1
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Kawashima T, Nakamura M, Sakono M. A one-process production of completely biotinylated proteins in a T7 expression system. Biotechnol Appl Biochem 2024. [PMID: 38770738 DOI: 10.1002/bab.2598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
Streptavidin is a tetrameric protein with high specificity and affinity for biotin. The interaction between avidin and biotin has become a valuable tool in nanotechnology. In recent years, the site-specific biotin modification of proteins using biotin ligases, such as BirA, has attracted attention. This study established an in vivo method for achieving the complete biotinylation of target proteins using a single plasmid co-expressing BirA and its target proteins. Specifically, a biotin-modified protein was produced in Escherichia coli strain BL21(DE3) using a single plasmid containing genes encoding both BirA and a protein fused to BirA's substrate sequence, Avitag. This approach simplifies the production of biotinylated proteins in E. coli and allows the creation of various biotinylated protein types through gene replacement. Furthermore, the biotin modification rate of the obtained target protein could be evaluated using Native-PAGE without performing complicated isolation operations of biotinylated proteins. In Native-PAGE, biotin-modified proteins and unmodified proteins were confirmed as clearly different bands, and it was possible to easily derive the modification rate from the respective band intensities.
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Affiliation(s)
- Takuma Kawashima
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
| | - Mitsuki Nakamura
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
| | - Masafumi Sakono
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
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2
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Ling M, Cardle II, Song K, Yan AJ, Kacherovsky N, Jensen MC, Pun SH. Aptamer-Based Chromatographic Methods for Efficient and Economical Separation of Leukocyte Populations. ACS Biomater Sci Eng 2023; 9:5062-5071. [PMID: 37467493 PMCID: PMC11016351 DOI: 10.1021/acsbiomaterials.3c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
The manufacturing process of chimeric antigen receptor T cell therapies includes isolation systems that provide pure T cells. Current magnetic-activated cell sorting and immunoaffinity chromatography methods produce desired cells with high purity and yield but require expensive equipment and reagents and involve time-consuming incubation steps. Here, we demonstrate that aptamers can be employed in a continuous-flow resin platform for both depletion of monocytes and selection of CD8+ T cells from peripheral blood mononuclear cells at low cost with high purity and throughput. Aptamer-mediated cell selection could potentially enable fully synthetic, traceless isolations of leukocyte subsets from a single isolation system.
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Affiliation(s)
- Melissa Ling
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195
| | - Ian I. Cardle
- Department of Bioengineering, University of Washington, Seattle, WA 98195
- Seattle Children’s Therapeutics, Seattle, WA 98101
| | - Kefan Song
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Alexander J. Yan
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | | | - Suzie H. Pun
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
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3
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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4
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Mechanistic investigation of human maturation of Okazaki fragments reveals slow kinetics. Nat Commun 2022; 13:6973. [PMID: 36379932 PMCID: PMC9666535 DOI: 10.1038/s41467-022-34751-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The final steps of lagging strand synthesis induce maturation of Okazaki fragments via removal of the RNA primers and ligation. Iterative cycles between Polymerase δ (Polδ) and Flap endonuclease-1 (FEN1) remove the primer, with an intermediary nick structure generated for each cycle. Here, we show that human Polδ is inefficient in releasing the nick product from FEN1, resulting in non-processive and remarkably slow RNA removal. Ligase 1 (Lig1) can release the nick from FEN1 and actively drive the reaction toward ligation. These mechanisms are coordinated by PCNA, which encircles DNA, and dynamically recruits Polδ, FEN1, and Lig1 to compete for their substrates. Our findings call for investigating additional pathways that may accelerate RNA removal in human cells, such as RNA pre-removal by RNase Hs, which, as demonstrated herein, enhances the maturation rate ~10-fold. They also suggest that FEN1 may attenuate the various activities of Polδ during DNA repair and recombination.
