1
|
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.
Collapse
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
| |
Collapse
|
2
|
Zhou M, Li C, Wei R, Wang H, Jia H, Yan C, Huang L. Exponential Amplification-Induced Activation of CRISPR/Cas9 for Sensitive Detection of Exosomal miRNA. Anal Chem 2024; 96:4322-4329. [PMID: 38422550 DOI: 10.1021/acs.analchem.4c00313] [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: 03/02/2024]
Abstract
As an important component of highly heterogeneous exosomes, exosomal microRNAs (miRNAs) have great potential as noninvasive biomarkers for cancer diagnosis. Therefore, a sensitive and simple sensor is the key for its clinical application. Herein, we designed an exponential amplification reaction (EXPAR) to induce the reactivation of the CRISPR-associated protein 9/small guide RNA (Cas9/sgRNA) complex, thus achieving sensitive and visual exosomal miRNAs-21 (miR-21) fluorescence sensing. In this design, we inactivated the sgRNA by hybridizing sgRNA and blocker DNA. Then, we used a trigger DNA to hybridize with miR-21 and produced a lot of activated DNA by EXPAR. Those activated DNA further hybridized with blocker DNA and released the free sgRNA to form the activated Cas9/sgRNA complex. Based on the quick cleavage of activated Cas9/sgRNA complex, the reporter DNA labeled by SYBR Green I was released from the surface of the magnetic nanoparticles (MNPs) into the supernatant, and thus was used to sensitively quantify the miRNAs concentration with a limit of detection of 3 × 103 particles/mL. In addition, this fluorescence sensor has also been successfully employed to distinguish healthy people and cancer patients by naked-eye observation of the fluorescence, thus demonstrating its great potential for accurate and point-of-care cancer diagnosis.
Collapse
Affiliation(s)
- Mengyang Zhou
- School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Chao Li
- School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Rong Wei
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, Anhui 230000, China
| | - Haoyu Wang
- School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Haojie Jia
- School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Chao Yan
- School of Life Science, Anhui University, Hefei 230601, China
| | - Lin Huang
- School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| |
Collapse
|
3
|
An Y, Yu Z, Liu D, Han L, Zhang X, Xin X, Li C. HpaII-assisted and linear amplification-enhanced isothermal exponential amplification fluorescent strategy for rapid and sensitive detection of DNA methyltransferase activity. Anal Bioanal Chem 2023; 415:2271-2280. [PMID: 36961574 DOI: 10.1007/s00216-023-04647-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/25/2023]
Abstract
The detection of methyltransferase (MTase) activity is of great significance in methylation-related disease diagnosis and drug screening. Herein, a HpaII-assisted and linear amplification-enhanced exponential amplification strategy is proposed for sensitive and label-free detection of M.SssI MTase activity. The P1 probe contains self-complementary sequence 5'-CTAGCCGGCTAG-3' at 3'-terminal. After denaturation and annealing, P1 probes hybridize with itself to generate P1 duplexes. M.SssI MTase induces methylation of cytosine at 5'-CG-3' in P1 duplexes, and thus, HpaII fails to cleave at 5'-CCGG-3' due to methylation sensitivity, leaving P1 duplex intact. Then, these intact P1 duplexes are extended along 3'-terminal through Vent (exo-) DNA polymerase to generate dsDNA, which is recognized and nicked at the recognition sites by Nt.BstNBI, releasing two copies of primer X. Primer X hybridizes with X' at the amplification template T1 (X'-Y'-X') and then serves as primers to trigger the exponential amplification reaction (EXPAR). The point of inflection (POI) values of real-time fluorescence curves is linearly correlated with the logarithm of M.SssI MTase concentration in the range of 0.125 [Formula: see text] 8 U mL-1 with a low detection limit of 0.034 U mL-1. In the absence of M.SssI, P1 duplexes are cut by HpaII and separated into ssDNA under the executed temperature of EXPAR and thus unable to trigger the amplification. The strategy provides good selectivity against other types of MTases and protein and is able to detect M.SssI activity in human serum. Furthermore, the analytical method has the generality and can be extended to the analysis of other types of DNA MTases.
Collapse
Affiliation(s)
- Yaqian An
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China
| | - Zhiqi Yu
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China
| | - Di Liu
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China
| | - Lirong Han
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China
| | - Xian Zhang
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China
| | - Xuelian Xin
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China
| | - Cuiping Li
- Key Laboratory of Public Health Safety of Hebei Province, School of Public Health, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding, 071002, People's Republic of China.
| |
Collapse
|
4
|
Zhang X, Shi Y, Chen G, Wu D, Wu Y, Li G. CRISPR/Cas Systems-Inspired Nano/Biosensors for Detecting Infectious Viruses and Pathogenic Bacteria. SMALL METHODS 2022; 6:e2200794. [PMID: 36114150 DOI: 10.1002/smtd.202200794] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Infectious pathogens cause severe human illnesses and great deaths per year worldwide. Rapid, sensitive, and accurate detection of pathogens is of great importance for preventing infectious diseases caused by pathogens and optimizing medical healthcare systems. Inspired by a microbial defense system (i.e., CRISPR/ CRISPR-associated proteins (Cas) system, an adaptive immune system for protecting microorganisms from being attacked by invading species), a great many new biosensors have been successfully developed and widely applied in the detection of infectious viruses and pathogenic bacteria. Moreover, advanced nanotechnologies have also been integrated into these biosensors to improve their detection stability, sensitivity, and accuracy. In this review, the recent advance in CRISPR/Cas systems-based nano/biosensors and their applications in the detection of infectious viruses and pathogenic bacteria are comprehensively reviewed. First of all, the categories and working principles of CRISPR/Cas systems for establishing the nano/biosensors are simply introduced. Then, the design and construction of CRISPR/Cas systems-based nano/biosensors are comprehensively discussed. In the end, attentions are focused on the applications of CRISPR/Cas systems-based nano/biosensors in the detection of infectious viruses and pathogenic bacteria. Impressively, the remaining opportunities and challenges for the further design and development of CRISPR/Cas system-based nano/biosensors and their promising applications are proposed.
