Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
Bibliography
- 1 Jolly CJ, Cook JLA, Manis JP. Fixing DNA breaks during class switch recombination. JEM205,509–513 (2008).
- 2 Raynard S, Niu H, Sung P. DNA double-strand break processing: the beginning of the end. Genes Dev.22,2903–2907 (2008).
- 3 Shrivastav M, De Haro LP, Nickoloff JA. Regulation of DNA double-strand break repair pathway choice. Cell Res.18,134–147 (2008).
- 4 Jackson SP, Bartek J. The DNA-damage response in human biology and disease, Nature461,1071–1078 (2009).
- 5 Niu H, Raynard S, Sung P. Multiplicity of DNA end resection machineries in chromosome break repair. Genes Develop.23,1481–1486 (2009).
- 6 Pontier DB, Tijsterman M. A robust network of double-strand break repair pathways governs genome integrity during C. elegans development. Curr. Biol.19,1384–1388 (2009).
- 7 Takashima Y, Sakuraba M, Koizumi T, Sakamoto H, Hayashi M, Honma M. Dependence of DNA double-strand break repair pathways on cell cycle phase in human lymphoblastoid cells. Environ. Mol. Mutagenesis50,815–822 (2009).
- 8 Mimitou EP, Symington LS. DNA end resection: many nucleases make light work. DNA Repair8,983–995 (2009).
- 9 Costanzo V, Chaudhuri J, Fung JC, Moran JV. Dealing with dangerous accidents: DNA double-strand breaks take centre stage. EMBO Reports10,837–842 (2009).
- 10 Rowe BP, Glazer PM. Emergence of rationally designed therapeutic strategies for breast cancer targeting DNA repair mechanisms. Breast Cancer Res.12,203 (2010).
- 11 Lieber MR. The mechanism of human nonhomologous DNA end joining. J. Biol. Chem.283,1–5 (2008).
- 12 Lieber MR, Lu H, Gu J, Schwarz K. Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining: relevance to cancer, aging, and the immune system. Cell Res.18,125–133 (2008).
- 13 Bibikova M, Carroll D, Segall DJ et al. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol. Cell. Biol.21,289–297 (2001).
- 14 Sung P, Klein H. Mechanism of homologous recombination: mediators and helicases take on regulatoy functions. Nat. Rev. Mol. Cell Biol.7,739–750 (2006).
- 15 Mimitou EP, Symington LS. Nucleases and helicases take center stage in homologous recombination. Trends Biochem. Sci.34,264–272 (2009).
- 16 Lieberman-Lazarovich M, Levy AA. Homologous recombination in plants: an antireview. Methods Mol. Biol.701,51–65 (2011).
- 17 Sharan SK, Thomason LC, Kuznetsov SG, Court DL. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc.4,206–223 (2009).
- 18 Pingoud A, Silva GH. Precision genome surgery. Nat. Biotechnol.25,743–744 (2007).
- 19 Harris KL, Lim S, Franklin SJ. Of folding and function: understanding active-site context through metalloenzyme design. Inorg. Chem.45,10002–10012 (2006).
- 20 Park HS, Nam SH, Lee JK et al. Design and evolution of new catalytic activity with an existing protein scaffold. Science311,535–538 (2006).
- 21 Stoddard BL. Homing endonuclease structure and function. Quart. Rev. Biophys.38,49–95 (2006).
- 22 Thyme SB, Jarjour J, Takeuchi R et al. Exploitation of binding energy for catalysis and design. Nature461,1300–1304 (2009).
- 23 Joachimiak LA, Kortemme T, Stoddard BL, Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein–protein interface. J. Mol. Biol.361,195–208 (2006).
- 24 Szczepek M, Brondani V, Buchel J, Serrano L, Segal DJ, Cathomen T. Structure-based redesign of the dimerization interface reduces the toxicity of zinc finger nucleases. Nat. Biotechnol.25,786–793 (2007).
- 25 Gao M, Skolnick J. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucl. Acids Res.36,3978–3992 (2008).
- 26 Ashworth J, Taylor GK, James J et al. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucl. Acids Res.38,5601–5608 (2010).
- 27 Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science302,1364–1368 (2003).
- 28 Dantas G, Watters AL, Lunde BM et al. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J. Mol. Biol.362,1004–1024 (2006).
- 29 Smith HO, Wilcox KW. A restriction enzyme from hemophilus influenzae. I. Purification and general properties. J. Mol. Biol.51,379–391 (1970).
- 30 Roberts RJ. How restriction enzymes became the workhorses of molecular biology. Proc. Natl Acad. Sci.102,5905–5908 (2005).
- 31 Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE—enzymes and genes for DNA restriction and modification. Nucl. Acids Res.35,D269–D270 (2007).
- 32 Hiraga K, Soga I, Dansereau JT et al. Selection and structure of hyperactive inteins: peripheral changes relayed to the catalytic center. J. Mol. Biol.393,1106–1117 (2009).
- 33 Barzel A, Naor A, Privman E, Kupiec M, Gophna U. Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions. Biochem. Soc. Trans.39,169–173 (2011).
- 34 Edgell DR. Selfish DNA: homing endonucleases find a home. Curr. Biol.19,R115–R117 (2009).
- 35 Dassa B, London N, Stoddard BL, Furman OS, Pietrokovski S. Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucl. Acids Res.37,2560–2573 (2009).
- 36 Eastberg JH, McConnell Smith A, Zhao L, Ashworth J, Shen BW, Stoddard BL. Thermodynamics of DNA target site recognition by homing endonucleases. Nucl. Acids Res.35,7209–7221 (2007).
- 37 Landthaler M, Shen BW, Stoddard BL, Shub DA. I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities. J. Mol. Biol.358,1137–1151 (2006).
- 38 Galburt EA, Stoddard BL. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry41,13851–13860 (2002).
- 39 Finn RD, Tate J, Mistry J et al. The Pfam protein families database. Nucl. Acids Res.36,D281–D288 (2008).
- 40 Niv MY, Ripoll DR, Vila JA et al. Topology of Type II REases revisited; structural classes and the common conserved core. Nucl. Acids Res.35,2227–2237 (2007).
- 41 Eastberg JH, Eklund J, Monnat R, Stoddard BL. Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism. Biochemistry46,7215–7225 (2007).
- 42 Orlowski J, Bujnicki JM. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucl. Acids Res.36,3552–3569 (2008).
- 43 Dupureur CM. Roles of metal ions in nucleases. Curr. Opin. Chem. Biol.12,250–255 (2008).
- 44 Xie F, Dupureur CM. Kinetic analysis of product release and metal ions in a metallonuclease. Arch. Biochem. Biophys.483,1–9 (2009).
- 45 Orlowski J, Boniecki M, Bujnicki JM. I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. Bioinformatics23,527–530 (2007).
- 46 Zhao L, Bonocora RP, Shub DA, Stoddard BL. The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J.26,2432–2442 (2007).
- 47 Zhao L, Pellenz S, Stoddard BL. Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I. J. Mol. Biol.385,1498–1510 (2009).
- 48 Pingoud A, Fuxreiter M, Pingoud V, Wende W. Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci.62,685–707 (2005).
- 49 Hiller DA, Rodriguez AM, Perona JJ. Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC. J. Mol. Biol.354,121–136 (2005).
- 50 Too PH, Zhu Z, Chan SH, Xu SY. Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs. Nucl. Acids Res.38,1294–1303 (2010).
- 51 Pingoud V, Wende W, Friedhoff P et al. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J. Mol. Biol.393,140–160 (2009).
- 52 Xie F, Qureshi SH, Papadakos GA, Dupureur CM. One- and two-metal ion catalysis: global single-turnover kinetic analysis of the PvuII endonuclease mechanism. Biochemistry47,12540–12550 (2008).
- 53 Dupureur CM. One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies. Metallomics2,609–620 (2010).
- 54 Lambert AR, Sussman D, Shen B et al. Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure16,558–569 (2008).
- 55 Mones L, Kulhánek P, Florián J, Simon I, Fuxreiter M. Probing the two-metal ion mechanism in the restriction endonuclease BamHI. Biochemistry46,14514–14523 (2007).
- 56 Mones L, Simon I, Fuxreiter M. Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism. Biol. Chem.388,73–78 (2007).
- 57 Grigorescu A, Horvath M, Wilkosz PA, Chandrasekhar K, Rosenberg JM. The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease. In: Restriction Endonucleases, Nucleic Acids and Molecular Biology. Pingoud A. (Ed.). Springer, Berlin, 14,137–177 (2004).
- 58 Hiller DA, Perona JJ. Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage. Biochemistry45,11453–11463 (2006).
- 59 Lukacs CM, Kucera R, Schildkraut I, Aggarwal A. Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Struct. Biol.7,134–140 (2000).
- 60 Ghosh M, Meiss G, Pingoud A, London RE, Pedersen LC. Structural insights into the mechanism of nuclease A, a ββα metal nuclease from anabaena. J. Biol. Chem.280,27990–27997 (2005).
- 61 Kriukiene E, Lubiene J, Lagunavicius A, Lubys A. MnlI—The member of HNH subtype of Type IIS restriction endonucleases. Biochim. Biophys. Acta1751,194–204 (2005).
- 62 Saravanan M, Vasu K, Ghosh S, Nagaraja V. Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease. J. Biol. Chem.282,32320–32326 (2007).
- 63 Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM. Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins: Struct. Func. Bioinf.65,867–876 (2006).
- 64 Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A. Identification of a single HNH active site in type IIs restriction endonuclease Eco31I. J. Mol. Biol.370,157–169 (2007).
- 65 Sokolowska M, Czapinska H, Bochtler M. Crystal structure of the ββα-Me type II restriction endonuclease Hpy99I with target DNA. Nucl. Acids Res.37,3799–3810 (2009).
- 66 Shen BW, Heiter DF, Chan SH et al. Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure18,734–743 (2010).
- 67 Veluchamy A, Mary S, Acharya V, Mehta P, Deva T, Krishnaswamy S. HNHDb: a database on pattern based classification of HNH domains reveals functional relevance of sequence patterns and domain associations. Bioinformatics6,80–83 (2009).
- 68 Sui MJ, Tsai LC, Hsia KC et al. Metal ions and phosphate binding in the HNH motif: Crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions. Protein Sci.11,2947–2957 (2002).
- 69 Doudeva LG, Huang H, Hsia KC et al. Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+. Protein Sci.15,269–280 (2006).
- 70 Hsia KC, Li CL, Yuan HS. Structural and functional insight into sugar-non-specific nucleases in host defense. Curr. Opin. Struct. Biol.15,126–134 (2005).
- 71 Huang H, Yuan HS. The conserved asparagine in the HNH motif serves an important structural role in metal finger endonucleases. J. Mol. Biol.368,812–821 (2007).
- 72 Shen BW, Landthaler M, Shub DA, Stoddard BL. DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J. Mol. Biol.342,43–56 (2004).
