1
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Bao M, Dollery SJ, Yuqing F, Tobin GJ, Du K. Micropillar enhanced FRET-CRISPR biosensor for nucleic acid detection. LAB ON A CHIP 2023; 24:47-55. [PMID: 38019145 DOI: 10.1039/d3lc00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
CRISPR technology has gained widespread adoption for pathogen detection due to its exceptional sensitivity and specificity. Although recent studies have investigated the potential of high-aspect-ratio microstructures in enhancing biochemical applications, their application in CRISPR-based detection has been relatively rare. In this study, we developed a FRET-based biosensor in combination with high-aspect-ratio microstructures and Cas12a-mediated trans-cleavage for detecting HPV 16 DNA fragments. Remarkably, our results show that micropillars with higher density exhibit superior molecular binding capabilities, leading to a tenfold increase in detection sensitivity. Furthermore, we investigated the effectiveness of two surface chemical treatment methods for enhancing the developed FRET assay. A simple and effective approach was also developed to mitigate bubble generation in microfluidic devices, a crucial issue in biochemical reactions within such devices. Overall, this work introduces a novel approach using micropillars for CRISPR-based viral detection and provides valuable insights into optimizing biochemical reactions within microfluidic devices.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | | | - Fnu Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Gregory J Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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2
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Lei Z, Lian L, Zhang L, Liu C, Zhai S, Yuan X, Wei J, Liu H, Liu Y, Du Z, Gul I, Zhang H, Qin Z, Zeng S, Jia P, Du K, Deng L, Yu D, He Q, Qin P. Detection of Frog Virus 3 by Integrating RPA-CRISPR/Cas12a-SPM with Deep Learning. ACS OMEGA 2023; 8:32555-32564. [PMID: 37720737 PMCID: PMC10500685 DOI: 10.1021/acsomega.3c02929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for frog virus 3 (FV3) is proposed. Combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, a limit of detection (LoD) of 100 aM (60.2 copies/μL) is achieved by optimizing RPA primers and CRISPR RNAs (crRNAs). For POC detection, smartphone microscopy is implemented, and an LoD of 10 aM is achieved in 40 min. The proposed system detects four positive animal-derived samples with a quantitation cycle (Cq) value of quantitative PCR (qPCR) in the range of 13 to 32. In addition, deep learning models are deployed for binary classification (positive or negative samples) and multiclass classification (different concentrations of FV3 and negative samples), achieving 100 and 98.75% accuracy, respectively. Without temperature regulation and expensive equipment, the proposed RPA-CRISPR/Cas12a combined with smartphone readouts and artificial-intelligence-assisted classification showcases the great potential for FV3 detection, specifically POC detection of DNA virus.
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Affiliation(s)
- Zhengyang Lei
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Lijin Lian
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Likun Zhang
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Changyue Liu
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Shiyao Zhai
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Xi Yuan
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Jiazhang Wei
- Department
of Otolaryngology & Head and Neck, The
People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi
Academy of Medical Sciences, 6 Taoyuan Road, Nanning, 530021, China
| | - Hong Liu
- Animal
and Plant Inspection and Quarantine Technical Centre, Shenzhen Exit and Entry Inspection and Quarantine Bureau, Shenzhen, Guangdong Province 518045, China
| | - Ying Liu
- Animal
and Plant Inspection and Quarantine Technical Centre, Shenzhen Exit and Entry Inspection and Quarantine Bureau, Shenzhen, Guangdong Province 518045, China
| | - Zhicheng Du
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Ijaz Gul
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Haihui Zhang
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Zhifeng Qin
- Animal
and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, Guangdong Province 518033, China
| | - Shaoling Zeng
- Animal
and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, Guangdong Province 518033, China
| | - Peng Jia
- Quality and
Standards Academy, Shenzhen Technology University, Shenzhen 518118, China
| | - Ke Du
- Department
of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Lin Deng
- Shenzhen
Bay Laboratory, Shenzhen 518132, China
| | - Dongmei Yu
- School
of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong 264209, China
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
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3
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Bao M, Dollery SJ, Yuqing F, Tobin GJ, Du K. Micropillar enhanced FRET-CRISPR biosensor for nucleic acid detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554533. [PMID: 37662406 PMCID: PMC10473682 DOI: 10.1101/2023.08.23.554533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