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5
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Chinthapatla R, Sotoudegan M, Anderson T, Moustafa IM, Passow KT, Kennelly SA, Moorthy R, Dulin D, Feng JY, Harki DA, Kirchdoerfer R, Cameron CE, Arnold JJ. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.11.503614. [PMID: 35982684 PMCID: PMC9387131 DOI: 10.1101/2022.08.11.503614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas Anderson
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A. Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y. Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert Kirchdoerfer
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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6
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Development of a streptavidin-bridged enhanced sandwich ELISA based on self-paired nanobodies for monitoring multiplex Salmonella serogroups. Anal Chim Acta 2022; 1203:339705. [DOI: 10.1016/j.aca.2022.339705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/01/2022] [Accepted: 03/07/2022] [Indexed: 01/01/2023]
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7
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Ali Z, Sánchez E, Tehseen M, Mahas A, Marsic T, Aman R, Sivakrishna Rao G, Alhamlan FS, Alsanea MS, Al-Qahtani AA, Hamdan S, Mahfouz M. Bio-SCAN: A CRISPR/dCas9-Based Lateral Flow Assay for Rapid, Specific, and Sensitive Detection of SARS-CoV-2. ACS Synth Biol 2022; 11:406-419. [PMID: 34939798 PMCID: PMC8751644 DOI: 10.1021/acssynbio.1c00499] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 12/26/2022]
Abstract
Simple, rapid, specific, and sensitive point-of-care detection methods are needed to contain the spread of SARS-CoV-2. CRISPR/Cas9-based lateral flow assays are emerging as a powerful alternative for COVID-19 diagnostics. Here, we developed Bio-SCAN (biotin-coupled specific CRISPR-based assay for nucleic acid detection) as an accurate pathogen detection platform that requires no sophisticated equipment or technical expertise. Bio-SCAN detects the SARS-CoV-2 genome in less than 1 h from sample collection to result. In the first step, the target nucleic acid sequence is isothermally amplified in 15 min via recombinase polymerase amplification before being precisely detected by biotin-labeled nuclease-dead SpCas9 (dCas9) on commercially available lateral flow strips. The resulting readout is visible to the naked eye. Compared to other CRISPR-Cas-based pathogen detection assays, Bio-SCAN requires no additional reporters, probes, enhancers, reagents, or sophisticated devices to interpret the results. Bio-SCAN is highly sensitive and successfully detected a clinically relevant level (4 copies/μL) of synthetic SARS-CoV-2 RNA genome. Similarly, Bio-SCAN showed 100% negative and 96% positive predictive agreement with RT-qPCR results when using clinical samples (86 nasopharyngeal swab samples). Furthermore, incorporating variant-specific sgRNAs in the detection reaction allowed Bio-SCAN to efficiently distinguish between the α, β, and δ SARS-CoV-2 variants. Also, our results confirmed that the Bio-SCAN reagents have a long shelf life and can be assembled locally in nonlaboratory and limited-resource settings. Furthermore, the Bio-SCAN platform is compatible with the nucleic acid quick extraction protocol. Our results highlight the potential of Bio-SCAN as a promising point-of-care diagnostic platform that can facilitate low-cost mass screening for SARS-CoV-2.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Edith Sánchez
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination,
Biological and Environmental Sciences and Engineering Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900,
Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Fatimah Saeed Alhamlan
- Department of Infection and Immunity, King
Faisal Specialist Hospital and Research Center, Riyadh 11211,
Saudi Arabia
| | - Madain S. Alsanea
- Department of Infection and Immunity, King
Faisal Specialist Hospital and Research Center, Riyadh 11211,
Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King
Faisal Specialist Hospital and Research Center, Riyadh 11211,
Saudi Arabia
| | - Samir Hamdan
- Laboratory of DNA Replication and Recombination,
