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Wu P, Li X, Yang M, Huang Z, Mo H, Li T, Zhang Y, Li H. High-throughput, one-step screening, cloning and expression based on the lethality of DpnI in Escherichia coli. Biochem Biophys Res Commun 2018; 504:177-183. [PMID: 30172375 DOI: 10.1016/j.bbrc.2018.08.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/25/2018] [Indexed: 11/17/2022]
Abstract
The manipulation of recombinant DNA has been an integral step in molecular biology to date. A number of strategies have been developed over the years, as traditional cloning methods are time consuming, have high backgrounds and low efficiency and are often limited by the number of suitable restriction sites available. Here, we constructed a series of new positive-selection-based cloning vectors that overcome most of the above mentioned drawbacks and can be applied in both eukaryotic and prokaryotic systems. This strategy is based on the extreme toxicity of DpnI in wild-type E. coli and the inactivation of this lethality by the introduction of target gene within multiple cloning sites. There are no rapid approaches for identifying soluble proteins for high-throughput screening. In this study, we combined this highly efficient cloning strategy with rapid identification of soluble proteins to construct vectors with multiple fusion tags, such as MBP, GST, CBD, NusA, and Sumo, to generate enzymes with potential diagnostic, industrial or therapeutic applications. Thus, this versatile positive-selection-based technology is appropriate for routine cloning, DNA library construction, and high-throughput screening for the expression of proteins of interest.
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Affiliation(s)
- Peijie Wu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Xiaoyan Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Maocheng Yang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Zhengzhi Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Hongya Mo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Ting Li
- Chinese Academy of Inspection and Quarantine, China
| | - Yuan Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Hongtao Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China.
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2
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Tafoya-Ramírez MD, Padilla-Vaca F, Ramírez-Saldaña AP, Mora-Garduño JD, Rangel-Serrano Á, Vargas-Maya NI, Herrera-Gutiérrez LJ, Franco B. Replacing Standard Reporters from Molecular Cloning Plasmids with Chromoproteins for Positive Clone Selection. Molecules 2018; 23:molecules23061328. [PMID: 29857551 PMCID: PMC6099721 DOI: 10.3390/molecules23061328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 11/23/2022] Open
Abstract
Cloning and expression plasmids are the workhorses of modern molecular biology. Despite the pathway paved by synthetic biology, laboratories around the globe still relay on standard cloning techniques using plasmids with reporter proteins for positive clone selection, such as β-galactosidase alpha peptide complementation for blue/white screening or ccdB, which encodes for a toxic DNA gyrase. These reporters, when interrupted, serve as a positive clone detection system. In the present report, we show that molecular cloning plasmids bearing the coding sequence for a 25.4 kDa protein, AmilCP, encoded by a 685 bp gene, that is well expressed in Escherichia coli, render blue-purple colonies. Using this reporter protein, we developed and tested a cloning system based on the constitutive expression of the non-toxic AmilCP protein, that once interrupted, the loss of purple color serves to facilitate positive clone selection. The main advantage of this system is that is less expensive than other systems since media do not contain chromogenic markers such as X-gal, which is both expensive and cumbersome to prepare and use, or inductors such as IPTG. We also designed an inducible expression plasmid suitable for recombinant protein expression that also contains AmilCP cloning selection marker, a feature not commonly found in protein expression plasmids. The use of chromogenic reporters opens an important avenue for its application in other organisms besides E. coli for clone selection or even for mutant selection.
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Affiliation(s)
| | - Felipe Padilla-Vaca
- Departamento de Biología, Universidad de Guanajuato, Noria Alta, 36050 Guanajuato, Mexico.
| | | | | | - Ángeles Rangel-Serrano
- Departamento de Biología, Universidad de Guanajuato, Noria Alta, 36050 Guanajuato, Mexico.
| | | | | | - Bernardo Franco
- Departamento de Biología, Universidad de Guanajuato, Noria Alta, 36050 Guanajuato, Mexico.
