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Vallejo D, Nikoomanzar A, Paegel BM, Chaput JC. Fluorescence-Activated Droplet Sorting for Single-Cell Directed Evolution. ACS Synth Biol 2019; 8:1430-1440. [PMID: 31120731 DOI: 10.1021/acssynbio.9b00103] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology aims to improve human health and the environment by repurposing biological enzymes for use in practical applications. However, natural enzymes often function with suboptimal activity when engineered into biological pathways or challenged to recognize unnatural substrates. Overcoming this problem requires efficient directed evolution methods for discovering new enzyme variants that function with a desired activity. Here, we describe the construction, validation, and application of a fluorescence-activated droplet sorting (FADS) instrument that was established to evolve enzymes for synthesizing and modifying artificial genetic polymers (XNAs). The microfluidic system enables droplet sorting at ∼2-3 kHz using fluorescent sensors that are responsive to enzymatic activity. The ability to evolve nucleic acid enzymes with customized properties will uniquely drive emerging applications in synthetic biology, biotechnology, and healthcare.
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Affiliation(s)
| | | | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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2
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Kapusi E, Stöger E. Detection of CRISPR/Cas9-Induced Genomic Fragment Deletions in Barley and Generation of Homozygous Edited Lines via Embryogenic Pollen Culture. Methods Mol Biol 2018; 1789:9-20. [PMID: 29916068 DOI: 10.1007/978-1-4939-7856-4_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The CRISPR/Cas9 system from Streptococcus pyogenes is an increasingly popular tool for genome editing due to its ease of application. Here we demonstrate genomic DNA fragment removal using RNA directed Cas9 nuclease in barley. The high mutation frequency confirms the exceptional efficiency of the system and its suitability for generating loss-of-function mutant lines that may be used in functional genetics approaches to study endomembrane trafficking pathways and posttranslational protein modifications. The generation of doubled haploids from genome edited plants allows the recovery of true breeding lines that are instantly homozygous for the edited alleles.
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Affiliation(s)
- Eszter Kapusi
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eva Stöger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
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3
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Genome engineering in Bacillus anthracis using tyrosine site-specific recombinases. PLoS One 2017; 12:e0183346. [PMID: 28829806 PMCID: PMC5567495 DOI: 10.1371/journal.pone.0183346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/02/2017] [Indexed: 01/07/2023] Open
Abstract
Tyrosine site-specific recombinases (T-SSR) are polynucleotidyltransferases that catalyze cutting and joining reactions between short specific DNA sequences. We developed three systems for performing genetic modifications in Bacillus anthracis that use T-SSR and their cognate target sequences, namely Escherichia coli bacteriophage P1 Cre-loxP, Saccharomyces cerevisiae Flp-FRT, and a newly discovered IntXO-PSL system from B. anthracis plasmid pXO1. All three tyrosine recombinase systems were used for creation of a B. anthracis sporulation-deficient, plasmid-free strain deleted for ten proteases which had been identified by proteomic analysis as being present in the B. anthracis secretome. This strain was used successfully for production of various recombinant proteins, including several that are candidates for inclusion in improved anthrax vaccines. These genetic tools developed for DNA manipulation in B. anthracis were also used for construction of strains having chromosomal insertions of 1, 2, or 3 adjacent atxA genes. AtxA is a B. anthracis global transcriptional regulator required for the response of B. anthracis virulence factor genes to bicarbonate. We found a positive correlation between the atxA copy number and the expression level of the pagA gene encoding B. anthracis protective antigen, when strains were grown in a carbon dioxide atmosphere. These results demonstrate that the three T-SSR systems described here provide effective tools for B. anthracis genome editing. These T-SSR systems may also be applicable to other prokaryotes and to eukaryotes.
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4
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Xu S, Cao S, Zou B, Yue Y, Gu C, Chen X, Wang P, Dong X, Xiang Z, Li K, Zhu M, Zhao Q, Zhou G. An alternative novel tool for DNA editing without target sequence limitation: the structure-guided nuclease. Genome Biol 2016; 17:186. [PMID: 27634179 PMCID: PMC5025552 DOI: 10.1186/s13059-016-1038-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/05/2016] [Indexed: 01/31/2023] Open
Abstract
Engineered endonucleases are a powerful tool for editing DNA. However, sequence preferences may limit their application. We engineer a structure-guided endonuclease (SGN) composed of flap endonuclease-1 (FEN-1), which recognizes the 3′ flap structure, and the cleavage domain of Fok I (Fn1), which cleaves DNA strands. The SGN recognizes the target DNA on the basis of the 3′ flap structure formed between the target and the guide DNA (gDNA) and cut the target through its Fn1 dimerization. Our results show that the SGN, guided by a pair of gDNAs, cleaves transgenic reporter gene and endogenous genes in zebrafish embryonic genome.