- 73 Gruenig MC, Lu D, Won SJ et al. Creating directed double-strand breaks with the Ref protein: a novel RecA-dependent nuclease from bacteriophage P1. J. Biol. Chem.286,8240–8251 (2011).
- 74 Raaijmakers H, Vix O, Törö I, Golz S, Kemper B, Suck D. X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture. EMBO J.18,1447–1458 (1999).
- 75 Flick KE, Jurica MA, Monnat RJ, Stoddard BL. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature394,96–101 (1998).
- 76 Galburt EA, Jurica MS. The His-Cys box homing endonuclease family. In: Homing Endonucleases and Inteins. Belfort M, Derbyshire V, Stoddard B, Wood D (Eds). Springer-Verlag, Berlin, Germany, 85–102 (2005).
- 77 Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL. Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases. Nucl. Acids Res.36,6988–6998 (2008).
- 78 Chevalier BS, Monnat RJ, Stoddard BL. The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nat. Struct. Biol.8,312–316 (2001).
- 79 Horton NC, Perona JJ. Making the most of metal ions. Nat. Struct. Biol.8,290–293 (2001).
- 80 Chevalier B, Sussman D, Otis C, et al. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry43,14015–14026 (2004).
- 81 Yang W, Lee JY, Nowotny M. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol. Cell22,5–13 (2006).
- 82 Prieto J, Redondo P, Padro D et al. The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage. Nucl. Acids Res.35,3262–3271 (2007).
- 83 Marcaida MJ, Prieto J, Redondo P et al. Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc. Natl Acad. Sci.105,16888–16893 (2008).
- 84 Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux C, Stoddard BL. The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure14,869–880 (2006).
- 85 Chevalier B, Turmel M, Lemieux C, Monnat RJ Jr, Stoddard BL. Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J. Mol. Biol.329,253–269 (2003).
- 86 Moure CM, Gimble FS, Quiocho FA. The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J. Mol. Biol.334,685–695 (2003).
- 87 Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K. Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. J. Mol. Biol.300,889–901 (2000).
- 88 Moure CM, Gimble FS, Quiocho FA. Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway. Nucl. Acids Res.36,3287–3296 (2008).
- 89 Werner E, Wende W, Pingoud A, Heinemann U. High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI. Nucl. Acids Res.30,3962–3971 (2002).
- 90 Moure CM, Gimble FS, Quiocho FA. Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity. Nat. Struct. Biol.9,764–770 (2002).
- 91 Bolduc JM, Spiegel PC, Chatterjee P et al. Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev.17,2875–2888 (2003).
- 92 Scalley-Kim M, McConnell-Smith A, Stoddard BL. Coevolution of a homing endonuclease and its host target sequence. J. Mol. Biol.372,1305–1319 (2007).
- 93 Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL. Optimization of in vitro activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucl. Acids Res.37,877–890 (2009).
- 94 Longo A, Leonard CW, Bassi GS et al. Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nat. Struct. Mol. Biol.12,779–787 (2005).
- 95 Kaiser BK, Clifton MC, Shen BW, Stoddard BL. The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease. Structure17,1368–1376 (2009).
- 96 Van Roey P, Meehan L, Kowalski JC, Belfort M, Derbyshire V. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nature Struct. Biol.9,806–811 (2002).
- 97 Truglio JJ, Rhau B, Croteau DL et al. Structural insights into the first incision reaction during nucleotide excision repair. EMBO J.24,885–894 (2005).
- 98 Mak AN, Lambert AR, Stoddard BL. Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI. Structure18,1321–1331 (2010).
- 99 Andersson CE, Lagerbäck P, Carlson K. Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. J. Mol. Biol.397,1003–1016 (2010).
- 100 Ibryashkina EM, Sasnauskas G, Solonin AS, Zakharova MV, Siksnys V. Oligomeric structure diversity within the GIY-YIG nuclease family. J. Mol. Biol.387,10–16 (2009).
- 101 Corina LE, Qiu W, Desai A, David L. Herrin DL. Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the HNH and GIY-YIG motifs. Nucl. Acids Res.37,5810–5821 (2009).
- 102 Livieri M, Mancin F, Saielli G, Chin J, Tonellato U. Mimicking enzymes: cooperation between organic functional groups and metal ions in the cleavage of phosphate diesters. Chem. Eur. J.13,2246–2256 (2007).
- 103 JingJing Z, Ying S, Li W et al. Design of artificial nucleases and studies of their interaction with DNA, Sci. China Ser. B-Chem.52,402–414 (2009).
- 104 Manchin F, Tecilla P. Artificial restriction agents: Hydrolytic agents for DNA cleavage. In: Metal complex – DNA interactions. Hadjiliadis N, Sletten E (Eds). Blackwell Publishing Ltd, Chichester, UK, 13,369–395 (2009).
- 105 Aoki SH, Kimura E. Zinc-nucleic acid interaction. Chem. Rev.104,769–784 (2004).
- 106 Sheng X, Guo X, Lu XM et al. DNA binding, cleavage, and cytotoxic activity of the preorganized dinuclear zinc(II) complex of triazacyclononane derivatives. Bioconjug. Chem.19,490–498 (2008).
- 107 Wang Q, Leino E, Jancso A et al. Zn2+ complexes of di- and tri-nucleating azacrown ligands as base-moiety-selective cleaving agents of RNA 3´,5´-phosphodiester bonds: binding to guanine base. ChemBioChem9,1739–1748 (2008).
- 108 Arjmand F, Aziz M. Synthesis and characterization of dinuclear macrocyclic cobalt(II), copper(II) and zinc(II) complexes derived from 2,2,2(‘),2(‘)-S,S[bis(bis-N,N-2-thiobenzimidazolyloxalato-1,2-ethane)]: DNA binding and cleavage studies. Eur. J. Med. Chem.44,834–844 (2009).
- 109 Bonomi R, Saielli G, Tonellato U, Scrimin P, Mancin F. Insights on nuclease mechanism: the role of proximal ammonium group on phosphate esters cleavage. J. Am. Chem. Soc.131,11278–11279 (2009).
- 110 Mohamed MF, Brown RS. Cleavage of an RNA model catalyzed by dinuclear Zn(II) complexes containing rate-accelerating pendants. Comparison of the catalytic benefits of H-bonding and hydrophobic substituents. J. Org. Chem.75,8471–8477 (2010).
- 111 Puckett CA, Barton JK. Fluorescein redirects a ruthenium-octaarginine conjugate to the nucleus. J. Am. Chem. Soc.131,8738–8739 (2009).
- 112 Ernst RJ, Song H, Barton JK. DNA mismatch binding and antiproliferative activity of rhodium metalloinsertors. J. Am. Chem. Soc.131,2359–2366 (2009).
- 113 Chen X, Fan J, Peng X et al. Bisintercalator-containing dinuclear iron(III) complex: An efficient artificial nuclease. Bioorg. Med. Chem. Lett.19,4139–4142 (2009).
- 114 Zeglis BM, Pierre VC, Barton JK. Metallo-intercalators and metallo-insertors. Chem. Commun. (Camb).4565–4579 (2007).
- 115 Zeglis BM, Barton JK. DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications. Nat. Protoc.2,357–371 (2007).
- 116 Brunner J, Barton JK. Site-specific DNA photocleavage by rhodium intercalators analyzed by MALDI-TOF mass spectrometry. J. Am. Chem. Soc.128,6772–6773 (2006).
- 117 Zeglis BM, Pierre VC, Kaiser JT, Barton JK. A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode. Biochemistry48,4247–4253 (2009).
- 118 Hart JR, Glebov O, Ernst RJ, Kirsch IR, Barton JK. DNA mismatch-specific targeting and hypersensitivity of mismatch-repair-deficient cells to bulky rhodium(III) intercalators. Proc. Natl Acad. Sci.103,15359–15363 (2006).
- 119 Lim MH, Lau IH, Barton JK. DNA strand cleavage near a CC mismatch directed by a metalloinsertor. Inorg. Chem.46,9528–9530 (2007).
- 120 Zeglis BM, Boland JA, Barton JK. Targeting abasic sites and single base bulges in DNA with metalloinsertors. J. Am. Chem. Soc.130,7530–7531 (2008).
- 121 Puckett CA, Barton JK. Targeting a ruthenium complex to the nucleus with short peptides. Bioorg. Med. Chem.18,3564–3569 (2010).
- 122 Puckett CA, Ernst RJ, Barton JK. Exploring the cellular accumulation of metal complexes. Dalton Trans.39,1159–1170 (2010).
- 123 Chen W, Komiyama M. Site-selective DNA hydrolysis by CeIV–EDTA with the use of one oligonucleotide additive bearing two monophosphates. ChemBioChem6,1825–1830 (2005).
- 124 Lönnberg T, Suzuki Y, Komiyama M. Prompt site-selective DNA hydrolysis by Ce(IV)-EDTA using oligonucleotide multiphosphonate conjugates. Org. Biomol. Chem.6,3580–3587 (2008).
- 125 Murtola M, Strömberg R. Development of 2´-o-methyloligoribonucleotide and peptide nucleic acid based artificial ribonucleases. Nucl. Acids Symp. Ser. (Oxf.).201–202 (2007).
- 126 Milton S, Murtola M, Sandbrink J, Yeheskiely E, Strömberg R. Making oligonucleotide conjugates and breaking oligonucleotides. Nucl. Acids Symp. Ser. (Oxf.).61 (2007).
- 127 Lönnberg T, Aiba Y, Hamano Y, Miyajima Y, Sumaoka J, Komiyama M. Oxidation of an oligonucleotide-bound Ce(III)/multiphosphonate complex for site-selective DNA scission. Chem. Eur. J.16,855–859 (2010).
- 128 Miller MJ, Li H, Foss CA. Novel antisense oligonucleotides containing hydroxamate linkages: targeted iron-triggered chemical nucleases. Biometals22,491–510 (2009).
- 129 Eisenschmidt K, Lanio T, Simoncsits A et al. Developing a programmed restriction endonuclease for highly specific DNA cleavage. Nucl. Acids Res.33,7039–7047 (2005).
- 130 Duca M, Guianvarc’h D, Oussedik K et al. Molecular basis of the targeting of topoisomerase II mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides. Nucl. Acids Res.34,1900–1911 (2006).
- 131 Majumdar A, Muniandy PA, Liu J et al. Targeted gene knock in and sequence modulation mediated by a psoralen-linked triplex-forming oligonucleotide. J. Biol. Chem.283,11244–11252 (2008).
- 132 Simon P, Cannata F, Concordet JP, Giovannangeli C. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie90,1109–1116 (2008).
- 133 Schleifman EB, Chin JY, Glazer PM. Triplex-mediated gene modification. Methods Mol. Biol.435,175–190 (2008).
- 134 Semenyuk A, Darian E, Liu J et al. Targeting of an interrupted polypurine:polypyrimidine sequence in mammalian cells by a triplex-forming oligonucleotide containing a novel base analogue. Biochemistry49,7867–7878 (2010).
