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Rational Design of an Artificial Nuclease by Engineering a Hetero-Dinuclear Center of Mg-Heme in Myoglobin. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04572] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Mori T, Mori K, Tobimatsu T, Sera T. Sandwiched zinc-finger nucleases demonstrating higher homologous recombination rates than conventional zinc-finger nucleases in mammalian cells. Bioorg Med Chem Lett 2014; 24:813-6. [PMID: 24412074 DOI: 10.1016/j.bmcl.2013.12.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 01/26/2023]
Abstract
We previously reported that our sandwiched zinc-finger nucleases (ZFNs), in which a DNA cleavage domain is inserted between two artificial zinc-finger proteins, cleave their target DNA much more efficiently than conventional ZFNs in vitro. In the present study, we compared DNA cleaving efficiencies of a sandwiched ZFN with those of its corresponding conventional ZFN in mammalian cells. Using a plasmid-based single-strand annealing reporter assay in HEK293 cells, we confirmed that the sandwiched ZFN induced homologous recombination more efficiently than the conventional ZFN; reporter activation by the sandwiched ZFN was more than eight times that of the conventional one. Western blot analysis showed that the sandwiched ZFN was expressed less frequently than the conventional ZFN, indicating that the greater DNA-cleaving activity of the sandwiched ZFN was not due to higher expression of the sandwiched ZFN. Furthermore, an MTT assay demonstrated that the sandwiched ZFN did not have any significant cytotoxicity under the DNA-cleavage conditions. Thus, because our sandwiched ZFN cleaved more efficiently than its corresponding conventional ZFN in HEK293 cells as well as in vitro, sandwiched ZFNs are expected to serve as an effective molecular tool for genome editing in living cells.
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Affiliation(s)
- Tomoaki Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Koichi Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takamasa Tobimatsu
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Sera
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
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[Application of artificial DNA-binding proteins and artificial nucleases to prevention of virus infection: development of virus-resistant plants and protein-based anti-viral drugs]. Uirusu 2014; 64:147-54. [PMID: 26437837 DOI: 10.2222/jsv.64.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Various DNA viruses are known to cause severe infectious diseases in both plants and mammals, including humans. For many of these infectious diseases, we have yet to find an effective prevention or treatment. Therefore, new methodologies for the prevention of virus infections in both agricultural crops and humans have been vigorously sought for a long time. One attractive approach to the prevention is inhibition of virus replication. We first inhibited virus replication by blocking binding of a viral replication protein, which initiates virus replication, to its replication origin, with using an artificial DNA-binding protein. We demonstrated that this new methodology was very effective in plants and mammalian cells: especially, we created transgenic plants that were immune to a geminivirus. We also developed novel protein-based antiviral drugs by fusing a cell-penetrating peptide to an artificial DNA-binding protein. Furthermore, we successfully generated a more effective protein-based antiviral, which was one hundred thousand times more active than the antiviral chemical drug Cidofovia, by alternatively fusing an DNA-cleaving enzyme to an artificial DNA-binding protein. Since this artificial protein has little cytotoxicity, it is expected that it will be used as a new antiviral drug.
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Mino T, Mori T, Aoyama Y, Sera T. Gene- and protein-delivered zinc finger-staphylococcal nuclease hybrid for inhibition of DNA replication of human papillomavirus. PLoS One 2013; 8:e56633. [PMID: 23437192 PMCID: PMC3577882 DOI: 10.1371/journal.pone.0056633] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 01/11/2013] [Indexed: 12/28/2022] Open
Abstract
Previously, we reported that artificial zinc-finger proteins (AZPs) inhibited virus DNA replication in planta and in mammalian cells by blocking binding of a viral replication protein to its replication origin. However, the replication mechanisms of viruses of interest need to be disentangled for the application. To develop more widely applicable methods for antiviral therapy, we explored the feasibility of inhibition of HPV-18 replication as a model system by cleaving its viral genome. To this end, we fused the staphylococcal nuclease cleaving DNA as a monomer to an AZP that binds to the viral genome. The resulting hybrid nuclease (designated AZP–SNase) cleaved its target DNA plasmid efficiently and sequence-specifically in vitro. Then, we confirmed that transfection with a plasmid expressing AZP–SNase inhibited HPV-18 DNA replication in transient replication assays using mammalian cells. Linker-mediated PCR analysis revealed that the AZP–SNase cleaved an HPV-18 ori plasmid around its binding site. Finally, we demonstrated that the protein-delivered AZP–SNase inhibited HPV-18 DNA replication as well and did not show any significant cytotoxicity. Thus, both gene- and protein-delivered hybrid nucleases efficiently inhibited HPV-18 DNA replication, leading to development of a more universal antiviral therapy for human DNA viruses.
