References
- Amberger, J., C. A. Bocchini, A. F. Scott, and A. Hamosh (2009) McKusick's Online Mendelian inheritance in man (OMIM(R)). Nucl. Acids Res. 37: D793-796. https://doi.org/10.1093/nar/gkn665
- O'Connor, T. P. and R. G. Crystal (2006) Genetic medicines: treatment strategies for hereditary disorders. Nat. Rev. Genet. 7: 261-276. https://doi.org/10.1038/nrg1829
- Capecchi, M. R. (1989) The new mouse genetics: Altering the genome by gene targeting. Trends Genet. 5: 70-76. https://doi.org/10.1016/0168-9525(89)90029-2
- Aiuti, A., S. Slavin, M. Aker, F. Ficara, S. Deola, A. Mortellaro, S. Morecki, G. Andolfi, A. Tabucchi, F. Carlucci, E. Marinello, F. Cattaneo, S. Vai, P. Servida, R. Miniero, M. G. Roncarolo, and C. Bordignon (2002) Correction of ADA-SCID by stem cell gene therapy combined with nonmyeloablative conditioning. Science. 296: 2410-2413. https://doi.org/10.1126/science.1070104
- Gaspar, H. B., K. L. Parsley, S. Howe, D. King, K. C. Gilmour, J. Sinclair, G. Brouns, M. Schmidt, C. Von Kalle, T. Barington, M. A. Jakobsen, H. O. Christensen, A. Al Ghonaium, H. N. White, J. L. Smith, R. J. Levinsky, R. R. Ali, C. Kinnon, and A. J. Thrasher (2004) Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector. Lancet. 364: 2181-2187. https://doi.org/10.1016/S0140-6736(04)17590-9
- Abbott, A. (2006) Questions linger about unexplained gene-therapy trial death. Nat. Med. 12: 597.
- Capecchi, M. R. (2001) Generating mice with targeted mutations. Nat. Med. 7: 1086-1090. https://doi.org/10.1038/nm1001-1086
- Smithies, O. (2001) Forty years with homologous recombination. Nat. Med. 7: 1083-1086. https://doi.org/10.1038/nm1001-1083
- Sedivy, J. M. and A. Dutriaux (1999) Gene targeting and somatic cell genetics: a rebirth or a coming of age? Trends Genet. 15: 88-90. https://doi.org/10.1016/S0168-9525(98)01689-8
- Friedhoff, P. and A. Pingoud (2007) Engineering Sitespecific Endonucleases. pp. 111-123 In: Arndt, K. M., and Kristian M. Müller (eds). Protein Engineering Protocols. Humana Press, Totowa, New Jersey.
- Albert Cotton F., E. E. H., Jr., and Margaret J. Legg (1979) Staphylococcal nuclease: Proposed mechanism of action based on structure of enzyme-thymidine 3′, 5′-bisphosphate-calcium ion complex at 1.5-A resolution. Proc. Natl. Acad. Sci. USA. 76: 2551-2555. https://doi.org/10.1073/pnas.76.6.2551
- Pei, D. and P. G. Schultz (1990) Site-specific cleavage of duplex DNA with a lambda. repressor-staphylococcal nuclease hybrid. J. Am. Chem. Soc. 112: 4579-4580. https://doi.org/10.1021/ja00167a085
- Chan, S.-h., Y. Bao, E. Ciszak, S. Laget, and S.-y. Xu (2007) Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities. Nucl. Acids Res. 35: 6238-6248. https://doi.org/10.1093/nar/gkm665
- Jurenaite-Urbanaviciene, S., J. Serksnaite, E. Kriukiene, J. Giedriene, C. Venclovas, and A. Lubys (2007) Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. Proceedings of the National Academy of Sciences. 104: 10358-10363. https://doi.org/10.1073/pnas.0610365104
- Katada, H. and M. Komiyama (2009) Artificial restriction DNA cutters as new tools for gene manipulation. Chembiochem. 10: 1279-1288. https://doi.org/10.1002/cbic.200900040
- Mimitou, E. P. and L. S. Symington (2009) Nucleases and helicases take center stage in homologous recombination. Trends Biochem. Sci. 34: 264-272. https://doi.org/10.1016/j.tibs.2009.01.010
- Coates, C. J., J. M. Kaminski, J. B. Summers, D. J. Segal, A. D. Miller, and A. F. Kolb (2005) Site-directed genome modification: derivatives of DNA-modifying enzymes as targeting tools. Trends Biotechnol. 23: 407-419. https://doi.org/10.1016/j.tibtech.2005.06.009
- Choulika, A., A. Perrin, B. Dujon, and J. Nicolas (1995) Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol. 15: 1968-1973. https://doi.org/10.1128/MCB.15.4.1968
- Stoddard, B. L. (2005) Homing endonuclease structure and function. Q. Rev. Biophys. 38: 49-95.