- 135 Chin JY, Schleifman EB, Glazer PM. Repair and recombination induced by triple helix DNA. Front. Biosci.12,4288–4297 (2007).
- 136 Chin JY, Glazer PM. Repair of DNA lesions associated with triplex-forming oligonucleotides. Mol. Carcinog.48,389–399 (2009).
- 137 Wang JT, Xia Q, Zheng XH et al. An effective approach to artificial nucleases using copper(II) complexes bearing nucleobases. Dalton Trans.39,2128–2136 (2010).
- 138 Radecke F, Peter I, Radecke S, Gellhaus K, Schwarz K, Cathomen T. Targeted chromosomal gene modification in human cells by single-stranded oligodeoxynucleotides in the presence of a DNA double-strand break. Mol. Ther.14,798–808 (2006).
- 139 Semir D, Aran JM. Targeted gene repair: the ups and downs of a promising gene therapy approach. Curr. Gene Ther.6,481–504 (2006).
- 140 Aarts M, Dekker M, de Vries S, van der Wal A, te Riele H. Generation of a mouse mutant by oligonucleotide-mediated gene modification in ES cells. Nucl. Acids Res.34,e147 (2006).
- 141 Dekker M, Brouwers C, Aarts M et al. Effective oligonucleotide-mediated gene disruption in ES cells lacking the mismatch repair protein MSH3. Gene Ther.13,686–694 (2006).
- 142 Disterer P, Simons JP, Owen JS. Validation of oligonucleotide-mediated gene editing. Gene Ther.16,824–826 (2009).
- 143 Papaioannou I, Disterer P, Owen JS. Use of internally nuclease-protected single-strand DNA oligonucleotides and silencing of the mismatch repair protein, MSH2, enhances the replication of corrected cells following gene editing. J. Gene Med.11,267–274 (2009).
- 144 Aarts M, Te Riele H. Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application. Gene Ther.18,213–219 (2011).
- 145 Aarts M, te Riele H. Parameters of oligonucleotide-mediated gene modification in mouse ES cells. J. Cell. Mol. Med.14,1657–1667 (2010).
- 146 Brunet E, Corgnali M, Cannata F, Perrouault L, Giovannangeli C. Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment. Nucl. Acids Res.34,4546–4553 (2006).
- 147 Saua SP, Kumara P, Anderson BA et al. Optimized DNA-targeting using triplex forming C5-alkynyl functionalized LNA. Chem. Commun.28,6756–6758 (2009).
- 148 Smith CI, Lundin KE, Simonson OE et al. Building biologically active nucleic acid nanocomplexes. Nucl. Acids Symp. Ser. (Oxf.).27–28 (2008).
- 149 Ge R, Heinonen JE, Svahn MG, Mohamed AJ, Lundin KE, Smith E. Zorro locked nucleic acid induces sequence-specific gene silencing. FASEB J.21,1902–1914 (2007).
- 150 Lundin KE, Simonson OE, Moreno P et al. Nanotechnology approaches for gene transfer. Genetica137,47–56 (2009).
- 151 Boll I, Kovbasyuk L, Krämer R, Oeser T, Mokhir A. Zn2+ dependent DNA binders based on terminally modified peptide nucleic acids. Bioorg. Med. Chem. Lett.16,2781–2785 (2006).
- 152 Ye SH, Miyajima Y, Ohnishi T, Yamamoto Y, Komiyama M. Combination of peptide nucleic acid beacon and nuclease S1 for clear-cut genotyping of single nucleotide polymorphisms. Anal. Biochem.363,300–302 (2007).
- 153 Kumagai I, Takahashi T, Hamasaki K, Ueno A, Mihara H. HIV Rev peptides conjugated with peptide nucleic acids and their efficient binding to RRE RNA. Bioorg. Med. Chem. Lett.11,1169–1172 (2001).
- 154 Takahashi T, Ueno A, Mihara H. Nucleobase amino acids incorporated into the HIV-1 nucleocapsid protein increased the binding affinity and specificity for a hairpin RNA ChemBioChem3,543–549 (2002).
- 155 Hansen ME, Bentin TH, Nielsen PE. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers. Nucl. Acids Res.37,4498–4507 (2009).
- 156 Lonkar P, Kim KH, Kuan JY et al. Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids. Nucl. Acids Res.37,3635–3644 (2009).
- 157 Yamamoto Y, Uehara A, Miura K, Watanabe A, Aburatani H, Komiyama M. Development of artificial restriction DNA cutter composed of Ce(IV)/EDTA and PNA. Nucleosides Nucleotides Nucl. Acids26,1265–1268 (2007).
- 158 Yamamoto Y, Mori M, Aiba Y et al. Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA. Nucl. Acids Res.35,e53 (2007).
- 159 Katada H, Komiyama M. Artificial restriction DNA cutters as new tools for gene manipulation. ChemBioChem10,1279–1288 (2009).
- 160 Ito K, Katada H, Shigi N, Komiyama M. Site-selective scission of human genome by artificial restriction DNA cutter. Chem. Comm. (Camb).6542–6544 (2009).
- 161 Komiyama M, Aiba Y, Yamamoto Y, Sumaoka J. Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity. Nat. Protoc.3,655–662 (2008).
- 162 Katada H, Chen HJ, Shigi N, Komiyama M. Homologous recombination in human cells using artificial restriction DNA cutter. Chem. Comm. (Camb).6545–6547 (2009).
- 163 Ishizuka T, Tedeschi T, Corradini R, Komiyama M, Sforza S, Marchelli R. SSB-assisted duplex invasion of preorganized PNA into double-stranded DNA. ChemBioChem10,2607–2612 (2009).
- 164 Ishizuka T, Yoshida J, Yamamoto Y et al. Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucl. Acids Res.36,1464–1471 (2008).
- 165 Aiba Y, Komiyama M. Handy and prompt DNA separation using PNA with internal disulfide bond. Nucl. Acids Symp. Ser. (Oxf).175–176 (2009).
- 166 Yamamoto Y, Uehara A, Watanabe A, Aburatani H, Komiyama M. Chemical-reaction-based site-selective DNA cutter for PCR-free gene manipulation. ChemBioChem7,673–677 (2006).
- 167 Kitamura Y, Mori S, Chen W, Sumaoka J, Komiyama M. Recombination of the GFP gene to the BFP gene using a man-made site-selective DNA cutter. J. Biol. Inorg. Chem.11,13–16 (2006).
- 168 Kovbasyuk L, Krämer R. Allosteric supramolecular receptors and catalysts. Chem. Rev.104,3161–3187 (2004).
- 169 Kovbasyuk L, Pritzkow H, Krämer R, Fritsky IO. On/off regulation of catalysis by allosteric control of metal complex nuclearity. Chem. Commun.880–881 (2004).
- 170 Goritz M, Krämer R. Allosteric control of oligonucleotide hybridization by metal-induced cyclization. J. Am. Chem. Soc.127,18016–18017 (2005).
- 171 Murtola M, Strömberg R. PNA based artificial nucleases displaying catalysis with turnover in the cleavage of a leukemia related RNA model. Org. Biomol. Chem.6,3837–3842 (2008).
- 172 Murtola M, Wenska M, Strömberg R. PNAzymes that are artificial RNA restriction enzymes. J. Am. Chem. Soc.132,8984–8990 (2010).
- 173 Mokhir A, Krämer R, Wolf H. Zn2+-dependent peptide nucleic acids probes. J. Am. Chem. Soc.126,6208–6209 (2004).
- 174 Boll I, Krämer R, Mokhir A. Hybridization dependent cleavage of internally modified disulfide–peptide nucleic acids. Bioorg. Med. Chem. Lett.15,505–509 (2006).
- 175 Boll I, Jentzsch E, Krämer R, Mokhir A. Metal complex catalysis on a double-stranded DNA template. Chem. Commun.3447–3449 (2006).
- 176 Fussl A, Schleifenbaum A, Goritz M, Riddell A, Schultz C, Krämer R. Cellular Uptake of PNA-terpyridine conjugates and its enhancement by Zn2+-ions. J. Am. Chem. Soc.128,5986–5987 (2006).
- 177 Graf N, Goritz M, Krämer R. A metal-ion-releasing probe for DNA detection by catalytic signal amplification. Angew. Chem. Int. Ed.45,4013–4015 (2006).
- 178 Graf N, Krämer R. Enzymatic amplification in a bioinspired, autonomous signal cascade. Chem. Commun.4375–4376 (2006).
- 179 Kiel A, Kovacs J, Mokhir A, Krämer R, Herten DP. Direct monitoring of formation and dissociation of individual metal complexes by single-molecule fluorescence spectroscopy. Angew. Chem. Int. Ed.46,3363–3366 (2007).
- 180 McNeer NA, Chin JY, Schleifman EB, Fields RJ, Glazer PM, Saltzman WM. Nanoparticles deliver triplex-forming PNAs for site-specific genomic recombination in CD34(+) human hematopoietic progenitors. Mol. Ther.19,172–180 (2010).
- 181 Nakagawa O, Ming X, Huang L, Juliano RL. Targeted intracellular delivery of antisense oligonucleotides via conjugation with small-molecule ligands. J. Am. Chem. Soc.132,8848–8849 (2010).
- 182 Jakab NI, Jancsó A, Gajda T, Gyurcsik B, Rockenbauer A. Copper(II), nickel(II) and zinc(II) complexes of N-acetyl-His-Pro-His-His-NH2: Equilibria, solution structure and enzyme mimicking. J. Inorg. Biochem.102,1438–1448 (2008).
- 183 Kolozsi A, Vosekalna I, Martinek T, Larsen E, Gyurcsik B. Copper(II) and zinc(II)ion binding properties of a MAP type branched ligand with histidines as surface functionalities. Dalton Trans.5647–5654 (2009).
- 184 Jakab NI, Lorincz O, Jancsó A, Gajda T, Gyurcsik B. Approaching the minimal metal ion binding peptide for structural and functional metalloenzyme mimicking. Dalton Trans.6987–6995 (2008).
- 185 González-Díaz H, Sánchez-González A, González-Díaz Y. 3D-QSAR study for DNA cleavage proteins with a potential anti-tumor ATCUN-like motif. J. Inorg. Biochem.100,1290–1297 (2006).
- 186 Jin Y, Lewis MA, Gokhale NH, Long EC, Cowan JA. Influence of stereochemistry and redox potentials on the single- and double-strand DNA cleavage efficiency of Cu(II) and Ni(II) Lys-Gly-His-derived ATCUN metallopeptides. J. Am. Chem. Soc.129,8353–8361 (2007).
- 187 Long EC, Fang YY, Lewis MA. DNA minor groove recognition by Ni(II)·and Cu(II)·Gly-Gly-His derived metallopeptides, models of protein and natural product DNA recognition. In: Bioinorganic Chemistry; Cellular Systems and Synthetic Models (Volume 1012). Long EC, Baldwin MJ (Eds). American Chemical Society, Washington, DC, USA, 219–241 (2009).
