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Qin L, Lou F, Wang Y, Zhang Y, Liu S, Hun X. CRISPR/Cas12a Coupled with Enzyme-DNA Molecular Switch Photoelectrochemical Assay for HIV Nucleic Acid. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Wang L, Xu M, Zhou H, Yan K, Duan S, Xue D, Wang Y, Di B, Hu C. Teaching PCR for Simultaneous Sensing of Gene Transcription and Downstream Metabolites by Cucurbit[8]uril-Mediated Intervention of Polymerase Activity. Anal Chem 2022; 94:8715-8723. [PMID: 35671188 DOI: 10.1021/acs.analchem.2c01103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The target of typical PCR analysis is restricted to nucleic acids. To this end, we report here a novel strategy to simultaneously detect genetic and metabolic markers using commercial PCR kits with cucurbit[8]urils (CB[8]) implemented to manipulate the activity of Taq DNA polymerase. CB[8] binds with the nonionic surfactants and displaces them from the polymerase surface, resulting in decreased enzyme activity. Meanwhile, the inhibited enzyme can be reversibly activated when spermine, the downstream metabolite of ornithine decarboxylase (ODC), is present in the sample, which competitively binds to CB[8] and recovers polymerase activity. CB[8] was implemented in conventional PCR kits not only to reduce false-positive results but also to extend the detection range of PCR technology. With this novel method to detect ODC in cell lysates containing both the nucleotides and intracellular metabolites, positive results were only observed in highly active HEK 293T cells, whereas silent cells treated with ODC inhibitor showed negative readouts, therefore providing a simple but elegant dual-modality PCR method for precision diagnosis.
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Affiliation(s)
- Lancheng Wang
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Mingjie Xu
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Huimin Zhou
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Kun Yan
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Shiqi Duan
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Dandan Xue
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Youmei Wang
- Key Laboratory of Drug Monitoring and Control, Drug Intelligence and Forensic Center, Ministry of Public Security, No. 18 Dongbeiwang West Road, Beijing 100193, China
| | - Bin Di
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Chi Hu
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
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An Aptamer-Array-Based Sample-to-Answer Biosensor for Ochratoxin A Detection via Fluorescence Resonance Energy Transfer. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9110309] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Food toxins are a hidden threat that can cause cancer and tremendously impact human health. Therefore, the detection of food toxins in a timely manner with high sensitivity is of paramount importance for public health and food safety. However, the current detection methods are relatively time-consuming and not practical for field tests. In the present work, we developed a novel aptamer-chip-based sample-to-answer biosensor (ACSB) for ochratoxin A (OTA) detection via fluorescence resonance energy transfer (FRET). In this system, a cyanine 3 (Cy3)-labeled OTA-specific biotinylated aptamer was immobilized on an epoxy-coated chip via streptavidin-biotin binding. A complementary DNA strand to OTA aptamer at the 3′-end was labeled with a black hole quencher 2 (BHQ2) to quench Cy3 fluorescence when in proximity. In the presence of OTA, the Cy3-labeled OTA aptamer bound specifically to OTA and led to the physical separation of Cy3 and BHQ2, which resulted in an increase of fluorescence signal. The limit of detection (LOD) of this ACSB for OTA was 0.005 ng/mL with a linearity range of 0.01–10 ng/mL. The cross-reactivity of ACSB against other mycotoxins, ochratoxin B (OTB), aflatoxin B1 (AFB1), zearalenone (ZEA), or deoxynilvalenol (DON), was less than 0.01%. In addition, this system could accurately detect OTA in rice samples spiked with OTA, and the mean recovery rate of the spiked-in OTA reached 91%, with a coefficient of variation (CV) of 8.57–9.89%. Collectively, the ACSB may represent a rapid, accurate, and easy-to-use platform for OTA detection with high sensitivity and specificity.