CRISPR technology has gained widespread adoption for pathogen detection due to its exceptional sensitivity and specificity. Although recent studies have investigated the potential of high-aspect-ratio microstructures in enhancing biochemical applications, their application in CRISPR-based detection has been relatively rare. In this study, we developed a FRET-based biosensor in combination with high-aspect-ratio microstructures and Cas12a-mediated trans-cleavage for detecting HPV 16 DNA fragments. Remarkably, our results show that micropillars with higher density exhibit superior molecular binding capabilities, leading to a tenfold increase in detection sensitivity. Furthermore, we investigated the effectiveness of two surface chemical treatment methods for enhancing the developed FRET assay. A simple and effective approach was also developed to mitigate bubble generation in microfluidic devices, a crucial issue in biochemical reactions within such devices. Overall, this work introduces a novel approach using micropillars for CRISPR-based viral detection and provides valuable insights into optimizing biochemical reactions within microfluidic devices.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Stephen J Dollery
- Biological Mimetics, Inc. 124 Byte Drive, Frederick, MD 21702, United States
| | - Fnu Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Gregory J Tobin
- Biological Mimetics, Inc. 124 Byte Drive, Frederick, MD 21702, United States
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
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4
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Liu FX, Cui JQ, Wu Z, Yao S. Recent progress in nucleic acid detection with CRISPR. LAB ON A CHIP 2023; 23:1467-1492. [PMID: 36723235 DOI: 10.1039/d2lc00928e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.
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Affiliation(s)
- Frank X Liu
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Johnson Q Cui
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Zhihao Wu
- IIP-Advanced Materials, Interdisciplinary Program Office (IPO), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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5
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Avaro AS, Santiago JG. A critical review of microfluidic systems for CRISPR assays. LAB ON A CHIP 2023; 23:938-963. [PMID: 36601854 DOI: 10.1039/d2lc00852a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Reviewed are nucleic acid detection assays that incorporate clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics and microfluidic devices and techniques. The review serves as a reference for researchers who wish to use CRISPR-Cas systems for diagnostics in microfluidic devices. The review is organized in sections reflecting a basic five-step workflow common to most CRISPR-based assays. These steps are analyte extraction, pre-amplification, target recognition, transduction, and detection. The systems described include custom microfluidic chips and custom (benchtop) chip control devices for automated assays steps. Also included are partition formats for digital assays and lateral flow biosensors as a readout modality. CRISPR-based, microfluidics-driven assays offer highly specific detection and are compatible with parallel, combinatorial implementation. They are highly reconfigurable, and assays are compatible with isothermal and even room temperature operation. A major drawback of these assays is the fact that reports of kinetic rates of these enzymes have been highly inconsistent (many demonstrably erroneous), and the low kinetic rate activity of these enzymes limits achievable sensitivity without pre-amplification. Further, the current state-of-the-art of CRISPR assays is such that nearly all systems rely on off-chip assays steps, particularly off-chip sample preparation.
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Affiliation(s)
- Alexandre S Avaro
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.
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6
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Wang D, Ma Z, Tian X. Effectiveness of organic solvents for recovering collapsed PDMS micropillar arrays. RSC Adv 2023; 13:4874-4879. [PMID: 36762086 PMCID: PMC9901194 DOI: 10.1039/d2ra08109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Polydimethylsiloxane (PDMS) micropillar arrays are widely used in research labs and engineering fields as analytical tools for various purposes. When the micropillar length or density surpasses a critical value, micropillars tend to collapse with each other and become unusable. Restoring collapsed PDMS micropillars typically involves the use of low surface tension solvents and ultrasound sonication, but such approach has received little success to date. In this work, we examined the effectiveness of different types of solvents for restoring collapsed PDMS micropillar arrays and show that the swelling ratio of PDMS in selected solvents constitutes an important factor in the effectiveness of restoring collapsed PDMS micropillars. Our results could be a promoter in recycling PDMS micropillar arrays and achieving economic and social benefits.