Biological and Environmental Sciences and Engineering Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900,
Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic
Biology, Division of Biological Sciences, 4700 King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
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8
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Gao S, Guisán JM, Rocha-Martin J. Oriented immobilization of antibodies onto sensing platforms - A critical review. Anal Chim Acta 2022; 1189:338907. [PMID: 34815045 DOI: 10.1016/j.aca.2021.338907] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/08/2021] [Accepted: 07/31/2021] [Indexed: 12/26/2022]
Abstract
The immunosensor has been proven a versatile tool to detect various analytes, such as food contaminants, pathogenic bacteria, antibiotics and biomarkers related to cancer. To fabricate robust and reproducible immunosensors with high sensitivity, the covalent immobilization of immunoglobulins (IgGs) in a site-specific manner contributes to better performance. Instead of the random IgG orientations result from the direct yet non-selective immobilization techniques, this review for the first time introduces the advances of stepwise yet site-selective conjugation strategies to give better biosensing efficiency. Noncovalently adsorbing IgGs is the first but decisive step to interact specifically with the Fc fragment, then following covalent conjugate can fix this uniform and antigens-favorable orientation irreversibly. In this review, we first categorized this stepwise strategy into two parts based on the different noncovalent interactions, namely adhesive layer-mediated interaction onto homofunctional support and layer-free interaction onto heterofunctional support (which displays several different functionalities on its surface that are capable to interact with IgGs). Further, the influence of ligands characteristics (synthesis strategies, spacer requirements and matrices selection) on the heterofunctional support has also been discussed. Finally, conclusions and future perspectives for the real-world application of stepwise covalent conjugation are discussed. This review provides more insights into the fabrication of high-efficiency immunosensor, and special attention has been devoted to the well-orientation of full-length IgGs onto the sensing platform.
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Affiliation(s)
- Shipeng Gao
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain
| | - José M Guisán
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain.
| | - Javier Rocha-Martin
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain.
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9
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Highly enhanced activity and stability via affinity induced immobilization β-glucosidase from Aspergillus niger onto amino-based silica for the biotransformation of ginsenoside Rb1. J Chromatogr A 2021; 1653:462388. [PMID: 34280789 DOI: 10.1016/j.chroma.2021.462388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 01/15/2023]
Abstract
In this study, an enzyme immobilization method for the effective biotransformation of ginsenoside Rb1 to impart activity and stability was developed. Using a hydrolase enzyme model, β-glucosidase from Aspergillus niger, immobilization within chemically affinity-linked amino-based silica provided an immobilization efficiency 5.86-fold higher than that of free enzyme. Compared with the free enzyme, the immobilized enzyme functioned optimally at a wider pH range and had higher thermostability. The optimum pH for the free and immobilized enzymes was 5.5. The optimal reaction temperature of the immobilized enzyme was 45 °C, which was 5 °C higher than that of the free enzyme. The Michaelis constant (Km) values before and after immobilization were 0.482 mmol•L-1 and 0.387 mmol•L-1, respectively. The catalytic rate (Kcat) for the immobilized and free enzymes was 22.269 mmol•L-1and 8.800 mmol•L-1, respectively, and the catalytic efficiency (Kcat/Km) activity of the immobilized enzyme was 3.30-fold higher than that of the free enzyme. The immobilized enzyme could preserve 97 % of the activity after 45 cycles of repeated use. The high catalytic activity and significant operational stability are beneficial for industrial applications.