Collapse
Affiliation(s)
- Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Yiheng Shi
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Guang Chen
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Di Wu
- Institute for Global Food Security, Queen's University Belfast, Belfast, BT95DL, UK
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| |
Collapse
|
5
|
Qin C, Liu J, Zhu W, Zeng M, Xu K, Ding J, Zhou H, Zhu J, Ke Y, Li LY, Sheng G, Li Z, Luo H, Jiang S, Chen K, Ding X, Meng H. One-Pot Visual Detection of African Swine Fever Virus Using CRISPR-Cas12a. Front Vet Sci 2022; 9:962438. [PMID: 35923823 PMCID: PMC9339671 DOI: 10.3389/fvets.2022.962438] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 12/26/2022] Open
Abstract
African swine fever virus (ASFV) is a leading cause of worldwide agricultural loss. ASFV is a highly contagious and lethal disease for both domestic and wild pigs, which has brought enormous economic losses to a number of countries. Conventional methods, such as general polymerase chain reaction and isothermal amplification, are time-consuming, instrument-dependent, and unsatisfactorily accurate. Therefore, rapid, sensitive, and field-deployable detection of ASFV is important for disease surveillance and control. Herein, we created a one-pot visual detection system for ASFV with CRISPR/Cas12a technology combined with LAMP or RPA. A mineral oil sealing strategy was adopted to mitigate sample cross-contamination between parallel vials during high-throughput testing. Furthermore, the blue fluorescence signal produced by ssDNA reporter could be observed by the naked eye without any dedicated instrument. For CRISPR-RPA system, detection could be completed within 40 min with advantageous sensitivity. While CRISPR-LAMP system could complete it within 60 min with a high sensitivity of 5.8 × 102 copies/μl. Furthermore, we verified such detection platforms display no cross-reactivity with other porcine DNA or RNA viruses. Both CRISPR-RPA and CRISPR-LAMP systems permit highly rapid, sensitive, specific, and low-cost Cas12a-mediated visual diagnostic of ASFV for point-of-care testing (POCT) applications.
Collapse
Affiliation(s)
- Chao Qin
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Jiajia Liu
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Wenqi Zhu
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Muchu Zeng
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ke Xu
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Jinmei Ding
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Hao Zhou
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Jianshen Zhu
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Yuqing Ke
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Lai Yan Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Gaoyuan Sheng
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhuoru Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Huaixi Luo
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Shengyao Jiang
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Kangchun Chen
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Xianting Ding
| | - He Meng
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- He Meng
| |
Collapse
|
6
|
Chi Z, Wu Y, Chen L, Yang H, Khan MR, Busquets R, Huang N, Lin X, Deng R, Yang W, Huang J. CRISPR-Cas14a-integrated strand displacement amplification for rapid and isothermal detection of cholangiocarcinoma associated circulating microRNAs. Anal Chim Acta 2022; 1205:339763. [DOI: 10.1016/j.aca.2022.339763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/23/2022]
|
7
|
Chen B, Li Y, Xu F, Yang X. Powerful CRISPR-Based Biosensing Techniques and Their Integration With Microfluidic Platforms. Front Bioeng Biotechnol 2022; 10:851712. [PMID: 35284406 PMCID: PMC8905290 DOI: 10.3389/fbioe.2022.851712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 12/20/2022] Open
Abstract
In the fight against the worldwide pandemic coronavirus disease 2019 (COVID-19), simple, rapid, and sensitive tools for nucleic acid detection are in urgent need. PCR has been a classic method for nucleic acid detection with high sensitivity and specificity. However, this method still has essential limitations due to the dependence on thermal cycling, which requires costly equipment, professional technicians, and long turnover times. Currently, clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors have been developed as powerful tools for nucleic acid detection. Moreover, the CRISPR method can be performed at physiological temperature, meaning that it is easy to assemble into point-of-care devices. Microfluidic chips hold promises to integrate sample processing and analysis on a chip, reducing the consumption of sample and reagent and increasing the detection throughput. This review provides an overview of recent advances in the development of CRISPR-based biosensing techniques and their perfect combination with microfluidic platforms. New opportunities and challenges for the improvement of specificity and efficiency signal amplification are outlined. Furthermore, their various applications in healthcare, animal husbandry, agriculture, and forestry are discussed.
Collapse
Affiliation(s)
- Bing Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ya Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Feng Xu, ; Xiaonan Yang,
| | - Xiaonan Yang
- Institute of Intelligent Sensing, Zhengzhou University, Zhengzhou, China
- *Correspondence: Feng Xu, ; Xiaonan Yang,
| |
Collapse
|
8
|
Xie S, Qin C, Zhao F, Shang Z, Wang P, Sohail M, Zhang X, Li B. The DNA-Cu nanocluster and exonuclease I integrated label-free reporting system for CRISPR/Cas12a-based SARS-CoV-2 detection with minimized background signal. J Mater Chem B 2022; 10:6107-6117. [DOI: 10.1039/d2tb00857b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CRISPR-driven biosensing is developing rapidly, but current works mostly adopt dye-labeled ssDNA as the signal reporter, which is costly and unstable. Herein, we developed a label-free and low-background reporter for...
Collapse
|
9
|
He S, Li P, Tang L, Chen M, Yang Y, Zeng Z, Xiong W, Wu X, Huang J. Dual-stage amplified fluorescent DNA sensor based on polymerase-Mediated strand displacement reactions. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|