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Ou X, Li K, Liu M, Song J, Zuo Z, Guo Y. EXPAR for biosensing: recent developments and applications. Analyst 2024; 149:4135-4157. [PMID: 39034763 DOI: 10.1039/d4an00609g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Emerging as a promising novel amplification technique, the exponential amplification reaction (EXPAR) offers significant advantages due to its potent exponential amplification capability, straightforward reaction design, rapid reaction kinetics, and isothermal operation. The past few years have witnessed swift advancements and refinements in EXPAR-based technologies, with numerous high-performance biosensing systems documented. A deeper understanding of the EXPAR mechanism has facilitated the proposal of novel strategies to overcome limitations inherent to traditional EXPAR. Furthermore, the synergistic integration of EXPAR with diverse amplification methodologies, including the use of a CRISPR/Cas system, metal nanoparticles, aptamers, alternative isothermal amplification techniques, and enzymes, has significantly bolstered analytical efficacy, aiming to enhance specificity, sensitivity, and amplification efficiency. This comprehensive review presents a detailed exposition of the EXPAR mechanism and analyzes its primary challenges. Additionally, we summarize the latest research advancements in the biomedical field concerning the integration of EXPAR with diverse amplification technologies for sensing strategies. Finally, we discuss the challenges and future prospects of EXPAR technology in the realms of biosensing and clinical applications.
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Affiliation(s)
- Xinyi Ou
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Kunxiang Li
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Miao Liu
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
| | - Jiajun Song
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Zhihua Zuo
- Department of Clinical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, Sichuan, 637003, PR China.
| | - Yongcan Guo
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
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Lin Q, Ye X, Chen H, Fang X, Chen H, Kong J. Binding Activity of Prokaryotic Argonaute for Background-Suppressed Exponential Isothermal Amplification. Anal Chem 2024; 96:620-623. [PMID: 38170960 DOI: 10.1021/acs.analchem.3c05263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Prokaryotic Argonautes (pAgos) have been recently used in many nucleic acid biosensing applications but have rarely been used for regulating the isothermal amplification system. Herein, we reported Thermus thermophilus Argonaute (TtAgo)-mediated background-suppressed exponential isothermal amplification (EXPAR) as the first example to explore the binding activity of pAgos toward regulation of the amplification template. It was demonstrated that thermophilic pAgos efficiently eliminated nonspecific hybridization between templates by their binding affinity with the template, resulting in greatly enhancing the specificity of EXPAR. TtAgo-mediated, background-suppressed EXPAR was employed to detect miRNA with a detection limit of 10-15 M, which was 1000 times and 100 times more sensitive than that of traditional RT-PCR and EXPAR, respectively. This method further showed good performance in discriminating cancer patients from healthy individuals, indicating its potential for practical clinical applications.
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Affiliation(s)
- Qiuyuan Lin
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Technology for Precision Medicine, School of Medical Technology and Engineering Fujian Medical University, Fuzhou 350005, China
| | - Xin Ye
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi PR China
| | - Hongyuan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200437, China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai 200437, China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai 200437, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai 200437, China
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CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction. Anal Chim Acta 2023; 1251:340998. [PMID: 36925288 DOI: 10.1016/j.aca.2023.340998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.
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Hu X, Qin W, Yuan R, Zhang L, Wang L, Ding K, Liu R, Huang W, Zhang H, Luo Y. Programmable molecular circuit discriminates multidrug-resistant bacteria. Mater Today Bio 2022; 16:100379. [PMID: 36042850 PMCID: PMC9420371 DOI: 10.1016/j.mtbio.2022.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022] Open
Abstract
Recognizing multidrug-resistant (MDR) bacteria with high accuracy and precision from clinical samples has long been a difficulty. For reliable detection of MDR bacteria, we investigated a programmable molecular circuit called the Background-free isothermal circuital kit (BRICK). The BRICK method provides a near-zero background signal by integrating four inherent modules equivalent to the conversion, amplification, separation, and reading modules. Interference elimination is largely owing to a molybdenum disulfide nanosheets-based fluorescence nanoswitch and non-specific suppression mediated by molecular inhibitors. In less than 70 min, an accurate distinction of various MDR bacteria was achieved without bacterial lysis. The BRICK technique detected 6.73 CFU/mL of methicillin-resistant Staphylococcus aureus in clinical samples in a proof-of-concept trial. By simply reprogramming the sequence panel, such a high signal-to-noise characteristic has been proven in the four other superbugs. The proposed BRICK method can provide a universal platform for infection surveillance and environmental management thanks to its superior programmability.
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Affiliation(s)
- Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Weichao Qin
- Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
| | - Rui Yuan
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Liangliang Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Liangting Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Ke Ding
- Department of Oncology, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
| | - Ruining Liu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Wanyun Huang
- Life Science Laboratories, Biology Department, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA, 01002, USA
| | - Hong Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
- Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
- Department of Clinical Laboratory, Fuling Hospital, Chongqing University, 2 Gaosuntang Road, Fuling District, Chongqing, 408099, China
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