- 188 Lim S, Franklin SJ. Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution. Protein Sci.15,2159–2165 (2006).
- 189 Wong-Deyrup SW, Kim Y, Franklin SJ. Sequence preference in DNA binding: de novo designed helix–turn–helix metallopeptides recognize a family of DNA target sites. J. Biol. Inorg. Chem.11,17–25 (2006).
- 190 Caprara MG, Chatterjee P, Solem A, Brady-Passerini KL, Kaspar BJ. An allosteric-feedback mechanism for protein-assisted group I intron splicing. RNA13,211–222 (2007).
- 191 Thibodeau-Beganny S, Maeder ML, Joung JK. Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system. Methods Mol. Biol.649,31–50 (2010).
- 192 Jarjour J, West-Foyle H, Certo MT et al. High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucl. Acids Res.37,6871–6880 (2009).
- 193 Arnould S, Chames P, Perez C 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).
- 194 Chames P, Epinat JCH, Guillier S, Patin A, Lacroix E, Pâques F. In vitro selection of engineered homing endonucleases using double-strand break induced homologous recombination. Nucl. Acids Res.33,e178 (2005).
- 195 Ashworth J, Havranek JJ, Duarte CM et al. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature441,656–659 (2006).
- 196 Redondo P, Prieto J, Munoz JG et al. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature456,107–111 (2008).
- 197 Mandell DJ, Kortemme T. Computer-aided design of functional protein interactions. Nat. Chem. Biol.5,797–807 (2009).
- 198 Wang YT, Wright JD, Doudeva LG, Jhang H-C, Lim C, Yuan HS. Redesign of high-affinity non-specific nucleases with altered sequence preference. J. Am. Chem. Soc.131,17345–17353 (2009).
- 199 Pingoud V, Sudina A, Geyer H et al. Specificity changes in the evolution of type II restriction endonucleases. J. Mol. Biol.280,4289–4298 (2005).
- 200 Reetz MT, Kahakeaw D, Lohmer R. Addressing the numbers problem in directed evolution. ChemBioChem9,1797–1804 (2008).
- 201 Morgan RD, Luyten YA. Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity. Nucl. Acids Res.37,5222–5233 (2009).
- 202 Sussman D, Chadsey M, Fauce S et al. Isolation and characterization of new homing endonuclease specificities at individual target site positions. J. Mol. Biol.342,31–41 (2004).
- 203 Rosen LE, Morrison HA, Masri S et al. Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucl. Acids Res.34,4791–4800 (2006).
- 204 Gimble FS, Moure CM, Posey KL. Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system. J. Mol. Biol.334,993–1008 (2003).
- 205 Silva GH, Belfort M, Wende W, Pingoud A. From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes. J. Mol. Biol.361,744–754 (2006).
- 206 Fajardo-Sanchez E, Stricher F, Pâques F, Isalan M, Serrano L. Computer design of obligate heterodimer meganucleases allows eficient cutting of custom DNA sequences. Nucl. Acids Res.36,2163–2173 (2008).
- 207 Smith J, Grizot S, Arnold S et al. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucl. Acid Res.34,e149 (2006).
- 208 Arnould S, Perez C, Cabaniols J et al. Engineered I-CreI derivatives cleaving sequences from the human xpc gene can induce highly efficient gene correction in mammmalian cells. J. Mol. Biol.371,49–65 (2007).
- 209 Grizot S, Smith J, Daboussi F et al. Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease. Nucl. Acids Res.37,5405–5419 (2009).
- 210 Muñoz IG, Prieto J, Subramanian S et al. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucl. Acids Res.39,729–743 (2011).
- 211 Grosse S, Huot N, Mahiet C et al. Meganuclease-mediated inhibition of HSV1 infection in cultured cells. Mol. Ther.19,694–702 (2011).
- 212 Prieto J, Epinat JC, Redondo P et al. Generation and analysis of mesophilic variants of the thermostable archaeal i-dmoi homing endonuclease. J. Biol. Chem.283,4364–4374 (2008).
- 213 Goyal K, Mande SC. Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins10,1206–1218 (2008).
- 214 Lee Y, Lim C. Physical basis of structural and catalytic Zn-binding sites in proteins. J. Mol. Biol.379,545–553 (2008).
- 215 Kozísek M, Svatos A, Budesínsky M et al. Molecular design of specific metal-binding peptide sequences from protein fragments: theory and experiment. Chem. Eur. J.14,7836–7846 (2008).
- 216 Levy R, Edelman M, Sobolev V. Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates. Proteins76,365–374 (2009).
- 217 Podtetenieff J, Taglieber A, Bill E, Reijerse EJ, Reetz MT. An artificial metalloenzyme: creation of a designed copper binding site in a thermostable protein. Angew. Chem. Int. Ed.49,5151–5155 (2010).
- 218 Steuer SH, Pingoud V, Pingoud A, Wende W. Chimeras of the homing endonuclease pI-SceI and the homologous candida tropicalis intein: a study to explore the possibility of exchanging DNA-binding modules to obtain highly specific endonucleases with altered specificity. ChemBioChem5,206–213 (2004).
- 219 Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell.10,895–905 (2002).
- 220 Grizot S, Epinat JC, Thomas S et al. Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucl. Acids Res.38,2006–2018 (2010).
- 221 Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ Jr. Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins. Nucl. Acids Res.37,1650–1662 (2009).
- 222 Yoshitake K, Aoyagi H, Fujiwara H. Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1. Mob. DNA1,13 (2010).
- 223 Tamulaitiene G, Jakubauskas A, Urbanke C, Huber R, Grazulis S, Siksnys V. The crystal structure of the rare-cutting restriction enzyme sdai reveals unexpected domain architecture. Structure14,1389–1400 (2006).
- 224 Chan S, Bao Y, Ciszak E, Laget S, Xu S. Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities. Nucl. Acids Res.35,186238–186248 (2007).
- 225 Fomenkov A, Too PH, Chan SH et al. Targeting DNA 5mCpG sites with chimeric endonucleases. Anal. Biochem.381,135–141 (2008).
- 226 Zhang P, Bao Y, Higgins L, Xu S. Rational design of a chimeric endonuclease targeted to NotI recognition site. Prot. Eng. Des. Sel.20,497–504 (2007).
- 227 Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Siksnys V, Bochtler M. Restriction endonucleases that resemble a component of the bacterial DNA repair machinery. Cell. Mol. Life Sci.64,2351–2357 (2007).
- 228 Chuluunbaatar T, Ivanenko-Johnston T, Fuxreiter M et al. An EcoRI–RsrI chimeric restriction endonuclease retains parental sequence specificity. Biochim. Biophys. Acta1774,583–594 (2007).
- 229 Saravanan M, Vasu K, Nagaraja V. Evolution of sequence specificity in a restriction endonuclease by a point mutation. Proc. Natl Acad. Sci.105,10344–10347 (2008).
- 230 Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V. How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets. Nucl. Acids Res.36,6101–6108 (2008).
- 231 Gilmore JL, Suzuki Y, Tamulaitis G, Siksnys V, Takeyasu K, Lyubchenko YL. Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy. Biochemistry48,10492–10498 (2009).
- 232 Alam N, Sittman DB. Characterization of cytotoxic effect of a chimeric restriction enzyme, H10-FokI. Gen. Ther. Mol. Biol.10,147–160 (2006).
- 233 Lippow SM, Aha PM, Parker MH, Blake WJ, Baynes BM, Lipovsek D. Creation of a type IIS restriction endonuclease with a long recognition sequence. Nucl. Acids Res.37,3061–3073 (2009).
- 234 Christian M, Cermak T, Doyle EL et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics186,757–761 (2010).
- 235 Miller JC, Tan S, Qiao G et al. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol.29,143–148 (2011).
- 236 Li T, Huang S, Jiang WZ et al. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucl. Acids Res.39,359–372 (2011).
- 237 Mishra SH, Shelley CM, Barrow DJ, Darby MK, Germann MW. Solution structures and characterization of human immunodeficiency virus rev responsive element IIB RNA targeting zinc finger proteins. Biopolymers83,352–364 (2006).
- 238 Mino T, Mori T, Aoyama Y, Sera T. Cell-permeable artificial zinc-finger proteins as potent antiviral drugs for human papillomaviruses. Arch. Virol.153,1291–1298 (2008).
- 239 Di Certo MG, Corbi N, Strimpakos G et al. The artificial gene Jazz, a transcriptional regulator of utrophin, corrects the dystrophic pathology in mdx mice. Hum. Mol. Genet.19,752–760 (2010).
- 240 Passananti C, Corbi N, Onori A, Certo MG, Mattei E. Transgenic mice expressing an artificial zinc finger regulator targeting an endogenous gene. Methods Mol. Biol.649,183–206 (2010).
- 241 Imanishi M, Nakaya T, Morisaki T, Noshiro D, Futaki S, Sugiura Y. Metal-stimulated regulation of transcription by an artificial zinc-finger protein. ChemBioChem11,1653–1655 (2010).
- 242 Stolzenburg S, Bilsland A, Keith WN, Rots MG. Modulation of gene expression using zinc finger-based artificial transcription factors. Methods Mol. Biol.649,257–270 (2010).
- 243 Lindhout BI, Meckel T, van der Zaal BJ. Zinc finger-mediated live cell imaging in Arabidopsis roots. Methods Mol. Biol.649,383–398 (2010).
- 244 Hoeksema KA, Tyrrell LJ. Inhibition of viral transcription using designed zinc finger proteins. Methods Mol. Biol.649,97–116 (2010).
- 245 Jantz D, Amann BT, Gatto JR, Berg GJ. The design of functional DNA-binding proteins based on zinc finger domains. Chem. Rev.104,789–799 (2004).
- 246 Heinz U, Hemmingsen L, Kiefer M, Adolph HW. Structural adaptability of zinc binding sites: different structures in partially, fully, and heavy-metal loaded states. Chem. Eur. J.15,7350–7358 (2009).
- 247 Hartwig A, Schwerdtle T, Bal W. Biophysical analysis of the interaction of toxic metal ions and oxidants with the zinc finger domain of XPA. Methods Mol. Biol.649,399–410 (2010).
- 248 Kim AC, Berg MJ. A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA. Nat. Struct. Biol.3,940–945 (1996).
- 249 Erickson ME, Benson TE, Pabo CO. High-resolution structures of variant Zif268–DNA complexes: implications for understanding zinc finger–DNA recognition. Structure6,451–464 (1998).
- 250 Horton NC, Park CK. Crystallization of zinc finger proteins bound to DNA. Methods Mol. Biol.649,457–477 (2010).
- 251 Shiraishi Y, Imanishi M, Morisaki T, Sugiura Y. Swapping of the β-hairpin region between Sp1 and GLI zinc fingers: significant role of the β-hairpin region in DNA binding properties of C2H2-type zinc finger peptides. Biochemistry44,2523–2528 (2005).