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3
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Use of adenylate kinase as a solubility tag for high level expression of T4 DNA ligase in Escherichia coli. Protein Expr Purif 2015; 109:79-84. [PMID: 25700573 DOI: 10.1016/j.pep.2015.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 11/20/2022]
Abstract
The discovery of T4 DNA ligase in 1960s was pivotal in the spread of molecular biotechnology. The enzyme has become ubiquitous for recombinant DNA routinely practiced in biomedical research around the globe. Great efforts have been made to express and purify T4 DNA ligase to meet the world demand, yet over-expression of soluble T4 DNA ligase in E. coli has been difficult. Here we explore the use of adenylate kinase to enhance T4 DNA ligase expression and its downstream purification. E.coli adenylate kinase, which can be expressed in active form at high level, was fused to the N-terminus of T4 DNA ligase. The resulting His-tagged AK-T4 DNA ligase fusion protein was greatly over-expressed in E. coli, and readily purified to near homogeneity via two purification steps consisting of Blue Sepharose and Ni-NTA chromatography. The purified AK-T4 DNA ligase not only is fully active for DNA ligation, but also can use ADP in addition to ATP as energy source since adenylate kinase converts ADP to ATP and AMP. Thus adenylate kinase may be used as a solubility tag to facilitate recombinant protein expression as well as their downstream purification.
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4
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Ma Z, Luo D, Huang A, Xu Y, Wang Y, Wei Y, Liang P. pKILLIN: a versatile positive-selection cloning vector based on the toxicity of Killin in Escherichia coli. Gene 2014; 544:228-35. [PMID: 24768186 DOI: 10.1016/j.gene.2014.04.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/16/2014] [Accepted: 04/19/2014] [Indexed: 11/26/2022]
Abstract
The invention of DNA cloning over 40 years ago marked the advent of molecular biology. The technique has now become a routine practice in any modern biomedical laboratory. Although positive-selection of recombinants in DNA cloning seems to be superior to blue/white selection based on the disruption of the lacZ gene, it is rarely practiced due to its high background, lack of multiple cloning sites, and inability to express the genes of interest or purify the protein products. Here we report the creation of a new positive-selection cloning vector dubbed pKILLIN, which overcomes all of the above pitfalls. The essence behind its high cloning efficiency is the extreme toxicity and small size of the toxic domain of killin, a recently discovered p53 target gene. Insertion inactivation of killin within the multiple cloning site via either blunt- or sticky-end ligation not only serves as a highly efficient cloning trap, but also may allow any cloned genes to be expressed as His-tagged fusion proteins for subsequent purification. Thus, pKILLIN is a versatile positive-selection vector ideal for cloning PCR products, making DNA libraries, as well as routine cloning and bacterial expression of genes.
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Affiliation(s)
- Zelong Ma
- Center for Growth, Metabolism and Aging, School of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Dan Luo
- Center for Growth, Metabolism and Aging, School of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Anliang Huang
- State Key Laboratory for Gene and Cell Therapy, Sichuan University, Chengdu, China
| | - Yang Xu
- Center for Growth, Metabolism and Aging, School of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yunxiao Wang
- Clover Biopharmaceuticals, Chengdu, China; State Key Laboratory for Gene and Cell Therapy, Sichuan University, Chengdu, China
| | - Yuquan Wei
- State Key Laboratory for Gene and Cell Therapy, Sichuan University, Chengdu, China
| | - Peng Liang
- Center for Growth, Metabolism and Aging, School of Life Sciences, Sichuan University, Chengdu 610064, China; Clover Biopharmaceuticals, Chengdu, China; State Key Laboratory for Gene and Cell Therapy, Sichuan University, Chengdu, China; GenHunter Corporation, 624 Grassmere Park, Nashville, TN 37211, USA.
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5
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Speltz EB, Regan L. White and green screening with circular polymerase extension cloning for easy and reliable cloning. Protein Sci 2013; 22:859-64. [PMID: 23592493 DOI: 10.1002/pro.2268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 11/08/2022]
Abstract
Cloning is an essential prerequisite to test protein design and engineering ideas. However, it is often time consuming, unreliable, and therefore frustrating. Here, we present a streamlined cloning strategy that incorporates a powerful white and green screening protocol to identify colonies with inserts. We use circular polymerase extension cloning, which is both ligation and sequence independent. Furthermore, our entire procedure requires only three quick steps and one enzyme making it easy to use, inexpensive, and tractable. We anticipate that this method will be particularly useful for protein engineers who frequently subclone or make focused deletion, insertion, or substitution libraries.