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10
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Han Z, Sun T, Xu Z, Fan L, Yun H, Ge X, Liu X, Liu Y, Ning B. Detection of 4 quinolone antibiotics by chemiluminescence based on a novel Nor-Biotin bifunctional ligand and SA-ALP technology. Biosci Biotechnol Biochem 2021; 85:1720-1728. [PMID: 33960377 DOI: 10.1093/bbb/zbab081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022]
Abstract
A simple and effective direct competitive chemiluminescence immunoassay for the detection of 4 kinds of quinolone antibiotics in milk was established using Nor-Biotin (biotin-modified norfloxacin [NOR]) bifunctional ligand and alkaline phosphatase-conjugated streptavidin signal amplification technology. The polyclonal antibody was obtained after the immunization of New Zealand White rabbits using norfloxacin-derived antigen. "Click chemistry" was used for the rapid and facile synthesis of the Nor-Biotin bifunctional ligand. After the optimization of the incubation time and reaction buffer, the direct competitive chemiluminescence assay method was developed and used for sensitive detection of 4 kinds of quinolone drugs (NOR, pefloxacin, ciprofloxacin, and danofloxacin). The IC50 of the 4 kinds of quinolone drugs ranged from 7.35 to 24.27 ng/mL, and the lowest detection limits ranged from 0.05 to 0.16 ng/mL, which were below their maximum residue levels, approved by the EU for treatment of food-producing animals. To demonstrate the applicability of the assay, artificially contaminated milk samples with the 4 quinolone drugs were analyzed. The mean recovery rates of the drugs ranged from 86.31% to 112.11%.
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Affiliation(s)
- Zhenyu Han
- School of Public Health, Inner Mongolia Medical University, Hohhot, China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Tieqiang Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zehua Xu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Longxing Fan
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.,Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, China
| | - Hanxuan Yun
- School of Public Health, Inner Mongolia Medical University, Hohhot, China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xuejiao Ge
- School of Public Health, Inner Mongolia Medical University, Hohhot, China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiao Liu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Ying Liu
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
| | - Bao'an Ning
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
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11
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Takahashi M, Tehseen M, Salunke R, Takahashi E, Mfarrej S, Sobhy MA, Alhamlan FS, Hala S, Ramos-Mandujano G, Al-Qahtani AA, Alofi FS, Alsomali A, Hashem AM, Khogeer A, Almontashiri NAM, Lee JM, Mon H, Sakashita K, Li M, Kusakabe T, Pain A, Hamdan SM. Quick and Easy Assembly of a One-Step qRT-PCR Kit for COVID-19 Diagnostics Using In-House Enzymes. ACS OMEGA 2021; 6:7374-7386. [PMID: 33778250 PMCID: PMC7986002 DOI: 10.1021/acsomega.0c05635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
One-step reverse-transcription quantitative polymerase chain reaction (qRT-PCR) is the most widely applied method for COVID-19 diagnostics. Notwithstanding the facts that one-step qRT-PCR is well suited for the diagnosis of COVID-19 and that there are many commercially available one-step qRT-PCR kits in the market, their high cost and unavailability due to airport closures and shipment restriction became a major bottleneck that had driven the desire to produce the key components of such kits locally. Here, we provide a simple, economical, and powerful one-step qRT-PCR kit based on patent-free, specifically tailored versions of Moloney murine leukemia virus reverse transcriptase and Thermus aquaticus DNA polymerase and termed R3T (Rapid Research Response Team) one-step qRT-PCR. We also demonstrate the robustness of our enzyme production strategies and provide the optimal reaction conditions for their efficient augmentation in a one-step approach. Our kit was routinely able to reliably detect as low as 10 copies of the synthetic RNAs of SARS-CoV-2. More importantly, our kit successfully detected COVID-19 in clinical samples of broad viral titers with similar reliability and selectivity to that of the Invitrogen SuperScript III Platinum One-step qRT-PCR and TaqPath one-step RT-qPCR kits. Overall, our kit has shown robust performance in both laboratory settings and the Saudi Ministry of Health-approved testing facility.