- 252 Dhanasekaran M, Negi S, Imanishi M, Sugiura Y. DNA-binding ability of GAGA zinc finger depends on the nature of amino acids present in the β-hairpin. Biochemistry46,7506–7513 (2007).
- 253 Peisach E, Pabo CO. Constraints for zinc finger linker design as inferred from x-ray crystal structure of tandem Zif268–DNA complexes. J. Mol. Biol.330,1–7 (2003).
- 254 Händel EM, Alwin S, Cathomen T. Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity. Mol. Ther.17,104–111 (2009).
- 255 Nomura W, Sugiura Y. Design and synthesis of artificial zinc finger proteins. Methods Mol Biol.352,83–93 (2007).
- 256 Dhanasekaran M, Negi SH, Sugiura Y. Designer zinc finger proteins: Tools for creating artificial DNA-binding functional proteins. Acc. Chem. Res.39,45–52 (2006).
- 257 Mandell JG, Barbas CF. Zinc Finger Tools. custom DNA-binding domains for transcription factors and nucleases. Nucl. Acids Res.34,W516–W523 (2006).
- 258 Segall DJ, Barbas CF. Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins. Curr. Opin. Biotechnol.12,632–637 (2001).
- 259 Liu Q, Xia Z, Zhong X, Case CC. Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol. Chem.277,3850–3856 (2002).
- 260 Bulyk ML, Huang X, Choo Y, Church GM. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl Acad. Sci.98,7158–7163 (2001).
- 261 Rebarand EJ, Pabo CO. Zinc finger phage: affinity selection of finger with new DNA-binding specificities. Science263,671–673 (1994).
- 262 Jamieson AC, Wang H, Kim SH. A zinc finger directory for high-affinity DNA recognition. Proc. Natl Acad. Sci.93,12834–12839 (1996).
- 263 Greisman HA, Pabo CO. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science275,657–661 (1997).
- 264 Shieh JC. Bipartite selection of zinc fingers by phage display for any 9-bp DNA target site. Methods Mol. Biol.649,51–76 (2010).
- 265 Ihara H, Mie M, Funabashi H et al. In vitro selection of zinc finger DNA-binding proteins through ribosome display. Biochem. Biophys. Res. Comm.345,1149–1154 (2006).
- 266 Tateyama S, Horisawa K, Takashima H, Miyamoto-Sato E, Doi N, Yanagawa H. Affinity selection of DNA-binding protein complexes using mRNA display. Nucl. Acids Res.34,e27 (2006).
- 267 Lund CV, Blancafort P, Popkov M, Barbas CF. Promoter-targeted phage display selections with preassembled synthetic zinc finger libraries for endogenous gene regulation. J. Mol. Biol.340,599–613 (2004).
- 268 Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK. Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc. Natl Acad. Sci.100,12271–12276 (2003).
- 269 Bae KH, Kim JS. One-step selection of artificial transcription factors using an in vitro screening system. Mol. Cells21,376–380 (2006).
- 270 Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D. An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins. Nucl. Acids Res.37,506–515 (2009).
- 271 Dreier B, Fuller RP, Segal DJ et al. 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.280,35588–35597 (2005).
- 272 Bhakta MS, Segal DJ. The generation of zinc finger proteins by modular assembly. Methods Mol. Biol.649,3–30 (2010).
- 273 Morisaki T, Imanishi M, Futaki S, Sugiura Y. Artificial transcription factors based on multi-zinc finger motifs. Yakugaku Zasshi130,45–48 (2010).
- 274 Ramirez CL, Foley JE, Wright DA et al. Unexpected failure rates for modular assembly of engineered zinc fingers. Nat. Methods5,374–375 (2008).
- 275 Segal DJ, Crotty JW, Bhakta MS, Barbas CF 3rd, Horton NC. Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J. Mol. Biol.363,405–421 (2006).
- 276 Sakai-Kato K, Ishiguro A, Mikoshiba K, Aruga J, Utsunomiya-Tate N. CD spectra show the relational style between Zic-, Gli-, Glis-zinc finger protein and DNA. Biochim. Biophys. Acta1784,1011–1019 (2008).
- 277 Sakai-Kato K, Umezawa Y, Mikoshiba K, Aruga J, Utsunomiya-Tate N. Stability of folding structure of Zic zinc finger proteins. Biochem. Biophys. Res. Comm.384,362–365 (2009).
- 278 Yan W, Imanishi M, Futaki S, Sugiura Y. Alpha-helical linker of an artificial 6-zinc finger peptide contributes to selective DNA binding to a discontinuous recognition sequence. Biochemistry46,8517–8524 (2007).
- 279 Mineta Y, Okamoto T, Takenaka K, Doi N, Aoyama Y, Sera T. Enhanced cleavage of double-stranded DNA by artificial zinc-finger nuclease sandwiched between two zinc-finger proteins. Biochemistry47,12257–12259 (2008).
- 280 Mineta Y, Okamoto T, Takenaka K, Doi N, Aoyama Y, Sera T. Multiple-turnover cleavage of double-stranded DNA by sandwiched zinc-finger nuclease. Nucl. Acids Symp. Ser. (Oxf.).53,279–280 (2009).
- 281 Negi S, Imanishi M, Matsumoto M, Sugiura Y. New redesigned zinc-finger proteins: design strategy and its application. Chem. Eur. J.14,3236–3249 (2008).
- 282 Papworth M, Kolasinska P, Minczuk M. Designer zinc-finger proteins and their applications. Gene366,27–38 (2006).
- 283 Dion S, Demattéi MV, Renault S. Les domainesà doigts de zinc Vers la modification de la structure et de l’activé des génomes. Med. Sci.23,834–839 (2007).
- 284 Gamsjaeger R, Swanton MK, Kobus FJ et al. Structural and biophysical analysis of the DNA binding properties of myelin transcription factor 1. J. Biol. Chem.283,5158–5167 (2008).
- 285 Minczuk M, Kolasinska-Zwierz P, Murphy MP, Papworth MA. Construction and testing of engineered zinc-finger proteins for sequence-specific modification of mtDNA. Nat. Protoc.5,342–356 (2010).
- 286 Ding G, Lorenz P, Kreutzer M, Li Y, Thiesen HJ. SysZNF: the C2H2 zinc finger gene database. Nucl. Acids Res.37,D267–273 (2009).
- 287 Fu F, Sander JD, Maeder M et al. Zinc finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucl. Acids Res.37,D279–D283 (2009).
- 288 Liu J, Stormo GD. Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinformatics24,1850–1857 (2008).
- 289 Stormo GD, Zhao Y. Determining the specificity of protein-DNA interactions. Nat. Rev. Genet.11,751–760 (2010).
- 290 Hermsen R, Tans S, Wolde PR. Transcriptional regulation by competing transcription factor modules. PLoS Comp. Biol.2,e164 (2006).
- 291 Siggers TW, Honig B. Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucl. Acids Res.35,41085–41097 (2007).
- 292 Mori H, Ueno-Noto K. A theoretical study of the physicochemical mechanisms associated with DNA recognition modulation in artificial zinc-finger proteins. J. Phys. Chem. B115,4774–4780 (2011).
- 293 Nagy G, Gyurcsik B, Hoffmann EA, Körtvélyesi T. Theoretical design of specific DNA – zinc-finger protein interaction by semiempirical quantum chemical methods. J. Mol. Graph. Mol. Model.29,928–934 (2011).
- 294 Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucl. Acids Res.35,W599–W605 (2007).
- 295 Sander JD, Maeder ML, Reyon D, Voytas DF, Joung K, Dobbs D. ZiFiT (zinc finger targeter): an updated zinc finger engineering tool. Nucl. Acids Res.38,W462–W468 (2010).
- 296 Reyon D, Kirkpatrick JR, Sander JD et al. Zinc fingerNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. BMC Genomics12,83 (2011).
- 297 Persikov AV, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics25,22–29 (2009).
- 298 Alibés A, Serrano L, Nadra AD. Structure-based DNA-binding prediction and design. Methods Mol. Biol.649,77–88 (2010).
- 299 Ladame S, Schouten JA, Roldan J, Redman JE, Neidle S, Balasubramanian S. Exploring the recognition of quadruplex DNA by an engineered Cys2-His2 zinc finger protein. Biochemistry45,1393–1399 (2006).
- 300 Addepalli B, Hunt AG. A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor. Nucl. Acids Res.35,4453–4463 (2007).
- 301 Kelly SM, Pabit SA, Kitchen CM et al. Recognition of polyadenosine RNA by zinc finger proteins. Proc. Natl Acad. Sci.104,12306–12311 (2007).
- 302 Font J, Mackay JP. Beyond DNA: zinc finger domains as RNA-binding modules. Methods Mol. Biol.649,479–491 (2010).
- 303 Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci.93,1156–1160 (1996).
- 304 Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK. Structure of the multimodular endonuclease FokI bound to DNA. Nature388,97–100 (1997).
- 305 Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK. Structure of FokI has implications for DNA cleavage. Proc. Natl Acad. Sci.95,10564–10569 (1998).
- 306 Gemmen GJ, Millin R, Smith DE. Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are ‘‘switched off’’ at low force. Proc. Natl Acad. Sci.103,11555–11560 (2006).
- 307 Gemmen GJ, Millin R, Smith DE. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Nucl. Acids Res.34,2864–2877 (2006).
- 308 Catto LE, Ganguly S, Milsom SE, Welsh AJ, Halford SE. Protein assembly and DNA looping by the FokI restriction endonuclease. Nucl. Acids Res.34,1711–1720 (2006).
- 309 Catto LE, Bellamy SR, Retter SE, Halford SE. Dynamics and consequences of DNA looping by the FokI restriction endonuclease. Nucl. Acids Res.2073–2081 (2008).
- 310 Mani M, Smith J, Kandavelou K, Berg JM, Chandrasegaran S. Binding of two zinc finger nuclease monomers to two specific sites is required for effective double-strand DNA cleavage. Biochem. Biophys. Res. Comm.334,1191–1197 (2005).
- 311 Shimizu Y, Bhakta MS, Segal DJ. Restricted spacer tolerance of a zinc finger nuclease with a six amino acid linker. Bioorg. Med. Chem. Lett.19,3970–3972 (2009).
- 312 Miller JC, Holmes MC, Wang J et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol.25,778–785 (2007).
- 313 Doyon Y, Vo T, Mendel MC et al. Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat. Methods8,74–79 (2011).
- 314 Zeevi V, Tovkach A, Tzfira T. Increasing cloning possibilities using artificial zinc finger nucleases. Proc. Natl Acad. Sci.105,12785–12790 (2008).
- 315 Zeevi V, Tovkach A, Tzfira T. Artificial zinc finger nucleases for DNA cloning. Methods Mol. Biol.649,209–225 (2010).
- 316 Porteus M. Design and testing of zinc finger nucleases for use in mammalian cells. Methods Mol. Biol.435,47–61 (2008).