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Affiliation(s)
- Elizabeth B Speltz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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6
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Cheong DE, Chang WS, Kim GJ. A cloning vector employing a versatile β-glucosidase as an indicator for recombinant clones. Anal Biochem 2012; 425:166-8. [PMID: 22425541 DOI: 10.1016/j.ab.2012.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/06/2012] [Accepted: 03/08/2012] [Indexed: 11/17/2022]
Abstract
A mutant glucosidase, cpGluT, with activity toward chromogenic substrates (X-gal [5-bromo-4-chloro-3-idolyl-β-d-galactoside] and indican) and a fluorogenic 4-methylumbeliferyl-β-d-glucopyranoside (MUG) was constructed by replacing the monomeric β-glucosidase region (E314-N326) with designed multiple cloning sites. When expressed in hosts (lacZ+ and lacZ-), a vector containing the cpGluT produced a colored or fluorescent phenotype according to the substrate supplemented on LB plates without any inducer. cpGluT is readily incorporable into customized vectors and does not require special hosts to detect recombinant plasmids, thereby making screening recombinants more effective and less expensive.
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Affiliation(s)
- Dea-Eun Cheong
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Yong-Bong Dong, Buk-Gu, Gwangju 500-757, Republic of Korea
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7
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pGreen–S: A clone vector bearing absence of enhanced green fluorescent protein for screening recombinants. Anal Biochem 2009; 388:173-4. [DOI: 10.1016/j.ab.2009.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 01/26/2009] [Accepted: 02/03/2009] [Indexed: 11/20/2022]
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8
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A novel chromate reductase from Thermus scotoductus SA-01 related to old yellow enzyme. J Bacteriol 2008; 190:3076-82. [PMID: 18263719 DOI: 10.1128/jb.01766-07] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria can reduce toxic and carcinogenic Cr(VI) to insoluble and less toxic Cr(III). Thermus scotoductus SA-01, a South African gold mine isolate, has been shown to be able to reduce a variety of metals, including Cr(VI). Here we report the purification to homogeneity and characterization of a novel chromate reductase. The oxidoreductase is a homodimeric protein, with a monomer molecular mass of approximately 36 kDa, containing a noncovalently bound flavin mononucleotide cofactor. The chromate reductase is optimally active at a pH of 6.3 and at 65 degrees C and requires Ca(2+) or Mg(2+) for activity. Enzyme activity was also dependent on NADH or NADPH, with a preference for NADPH, coupling the oxidation of approximately 2 and 1.5 mol NAD(P)H to the reduction of 1 mol Cr(VI) under aerobic and anaerobic conditions, respectively. The K(m) values for Cr(VI) reduction were 3.5 and 8.4 microM for utilizing NADH and NADPH as electron donors, respectively, with corresponding V(max) values of 6.2 and 16.0 micromol min(-1) mg(-1). The catalytic efficiency (k(cat)/K(m)) of chromate reduction was 1.14 x 10(6) M(-1) s(-1), which was >50-fold more efficient than that of the quinone reductases and >180-fold more efficient than that of the nitroreductases able to reduce Cr(VI). The chromate reductase was identified to be encoded by an open reading frame of 1,050 bp, encoding a single protein of 38 kDa under the regulation of an Escherichia coli sigma(70)-like promoter. Sequence analysis shows the chromate reductase to be related to the old yellow enzyme family, in particular the xenobiotic reductases involved in the oxidative stress response.
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Dietrich C, Miller J, McKenzie G, Palkovics L, Balázs E, Palukaitis P, Maiss E. No recombination detected in artificial potyvirus mixed infections and between potyvirus derived transgenes and heterologous challenging potyviruses. ENVIRONMENTAL BIOSAFETY RESEARCH 2007; 6:207-18. [PMID: 18001687 DOI: 10.1051/ebr:2007042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Risk-assessment studies of virus-resistant transgenic plants (VRTPs) focussing on recombination of a plant virus with a transgenic sequence of a different virus should include a comparison of recombination frequencies between viruses in double-infected non-transgenic plants with those observed in singly infected transgenic plants to estimate recombination incidence in VRTPs. In this study, the occurrence of recombination events was investigated in non-transgenic plants double-infected with two different potyviruses, as well as in potyviral genomes in singly infected transgenic plants expressing potyvirus sequences. Different potyviruses, namely Potato virus A (PVA), Tobacco vein mottling virus (TVMV), two strains of Potato virus Y (PVY-O, PVY-H) and two strains of Plum pox virus (PPV-NAT, PPV-SK68), were used in three combinations for double infection of a common host. Furthermore, transgenic plants expressing either potyviral coat protein (CP), helicase (CI) or polymerase (NIb) coding sequences (PPV-NAT-CP, PVY-CI, PVY-NIb) were singly-infected with a heterologous potyvirus, which was not targeted by the respective transgenic resistance. To identify recombinant potyviral sequences, a sensitive RT-PCR was developed to detect up to one recombinant molecule out of 10(6) parental molecules. In 304 mixed infected non-transgenic plants, 92 mixed and 164 single infected transgenic plants screened for recombinant sequences no recombinant potyviral sequence was found. These results indicate that recombination events between different potyviruses in mixed infections and between a potyvirus infecting a potyvirus-resistant transgenic plant are likely to be very infrequent.