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Affiliation(s)
- Shu Xu
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Shasha Cao
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Yunyun Yue
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Chun Gu
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Xin Chen
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Pei Wang
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Xiaohua Dong
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Zheng Xiang
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Kai Li
- College of Pharmaceutical Science, Soochow University, No. 199, Renai Road, Suzhou, 215123, People's Republic of China
| | - Minsheng Zhu
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China.
| | - Qingshun Zhao
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China.
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China.
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5
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Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering. Sci Rep 2016; 6:30130. [PMID: 27444945 PMCID: PMC4957104 DOI: 10.1038/srep30130] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets.
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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Xiao X, Wu T, Gu F, Zhao M. Generation of artificial sequence-specific nucleases via a preassembled inert-template. Chem Sci 2015; 7:2051-2057. [PMID: 29899930 PMCID: PMC5968549 DOI: 10.1039/c5sc04398k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/07/2015] [Indexed: 02/01/2023] Open
Abstract
Sequence specific nucleases are important tools for processing nucleic acids in a predictable way. Herein, we demonstrate a conceptually new approach for generating sequence-specific nucleases via a preassembled inert-template (PAIT). A fairly stable DNase I/inert-DNA complex was prepared with a customized sequence specificity for a target DNA which contains a sequence complementary to the inert-DNA template. The complex could efficiently cleave the targeted sequence within either a long double-stranded DNA or a single-stranded DNA without affecting other unrelated DNA strands. The discrimination factor against single-base mismatch strands within a 14 nt target region was as high as 25.3. The strategy was also successfully applied to RNase A. Our findings may hold great potential for the development of a number of new powerful enzymatic tools.
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Affiliation(s)
- Xianjin Xiao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Feidan Gu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
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8
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Wang H, Hurt N, Dunbar WB. Measuring and modeling the kinetics of individual DNA-DNA polymerase complexes on a nanopore. ACS NANO 2013; 7:3876-3886. [PMID: 23565679 PMCID: PMC3682681 DOI: 10.1021/nn401180j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The assembly of a DNA-DNA polymerase binary complex is the precursory step in genome replication, in which the enzyme binds to the 3' junction created when a primer binds to its complementary substrate. In this study, we use an active control method for observing the binding interaction between Klenow fragment (exo-) (KF) in the bulk-phase chamber above an α-hemolysin (α-HL) nanopore and a single DNA molecule tethered noncovalently in the nanopore. Specifically, the control method regulates the temporal availability of the primer-template DNA to KF binding and unbinding above the nanopore, on millisecond-to-second time scales. Our nanopore measurements support a model that incorporates two mutually exclusive binding states of KF to DNA at the primer-template junction site, termed "weakly bound" and "strongly bound" states. The composite binding affinity constant, the equilibrium constant between the weak and strong states, and the unbound-to-strong association rate are quantified from the data using derived modeling analysis. The results support that the strong state is in the nucleotide incorporation pathway, consistent with other nanopore assays. Surprisingly, the measured unbound-to-strong association process does not fit a model that admits binding of only free (unbound) KF to the tethered DNA but does fit an association rate that is proportional to the total (unbound and DNA-bound) KF concentration in the chamber above the nanopore. Our method provides a tool for measuring pre-equilibrium kinetics one molecule at a time, serially and for tens of thousands of single-molecule events, and can be used for other polynucleotide-binding enzymes.
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Affiliation(s)
- Hongyun Wang
- Department of Applied Mathematics and Statistics, University of California, Santa Cruz, 95064
| | - Nicholas Hurt
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 95064
| | - William B. Dunbar
- Department of Computer Engineering, University of California, Santa Cruz, 95064
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9
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Yau YY, Stewart CN. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol 2013; 13:36. [PMID: 23617583 PMCID: PMC3689633 DOI: 10.1186/1472-6750-13-36] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.