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Affiliation(s)
- Masateru Takahashi
- Laboratory
of DNA Replication and Recombination, Biological and Environmental
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory
of DNA Replication and Recombination, Biological and Environmental
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Rahul Salunke
- Pathogen
Genomics Laboratory, BESE Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Etsuko Takahashi
- Laboratory
of DNA Replication and Recombination, Biological and Environmental
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sara Mfarrej
- Pathogen
Genomics Laboratory, BESE Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed A. Sobhy
- Laboratory
of DNA Replication and Recombination, Biological and Environmental
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Fatimah S. Alhamlan
- Department
of Infection and Immunity, King Faisal Specialist
Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sharif Hala
- Pathogen
Genomics Laboratory, BESE Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- King
Saud Bin Abdulaziz University of Health Sciences, Jeddah 22384, Saudi Arabia
- King
Abdullah International Medical Research Centre, Jeddah, Makkah, Ministry of National Guard Health Affairs, Jeddah, Makkah 22384, Saudi Arabia
| | - Gerardo Ramos-Mandujano
- Stem
Cell
and Regenration Laboratory. Biological and Environmental Sciences
and Engineering Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department
of Infection and Immunity, King Faisal Specialist
Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Fadwa S. Alofi
- Infectious
Diseases Department, King Fahad Hospital, Madinah 3177, Saudi Arabia
| | - Afrah Alsomali
- King
Abdullah Medical Complex (KAMC), Jeddah 23816, Saudi Arabia
| | - Anwar M. Hashem
- Vaccines
and Immunotherapy Unit, King Fahd Medical Research Center; King Abdulaziz University, Jeddah, Saudi Arabia
- Department
of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Asim Khogeer
- Plan and Research Department, General Directorate
of Health Affairs Makkah Region, MOH Mecca 24321, Saudi Arabia
| | - Naif A. M. Almontashiri
- College of Applied Medical Sciences, Taibah
University, Madinah 41311, Saudi Arabia
- Center for Genetics and Inherited Diseases, Taibah University, Madinah 42353, Saudi Arabia
| | - Jae Man Lee
- Laboratory of Insect Genome Science, Kyushu
University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu
University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kosuke Sakashita
- Department of Infection and Immunity, King Faisal Specialist
Hospital
and Research Centre, King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mo Li
- Stem
Cell
and Regenration Laboratory. Biological and Environmental Sciences
and Engineering Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu
University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Arnab Pain
- Pathogen
Genomics Laboratory, BESE Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Samir M. Hamdan
- Laboratory
of DNA Replication and Recombination, Biological and Environmental
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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12
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Raducanu V, Raducanu D, Ouyang Y, Tehseen M, Takahashi M, Hamdan SM. TSGIT: An N- and C-terminal tandem tag system for purification of native and intein-mediated ligation-ready proteins. Protein Sci 2021; 30:497-512. [PMID: 33150985 PMCID: PMC7784762 DOI: 10.1002/pro.3989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 11/26/2022]
Abstract
A large variety of fusion tags have been developed to improve protein expression, solubilization, and purification. Nevertheless, these tags have been combined in a rather limited number of composite tags and usually these composite tags have been dictated by traditional commercially-available expression vectors. Moreover, most commercially-available expression vectors include either N- or C-terminal fusion tags but not both. Here, we introduce TSGIT, a fusion-tag system composed of both N- and a C-terminal composite fusion tags. The system includes two affinity tags, two solubilization tags and two cleavable tags distributed at both termini of the protein of interest. Therefore, the N- and the C-terminal composite fusion tags in TSGIT are fully orthogonal in terms of both affinity selection and cleavage. For using TSGIT, we streamlined the cloning, expression, and purification procedures. Each component tag is selected to maximize its benefits toward the final construct. By expressing and partially purifying the protein of interest between the components of the TSGIT fusion, the full-length protein is selected over truncated forms, which has been a long-standing problem in protein purification. Moreover, due to the nature of the cleavable tags in TSGIT, the protein of interest is obtained in its native form without any additional undesired N- or C-terminal amino acids. Finally, the resulting purified protein is ready for efficient ligation with other proteins or peptides for downstream applications. We demonstrate the use of this system by purifying a large amount of native fluorescent mRuby3 protein and bacteriophage T7 gp2.5 ssDNA-binding protein.