- Lee, G. S., M. B. Neiditch, S. S. Salus, and D. B. Roth (2004) RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAGNicking initiates homologous recombination. Cell. 117: 171-184. https://doi.org/10.1016/S0092-8674(04)00301-0
- McConnell Smith, A., R. Takeuchi, S. Pellenz, L. Davis, N. Maizels, R. J. Monnat, and B. L. Stoddard (2009) Generation of a nicking enzyme that stimulates sitespecific gene conversion from the I-AniI LAGLIDADG homing endonuclease. Proceedings of the National Academy of Sciences. 106: 5099-5104. https://doi.org/10.1073/pnas.0810588106
- Flick, K. E., M. S. Jurica, R. J. Monnat, Jr., and B. L. Stoddard (1998) DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature. 394: 96-101. https://doi.org/10.1038/27952
- Eklund, J. L., U. Y. Ulge, J. Eastberg, and R. J. Monnat, Jr (2007) Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease. Nucl. Acids Res. 35: 5839-5850. https://doi.org/10.1093/nar/gkm624
- Redondo, P., J. Prieto, I. G. Munoz, A. Alibes, F. Stricher, L. Serrano, J.-P. Cabaniols, F. Daboussi, S. Arnould, C. Perez, P. Duchateau, F. Paques, F. J. Blanco, and G. Montoya (2008) Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature. 456: 107-111. https://doi.org/10.1038/nature07343
- Chica, R. A., N. Doucet, and J. N. Pelletier (2005) Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr. Opin. Biotechnol. 16: 378-384. https://doi.org/10.1016/j.copbio.2005.06.004
- Ashworth, J., J. J. Havranek, C. M. Duarte, D. Sussman, R. J. Monnat, B. L. Stoddard, and D. Baker (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441: 656-659. https://doi.org/10.1038/nature04818
- Desjarlais, J. R. and J. M. Berg (1992) Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc. Natl. Acad. Sci. USA. 89: 7345-7349. https://doi.org/10.1073/pnas.89.16.7345
- Greisman, H. A. and C. O. Pabo (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science. 275: 657-661. https://doi.org/10.1126/science.275.5300.657
- Urnov, F. D., J. C. Miller, Y.-L. Lee, C. M. Beausejour, J. M. Rock, S. Augustus, A. C. Jamieson, M. H. Porteus, P. D. Gregory, and M. C. Holmes (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature. 435: 646-651. https://doi.org/10.1038/nature03556
- Isalan, M., A. Klug, and Y. Choo (2001) A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat Biotech. 19: 656-660. https://doi.org/10.1038/90264
- Wright, D. A., S. Thibodeau-Beganny, J. D. Sander, R. J. Winfrey, A. S. Hirsh, M. Eichtinger, F. Fu, M. H. Porteus, D. Dobbs, D. F. Voytas, and J. K. Joung (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat. Protocols. 1: 1637-1652. https://doi.org/10.1038/nprot.2006.259
- Maeder, M. L., S. Thibodeau-Beganny, A. Osiak, D. A. Wright, R. M. Anthony, M. Eichtinger, T. Jiang, J. E. Foley, R. J. Winfrey, J. A. Townsend, E. Unger- Wallace, J. D. Sander, F. Muller-Lerch, F. Fu, J. Pearlberg, C. Gobel, JustinDassie, S. M. Pruett-Miller, M. H. Porteus, D. C. Sgroi, A. J. Iafrate, D. Dobbs, P. B. McCray Jr, T. Cathomen, D. F. Voytas, and J. K. Joung (2008) Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol. Cell. 31: 294-301. https://doi.org/10.1016/j.molcel.2008.06.016