- 317 Cathomen T, Joung JK. Zinc-finger nucleases: the next generation emerges. Mol. Ther.16,1200–1207 (2008).
- 318 Cathomen T, Segal DJ, Brondani V, Müller-Lerch F. Generation and functional analysis of zinc finger nucleases. Methods Mol. Biol.434,277–290 (2008).
- 319 Wright DA, Thibodeau-Beganny S, Sander JD. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat. Protoc.1,1637–1652 (2006).
- 320 Carroll D, Morton JJ, Beumer KJ, Segal DJ. Design, construction and in vitro testing of zinc finger nucleases. Nat. Protoc.1,1329–1341 (2006).
- 321 Kandavelou K, Chandrasegaran S. Custom-designed molecular scissors for site-specific manipulation of the plant and mammalian genomes. Methods Mol. Biol.544,617–636 (2009).
- 322 Tovkach A, Zeevi V, Tzfira T. A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells. Plant J.57,747–757 (2009).
- 323 Sander JD, Reyon D, Maeder ML et al. Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinformatics11,543 (2010).
- 324 Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK. Oligomerized pool engineering (OPEN): an ‘open-source’ protocol for making customized zinc-finger arrays. Nat. Protoc.4,471–501 (2009).
- 325 Cathomen T, Söllü C. In vitro assessment of zinc finger nuclease activity. Methods Mol. Biol.649,227–235 (2010).
- 326 Kim JS, Lee HJ, Carroll D. Genome editing with modularly assembled zinc-finger nucleases. Nat. Methods7,91 (2010).
- 327 Porteus M. Creating zinc finger nucleases using a modular-assembly approach. Cold Spring Harb. Protoc. 2010:pdb.prot5530 (2010).
- 328 Porteus M. Creating zinc finger nucleases to manipulate the genome in a site-specific manner using a modular-assembly approach. Cold Spring Harb. Protoc. 2010:pdb.top93 (2010).
- 329 Tovkach A, Zeevi V, Tzfira T. Expression, purification and characterization of cloning-grade zinc finger nuclease. J. Biotechnol.151,1–8 (2011).
- 330 Chandrasekharan S, Kumar S, Valley CM, Rai A. Proprietary science, open science and the role of patent disclosure: the case of zinc-finger proteins. Nat. Biotechnol.27,140–144 (2009).
- 331 Lippow S, Lipovsek D, Aha PM. Engineered nucleases and their uses for nucleic acid assembly. WO/2008/130629 International Patent Office (2008).
- 332 Minczuk M, Papworth MA, Kolasinska P, Murphy MP, Klug A. Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase. Proc. Natl Acad. Sci.103,19689–19694 (2006).
- 333 Krichevsky A, Gutgarts H, Kozlovsky SV et al. C2H2 zinc finger-SET histone methyltransferase is a plant-specific chromatin modifier. Dev. Biol.303,259–269 (2007).
- 334 Meister GE, Chandrasegaran S, Ostermeier M. Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells. Nucl. Acids Res.38,1749–1759 (2010).
- 335 Jurkowska RZ, Jeltsch A. Silencing of gene expression by targeted DNA methylation: concepts and approaches. Methods Mol. Biol.649,149–161 (2010).
- 336 Imanishi M, Negi S, Sugiura Y. Non-FokI-based zinc finger nucleases. Methods Mol. Biol.649,337–349 (2010).
- 337 Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S. Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucl. Acids Res.33,5978–5990 (2005).
- 338 Porteus MH, Caroll D. Gene targeting using zinc finger nucleases. Nat. Biotechnol.23,967–973 (2005).
- 339 Dolan P. Targeted gene repair using engineered zinc finger. MMG445 Basic Biotechnol.2,7–13 (2006).
- 340 Wu J, Kandavelou K, Chandrasegaran S. Custom-designed zinc finger nucleases: what is next? Cell. Mol. Life Sci.64,2933–2944 (2007).
- 341 Carroll D. Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther.15,1463–1468 (2008).
- 342 Porteus MH. Plant biotechnology: zinc fingers on target. Nature459,337–338 (2009).
- 343 Yan Z, Sun X, Engelhardt JF. Progress and prospects: techniques for site-directed mutagenesis in animal models. Gene Ther.16,581–588 (2009).
- 344 Davis D, Stokoe D. Zinc finger nucleases as tools to understand and treat human diseases. BMC Med.42,1–11 (2010).
- 345 Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet.11,636–647 (2010).
- 346 Weinthal D, Tovkach A, Zeevi V, Tzfira T. Genome editing in plant cells by zinc finger nucleases. Trends Plant Sci.15,308–321 (2010).
- 347 Carroll D. Zinc-finger nucleases: a panoramic view. Curr. Gene Ther.11,2–10 (2011).
- 348 Pâques F, Duchateau P. Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Curr. Gene Ther.7,49–66 (2007).
- 349 Stoddard BL. Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure19,7–15 (2011).
- 350 Galetto R, Duchateau P, Pâques F. Targeted approaches for gene therapy and the emergence of engineered meganucleases. Expert Opin. Biol. Ther.9,1289–1303 (2009).
- 351 Arnould S, Delenda C, Grizot S et al. The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy. Prot. Eng. Des. Sel.24,27–31 (2011).
- 352 Silva G, Poirot L, Galetto R et al. Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy. Curr. Gene Ther.11,11–27 (2011).
- 353 Cabaniols JP, Pâques F. Robust cell line development using meganucleases. Methods Mol. Biol.435,31–45 (2008).
- 354 Cabaniols JP, Ouvry C, Lamamy V et al. Meganuclease-driven targeted integration in CHO-K1 cells for the fast generation of HTS-compatible cell-based assays. J. Biomol. Screen15,956–967 (2010).
- 355 Geurts AM, Cost GJ, Freyvert Y et al. Knockout rats produced using designed zinc finger nucleases. Science24,1–3 (2009).
- 356 Gondo Y. Now and future of mouse mutagenesis for human disease models. J. Genet. Genomics37,559–572 (2010).
- 357 Connelly JP, Barker JC, Pruett-Miller S, Porteus MH. Gene correction by homologous recombination with zinc finger nucleases in primary cells from a mouse model of a generic recessive genetic disease. Mol. Ther.18,1103–1110 (2010).
- 358 Gondo Y, Murata T, Makino S, Fukumura R, Ishitsuka Y. Mouse mutagenesis and disease models for neuropsychiatric disorders. Curr. Top. Behav. Neurosci.7,1–35 (2011).
- 359 Meyer M, de Angelis MH, Wurst W, Kühn R. Gene targeting by homologous recombination in mouse zygotes mediated by zinc-finger nucleases. Proc. Natl Acad. Sci.107,15022–15026 (2010).
- 360 Friedel RH, Wurst W, Wefers B, Kühn R. Generating conditional knockout mice. Methods Mol. Biol.693,205–231 (2011).
- 361 Smedley D, Salimova E, Rosenthal N. Cre recombinase resources for conditional mouse mutagenesis. Methods53,411–416 (2011).
- 362 Cavazzana-Calvo M, Fischer A. Gene therapy for severe combined immunodeficiency: are we there yet? J. Clin. Invest.114,1456–1465 (2007).
- 363 Mashimo T, Takizawa A, Voigt B et al. Generation of knockout rats with x-linked severe combined immunodeficiency (x-scid) using zinc-finger nucleases. PLoS ONE5,e8870 (2010).
- 364 Benjelloun F, Garrigue A, Chappedelaine C et al. Stable and functional lymphoid reconstitution in artemis-deficient mice following lentiviral artemis gene transfer into hematopoietic stem cells. Mol. Ther.16,1490–1499 (2008).
- 365 Klymiuk N, Aigner B, Brem G, Wolf E. Genetic modification of pigs as organ donors for xenotransplantation. Mol. Reprod. Dev.77,209–221 (2010).
- 366 Porteus M. Testing a three-finger zinc finger nuclease using a GFP reporter system. Cold Spring Harb. Protoc. DOI: 10.1101/pdb.prot5531 (2010).
- 367 Hockemeyer D, Soldner F, Beard C et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat. Biotechnol.27,851–857 (2009).
- 368 Porteus MH. Mammalian gene targeting with designed zinc finger nucleases. Mol. Ther.13,438–446 (2006).
- 369 Cornu T, Cathomen T. Targeted genome modifications using integrase-deficient lentiviral vectors. Mol. Ther.15,2107–2113 (2007).
- 370 Porteus MH, Baltimore D. Chimeric nucleases stimulate gene targeting in human cells. Science300,763 (2003).
- 371 Kandavelou K, Ramalingam S, London V et al. Targeted manipulation of mammalian genomes using designed zinc finger nucleases. Biochem. Biophys. Res. Comm.388,56–61 (2009).
- 372 Zou J, Maeder ML, Mali P et al. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell5,97–110, (2009).
- 373 DeKelver RC, Choi VM, Moehle EA et al. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res.20,1133–1142 (2010).
- 374 Benabdallah BF, Allard E, Yao S et al. Targeted gene addition to human mesenchymal stromal cells as a cell-based plasma-soluble protein delivery platform. Cytotherapy12,394–399 (2010).
- 375 Cathomen T, Weitzman MD. Pointing the finger at genetic disease. Gene Ther.12,1415–1416 (2005).
- 376 Urnov FD, Miller JC, Lee YL et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature435,646–651 (2005).
- 377 Lombardo A, Genovese P, Beausejour CM et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat. Biotechnol.25,1298–1306 (2007).
- 378 Qasim W, Gaspar HB, Thrasher AJ. Progress and prospects: gene therapy for inherited immunodeficiencies. Gene Ther.16,1285–1291 (2009).
- 379 Porteus MH, Cathomen T, Matthew D, Weitzman MD, Baltimore D. efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks. Mol. Cell. Biol.23,3558–3565 (2003).
- 380 Hirsch ML, Green L, Porteus MH, Samulski RJ. Self-complementary AAV mediates gene targeting and enhances endonuclease delivery for double-strand break repair. Gene Ther.17,1175–1180 (2010).
- 381 Cathomen T. AAV vectors for gene correction. Curr. Op. Mol. Ther.6,360–366 (2004).
- 382 Gouble A, Smith J, Bruneau S et al. Efficient in toto targeted recombination in mouse liver by meganuclease-induced double-strand break. J. Gene. Med.8,616–622 (2006).
- 383 Marton I, Zuker A, Shklarman E et al. Nontransgenic genome modification in plant cells. Plant Physiol.154,1079–1087 (2010).
- 384 Wright DA, Townsend JA, Winfrey RJ et al. High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J.44,693–705 (2005).
- 385 Cai CQ, Doyon Y, Ainley WM et al. Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol. Biol.69,699–709 (2009).
- 386 Shukla VK, Doyon Y, Miller JC et al. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature459,437–441 (2009).
- 387 Moehle EA, Rock JM, Lee YL et al. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc. Natl Acad. Sci.104,3055–3060 (2007).
