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Zhu B, Gan R, Cabezas MD, Kojima T, Nicol R, Jewett MC, Nakano H. Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins. Biotechnol Bioeng 2020; 117:3849-3857. [PMID: 32816360 DOI: 10.1002/bit.27538] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022]
Abstract
In crude extract-based cell-free protein synthesis (CFPS), DNA templates are transcribed and translated into functional proteins. Although linear expression templates (LETs) are less laborious and expensive to generate, plasmid templates are often desired over polymerase chain reaction-generated LETs due to increased stability and protection against exonucleases present in the extract of the reaction. Here we demonstrate that addition of a double stranded DNA-binding protein to the CFPS reaction, termed single-chain Cro protein (scCro), achieves terminal protection of LETs. This CroP-LET (scCro-based protection of LET) method effectively increases superfolder green fluorescent protein (sfGFP) expression levels from LETs in Escherichia coli CFPS reactions by sixfold. Our yields are comparable to other strategies that provide chemical and enzymatic DNA stabilization in E. coli CFPS. Notably, we also report that the CroP-LET method successfully enhanced yields in CFPS platforms derived from nonmodel organisms. Our results show that CroP-LET increased sfGFP yields by 18-fold in the Vibrio natriegens CFPS platform. With the fast-expanding applications of CFPS platforms, this method provides a practical and generalizable solution to protect linear expression DNA templates.
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Affiliation(s)
- Bo Zhu
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Maria D Cabezas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Robert Nicol
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois.,Simpson Querrey Institute, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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2
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Kojima T. Ultra-high-throughput analysis of functional biomolecules using in vitro selection and bioinformatics. Biosci Biotechnol Biochem 2020; 84:1767-1774. [PMID: 32441212 DOI: 10.1080/09168451.2020.1768823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Functional analysis of biomolecules, including nucleic acids and proteins, is important for understanding biological mechanisms in living cells such as gene expression and metabolism. To analyze diverse biomolecular functions, large-scale screening systems for biomolecules have been developed for various applications such as to improve enzyme activity and identify target binding molecules. One of these systems, the Bead Display system, utilizes emulsion technology and is a powerful tool for rapidly screening functional nucleic acids or proteins in vitro. Furthermore, an analytical pipeline that consists of genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq, gene expression analysis, and bioinformatics was shown to be a robust platform for comprehensively identifying genes regulated by a transcription factor. This review provides an overview of the biomolecular screening methods developed to date.
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Affiliation(s)
- Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Japan
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3
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Kojima T, Nakane A, Zhu B, Alfi A, Nakano H. A simple, real-time assay of horseradish peroxidase using biolayer interferometry. Biosci Biotechnol Biochem 2019; 83:1822-1828. [PMID: 31119970 DOI: 10.1080/09168451.2019.1621156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Horseradish peroxidase (HRP) isoenzyme C1a is one of the most widely used enzymes for various analytical methods in bioscience research and medical fields. In these fields, real-time monitoring of HRP activity is highly desirable because the utility of HRP as a reporter enzyme would be expanded. In this study, we developed a simple assay system enabling real-time monitoring of HRP activity by using biolayer interferometry (BLI). The HRP activity was quantitatively detected on a BLI sensor chip by tracing a binding response of tyramide, a substrate of HRP, onto an immobilized protein. This system could be applied to analyses related to oxidase activity, as well as to the functional analysis of recombinant HRP.
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Affiliation(s)
- Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Ayako Nakane
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Bo Zhu
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Almasul Alfi
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Hideo Nakano
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
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4
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Optimization of a dual-functional biocatalytic system for continuous hydrolysis of lactose in milk. J Biosci Bioeng 2019; 127:38-44. [DOI: 10.1016/j.jbiosc.2018.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/17/2018] [Accepted: 07/10/2018] [Indexed: 01/16/2023]
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5
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Parsa SF, Vafajoo A, Rostami A, Salarian R, Rabiee M, Rabiee N, Rabiee G, Tahriri M, Yadegari A, Vashaee D, Tayebi L, Hamblin MR. Early diagnosis of disease using microbead array technology: A review. Anal Chim Acta 2018; 1032:1-17. [PMID: 30143206 PMCID: PMC6152944 DOI: 10.1016/j.aca.2018.05.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 12/31/2022]
Abstract
Early diagnosis of diseases (before they become advanced and incurable) is essential to reduce morbidity and mortality rates. With the advent of novel technologies in clinical laboratory diagnosis, microbead-based arrays have come to be recognized as an efficient approach, that demonstrates useful advantages over traditional assay methods for multiple disease-related biomarkers. Multiplexed microbead assays provide a robust, rapid, specific, and cost-effective approach for high-throughput and simultaneous screening of many different targets. Biomolecular binding interactions occur after applying a biological sample (such as blood plasma, saliva, cerebrospinal fluid etc.) containing the target analyte(s) to a set of microbeads with different ligand-specificities that have been coded in planar or suspension arrays. The ligand-receptor binding activity is tracked by optical signals generated by means of flow cytometry analysis in the case of suspension arrays, or by image processing devices in the case of planar arrays. In this review paper, we discuss diagnosis of cancer, neurological and infectious diseases by using optically-encoded microbead-based arrays (both multiplexed and single-analyte assays) as a reliable tool for detection and quantification of various analytes.
