of Target Site Selectivity. In: Molecular Therapy. 17, 2008, pp. 104–111, doi : 10.1038 / mt.2008.233 .
  5. ↑ doi : 10.1016 / j.jmb.2010.04.060
  6. ↑ DOI: 10.1038 / nbt1317
  7. ↑ Jeffrey C Miller, Michael C Holmes et al. a .: An improved zinc-finger nuclease architecture for highly specific genome editing. In: Nature Biotechnology. 25, 2007, pp. 778-785, doi : 10.1038 / nbt1319 .
  8. ↑ Yannick Doyon, Thuy D Vo u. a .: Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. In: Nature Methods. 8, 2010, pp. 74-79, doi : 10.1038 / nmeth.1539 .
  9. ↑ DOI: 10.1016 / j.jmb.2010.10.043
  10. ↑ CO Pabo, E. Peisach, RA Grant: Design and Selection of Novel Cys2His2 Zinc Finger Proteins . In: Annu. Rev. Biochem. . 70, 2001, pp. 313-340. doi : 10.1146 / annurev.biochem.70.1.313 . PMID 11395410 .
  11. ↑ Cherie L Ramirez, Jonathan E Foley et al. a .: Unexpected failure rates for modular assembly of engineered zinc fingers. In: Nature Methods. 5, 2008, pp. 374-375, doi : 10.1038 / nmeth0508-374 .
  12. ↑ F. Zhang, ML Maeder, E. Unger-Wallace, JP Hoshaw, D. Reyon, M. Christian, X. Li, CJ Pierick, D. Dobbs, T. Peterson, JK Joung, DF Voytas: High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases . In: Proceedings of the National Academy of Sciences . 107, No. 26, 2010, pp. 12028-12033. doi : 10.1073 / pnas.0914991107 .
  13. ↑ K. Osakabe, Y. Osakabe, S. Toki: Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases . In: Proceedings of the National Academy of Sciences . 107, No. 26, 2010, pp. 12034-12039. doi : 10.1073 / pnas.1000234107 .
  14. ↑ CQ Cai, Y. Doyon, WM Ainley, JC Miller, RC Dekelver, EA Moehle, JM Rock, YL Lee, R. Garrison, L. Schulenberg, R. Blue, A. Worden, L. Baker, F. Faraji, L. Zhang, MC Holmes, EJ Rebar, TN Collingwood, B. Rubin-Wilson, PD Gregory, FD Urnov, JF Petolino: Targeted transgene integration in plant cells using designed zinc finger nucleases . In: Plant Molecular Biology . 69, No. 6, 2008, ISSN  0167-4412 , pp. 699-709. doi : 10.1007 / s11103-008-9449-7 . PMID 19112554 .
  15. ↑ JA Townsend, DA Wright, RJ Winfrey, F. Fu, ML Maeder, JK Joung, DF Voytas: High-frequency modification of plant genes using engineered zinc-finger nucleases . In: Nature . 459, No. 7245, 2009, pp. 442-445. bibcode : 2009Natur.459..442T . doi : 10.1038 / nature07845 . PMID 19404258 . PMC 2743854 (free full text).
  16. ^ SJ Curtin, F. Zhang, JD Sander, WJ Haun, C. Starker, NJ Baltes, D. Reyon, EJ Dahlborg, MJ Goodwin, AP Coffman, D. Dobbs, JK Joung, DF Voytas, RM Stupar: Targeted Mutagenesis of Duplicated Genes in Soybean with Zinc-Finger Nucleases . In: Plant Physiology . 156, No. 2, 2011, pp. 466-473. doi : 10.1104 / pp.111.172981 . PMID 21464476 . PMC 3177250 (free full text).
  17. ^ VK Shukla, Y. Doyon, JC Miller: Precise genome modification in the crop species Zea mays using zinc-finger nucleases . In: Nature . 459, No. 7245, May 2009, pp. 437-41. bibcode : 2009Natur.459..437S . doi : 10.1038 / nature07992 . PMID 19404259 .
  18. ↑ M. Bibikova, K. Beumer, J. Trautman, D. Carroll: Enhancing Gene Targeting with Designed Zinc Finger Nucleases . In: Science . 300, No. 5620, 2003, p. 764. doi : 10.1126 / science.1079512 . PMID 12730594 .
  19. ^ AJ Wood, T. -W. Lo, B. Zeitler, CS Pickle, EJ Ralston, AH Lee, R. Amora, JC Miller, E. Leung, X. Meng, L. Zhang, EJ Rebar, PD Gregory, FD Urnov, BJ Meyer: Targeted Genome Editing Across Species Using ZFNs and TALENs . In: Science . 333, No. 6040, 2011, p. 307. doi : 10.1126 / science.1207773 . PMID 21700836 . PMC 3489282 (free full text).
  20. ↑ Martin Gühmann, Huiyong Jia, Nadine Randel, Csaba Verasztó, Luis A. Bezares-Calderón, Nico K. Michiels, Shozo Yokoyama, Gáspár Jékely: Spectral Tuning of Phototaxis by a Go-Opsin in the Rhabdomeric Eyes of Platynereis . In: Current Biology . 25, No. 17, August 2015, pp. 2265–2271. doi : 10.1016 / j.cub.2015.07.017 .
  21. ↑ H. Ochiai, K. Fujita, KI Suzuki, M. Nishikawa, T. Shibata, N. Sakamoto, T. Yamamoto: Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases . In: Genes to Cells . 15, No. 8, 2010, p. No. Doi : 10.1111 / j.1365-2443.2010.01425.x . PMID 20604805 .