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Tsukakoshi K, Yamagishi Y, Kanazashi M, Nakama K, Oshikawa D, Savory N, Matsugami A, Hayashi F, Lee J, Saito T, Sode K, Khunathai K, Kuno H, Ikebukuro K. G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Res 2021; 49:6069-6081. [PMID: 34095949 PMCID: PMC8216272 DOI: 10.1093/nar/gkab388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/07/2023] Open
Abstract
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasuko Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Mana Kanazashi
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kenta Nakama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daiki Oshikawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | | | - Hitoshi Kuno
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Song K, Chen W. An electrochemical sensor for high sensitive determination of lysozyme based on the aptamer competition approach. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Protein is a kind of basic substance that constitutes a life body. The determination of protein is very important for the research of biology, medicine, and other fields. Lysozyme is relatively small and simple in structure among all kinds of proteins, so it is often used as a standard target detector in the study of aptamer sensor for protein detection. In this paper, a lysozyme electrochemical sensor based on aptamer competition mechanism is proposed. We have successfully prepared a signal weakening electrochemical sensor based on the lysozyme aptamer competition mechanism. The carboxylated multi-walled carbon nanotubes (MWCNTs) were modified on the glassy carbon electrode, and the complementary aptamer DNA with amino group was connected to MWCNTs. Because of the complementary DNA of daunomycin into the electrode, the electrochemical signal is generated. When there is a target, the aptamer binds to lysozyme with higher binding power, and the original complementary chain breaks down, resulting in the loss of daunomycin inserted into the double chain and the weakening of electrochemical signal. Differential pulse voltammetry was used to determine lysozyme, the response range was 1–500 nM, the correlation coefficient was 0.9995, and the detection limit was 0.5 nM. In addition, the proposed sensor has good selectivity and anti-interference.
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Affiliation(s)
- Kai Song
- School of Drug and Food, Xuzhou Vocational College of Bioengineering , Xuzhou 221006 , China
| | - Wenwu Chen
- School of Drug and Food, Xuzhou Vocational College of Bioengineering , Xuzhou 221006 , China
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Hu Y, Wang Z, Chen Z, Pan L. Switching the activity of Taq polymerase using clamp-like triplex aptamer structure. Nucleic Acids Res 2020; 48:8591-8600. [PMID: 32644133 PMCID: PMC7470972 DOI: 10.1093/nar/gkaa581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/31/2020] [Accepted: 06/27/2020] [Indexed: 01/22/2023] Open
Abstract
In nature, allostery is the principal approach for regulating cellular processes and pathways. Inspired by nature, structure-switching aptamer-based nanodevices are widely used in artificial biotechnologies. However, the canonical aptamer structures in the nanodevices usually adopt a duplex form, which limits the flexibility and controllability. Here, a new regulating strategy based on a clamp-like triplex aptamer structure (CLTAS) was proposed for switching DNA polymerase activity via conformational changes. It was demonstrated that the polymerase activity could be regulated by either adjusting structure parameters or dynamic reactions including strand displacement or enzymatic digestion. Compared with the duplex aptamer structure, the CLTAS possesses programmability, excellent affinity and high discrimination efficiency. The CLTAS was successfully applied to distinguish single-base mismatches. The strategy expands the application scope of triplex structures and shows potential in biosensing and programmable nanomachines.
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Affiliation(s)
- Yingxin Hu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, Hebei 050043, China
| | - Zhiyu Wang
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Linqiang Pan
- To whom correspondence should be addressed. Tel: +86 27 87556070; Fax: +86 27 87543130;
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Wang Z, Meng Z, Xue M, Zhang H, Shea KJ, Kang L. Detection of lysozyme in body fluid based on two-dimensional colloidal crystal sensor. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Gao Y, Guo X, Wang S, Chen F, Ren X, Xiao H, Wang L. Perfluorooctane sulfonate enhances mRNA expression of PPARγ and ap2 in human mesenchymal stem cells monitored by long-retained intracellular nanosensor. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114571. [PMID: 32320904 DOI: 10.1016/j.envpol.2020.114571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Perfluorooctane sulfonate (PFOS) has been widely used as a surface coating for household products. It still exists in living environments despite being restricted, due to its bioaccumulation and long half-life. Studies have shown that PFOS has the ability to induce adipogenic differentiation of human cells. Human mesenchymal stem cells (hMSCs) distributed within the adipose tissue might be a potential target of accumulated PFOS. However, traditional end-point toxicity assays failed to examine the subtle changes of cellular function exposed to low-dose persistent organic pollutants in real time. In the present work, highly sensitive and long-retained (more than 30 days) fluorescence based polymeric nanosensors were developed and employed for real-time assessment of cellular functions. hMSCs were engineered with sensor molecules encapsulated poly (lactic-co-glycolic acid) (PLGA) particles. Once internalized by hMSCs, PLGA particles continuously release and replenish sensor molecules to cytoplasm, resulting in prolonged fluorescence signal against photo bleaching and dilution by exocytosis. With this method, the dynamic changes of viability, ROS induction, and adipogenic differentiation related mRNA expression of hMSCs were monitored. PFOS with the concentration as low as 0.1 μM can induce cellular ROS and enhance the PPARγ and ap2 mRNA expression, suggesting the effect on promoting adipogenic differentiation of hMSCs.
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Affiliation(s)
- Yu Gao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Xixi Guo
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Siyu Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Fubin Chen
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Xiaomin Ren
- State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, P.O. Box 2871, Beijing, 100085, China
| | - Huaxin Xiao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China.
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