- Sander, J. D., P. Zaback, J. K. Joung, D. F. Voytas, and D. Dobbs (2007) Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucl. Acids Res. 35: W599-605. https://doi.org/10.1093/nar/gkm349
- Wah, D. A., J. Bitinaite, I. Schildkraut, and A. K. Aggarwal (1998) Structure of FokI has implications for DNA cleavage. Proc. Natl. Acad. Sci. USA. 95: 10564-10569. https://doi.org/10.1073/pnas.95.18.10564
- Bitinaite, J., D. A. Wah, A. K. Aggarwal, and I. Schildkraut (1998) FokI dimerization is required for DNA cleavage. Proc. Natl. Acad. Sci. USA. 95: 10570-10575. https://doi.org/10.1073/pnas.95.18.10570
- Vanamee, E. S., S. Santagata, and A. K. Aggarwal (2001) FokI requires two specific DNA sites for cleavage. J. Mol. Biol. 309: 69-78. https://doi.org/10.1006/jmbi.2001.4635
- Guo, J., T. Gaj, and C. F. Barbas Iii (2010) Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J. Mol. Biol. 400: 96-107. https://doi.org/10.1016/j.jmb.2010.04.060
- Szczepek, M., V. Brondani, J. Buchel, L. Serrano, D. J. Segal, and T. Cathomen (2007) Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotech. 25: 786-793. https://doi.org/10.1038/nbt1317
- Mino, T., Y. Aoyama, and T. Sera (2009) Efficient double-stranded DNA cleavage by artificial zinc-finger nucleases composed of one zinc-finger protein and a single-chain FokI dimer. J. Biotechnol. 140: 156-161. https://doi.org/10.1016/j.jbiotec.2009.02.004
- Cai, C., Y. Doyon, W. Ainley, J. Miller, R. DeKelver, E. Moehle, J. Rock, Y.-L. Lee, R. Garrison, L. Schulenberg, R. Blue, A. Worden, L. Baker, F. Faraji, L. Zhang, M. Holmes, E. Rebar, T. Collingwood, B. Rubin-Wilson, P. Gregory, F. Urnov, and J. Petolino (2009) Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol. Biol. 69: 699-709. https://doi.org/10.1007/s11103-008-9449-7
- Beumer, K. J., J. K. Trautman, A. Bozas, J.-L. Liu, J. Rutter, J. G. Gall, and D. Carroll (2008) Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proceedings of the National Academy of Sciences. 105: 19821-19826. https://doi.org/10.1073/pnas.0810475105
- Bronson, S. K., E. G. Plaehn, K. D. Kluckman, J. R. Hagaman, N. Maeda, and O. Smithies (1996) Singlecopy transgenic mice with chosen-site integration. Proc. Natl. Acad. Sci. USA. 93: 9067-9072. https://doi.org/10.1073/pnas.93.17.9067
- Bibikova, M., M. Golic, K. G. Golic, and D. Carroll (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics. 161: 1169-1175.
- Carroll, D., K. J. Beumer, J. J. Morton, A. Bozas, and J. K. Trautman (2008) Gene Targeting in Drosophila and Caenorhabditis elegans With Zinc-Finger Nucleases. pp. 63-77. In: Davis, D. G, and Kevin J. Kayser (eds.). Chromosomal Mutagenesis. Humana Press, Totowa, New Jersey.
- Foley, J. E., J.-R. J. Yeh, M. L. Maeder, D. Reyon, J. D. Sander, R. T. Peterson, and J. K. Joung (2009) Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS ONE. 4: e4348. https://doi.org/10.1371/journal.pone.0004348
- Doyon, Y., J. M. McCammon, J. C. Miller, F. Faraji, C. Ngo, G. E. Katibah, R. Amora, T. D. Hocking, L. Zhang, E. J. Rebar, P. D. Gregory, F. D. Urnov, and S. L. Amacher (2008) Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat Biotech. 26: 702-708. https://doi.org/10.1038/nbt1409