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Affiliation(s)
- Christof Dietrich
- German Collection of Microorganisms and Cell Cultures, Plant Virus Division, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
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Abstract
We describe a method for tracking RNA molecules in Escherichia coli that is sensitive to single copies of mRNA, and, using the method, we find that individual molecules can be followed for many hours in living cells. We observe distinct characteristic dynamics of RNA molecules, all consistent with the known life history of RNA in prokaryotes: localized motion consistent with the Brownian motion of an RNA polymer tethered to its template DNA, free diffusion, and a few examples of polymer chain dynamics that appear to be a combination of chain fluctuation and chain elongation attributable to RNA transcription. We also quantify some of the dynamics, such as width of the displacement distribution, diffusion coefficient, chain elongation rate, and distribution of molecule numbers, and compare them with known biophysical parameters of the E. coli system.
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Affiliation(s)
- Ido Golding
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Gutkina N, Varlakhanova NV, Lysova MV, Kovalenko SP. Limitations on the recombinant plasmid selection by Lac(+)/Lac(-) colony phenotype detection. Biochem Biophys Res Commun 2002; 298:37-40. [PMID: 12379216 DOI: 10.1016/s0006-291x(02)02392-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lac(+)/Lac(-) selection of recombinant plasmids based on the insertional inactivation of LacZalpha gene cannot differentiate recombinant clones in some cases. Several fragments of exon 11 of human brca1 gene were cloned in LacZalpha-containing plasmids so that frameshift appeared at the 5(')-end of the fragments tested but these fragments were in frame with the part of LacZalpha situated downstream of the polylinker. All plasmids except one caused blue colonies formation after being transformed in Escherichia coli LacZDeltaM15 cells in spite of the frameshift. The fact may be explained by reinitiation of translation within the mRNA transcribed from the inserted DNA fragments at in-frame AUG, GUG, and UUG. The data demonstrated limitations on the Lac(+)/Lac(-) selection of LacZalpha-based recombinant plasmids.
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Affiliation(s)
- Nadezhda Gutkina
- Institute of Molecular Biology and Biophysics, Academy of Medical Sciences, Siberian Branch, Timakov str. 2, Novosibirsk 630117, Russia
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Wild J, Hradecna Z, Szybalski W. Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. Genome Res 2002; 12:1434-44. [PMID: 12213781 PMCID: PMC186656 DOI: 10.1101/gr.130502] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The widely used, very-low-copy BAC (bacterial artificial chromosome) vectors are the mainstay of present genomic research. The principal advantage of BACs is the high stability of inserted clones, but an important disadvantage is the low yield of DNA, both for vectors alone and when carrying genomic inserts. We describe here a novel class of single-copy/high-copy (SC/HC) pBAC/oriV vectors that retain all the advantages of low-copy BAC vectors, but are endowed with a conditional and tightly controlled oriV/TrfA amplification system that allows: (1) a yield of ~100 copies of the vector per host cell when conditionally induced with L-arabinose, and (2) analogous DNA amplification (only upon induction and with copy number depending on the insert size) of pBAC/oriV clones carrying >100-kb inserts. Amplifiable clones and libraries facilitate high-throughput DNA sequencing and other applications requiring HC plasmid DNA. To turn on DNA amplification, which is driven by the oriV origin of replication, we used copy-up mutations in the gene trfA whose expression was very tightly controlled by the araC-P(araBAD) promoter/regulator system. This system is inducible by L-arabinose, and could be further regulated by glucose and fucose. Amplification of DNA upon induction with L-arabinose and its modulation by glucose are robust and reliable. Furthermore, we discovered that addition of 0.2% D-glucose to the growth medium helped toward the objective of obtaining a real SC state for all BAC systems, thus enhancing the stability of their maintenance, which became equivalent to cloning into the host chromosome
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Affiliation(s)
- Jadwiga Wild
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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