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Iijima M, Yamada Y, Nakano H, Nakayama T, Kuroda S. Bio-nanocapsules for oriented immobilization of DNA aptamers on aptasensors. Analyst 2022; 147:489-495. [PMID: 35023508 DOI: 10.1039/d1an02278d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The oriented immobilization of sensing molecules (e.g., IgGs, receptors, lectins, and DNA aptamers) on sensor chips is particularly important for maximizing the potential of the sensing molecules, thereby enhancing the sensitivity and target-binding capacity of biosensors. We previously developed ∼30 nm bio-nanocapsules (ZZ-BNCs) consisting of the hepatitis B virus envelope L protein fused with the tandem form of protein A-derived IgG Fc-binding Z domain (ZZ-L protein). ZZ-BNC acts successfully as a scaffold, enhancing both the sensitivity and binding capacity of IgG, a Fc-fused receptor, and Fc-fused lectin to antigens, cytokines, and sugar chains through an oriented immobilization on a biosensor surface. To expand the versatility of ZZ-BNC, we modified ZZ-BNC by replacing the ZZ domain with a DNA-binding single-chain lambda Cro (scCro) domain, thereby developing scCro-BNC. The scCro-BNC was synthesized in yeast cells and homogeneously purified as ∼30 nm sized nanoparticles. In a quartz crystal microbalance, an scCro-BNC-coated sensor chip immobilized with thrombin-binding DNA aptamers showed an ∼5.5-fold higher thrombin-binding capacity and ∼6000-fold higher detection sensitivity than a sensor chip directly coated with DNA aptamers. In addition, the number of bound thrombin molecules per molecule of DNA aptamer increased by ∼7.8-fold with an scCro-BNC coating, consistent with the theoretical thrombin-binding capacity. Collectively, scCro-BNC was shown to perform as an ideal scaffold for maximizing the potential of the DNA aptamer by immobilizing it in an oriented manner. Facilitating a highly sensitive detection of various target molecules, these BNC-based scaffolds are expected to improve a wide range of biosensors while minimizing the number of sensing molecules required.
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Affiliation(s)
- Masumi Iijima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.,Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Yuki Yamada
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideo Nakano
- Department of Applied Biosciences, Graduate School of Bioagricultural Science, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Tsutomu Nakayama
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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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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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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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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