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Affiliation(s)
- Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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10
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Abi-Ghanem J, Chusainow J, Karimova M, Spiegel C, Hofmann-Sieber H, Hauber J, Buchholz F, Pisabarro MT. Engineering of a target site-specific recombinase by a combined evolution- and structure-guided approach. Nucleic Acids Res 2012; 41:2394-403. [PMID: 23275541 PMCID: PMC3575804 DOI: 10.1093/nar/gks1308] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Site-specific recombinases (SSRs) can perform DNA rearrangements, including deletions, inversions and translocations when their naive target sequences are placed strategically into the genome of an organism. Hence, in order to employ SSRs in heterologous hosts, their target sites have to be introduced into the genome of an organism before the enzyme can be practically employed. Engineered SSRs hold great promise for biotechnology and advanced biomedical applications, as they promise to extend the usefulness of SSRs to allow efficient and specific recombination of pre-existing, natural genomic sequences. However, the generation of enzymes with desired properties remains challenging. Here, we use substrate-linked directed evolution in combination with molecular modeling to rationally engineer an efficient and specific recombinase (sTre) that readily and specifically recombines a sequence present in the HIV-1 genome. We elucidate the role of key residues implicated in the molecular recognition mechanism and we present a rationale for sTre’s enhanced specificity. Combining evolutionary and rational approaches should help in accelerating the generation of enzymes with desired properties for use in biotechnology and biomedicine.
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Affiliation(s)
- Josephine Abi-Ghanem
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01037 Dresden, Germany
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Karimova M, Abi-Ghanem J, Berger N, Surendranath V, Pisabarro MT, Buchholz F. Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system. Nucleic Acids Res 2012; 41:e37. [PMID: 23143104 PMCID: PMC3553980 DOI: 10.1093/nar/gks1037] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the 'genetic toolbox' that can be used alone or in combination with other SSRs in heterologous hosts.
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Affiliation(s)
- Madina Karimova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, University of Technology, Fetscherstrasse 74, 01307 Dresden, Germany
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12
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Staining-free gel electrophoresis-based multiplex enzyme assay using DNA and peptide dual-functionalized gold nanoparticles. Electrophoresis 2012; 33:1288-91. [DOI: 10.1002/elps.201100591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Proudfoot C, McPherson AL, Kolb AF, Stark WM. Zinc finger recombinases with adaptable DNA sequence specificity. PLoS One 2011; 6:e19537. [PMID: 21559340 PMCID: PMC3084882 DOI: 10.1371/journal.pone.0019537] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/31/2011] [Indexed: 12/31/2022] Open
Abstract
Site-specific recombinases have become essential tools in genetics and molecular biology for the precise excision or integration of DNA sequences. However, their utility is currently limited to circumstances where the sites recognized by the recombinase enzyme have been introduced into the DNA being manipulated, or natural 'pseudosites' are already present. Many new applications would become feasible if recombinase activity could be targeted to chosen sequences in natural genomic DNA. Here we demonstrate efficient site-specific recombination at several sequences taken from a 1.9 kilobasepair locus of biotechnological interest (in the bovine β-casein gene), mediated by zinc finger recombinases (ZFRs), chimaeric enzymes with linked zinc finger (DNA recognition) and recombinase (catalytic) domains. In the "Z-sites" tested here, 22 bp casein gene sequences are flanked by 9 bp motifs recognized by zinc finger domains. Asymmetric Z-sites were recombined by the concomitant action of two ZFRs with different zinc finger DNA-binding specificities, and could be recombined with a heterologous site in the presence of a third recombinase. Our results show that engineered ZFRs may be designed to promote site-specific recombination at many natural DNA sequences.
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Affiliation(s)
- Chris Proudfoot
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Arlene L. McPherson
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Andreas F. Kolb
- Nutrition and Epigenetics Group, Life Long Health Division, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - W. Marshall Stark
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- * E-mail:
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Buchholz F, Hauber J. In vitro evolution and analysis of HIV-1 LTR-specific recombinases. Methods 2010; 53:102-9. [PMID: 20600935 DOI: 10.1016/j.ymeth.2010.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Revised: 06/14/2010] [Accepted: 06/18/2010] [Indexed: 12/01/2022] Open
Abstract
Current antiretroviral therapies would greatly benefit from the concurrent removal of integrated HIV-1 proviral DNA from the patient's cells. In this review, we describe an experimental strategy that allowed the engineering and functional analysis of a HIV-1 LTR-specific recombinase (Tre-recombinase). We furthermore provide protocols that are utilized for the investigation of Tre's antiretroviral activity in infected tissue cultures as well as in infected humanized Rag2(-/-)γc(-/-) mice.
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Affiliation(s)
- Frank Buchholz
- Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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