- 388 Orlando SJ, Santiago Y, DeKelver RC et al. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucl. Acids Res.38,e152 (2010).
- 389 Radecke S, Radecke F, Cathomen T, Schwarz K. Zinc-finger nuclease-induced gene repair with oligodeoxynucleotides: wanted and unwanted target locus modifications. Mol. Ther.18,743–753 (2010).
- 390 McConnell-Smith A, Takeuchi R, Pellenz S et al. Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease. Proc. Natl Acad. Sci.106,5099–5104 (2009).
- 391 Metzger MJ, McConnell-Smith A, Stoddard BL, Miller AD. Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template. Nucl. Acids Res.39,1–18 (2011).
- 392 Zhang P, Too PH, Samuelson JC et al. Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA. Protein Expr. Purif.69,226–234 (2010).
- 393 Zheleznaya LA, Kachalova GS, Artyukh RI, Yunusova AK, Perevyazova TA, Matvienko NI. Nicking endonucleases. Biochemistry (Mosc).74,1457–1466 (2009).
- 394 Chan SH, Stoddard BL, Xu SY Natural and engineered nicking endonucleases – from cleavage mechanism to engineering of strand-specificity. Nucl. Acids Res.39,1–18 (2011).
- 395 Bibikova M, Golic M, Golic KG, Carroll D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics161,1169–1175 (2002).
- 396 Beumer K, Bhattacharyya G, Bibikova M, Trautman JK, Carroll D. Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics172,2391–2403 (2006).
- 397 Bibikova M, Beumer K, Trautman JK, Carroll D. Enhancing gene targeting with designed zinc finger nucleases. Science300,764 (2003).
- 398 Beumer JK, Trautman JK, Bozas A et al. Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc. Natl Acad. Sci.105,19821–19826 (2008).
- 399 Bozas A, Beumer KJ, Trautman JK, Carroll D. Genetic analysis of zinc-finger nuclease-induced gene targeting in drosophila. Genetics182,641–651 (2009).
- 400 Morton J, Davis MW, Jorgensen EM, Carroll D. Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc. Natl Acad. Sci.103,16370–16375 (2006).
- 401 Carroll D, Beumer KJ, Morton JJ, Bozas A, Trautman JK. Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases. Methods Mol. Biol.435,63–77 (2008).
- 402 Huang J, Zhou W, Watson AM, Jan YN, Hong Y. Efficient ends-out gene targeting in Drosophila. Genetics180,703–707 (2008).
- 403 Carroll D, Beumer KJ, Trautman JK. High-efficiency gene targeting in Drosophila with zinc finger nucleases. Methods Mol. Biol.649,271–280 (2010).
- 404 Doyon Y, McCammon JM, Miller JC et al. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol.26,702–708 (2008).
- 405 Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat. Biotechnol.26,695–701 (2008).
- 406 Kiermer V. Fish fingers on the menu. Nat. Methods5,579 (2008).
- 407 Foley JE, Yeh JJ, Maeder ML et al. Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by oligomerized pool engineering (OPEN). PLoS ONE4,e4348 (2009).
- 408 Maeder ML, Thibodeau-Begannym S, Osiak A et al. Rapid ‘‘open-source’’ engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol. Cell31,294–301 (2008).
- 409 Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR. Targeted mutagenesis in zebrafish using customized zinc-finger nucleases. Nat. Protoc.4,1855–1867 (2009).
- 410 McCammon JM, Amacher SL. Using zinc finger nucleases for efficient and heritable gene disruption in zebrafish. Methods Mol. Biol.649,281–298 (2010).
- 411 Takasu Y, Kobayashi I, Beumer K et al. Targeted mutagenesis in the silkworm Bombyx mori using zinc finger nuclease mRNA injection. Insect Biochem. Mol. Biol.40,759–765 (2010).
- 412 Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A. Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos. Nucl. Acids Res.35,5922–5933 (2007).
- 413 Mittelmana D, Moyea C, Morton J et al. Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells. Proc. Natl Acad. Sci.106,9607–9612 (2009).
- 414 Santiago Y, Chan E, Liu PQ et al. Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc. Natl Acad. Sci.105,5809–5814 (2008).
- 415 Cristea S, Gregory PD, Urnov FD, Cost GJ. Dissection of splicing regulation at an endogenous locus by zinc-finger nuclease-mediated gene editing. PLoS One6,e16961 (2011).
- 416 Mino T, Mori T, Aoyama Y, Sera T. Inhibition of human papillomavirus replication by using artificial zinc-finger nucleases. Nucl. Acids Symp. Ser. (Oxf).185–186 (2008).
- 417 Perez EE, Wang J, Miller JC et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat. Biotechnol.26,808–816 (2008).
- 418 Holt N, Wang J, Kim K et al. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vitro. Nat. Biotechnol.28,839–847 (2010).
- 419 Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS. Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res.19,1279–1288 (2009).
- 420 Babcock MA, Kostova FV, Moxley III RT, Chamberlain JS, Maria BL. Muscular dystrophy: new opportunities for diagnosis and treatment. J. Child. Neurol.25,1080–1097 (2010).
- 421 Goyenvalle A, Babbs A, Powell D et al. Prevention of dystrophic pathology in severely affected dystrophin/utrophin-deficient mice by morpholino-oligomer-mediated exon-skipping. Mol. Ther.18,198–205 (2010).
- 422 Quattrocelli M, Cassano M, Crippa S, Perini I, Sampaolesi M. Cell therapy strategies and improvements for muscular dystrophy. Cell Death Diff.17,1222–1229 (2010).
- 423 Chapdelaine P, Pichavant C, Rousseau J, Pâques F, Tremblay JP. Meganucleases can restore the reading frame of a mutated dystrophin. Gene Ther.1–13, (2010).
- 424 de Pater S, Neuteboom LW, Pinas JE, Hooykaas P, Zaal B. Zinc fingerN-induced mutagenesis and gene-targeting in Arabidopsis through Agrobacterium-mediated floral dip transformation. Plant Biotechnol. J.7,821–835 (2009).
- 425 Zhang F, Maeder ML, Unger-Wallace E et al. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc. Natl Acad. Sci.107,12028–12033 (2010).
- 426 Osakabe K, Osakabe Y, Toki S. Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc. Natl Acad. Sci.107,12034–12039 (2010).
- 427 Zhang F, Voytas DF. Targeted mutagenesis in Arabidopsis using zinc-finger nucleases. Methods Mol. Biol.701,167–177 (2011).
- 428 Lloyd MA, Plaisier CL, Carroll D, Drews GN. Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc. Natl Acad. Sci.102,2232–2237 (2005).
- 429 Yang M, Djukanovic V, Stagg J et al. Targeted mutagenesis in the progeny of maize transgenic plants. Plant Mol. Biol.70,669–679 (2009).
- 430 Gao H, Smith J, Yang M et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J.6,176–187 (2010).
- 431 Petolino JF, Worden A, Curlee K et al. Zinc finger nuclease-mediated transgene deletion. Plant Mol. Biol.73,617–628 (2010).
- 432 Townsend JA, Wright DA, Winfrey RJ et al. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature21,442–445 (2009).
- 433 Lee HJ, Kim E, Kim JS. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res.20,81–89 (2010).
- 434 Söllü C, Pars K, Cornu TI et al. Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion. Nucl. Acids Res.38,8269–8276 (2010).
- 435 Bruneta E, Simseka D, Tomishima M. Chromosomal translocations induced at specified loci in human stem cells. Proc. Natl Acad. Sci.106,10620–10625 (2009).
- 436 Feng X, Bednarz AL, Colloms SD. Precise targeted integration by a chimaeric transposase zinc-finger fusion protein. Nucl. Acids Res.38,1204–1216 (2010).
- 437 Wilson MH, George AL. Designing and testing chimeric zinc finger transposases. Methods Mol. Biol.649,353–363 (2010).
- 438 Gordley RM, Gersbach CA, Barbas CF. Synthesis of programmable integrases. Proc. Natl Acad. Sci.106,5053–5058 (2009).
- 439 Soroldoni D, Hogan BM, Oates AC. Simple and efficient transgenesis with meganuclease constructs in zebrafish. Methods Mol. Biol.546,117–130 (2009).
- 440 Lee DJ, Bingle LE, Heurlier K. Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiol.9,1–14 (2009).
- 441 Uemura M, Niwa Y, Kakazu N, Adachi N, Kinoshita K. Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors. PLoS One5,e9846 (2010).
- 442 Brown WRA, Lee NCO, Xu Z, Smith MCM. Serine recombinases as tools for genome engineering. Methods53,372–379 (2011).
- 443 Tate PH, Skarnes WC. Bi-allelic gene targeting in mouse embryonic stem cells. Methods53,331–338 (2011).
- 444 Patsch C, Kesseler D, Edenhofer F. Genetic engineering of mammalian cells by direct delivery of FLP recombinase protein. Methods53,386–393 (2011).
- 445 Monetti C, Nishino K, Biechele S et al. PhiC31 integrase facilitates genetic approaches combining multiple recombinases. Methods53,380–385 (2011).
- 446 Anastassiadis K, Fu J, Patsch C et al. Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice. Dis. Model Mech.2,508–515 (2009).
- 447 Huang J, Zhou W, Dong W, Watson AM, Hong Y. Directed, efficient, and versatile modifications of the Drosophila genome by genomic engineering. Proc. Natl Acad. Sci.106,8284–8289 (2009).
- 448 Huang J, Zhou W, Dong W, Hong Y. Targeted engineering of the Drosophila genome. Fly (Austin)3,274–277 (2009).
- 449 Shaked H, Avivi-Ragolsky N, Levy AA. Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics173,985–994 (2006).
- 450 Hiom K. DNA repair: Common approaches to fixing double-strand breaks. Curr. Biol.19,R523–R525 (2009).
- 451 Yano K, Morotomi-Yano K, Adachi N, Akiyama H. Molecular mechanism of protein assembly on DNA double-strand breaks in the non-homologous end-joining pathway. J. Radiat. Res. (Tokyo)50,97–108 (2009).
- 452 Agmon N, Pur S, Liefshitz B, Kupiec M. Analysis of repair mechanism choice during homologous recombination. Nucl. Acids Res.37,5081–5092 (2009).
- 453 Rivera-Munoz P, Soulas-Sprauel P, Le Guyader G et al. Reduced immunoglobulin class switch recombination in the absence of Artemis. Blood114,3601–3609 (2009).
- 454 Kurosawa A, Adachi N. Functions and regulation of Artemis: a goddess in the maintenance of genome integrity. J. Radiat. Res. (Tokyo)51,503–509 (2010).
- 455 Sharma GG, So S, Gupta A et al. MOF and histone H4 acetylation at lysine 16 are critical for DNA damage response and double-strand break repair. Mol. Cell. Biol.30,3582–3595 (2010).
