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Matsuura SI, Baba T, Ikeda T, Yamamoto K, Tsunoda T, Yamaguchi A. Highly Precise and Sensitive Polymerase Chain Reaction Using Mesoporous Silica-Immobilized Enzymes. ACS APPLIED MATERIALS & INTERFACES 2022; 14:29483-29490. [PMID: 35700238 PMCID: PMC9266630 DOI: 10.1021/acsami.2c01992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A highly precise and sensitive technology that enables DNA amplification/detection from minimal amounts of nucleic acid is expected to find applicability in genetic testing involving small amounts of samples. The use of a free enzyme in conventional DNA amplification techniques, such as the polymerase chain reaction (PCR), frequently causes side reactions (i.e., nonspecific DNA amplification) when ≤103 substrate DNA molecules are present, thereby preventing selective amplification of the target DNA. To address this issue, we have developed a novel DNA amplification system, mesoporous silica-enhanced PCR (MSE-PCR), which involves the immobilization of a thermostable DNA polymerase from Thermococcus kodakaraensis (KOD DNA polymerase) into highly ordered nanopores of the mesoporous silica to control the reaction environment around the enzyme. In the MSE-PCR system using immobilized KOD DNA polymerase, such nonspecific DNA amplification was remarkably inhibited under the same conditions. Furthermore, the optimization of mesoporous silica pore sizes enabled selective and efficient DNA amplification from DNA substrates at the single-molecule level, i.e., one ten-thousandth of the amount of substrate DNA required for a DNA amplification reaction using a free enzyme. The results obtained in this study have shown that the nanopores of mesoporous silica can inhibit nonspecific reactions in DNA amplification, thereby considerably improving the specificity and sensitivity of the DNA polymerase reaction.
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Affiliation(s)
- Shun-ichi Matsuura
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Tomoya Baba
- Advanced
Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Joint
Support-Center for Data Science Research, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-0014, Japan
| | - Takuji Ikeda
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Katsutoshi Yamamoto
- Faculty
of Environmental Engineering, The University
of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Tatsuo Tsunoda
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Aritomo Yamaguchi
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
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Matsuura SI, Ikeda T, Hiyoshi N, Chiba M, Yamaguchi A. Assemblies of two multimeric enzymes using mesoporous silica microspheres toward cascade reaction fields. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Matsuura SI, Ikeda T, Chiba M, Yamamoto K. Efficient production of γ-aminobutyric acid by glutamate decarboxylase immobilized on an amphiphilic organic-inorganic hybrid porous material. J Biosci Bioeng 2020; 131:250-255. [PMID: 33191128 DOI: 10.1016/j.jbiosc.2020.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 01/24/2023]
Abstract
A novel organic-inorganic hybrid porous material (KCS-2), containing both lipophilic and hydrophilic nanospaces to mimic a lipid bilayer, was utilized as an immobilization support and reaction accelerator for glutamate decarboxylase (GADβ). Upon evaluation of the adsorption of GADβ on KCS-2, the amount of immobilization was found to be approximately four times higher than that on non-porous silica, and a comparable adsorbability to mesoporous silica was observed. Following γ-aminobutyric acid (GABA) production by the decarboxylation of l-glutamic acid using these immobilized enzymes, the enzymatic activity of the GADβ-KCS-2 composite was found to be significantly higher than that of the free enzyme. In contrast, the activity of the more common GADβ-mesoporous silica composite decreased. Furthermore, the enzymatic activity of the GADβ-KCS-2 composite was superior to those of the un-immobilized free enzyme and the amorphous material itself over a wide temperature range. Thereby, these findings suggest that the amphiphilic nanospace of KCS-2 is suitable as a stable enzyme immobilization field and reaction acceleration field under such conditions. In addition, the durability of the immobilized enzyme was examined in terms of GABA production, with approximately 20% activity retention being observed after 10 cycles using KCS-2. Such durability was not observed for the non-porous silica material due to enzyme desorption.
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Affiliation(s)
- Shun-Ichi Matsuura
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan.
| | - Takuji Ikeda
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Manami Chiba
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Katsutoshi Yamamoto
- Faculty of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu 808-0135, Japan
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Nie X, Chen J, Sheng N, Zeng L, Yang H, Wang C. Effect of water molecules on nanoscale wetting behaviour of molecular ethanol on hydroxylated SiO2 substrate. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1353692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Xuechuan Nie
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jige Chen
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Nan Sheng
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Li Zeng
- College of Physics and Electronic Engineering, Guangxi Teachers Education University, Nanning, China
| | - Haijun Yang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Chunlei Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
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Albert E, Basa P, Deák A, Németh A, Osváth Z, Sáfrán G, Zolnai Z, Hórvölgyi Z, Nagy N. Introducing nanoscaled surface morphology and percolation barrier network into mesoporous silica coatings. RSC Adv 2015. [DOI: 10.1039/c5ra09357k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The advantages of surface pattern and mesoporous character of silica thin films were combined, while preserving the interconnected pore system or creating laterally separated porous volumes surrounded by nonpermeable compact zones.
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Affiliation(s)
- E. Albert
- Budapest University of Technology and Economics
- Department of Physical Chemistry and Materials Science
- H-1521 Budapest
- Hungary
| | - P. Basa
- Semilab Semiconductor Physics Laboratory Co. Ltd
- H-1117 Budapest
- Hungary
| | - A. Deák
- Hungarian Academy of Sciences
- Centre for Energy Research
- Institute of Technical Physics and Materials Science
- H-1525 Budapest
- Hungary
| | - A. Németh
- Hungarian Academy of Sciences
- Wigner Research Centre for Physics
- Institute for Particle and Nuclear Physics
- H-1525 Budapest
- Hungary
| | - Z. Osváth
- Hungarian Academy of Sciences
- Centre for Energy Research
- Institute of Technical Physics and Materials Science
- H-1525 Budapest
- Hungary
| | - G. Sáfrán
- Hungarian Academy of Sciences
- Centre for Energy Research
- Institute of Technical Physics and Materials Science
- H-1525 Budapest
- Hungary
| | - Z. Zolnai
- Hungarian Academy of Sciences
- Centre for Energy Research
- Institute of Technical Physics and Materials Science
- H-1525 Budapest
- Hungary
| | - Z. Hórvölgyi
- Budapest University of Technology and Economics
- Department of Physical Chemistry and Materials Science
- H-1521 Budapest
- Hungary
| | - N. Nagy
- Hungarian Academy of Sciences
- Centre for Energy Research
- Institute of Technical Physics and Materials Science
- H-1525 Budapest
- Hungary
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Zlateski V, Keller TC, Pérez-Ramírez J, Grass RN. Immobilizing and de-immobilizing enzymes on mesoporous silica. RSC Adv 2015. [DOI: 10.1039/c5ra19568c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
β-Glucosidase was immobilised as a model enzyme within silica mesocellular foam (MCF) at a high loading, further entrapped to achieve higher stability and released unharmed upon need by applying fluoride buffered solutions.
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Affiliation(s)
- Vladimir Zlateski
- Institute for Chemical and Bioengineering
- ETH Zurich
- Zurich
- Switzerland
| | - Tobias C. Keller
- Institute for Chemical and Bioengineering
- ETH Zurich
- Zurich
- Switzerland
| | | | - Robert N. Grass
- Institute for Chemical and Bioengineering
- ETH Zurich
- Zurich
- Switzerland
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