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Affiliation(s)
- Takashi Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Tomoaki Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Yasuhiro Aoyama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyoto, Japan
| | - Takashi Sera
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
- * E-mail:
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Xiao A, Wu Y, Yang Z, Hu Y, Wang W, Zhang Y, Kong L, Gao G, Zhu Z, Lin S, Zhang B. EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering. Nucleic Acids Res 2012. [PMID: 23203870 PMCID: PMC3531095 DOI: 10.1093/nar/gks1144] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We report here the construction of engineered endonuclease database (EENdb) (http://eendb.zfgenetics.org/), a searchable database and knowledge base for customizable engineered endonucleases (EENs), including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). EENs are artificial nucleases designed to target and cleave specific DNA sequences. EENs have been shown to be a very useful genetic tool for targeted genome modification and have shown great potentials in the applications in basic research, clinical therapies and agricultural utilities, and they are specifically essential for reverse genetics research in species where no other gene targeting techniques are available. EENdb contains over 700 records of all the reported ZFNs and TALENs and related information, such as their target sequences, the peptide components [zinc finger protein-/transcription activator-like effector (TALE)-binding domains, FokI variants and linker peptide/framework], the efficiency and specificity of their activities. The database also lists EEN engineering tools and resources as well as information about forms and types of EENs, EEN screening and construction methods, detection methods for targeting efficiency and many other utilities. The aim of EENdb is to represent a central hub for EEN information and an integrated solution for EEN engineering. These studies may help to extract in-depth properties and common rules regarding ZFN or TALEN efficiency through comparison of the known ZFNs or TALENs.
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Affiliation(s)
- An Xiao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, China
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Schierling B, Dannemann N, Gabsalilow L, Wende W, Cathomen T, Pingoud A. A novel zinc-finger nuclease platform with a sequence-specific cleavage module. Nucleic Acids Res 2012; 40:2623-38. [PMID: 22135304 PMCID: PMC3315325 DOI: 10.1093/nar/gkr1112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 12/18/2022] Open
Abstract
Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration, the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs, ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at addressed sites with a >1000-fold preference over unaddressed PvuII sites in vitro as well as in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results present the ZF-PvuII platform as a valid alternative to conventional ZFNs.
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Affiliation(s)
- Benno Schierling
- Institute of Biochemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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Zhang X, Chen Y. Photo-controlled metal-ion (Zn2+ and Cd2+) release in aqueous Tween-20 micelle solution. Phys Chem Chem Phys 2012; 14:2312-6. [DOI: 10.1039/c2cp23265k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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.