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Affiliation(s)
- Sanam Foroutan Parsa
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Atieh Vafajoo
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Azin Rostami
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Reza Salarian
- Biomedical Engineering Department, Maziar University, Noor, Royan, Iran
| | - Mohammad Rabiee
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Navid Rabiee
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - Ghazal Rabiee
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
| | | | - Amir Yadegari
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
| | - Daryoosh Vashaee
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC 27606, USA
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA; Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
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6
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Kojima T, Hata J, Oka H, Hayashi K, Hitomi K, Nakano H. Spatial arrangement of proteins using scCro-tag: application for an in situ enzymatic microbead assay. Biosci Biotechnol Biochem 2018; 82:1911-1921. [PMID: 30067465 DOI: 10.1080/09168451.2018.1501265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In natural systems, various metabolic reactions are often spatially organized to increase enzyme activity and specificity. Thus, by spatially arranging enzyme molecules in synthetic systems to imitate these natural systems, it is possible to promote a high rate of enzymatic turnover. In this present study, a normal and mutant form of the scCro DNA-binding protein were shown to bind orthogonally to specific recognition sequences under appropriate conditions. Furthermore, these DNA-binding tags were used to establish an enzyme assay system based on the spatial arrangement of transglutaminase and its substrate at the molecular level. Together, the results of the present study suggest that the scCro-tag may be a powerful tool to facilitate the synthetic spatial arrangement of proteins on a DNA ligand.
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Affiliation(s)
- Takaaki Kojima
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Jumpei Hata
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Hiroya Oka
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Kenta Hayashi
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Kiyotaka Hitomi
- b Graduate School of Pharmaceutical Sciences , Nagoya University , Nagoya , Japan
| | - Hideo Nakano
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
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Verma SK, Albrecht AK, Siebecke V, Klöck G, Kolesnikova TA, Springer S. Comparative validation of a microcapsule-based immunoassay for the detection of proteins and nucleic acids. PLoS One 2018; 13:e0201009. [PMID: 30028867 PMCID: PMC6054379 DOI: 10.1371/journal.pone.0201009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/06/2018] [Indexed: 01/12/2023] Open
Abstract
To detect and study diseases, research and clinical laboratories must quantify specific biomarkers in the plasma and urine of patients with precision, sensitivity, and cost-effectiveness. Newly developed techniques, such as particle-based immunoassays, must be validated in these terms against standard methods such as enzyme-linked immunosorbent assays (ELISAs). Here, we compare the performance of assays that use hollow polyelectrolyte microcapsules with assays based on solid plastic beads, and with standard microplate immunoassays. The polyelectrolyte microcapsules detect the disease biomarker beta-2 microglobulin with a fifty-fold increase in sensitivity than polystyrene (PS) beads. For sequence-specific nucleic acid detection, the oligonucleotide-coated microcapsules exhibit a two-fold lower increase in sensitivity over PS beads. The microcapsules also detect the presence of a monoclonal antibody in hybridoma supernatant at a fifty-six-fold increase in sensitivity compared to a microplate assay. Overall, polyelectrolyte microcapsule-based assays are more sensitive for the detection of protein and nucleic acid analytes than PS beads and microplate assays, and they are viable alternatives as a platform for the rapid quantitative detection of analytes at very low concentrations.
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Affiliation(s)
- Sujit Kumar Verma
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | | | | | - Gerd Klöck
- City University of Applied Sciences, Bremen, Germany
| | | | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
- * E-mail:
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