Artificial Restriction DNA Cutters as New Tools for Gene Manipulation

The final cut. Two types of artificial tools (artificial restriction DNA cutter and zinc finger nuclease) that cut double‐stranded DNA through hydrolysis of target phosphodiester linkages, have been recently developed. The chemical structures, preparation, properties, and typical applications of these two man‐made tools are reviewed.

[1]  P. Dervan,et al.  Orientation Preferences of Pyrrole−Imidazole Polyamides in the Minor Groove of DNA , 1997 .

[2]  C. Pabo,et al.  Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. , 1994, Science.

[3]  J. Cowan,et al.  Catalytic hydrolysis of DNA by metal ions and complexes , 2001, JBIC Journal of Biological Inorganic Chemistry.

[4]  A Klug,et al.  Design of polyzinc finger peptides with structured linkers. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[5]  David A Wright,et al.  High-frequency homologous recombination in plants mediated by zinc-finger nucleases. , 2005, The Plant journal : for cell and molecular biology.

[6]  P. Dervan,et al.  Sequence-specific cleavage of double helical DNA by triple helix formation. , 1987, Science.

[7]  M. Komiyama,et al.  Progress towards synthetic enzymes for phosphoester hydrolysis. , 1998, Current opinion in chemical biology.

[8]  B. Stoddard Homing endonuclease structure and function , 2005, Quarterly Reviews of Biophysics.

[9]  David R. Liu,et al.  Directed evolution and substrate specificity profile of homing endonuclease I-SceI. , 2006, Journal of the American Chemical Society.

[10]  P. Dervan,et al.  Recognition of seven base pair sequences in the minor groove of DNA by ten-ring pyrrole-imidazole polyamide hairpins , 1997 .

[11]  Hongzhe Sun,et al.  DNA hydrolysis promoted by di- and multi-nuclear metal complexes , 2004 .

[12]  C. Barbas,et al.  Building zinc fingers by selection: toward a therapeutic application. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[13]  N. Pavletich,et al.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.

[14]  Judith N. Burstyn,et al.  Toward the development of metal-based synthetic nucleases and peptidases: a rationale and progress report in applying the principles of coordination chemistry , 1998 .

[15]  Makoto Komiyama,et al.  Solid-phase synthesis of pseudo-complementary peptide nucleic acids , 2008, Nature Protocols.

[16]  S Chandrasegaran,et al.  A detailed study of the substrate specificity of a chimeric restriction enzyme. , 1999, Nucleic acids research.

[17]  Adam James Waite,et al.  An improved zinc-finger nuclease architecture for highly specific genome editing , 2007, Nature Biotechnology.

[18]  B. Dujon,et al.  Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae , 1995, Molecular and cellular biology.

[19]  J. Joung,et al.  Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Carl O. Pabo,et al.  Drug discovery with engineered zinc-finger proteins , 2003, Nature Reviews Drug Discovery.

[21]  K. Vasquez,et al.  Manipulating the mammalian genome by homologous recombination , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Komiyama,et al.  Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity , 2008, Nature Protocols.

[23]  B. Dujon,et al.  Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. , 1993, Nucleic acids research.

[24]  Zhilei Chen,et al.  Directed evolution of homing endonuclease I-SceI with altered sequence specificity. , 2009, Protein engineering, design & selection : PEDS.

[25]  S Chandrasegaran,et al.  Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[26]  S Chandrasegaran,et al.  Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. , 2000, Nucleic acids research.

[27]  Jeffrey C. Miller,et al.  Highly efficient endogenous human gene correction using designed zinc-finger nucleases , 2005, Nature.

[28]  J. Francois,et al.  Sequence-specific recognition and cleavage of duplex DNA via triple-helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[29]  A Klug,et al.  Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[30]  D. Baker,et al.  Computational redesign of endonuclease DNA binding and cleavage specificity , 2006, Nature.

[31]  Frédéric Pâques,et al.  Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. , 2007, Current gene therapy.

[32]  Tomoyuki Okamoto,et al.  Enhanced cleavage of double-stranded DNA by artificial zinc-finger nuclease sandwiched between two zinc-finger proteins. , 2008, Biochemistry.

[33]  A. Klug,et al.  A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter , 2001, Nature Biotechnology.

[34]  J. Joung,et al.  DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

[35]  P. Rouet,et al.  Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[36]  J. S. Kim,et al.  Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[37]  P. Dervan,et al.  Strand Selective Cleavage of DNA by Diastereomers of Hairpin Polyamide-seco-CBI Conjugates , 2000 .

[38]  J. Joung,et al.  A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[39]  J. Francois,et al.  Sequence-targeted cleavage of single- and double-stranded DNA by oligothymidylates covalently linked to 1,10-phenanthroline. , 1989, The Journal of biological chemistry.

[40]  M. Komiyama,et al.  Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex. , 2002, Nucleic acids research.

[41]  J. Orange,et al.  Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases , 2008, Nature Biotechnology.

[42]  M. Egholm,et al.  Sequence selective double strand DNA cleavage by peptide nucleic acid (PNA) targeting using nuclease S1. , 1993, Nucleic acids research.

[43]  David Baltimore,et al.  Chimeric Nucleases Stimulate Gene Targeting in Human Cells , 2003, Science.

[44]  Toni Cathomen,et al.  Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases , 2007, Nature Biotechnology.

[45]  J. Bashkin Hydrolysis of phosphates, esters and related substrates by models of biological catalysts. , 1999, Current opinion in chemical biology.

[46]  Barry L. Stoddard,et al.  Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins , 2009, Nucleic acids research.

[47]  M. Komiyama,et al.  Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA , 2007, Nucleic acids research.

[48]  B. Stoddard,et al.  Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. , 2001, Nucleic acids research.

[49]  T. C. Bruice,et al.  RECENT STUDIES OF NUCLEOPHILIC, GENERAL-ACID, AND METAL ION CATALYSIS OF PHOSPHATE DIESTER HYDROLYSIS , 1999 .

[50]  R. Krämer,et al.  DNA hydrolysis by inorganic catalysts , 1999, Applied Microbiology and Biotechnology.

[51]  P. Nielsen,et al.  Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[52]  M. Komiyama,et al.  Origin of high fidelity in target-sequence recognition by PNA-Ce(IV)/EDTA combinations as site-selective DNA cutters. , 2009, Journal of the American Chemical Society.

[53]  J. Trauger,et al.  RECOGNITION OF 16 BASE PAIRS IN THE MINOR GROOVE OF DNA BY A PYRROLE-IMIDAZOLE POLYAMIDE DIMER , 1998 .

[54]  S J Franklin,et al.  Lanthanide-mediated DNA hydrolysis. , 2001, Current opinion in chemical biology.

[55]  M. Komiyama,et al.  Hydrolysis of Oligonucleotides by Homogeneous Ce (IV)/EDTA Complex , 2000 .

[56]  J. Bitinaite,et al.  FokI dimerization is required for DNA cleavage. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Dana Carroll,et al.  Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.