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Affiliation(s)
- Vlad‐Stefan Raducanu
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Daniela‐Violeta Raducanu
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Yujing Ouyang
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Muhammad Tehseen
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Samir M. Hamdan
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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13
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Yang Q, Gao Y, Xu L, Hong W, She Y, Yang G. Enzyme-driven micro/nanomotors: Recent advances and biomedical applications. Int J Biol Macromol 2020; 167:457-469. [PMID: 33278445 DOI: 10.1016/j.ijbiomac.2020.11.215] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
Micro/nanomotors (MNMs), both self-propelled actuators and external fields-promoted machines, have joined forces in the past decade to accomplish versatile tasks such as precise detection and targeted cargo delivery with adequate propulsion and desirable locomotion. Amongst, enzyme-driven MNMs have been able to differentiate themselves from others owing to their distinct characteristics, such as absence of chemical fuel, enhanced cellular uptake and the possibility to be easily conjugated with many therapeutics, including both small molecules and biologics, displaying superior efficacy, enhanced specificity and diminished side effects. In the present review, we aim to highlight and summarize recent advances in enzyme-driven MNMs, particularly to provide an in-depth discussion focusing on the enzyme linking approaches onto those MNMs and motion control strategies of such MNMs with advantages and limitations thereof. Conclusions and future perspectives are also provided in brief.
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Affiliation(s)
- Qingliang Yang
- Research Institute of Pharmaceutical Particle Technology, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ying Gao
- Research Institute of Pharmaceutical Particle Technology, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lei Xu
- Research Institute of Pharmaceutical Particle Technology, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Weiyong Hong
- Research Institute of Pharmaceutical Particle Technology, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; Taizhou Municipal Hospital of Zhejiang Province, Taizhou 318000, China
| | - Yuanbin She
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Gensheng Yang
- Research Institute of Pharmaceutical Particle Technology, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.
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14
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Rodriguez EL, Poddar S, Iftekhar S, Suh K, Woolfork AG, Ovbude S, Pekarek A, Walters M, Lott S, Hage DS. Affinity chromatography: A review of trends and developments over the past 50 years. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122332. [PMID: 32871378 PMCID: PMC7584770 DOI: 10.1016/j.jchromb.2020.122332] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.
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Affiliation(s)
| | - Saumen Poddar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Ashley G Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Allegra Pekarek
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Morgan Walters
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Shae Lott
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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15
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Raducanu VS, Isaioglou I, Raducanu DV, Merzaban JS, Hamdan SM. Simplified detection of polyhistidine-tagged proteins in gels and membranes using a UV-excitable dye and a multiple chelator head pair. J Biol Chem 2020; 295:12214-12223. [PMID: 32647010 PMCID: PMC7443479 DOI: 10.1074/jbc.ra120.014132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/29/2020] [Indexed: 12/22/2022] Open
Abstract
The polyhistidine tag (His-tag) is one of the most popular protein tags used in the life sciences. Traditionally, the detection of His-tagged proteins relies on immunoblotting with anti-His antibodies. This approach is laborious for certain applications, such as protein purification, where time and simplicity are critical. The His-tag can also be directly detected by metal ion-loaded nickel-nitrilotriacetic acid-based chelator heads conjugated to fluorophores, which is a convenient alternative method to immunoblotting. Typically, such chelator heads are conjugated to either green or red fluorophores, the detection of which requires specialized excitation sources and detection systems. Here, we demonstrate that post-run staining is ideal for His-tag detection by metal ion-loaded and fluorescently labeled chelator heads in PAGE and blot membranes. Additionally, by comparing the performances of different chelator heads, we show how differences in microscopic affinity constants translate to macroscopic differences in the detection limits in environments with limited diffusion, such as PAGE. On the basis of these results, we devise a simple approach, called UVHis-PAGE, that uses metal ion-loaded and fluorescently labeled chelator heads to detect His-tagged proteins in PAGE and blot membranes. Our method uses a UV transilluminator as an excitation source, and the results can be visually inspected by the naked eye.
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Affiliation(s)
- Vlad-Stefan Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ioannis Isaioglou
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniela-Violeta Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jasmeen S Merzaban
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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