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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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Orientation Control of the Molecular Recognition Layer for Improved Sensitivity: a Review. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3103-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Karaballi RA, Nel A, Krishnan S, Blackburn J, Brosseau CL. Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization. Phys Chem Chem Phys 2016; 17:21356-63. [PMID: 25780805 DOI: 10.1039/c4cp05077k] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.
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Affiliation(s)
- R A Karaballi
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia B3H 3C3, Canada.
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Matsuura SI, Baba T, Chiba M, Tsunoda T. Nanoporous scaffold for DNA polymerase: pore-size optimisation of mesoporous silica for DNA amplification. RSC Adv 2014. [DOI: 10.1039/c4ra02725f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The simple and selective immobilisation of a thermostable DNA polymerase on mesoporous silicas was achieved, and DNA amplification activity was retained under the pore-size regulation of the mesoporous silicas.
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Affiliation(s)
- Shun-ichi Matsuura
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai, Japan
| | - Tomoya Baba
- Transdisciplinary Research Integration Center
- Research Organization of Information and Systems (ROIS)
- National Institute of Genetics
- Mishima, Japan
| | - Manami Chiba
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai, Japan
| | - Tatsuo Tsunoda
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai, Japan
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Lim G, Kim J, Kim JH. Optimization of the masking molecule for active-site-protected immobilization of Taq DNA polymerase and its application. Anal Biochem 2012; 432:139-41. [PMID: 23036837 DOI: 10.1016/j.ab.2012.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 11/17/2022]
Abstract
The method of oriented and activity-preserved immobilization of biologically active proteins based on concepts of active-site masking and kinetic control was further developed in this study. Minimal requirements for the masking DNA molecule were found to be a 5'overhang of 5-7 nucleotides and a double-stranded region of 11-13 bp to retain approximately 70% of the enzyme activity. The amplification range of protected immobilized (PIM) Taq DNA polymerase was over 1.2 kb. These data suggest that PIM Taq DNA polymerase can be used for various commercial applications.
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Affiliation(s)
- Gumjung Lim
- Department of Chemistry, Kyung Hee University, Seoul 130-701, Republic of Korea
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