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Shinomiya K, Mori T, Aoyama Y, Sera T. Unidirectional cloning by cleaving heterogeneous sites with a single sandwiched zinc finger nuclease. Biochem Biophys Res Commun 2011; 414:733-6. [PMID: 22001928 DOI: 10.1016/j.bbrc.2011.09.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
Abstract
We previously developed a novel type of zinc finger nucleases (ZFNs), sandwiched ZFNs that can discriminate DNA substrates from cleavage products and thus cleave DNA much more efficiently than conventional ZFNs as well as perform with multiple turnovers like restriction endonucleases. In the present study, we used the sandwiched ZFN to unidirectionally clone exogenous genes into target vectors by cleaving heterogeneous sites that contained heterogeneous spacer DNAs between two zinc-finger protein binding sites with a single sandwiched ZFN. We demonstrated that the sandwiched ZFN cleaved a 40-fold excess of both insert and vector plasmids within 1h and confirmed by sequencing that the resulting recombinants harbored the inserted DNA fragment in the desired orientation. Because sandwiched ZFNs can recognize and cleave a variety of long (≥ 26-bp) target DNAs, they may not only expand the utility of ZFNs for construction of recombinant plasmids, but also serve as useful meganucleases for synthesis of artificial genomes.
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Affiliation(s)
- Kazuki Shinomiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Lee SJ, Michalek JL, Besold AN, Rokita SE, Michel SLJ. Classical Cys2His2 Zinc Finger Peptides Are Rapidly Oxidized by Either H2O2 or O2 Irrespective of Metal Coordination. Inorg Chem 2011; 50:5442-50. [DOI: 10.1021/ic102252a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Seung Jae Lee
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Jamie L. Michalek
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Angelique N. Besold
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Steven E. Rokita
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-4454, United States
| | - Sarah L. J. Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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Zhang X, Chen Y. Construction and Properties of a Phototriggered Cd2+ Release System. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ling JQ, Hou A, Hoffman AR. Long-range DNA interactions are specifically altered by locked nucleic acid-targeting of a CTCF binding site. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:24-33. [PMID: 21111075 DOI: 10.1016/j.bbagrm.2010.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 11/10/2010] [Accepted: 11/15/2010] [Indexed: 01/21/2023]
Abstract
Long-range DNA interactions play an important role in gene expression. CCCTC-binding factor (CTCF), a ubiquitously expressed and evolutionarily conserved 11-zinc-finger DNA binding protein, is intimately involved in gene regulation, helping to establish and maintain chromatin architecture and long-range DNA interactions. In order to study the effects of manipulating long range chromatin interactions in the regulation of the neurofibromatosis gene NF1, we targeted Zorro locked nucleic acids (Zorro LNA) to a single CTCF binding site at an NF1 locus in human fibroblast cells. Using chromatin immunoprecipitation, we determined that this Zorro LNA altered CTCF and RNA polymerase II binding at three separate and distinct regions in the NF1 gene. This change in protein binding was associated with changes in long-range DNA interactions at the NF1 locus and downregulation of NF1 gene expression. This study describes an efficient and convenient method to manipulate chromatin structure and alter gene expression that is regulated by long-range DNA interactions without changing the DNA sequence. The use of specific Zorro LNA probes may facilitate our efforts to understand the interactions between chromatin architecture and gene expression.
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Affiliation(s)
- Jian Qun Ling
- Medical Service, VA Palo Alto Health Care System and Department of Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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Sandwiched zinc-finger nucleases harboring a single-chain FokI dimer as a DNA-cleavage domain. Biochem Biophys Res Commun 2009; 390:694-7. [DOI: 10.1016/j.bbrc.2009.10.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 10/07/2009] [Indexed: 11/23/2022]
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Abstract
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.Two types of artificial tools that cut double-stranded DNA through hydrolysis of target phosphodiester linkages have been recently developed. One is the chemistry-based artificial restriction DNA cutter (ARCUT) that is composed of a Ce(IV)-EDTA complex, which catalyses DNA hydrolysis, and a pair of pseudo-complementary peptide nucleic acid fragments for sequence recognition. Another type of DNA cutter, zinc finger nuclease (ZFN), is composed of the nuclease domain of naturally occurring FokI restriction endonuclease and a designed zinc finger DNA-binding domain. For both of these artificial tools, the scission site and specificity can be freely chosen according to our needs, so that even huge genomic DNA sequences can be selectively cut at the target site. In this article, the chemical structures, preparation, properties, and typical applications of these two man-made tools are described.
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Affiliation(s)
- Hitoshi Katada
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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