DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases

Molecular Therapy - Tập 16 - Trang 352-358 - 2008
Tatjana I Cornu1, Stacey Thibodeau-Beganny2, Eva Guhl1, Stephen Alwin1, Magdalena Eichtinger2,3, JK Joung2,3, Toni Cathomen1
1Charité Medical School, Institute of Virology (CBF), Berlin, Germany
2Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
3Department of Pathology, Harvard Medical School, Boston, Massachusetts USA

Tài liệu tham khảo

Pabo, 2001, Design and selection of novel Cys2His2 zinc finger proteins, Annu Rev Biochem, 70, 313, 10.1146/annurev.biochem.70.1.313 Jamieson, 2003, Drug discovery with engineered zinc-finger proteins, Nat Rev Drug Discov, 2, 361, 10.1038/nrd1087 Durai, 2005, Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells, Nucleic Acids Res, 33, 5978, 10.1093/nar/gki912 Porteus, 2005, Gene targeting using zinc finger nucleases, Nat Biotechnol, 23, 967, 10.1038/nbt1125 Paques, 2007, Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy, Curr Gene Ther, 7, 49, 10.2174/156652307779940216 Kim, 1996, Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain, Proc Natl Acad Sci USA, 93, 1156, 10.1073/pnas.93.3.1156 Smith, 2000, Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains, Nucleic Acids Res, 28, 3361, 10.1093/nar/28.17.3361 Vasquez, 2001, Manipulating the mammalian genome by homologous recombination, Proc Natl Acad Sci USA, 98, 8403, 10.1073/pnas.111009698 Choulika, 1995, Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae, Mol Cell Biol, 15, 1968, 10.1128/MCB.15.4.1968 Smih, 1995, Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells, Nucleic Acids Res, 23, 5012, 10.1093/nar/23.24.5012 Bibikova, 2003, Enhancing gene targeting with designed zinc finger nucleases, Science, 300, 764, 10.1126/science.1079512 Porteus, 2003, Chimeric nucleases stimulate gene targeting in human cells, Science, 300, 763, 10.1126/science.1078395 Alwin, 2005, Custom zinc-finger nucleases for use in human cells, Mol Ther, 12, 610, 10.1016/j.ymthe.2005.06.094 Urnov, 2005, Highly efficient endogenous human gene correction using designed zinc-finger nucleases, Nature, 435, 646, 10.1038/nature03556 Wright, 2005, High-frequency homologous recombination in plants mediated by zinc-finger nucleases, Plant J, 44, 693, 10.1111/j.1365-313X.2005.02551.x Beumer, 2006, Efficient gene targeting in Drosophila with zinc-finger nucleases, Genetics, 172, 2391, 10.1534/genetics.105.052829 Porteus, 2006, Mammalian gene targeting with designed zinc finger nucleases, Mol Ther, 13, 438, 10.1016/j.ymthe.2005.08.003 Miller, 2007, An improved zinc-finger nuclease architecture for highly specific genome editing, Nat Biotechnol, 25, 778, 10.1038/nbt1319 Szczepek, 2007, Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases, Nat Biotechnol, 25, 786, 10.1038/nbt1317 Pavletich, 1991, Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A, Science, 252, 809, 10.1126/science.2028256 Elrod-Erickson, 1996, Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions, Structure, 4, 1171, 10.1016/S0969-2126(96)00125-6 Choo, 1994, Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions, Proc Natl Acad Sci USA, 91, 11168, 10.1073/pnas.91.23.11168 Rebar, 1994, Zinc finger phage: affinity selection of fingers with new DNA-binding specificities, Science, 263, 671, 10.1126/science.8303274 Wu, 1995, Building zinc fingers by selection: toward a therapeutic application, Proc Natl Acad Sci USA, 92, 344, 10.1073/pnas.92.2.344 Jamieson, 1996, A zinc finger directory for high-affinity DNA recognition, Proc Natl Acad Sci USA, 93, 12834, 10.1073/pnas.93.23.12834 Segal, 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 USA, 96, 2758, 10.1073/pnas.96.6.2758 Dreier, 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, 10.1074/jbc.M102604200 Liu, 2002, Validated zinc finger protein designs for all 16 GNN DNA triplet targets, J Biol Chem, 277, 3850, 10.1074/jbc.M110669200 Blancafort, 2003, Scanning the human genome with combinatorial transcription factor libraries, Nat Biotechnol, 21, 269, 10.1038/nbt794 Dreier, 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, 280, 35588, 10.1074/jbc.M506654200 Bitinaite, 1998, FokI dimerization is required for DNA cleavage, Proc Natl Acad Sci USA, 95, 10570, 10.1073/pnas.95.18.10570 Bibikova, 2001, Stimulation of homologous recombination through targeted cleavage by chimeric nucleases, Mol Cell Biol, 21, 289, 10.1128/MCB.21.1.289-297.2001 Hurt, 2003, Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection, Proc Natl Acad Sci USA, 100, 12271, 10.1073/pnas.2135381100 Joung, 2000, A bacterial two-hybrid selection system for studying protein-DNA and protein–protein interactions, Proc Natl Acad Sci USA, 97, 7382, 10.1073/pnas.110149297 Miller, 2003, Human gene targeting by adeno-associated virus vectors is enhanced by DNA double-strand breaks, Mol Cell Biol, 23, 3550, 10.1128/MCB.23.10.3550-3557.2003 Porteus, 2003, Efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks, Mol Cell Biol, 23, 3558, 10.1128/MCB.23.10.3558-3565.2003 Rogakou, 1998, DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139, J Biol Chem, 273, 5858, 10.1074/jbc.273.10.5858 Wright, 2006, Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly, Nat Protocols, 1, 1637, 10.1038/nprot.2006.259 Segal, 2003, Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins, Biochemistry, 42, 2137, 10.1021/bi026806o Greisman, 1997, A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites, Science, 275, 657, 10.1126/science.275.5300.657 Isalan, 2001, A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter, Nat Biotechnol, 19, 656, 10.1038/90264 Desjarlais, 1993, Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins, Proc Natl Acad Sci USA, 90, 2256, 10.1073/pnas.90.6.2256 Kim, 1996, A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA, Nat Struct Biol, 3, 940, 10.1038/nsb1196-940 Isalan, 1998, Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers, Biochemistry, 37, 12026, 10.1021/bi981358z Dreier, 2000, Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc finger domains, J Mol Biol, 303, 489, 10.1006/jmbi.2000.4133 Cathomen, 2001, A genetic screen identifies a cellular regulator of adeno-associated virus, Proc Natl Acad Sci USA, 98, 14991, 10.1073/pnas.261567198 Cathomen, 2000, A chimeric protein containing the N terminus of the adeno-associated virus Rep protein recognizes its target site in an in vivo assay, J Virol, 74, 2372, 10.1128/JVI.74.5.2372-2382.2000 Thibodeau, 2004, High-throughput β-galactosidase assay for bacterial cell-based reporter systems, Biotechniques, 36, 410, 10.2144/04363BM07