Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases (original) (raw)
Cleaver, J. E. Cancer in xeroderma pigmentosum and related disorders of DNA repair. Nature Rev. Cancer5, 564–573 (2005) ArticleCAS Google Scholar
Pabo, C. O., Peisach, E. & Grant, R. A. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem.70, 313–340 (2001) ArticleCAS Google Scholar
Porteus, M. H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science300, 763 (2003) Article Google Scholar
Urnov, F. D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature435, 646–651 (2005) ArticleADSCAS Google Scholar
Bibikova, M., Beumer, K., Trautman, J. K. & Carroll, D. Enhancing gene targeting with designed zinc finger nucleases. Science300, 764 (2003) ArticleCAS Google Scholar
Lombardo, A. et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nature Biotechnol.25, 1298–1306 (2007) ArticleCAS Google Scholar
Bibikova, M., Golic, M., Golic, K. G. & Carroll, D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics161, 1169–1175 (2002) CASPubMedPubMed Central Google Scholar
Szczepek, M. et al. Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nature Biotechnol.25, 786–793 (2007) ArticleCAS Google Scholar
Miller, J. C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nature Biotechnol.25, 778–785 (2007) ArticleCAS Google Scholar
Jacquier, A. & Dujon, B. An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene. Cell41, 383–394 (1985) ArticleCAS Google Scholar
Chevalier, B. S. & Stoddard, B. L. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res.29, 3757–3774 (2001) ArticleCAS Google Scholar
Wang, J., Kim, H. H., Yuan, X. & Herrin, D. L. Purification, biochemical characterization and protein–DNA interactions of the I-CreI endonuclease produced in Escherichia coli . Nucleic Acids Res.25, 3767–3776 (1997) ArticleCAS Google Scholar
Jurica, M. S., Monnat, R. J. & Stoddard, B. L. DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. Mol. Cell2, 469–476 (1998) ArticleCAS Google Scholar
Arnould, S. et al. Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J. Mol. Biol.355, 443–458 (2006) ArticleCAS Google Scholar
Smith, J. et al. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res.34, e149 (2006) Article Google Scholar
Arnould, S. et al. Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells. J. Mol. Biol.371, 49–65 (2007) ArticleCAS Google Scholar
Silva, G. H. & Belfort, M. Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI. Nucleic Acids Res.32, 3156–3168 (2004) ArticleCAS Google Scholar
Schymkowitz, J. et al. The FoldX web server: an online force field. Nucleic Acids Res.33, W382–W388 (2005) ArticleCAS Google Scholar
Soutoglou, E. et al. Positional stability of single double-strand breaks in mammalian cells. Nature Cell Biol.9, 675–682 (2007) ArticleCAS Google Scholar
Saintigny, Y., Delacote, F., Boucher, D., Averbeck, D. & Lopez, B. S. XRCC4 in G1 suppresses homologous recombination in S/G2, in G1 checkpoint-defective cells. Oncogene26, 2769–2780 (2007) ArticleCAS Google Scholar
Rimseliene, R., Maneliene, Z., Lubys, A. & Janulaitis, A. Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco57I to select the mutant with a novel sequence specificity. J. Mol. Biol.327, 383–391 (2003) ArticleCAS Google Scholar
Samuelson, J. C. & Xu, S. Y. Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J. Mol. Biol.319, 673–683 (2002) ArticleCAS Google Scholar
Buchholz, F. & Stewart, A. F. Alteration of Cre recombinase site specificity by substrate-linked protein evolution. Nature Biotechnol.19, 1047–1052 (2001) ArticleCAS Google Scholar
Santoro, S. W. & Schultz, P. G. Directed evolution of the site specificity of Cre recombinase. Proc. Natl Acad. Sci. USA99, 4185–4190 (2002) ArticleADSCAS Google Scholar
Voziyanov, Y., Konieczka, J. H., Stewart, A. F. & Jayaram, M. Stepwise manipulation of DNA specificity in Flp recombinase: progressively adapting Flp to individual and combinatorial mutations in its target site. J. Mol. Biol.326, 65–76 (2003) ArticleCAS Google Scholar
Jamieson, A. C., Miller, J. C. & Pabo, C. O. Drug discovery with engineered zinc-finger proteins. Nature Rev. Drug Discov.2, 361–368 (2003) ArticleCAS Google Scholar
Ashworth, J. et al. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature441, 656–659 (2006) ArticleADSCAS Google Scholar
Bernerd, F. et al. Clues to epidermal cancer proneness revealed by reconstruction of DNA repair-deficient xeroderma pigmentosum skin in vitro . Proc. Natl Acad. Sci. USA98, 7817–7822 (2001) ArticleADSCAS Google Scholar
Prieto, J. et al. The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage. Nucleic Acids Res.35, 3262–3271 (2007) ArticleCAS Google Scholar
Zhang, Z. & Marshall, A. G. A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J. Am. Soc. Mass Spectrom.9, 225–233 (1998) ArticleCAS Google Scholar
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol.372, 774–797 (2007) ArticleCAS Google Scholar
Luscombe, N. M., Laskowski, R. A. & Thornton, J. M. NUCPLOT: a program to generate schematic diagrams of protein–nucleic acid interactions. Nucleic Acids Res.25, 4940–4945 (1997) ArticleCAS Google Scholar
Delacote, F., Han, M., Stamato, T. D., Jasin, M. & Lopez, B. S. An xrcc4 defect or Wortmannin stimulates homologous recombination specifically induced by double-strand breaks in mammalian cells. Nucleic Acids Res.30, 3454–3463 (2002) ArticleCAS Google Scholar