  22. ↑ Y. Takasu, I. Kobayashi, K. Beumer, K. Uchino, H. Sezutsu, S. Sajwan, D. Carroll, T. Tamura, M. Zurovec: Targeted mutagenesis in the silkworm Bombyx mori using zinc finger nuclease mRNA injection . In: Insect Biochemistry and Molecular Biology . 40, No. 10, 2010, pp. 759-765. doi : 10.1016 / j.ibmb.2010.07.012 . PMID 20692340 .
  23. ↑ SC Ekker: Zinc Finger-Based Knockout Punches for Zebrafish Genes . In: Zebrafish . 5, No. 2, 2008, pp. 1121-3. doi : 10.1089 / zeb.2008.9988 . PMID 18554175 . PMC 2849655 (free full text).
  24. ↑ JJ Young, JM Cherone, Y. Doyon, I. Ankoudinova, FM Faraji, AH Lee, C. Ngo, DY Guschin, DE Paschon, JC Miller, L. Zhang, EJ Rebar, PD Gregory, FD Urnov, RM Harland, B. Zeitler: Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases . In: Proceedings of the National Academy of Sciences . 108, No. 17, 2011, pp. 7052-7057. doi : 10.1073 / pnas.1102030108 .
  25. ↑ AD Goldberg, LA Banaszynski, KM Noh, PW Lewis, SJ Elsaesser, S. Stadler, S. Dewell, M. Law, X. Guo, X. Li, D. Wen, A. Chapgier, RC Dekelver, JC Miller, YL Lee, EA Boydston, MC Holmes, PD Gregory, JM Greally, S. Rafii, C. Yang, PJ Scambler, D. Garrick, RJ Gibbons, DR Higgs, IM Cristea, FD Urnov, D. Zheng, CD Allis: Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions . In: Cell . 140, No. 5, 2010, pp. 678-691. doi : 10.1016 / j.cell.2010.01.003 . PMID 20211137 . PMC 2885838 (free full text).
  26. ↑ AM Geurts, GJ Cost, Y. Freyvert, B. Zeitler, JC Miller, VM Choi, SS Jenkins, A. Wood, X. Cui, X. Meng, A. Vincent, S. Lam, M. Michalkiewicz, R. Schilling, J. Foeckler, S. Kalloway, H. Weiler, S. Menoret, I. Anegon, GD Davis, L. Zhang, EJ Rebar, PD Gregory, FD Urnov, HJ Jacob, R. Buelow: Knockout Rats via Embryo Microinjection of Zinc-Finger Nucleases . In: Science . 325, No. 5939, 2009, pp. 433-433. doi : 10.1126 / science.1172447 . PMID 19628861 . PMC 2831805 (free full text).
  27. ↑ T. Flisikowska, IS Thorey, S. Offner, F. Ros, V. Lifke, B. Zeitler, O. Rottmann, A. Vincent, L. Zhang, S. Jenkins, H. Niersbach, AJ Kind, PD Gregory, AE Schnieke, J. Platzer: Efficient Immunoglobulin Gene Disruption and Targeted Replacement in Rabbit Using Zinc Finger Nucleases . In: PLoS ONE . 6, No. 6, 2011, p. E21045. doi : 10.1371 / journal.pone.0021045 . PMID 21695153 . PMC 3113902 (free full text).
  28. ↑ J. Hauschild, B. Petersen, Y. Santiago, A. -L. Queisser, JW Carnwath, A. Lucas-Hahn, L. Zhang, X. Meng, PD Gregory, R. Schwinzer, GJ Cost, H. Niemann: Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases . In: Proceedings of the National Academy of Sciences . 108, No. 29, 2011, p. 12013. doi : 10.1073 / pnas.1106422108 .
  29. ↑ S. Yu, J. Luo, Z. Song, F. Ding, Y. Dai, N. Li: Highly efficient modification of beta-lactoglobulin (BLG) gene via zinc-finger nucleases in cattle . In: Cell Research . 2011. doi : 10.1038 / cr.2011.153 .
  30. ↑ D. Carroll : Zinc-finger Nucleases as Gene Therapy Agents . In: Gene Therapy . 15, No. 22, 2008, pp. 1463-1468. doi : 10.1038 / gt.2008.145 . PMID 18784746 . PMC 2747807 (free full text).
  31. ↑ H. Li, V. Haurigot, Y. Doyon, T. Li, SY Wong, AS Bhagwat, N. Malani, XM Anguela, R. Sharma, L. Ivanciu, SL Murphy, JD Finn, FR Khazi, S. Zhou , DE Paschon, EJ Rebar, FD Bushman, PD Gregory, MC Holmes, KA High: In vivo genome editing restores haemostasis in a mouse model of haemophilia . In: Nature . 475, No. 7355, 2011, pp. 217-221. doi : 10.1038 / nature10177 . PMID 21706032 . PMC 3152293 (free full text).
  32. ↑ Pablo Tebas, David Stein, Winson W. Tang, Ian Frank, Shelley Q. Wang, Gary Lee, S. Kaye Spratt, Richard T. Surosky, Martin A. Giedlin, Geoff Nichol, Michael C. Holmes, Philip D. Gregory , Dale G. Ando, ​​Michael Kalos, Ronald G. Collman, Gwendolyn Binder-Scholl, Gabriela Plesa, Wei-Ting Hwang, Bruce L. Levine, Carl H. June: Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV . In: New England Journal of Medicine . 370, No. 10, March 6, 2014, pp. 901-910. doi : 10.1056 / NEJMoa1300662 . PMID 24597865 .

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