- 456 Schaefer DG, Delacote F, Charlot F et al. RAD51 loss of function abolishes gene targeting and de-represses illegitimate integration in the moss Physcomitrella patens. DNA Repair (Amst).9,526–533 (2010).
- 457 Maresca M, Erler A, Fu J, Friedrich A, Zhang Y, Stewart AF. Single-stranded heteroduplex intermediates in lambda Red homologous recombination. BMC Mol. Biol.11,54 (2010).
- 458 Fattah F, Lee EH, Weisensel N, Wang Y, Lichter N, Hendrickson EA. Ku regulates the non-homologous end joining pathway choice of DNA double-strand break repair in human somatic cells. PLoS Genet.6,e1000855 (2010).
- 459 Emmanuel E, Yehuda E, Melamed-Bessudo C, Avivi-Ragolsky N, Levy AA. The role of AtMSH2 in homologous recombination in Arabidopsis thaliana. EMBO Rep.7,100–105 (2006).
- 460 Trouiller B, Schaefer DG, Charlot F, Nogué F. MSH2 is essential for the preservation of genome integrity and prevents homologous recombination in the moss Physcomitrella patens. Nucl. Acids Res.34,232–242 (2006).
- 461 Sharan SK, Kuznetsov SG. Resolving RAD51C function in late stages of homologous recombination. Cell Div.2,15 (2007).
- 462 Barzel A, Kupiec M. Finding a match: how do homologous sequences get together for recombination? Nat. Rev. Genet.9,27–37 (2008).
- 463 Zorin B, Lu Y, Sizova I, Hegemann P. Nuclear gene targeting in Chlamydomonas as exemplified by disruption of the PHOT gene. Gene432,91–96 (2009).
- 464 Porteus MH. Translating the lessons from gene therapy to the development of regenerative medicine. Mol. Ther.19,439–441 (2011).
- 465 Porteus MH, Connelly JP, Pruett SM. A look to future directions in gene therapy research for monogenic diseases. PLoS Genet.2,e133 (2006).
- 466 Porteus M. Using homologous recombination to manipulate the genome of human somatic cells. Biotechnol. Genet. Eng. Rev.24,195–212 (2007).
- 467 Bohne J, Cathomen T. Genotoxicity in gene therapy: An account of vector integration and designer nucleases. Curr. Op. Mol. Therap.10,214–223 (2008).
- 468 Pruett-Miller SM, Reading DW, Porter SN, Porteus MH. Attenuation of zinc finger nuclease toxicity by small- molecule regulation of protein levels. PLoS Genet.5,e1000376 (2009).
- 469 Cornu TI, Cathomen T. Quantification of zinc finger nuclease-associated toxicity. Methods Mol. Biol.649,237–245 (2010).
- 470 Sera T. Generation of cell-permeable artificial zinc finger protein variants. Methods Mol. Biol.649,91–96 (2010).
- 471 Zajakina A, Kozlovska T, Bruvere R, Aleksejeva J, Pumpens P, Garoff H. Translation of hepatitis B virus (HBV) surface proteins from the HBV pregenome and precore RNAs in Semliki Forest virus-driven expression. J. Gen. Virol.85,3343–3351 (2004).
- 472 Tissot AC, Renhofa R, Schmitz N et al. Versatile Virus-Like Particle Carrier for Epitope Based Vaccines. PLos One5,e9809 (2010).
- 473 Freivalds J, Dislers A, Ose V, Pumpens P, Tars K, Kazaks A. Highly efficient production of phosphorylated hepatitis B core particles in yeast Pichia pastoris. Prot. Expr. Purif.75,218–224 (2011).
- 474 Hummel HD, Kuntz G, Russell SJ et al. Genetically engineered attenuated measles virus specifically infects and kills primary multiple myeloma cells. J. Gen. Virol.90,693–701 (2009).
- 475 Hou Y, Rajagopal J, Irwin PA, Voytas DF. Retrotransposon vectors for gene delivery in plants. Mob. DNA1,19 (2010).
- 476 Narsinh KH, Wu JC. Gene correction in human embryonic and induced pluripotent stem cells. promises and challenges ahead. Mol. Ther.18,1061–1063 (2010).
- 477 Khan IF, Hirata RK, Wang PR et al. Engineering of human pluripotent stem cells by AAV-mediated gene targeting. Mol. Ther.18,1192–1199 (2010).
- 478 Evans M. Embryonic stem cells: the mouse source-vehicle for mammalian genetics and beyond. ChemBioChem9,1690–1696 (2008).
- 479 Qiu J. Trading on hope. Nat. Biotechnol.27,790–792 (2009).
- 480 Hoshaw JP, Unger-Wallace E, Zhang F, Voytas DF. A transient assay for monitoring zinc finger nuclease activity at endogenous plant gene targets. Methods Mol. Biol.649,299–313 (2010).
- 481 Potts PR, Porteus MH, Yu H. Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double-strand breaks. EMBO J.25,3377–3388 (2006).
- 482 Elefanty AG, Stanley EG. Reshaping pluripotent stem cells. Nat. Biotechnol.27,823–824 (2009).
- 483 Schambach A, Cantz T, Baum C, Cathomen T. Generation and genetic modification of induced pluripotent stem cells. Expert Opin. Biol. Ther.10,1089–1103 (2010).
- 484 Bobis-Wozowicz S, Osiak A, Rahman SH, Cathomen T. Targeted genome editing in pluripotent stem cells using zinc-finger nucleases. Methods53,339–346 (2011).
- 485 Cathomen T, Schambach A. Zinc positive: tailored genome engineering meets reprogramming. Gene Ther.17,1–3 (2010).
- 486 Olsen PA, Gelazauskaite M, Randøl M, Krauss S. Analysis of illegitimate genomic integration mediated by zinc-finger nucleases: implications for specificity of targeted gene correction. BMC Mol. Biol.11,1–11 (2010).
- 487 Li Y, Wang J. Faster human genome sequencing. Nat. Biotechnol.27,820–821 (2009).
- 488 Patterson N, Gabriel S. Combinatorics and next-generation sequencing. Nat. Biotechnol.27,826–827 (2009).
- 489 Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat. Biotechnol.27,847–850 (2009).
- 490 Nagy Z, Soutoglou E. DNA repair: easy to visualize, difficult to elucidate. Trends Cell Biol.19,617–629 (2009).
- 491 Feuerhahn S, Egly JM. Tools to study DNA repair: what’s in the box? Trends Genet.24,467–474 (2008).
- 492 Tovkach A, Zeevi V, Tzfira T. Validation and expression of zinc finger nucleases in plant cells. Methods Mol. Biol.649,315–336 (2010).
- 493 De Muyt A, Pereira L, Vezon D et al. A high throughput genetic screen identifies new early meiotic recombination functions in Arabidopsis thaliana. PLoS Genet.5,e1000654 (2009).
- 494 Gates H, Mallon AM, Brown SDM, EUMODIC Consortium: high-throughput mouse phenotyping. Methods53,394–404 (2011).
- 495 Ringwald M, Eppig JT. Mouse mutants and phenotypes: accessing information for the study of mammalian gene function. Methods53,405–410 (2011).
- 496 Eichele G, Diez-Roux G. High-throughput analysis of gene expression on tissue sections by in situ hybridization. Methods53,417–423 (2011).
- 497 Lindhout BI, Pinas JE, Hooykaas PJ, van der Zaal BJ. Employing libraries of zinc finger artificial transcription factors to screen for homologous recombination mutants in Arabidopsis. Plant J.48,475–483 (2006).
- 498 Gressel J, Levy AA. Agriculture: the selector of improbable mutations. Proc. Natl Acad. Sci.103,12215–12216 (2006).
- 499 Lim MH, Song H, Olmon ED, Dervan EE, Barton JK. Sensitivity of Ru(bpy)2dppz2+ luminescence to DNA defects. Inorg. Chem.48,5392–5397 (2009).
- 500 Boal AK, Genereux JC, Sontz PA, Gralnick JA, Newman DK, Barton JK. Redox signaling between DNA repair proteins for efficient lesion detection. Proc. Natl Acad. Sci.106,15237–15242 (2009).
- 501 Zonno KD, Terry PF, Terry SF. A measure of truth in genetic testing. Genet. Test. Mol. Biomarkers13,285–286 (2009).
- 502 Händel EM, Cathomen T. Zinc-finger nuclease based genome surgery: it’s all about specificity. Curr. Gene Ther.11,28–37 (2011).
- 503 Alwin S, Gere MB, Guhl E et al. Custom zinc-finger nucleases for use in human cells. Mol. Ther.12,610–617 (2005).
- 504 Cornu TI, Thibodeau-Beganny S, Guhl E et al. DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol. Ther.16,352–358 (2008).
- 505 Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH. Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol. Ther.16,707–717 (2008).
- 506 Segal DJ. Zinc-finger nucleases transition to the CoDA. Nat. Methods8,53–55 (2011).
- 507 Sander JD, Dahlborg EJ, Goodwin MJ et al. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat.Methods8,67–69 (2011).
- 508 Minczuk M, Papworth MA, Miller JC, Murphy MP, Klug A. Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA. Nucl. Acids Res.36,3926–3938 (2008).
- 509 Minczuk M. Engineered zinc finger proteins for manipulation of the human mitochondrial genome. Methods Mol. Biol.649,257–270 (2010).
- 510 Boch J, Scholze H, Schornack S et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science326,1509–1512 (2009).
- 511 Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science326,1501 (2009).
- 512 Scholze H, Boch J. TAL effector-DNA specificity. Virulence1,5, 428–432 (2010).
- 513 Li T, Huang S, Zhao X et al. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucl. Acids Res.39,6315–6325 (2011).
- 514 Hockemeyer D, Wang H, Kiani S et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat. Biotechnol.29,731–734 (2011).
- 515 Mussolino C, Morbitzer R, Lütge F, Dannemann N, Lahaye T, Cathomen T. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucl. Acids Res. DOI:10.1093/nar/gkr597 (2011).
- 516 Zaremba M, Siksnys V. Molecular scissors under light control. Proc. Natl Acad. Sci.107,1259–1260 (2010).
- 517 Yang WY, Breiner B, Kovalenko SV. C-Lysine conjugates: pH-controlled light-activated reagents for efficient double-stranded DNA cleavage with implications for cancer therapy. J. Am. Chem. Soc.131,11458–11470 (2009).
- 518 Strickland D, Moffat K, Sosnick TR. Light-activated DNA binding in a designed allosteric protein. Proc. Natl Acad. Sci.105,10709–10714 (2008).
- 519 Doyon Y, Choi VM, Xia DF, Thuy D, Gregory PD, Holmes MC. Transient cold shock enhances zinc-finger nuclease–mediated gene disruption. Nat. Methods7,459–460 (2010).
- 520 Xu SY, Corvaglia AR, Chan SH, Zheng Y, Linder P. A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300. Nucl. Acids Res.39(13),5597–5610 (2011).
- 601 PyMOL, DeLano Scientific LLC. www.delanoscientific.com