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Affiliation(s)
- Dong Wang
- School of Materials Science and Engineering, Beijing Institute of Technology Beijing 100081 China .,National Key Laboratory of Science and Technology on Material under Shock and Impact Beijing 100081 China.,Tangshan Research Institute, Beijing Institute of Technology Tangshan 063000 China
| | - Zhuang Ma
- School of Materials Science and Engineering, Beijing Institute of Technology Beijing 100081 China .,National Key Laboratory of Science and Technology on Material under Shock and Impact Beijing 100081 China.,Tangshan Research Institute, Beijing Institute of Technology Tangshan 063000 China.,Beijing Institute of Technology Chongqing Innovation Center Chongqing, 401120 China
| | - Xinchun Tian
- School of Materials Science and Engineering, Beijing Institute of Technology Beijing 100081 China .,National Key Laboratory of Science and Technology on Material under Shock and Impact Beijing 100081 China
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7
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Lu Y, Yang H, Bai J, He Q, Deng R. CRISPR-Cas based molecular diagnostics for foodborne pathogens. Crit Rev Food Sci Nutr 2022; 64:5269-5289. [PMID: 36476134 DOI: 10.1080/10408398.2022.2153792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Foodborne pathogenic infection has brought multifaceted issues to human life, leading to an urgent demand for advanced detection technologies. CRISPR/Cas-based biosensors have the potential to address various challenges that exist in conventional assays such as insensitivity, long turnaround time and complex pretreatments. In this perspective, we review the relevant strategies of CRISPR/Cas-assisted diagnostics on foodborne pathogens, focusing on biosensing platforms for foodborne pathogens based on fluorescence, colorimetric, (electro)chemiluminescence, electrochemical, and surface-enhanced Raman scattering detection. It summarizes their detection principles by the clarification of foodborne pathogenic bacteria, fungi, and viruses. Finally, we discuss the current challenges or technical barriers of these methods against broad application, and put forward alternative solutions to improve CRISPR/Cas potential for food safety.
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Affiliation(s)
- Yunhao Lu
- College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
| | - Jinrong Bai
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, P.R. China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
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8
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Bao M, Zhang S, Ten Pas C, Dollery SJ, Bushnell RV, Yuqing FNU, Liu R, Lu G, Tobin GJ, Du K. Computer vision enabled funnel adapted sensing tube (FAST) for power-free and pipette-free nucleic acid detection. LAB ON A CHIP 2022; 22:4849-4859. [PMID: 36111877 DOI: 10.1039/d2lc00586g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A simple, portable, and low-cost microfluidic system-funnel adapted sensing tube (FAST) is developed as an integrated, power-free, and pipette-free biosensor for viral nucleic acids. This FAST chip consists of four reaction chambers separated by carbon fiber rods, and the reagents in each chamber are transferred and mixed by manually removing the rods. Rather than using electrical heaters, only a hand warmer pouch is used for an isothermal recombinase polymerase amplification (RPA) and CRISPR-Cas12a reaction. The signal produced by the RPA-CRISPR reaction is observed by the naked eye using an inexpensive flashlight as a light source. The FAST chip is fabricated using water-soluble polyvinyl alcohol (PVA) as a sacrificial core, which is simple and environmentally friendly. Using a SARS-CoV-2 fragment as a target, a ∼10 fM (6 × 103 copies per μL) detection limit is achieved. To generalize standard optical readout for individuals without training, a linear kernel algorithm is created, showing an accuracy of ∼100% for identifying both positive and negative samples in FAST. This power-free, pipette-free, disposable, and simple device will be a promising tool for nucleic acid diagnostics in either clinics or low-resource settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Shuhuan Zhang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Chad Ten Pas
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | | | - Ruth V Bushnell
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - F N U Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Rui Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Guoyu Lu
- Department of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
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9
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Xie Y, Li H, Chen F, Udayakumar S, Arora K, Chen H, Lan Y, Hu Q, Zhou X, Guo X, Xiu L, Yin K. Clustered Regularly Interspaced short palindromic repeats-Based Microfluidic System in Infectious Diseases Diagnosis: Current Status, Challenges, and Perspectives. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204172. [PMID: 36257813 PMCID: PMC9731715 DOI: 10.1002/advs.202204172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/16/2022] [Indexed: 06/02/2023]
Abstract
Mitigating the spread of global infectious diseases requires rapid and accurate diagnostic tools. Conventional diagnostic techniques for infectious diseases typically require sophisticated equipment and are time consuming. Emerging clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) detection systems have shown remarkable potential as next-generation diagnostic tools to achieve rapid, sensitive, specific, and field-deployable diagnoses of infectious diseases, based on state-of-the-art microfluidic platforms. Therefore, a review of recent advances in CRISPR-based microfluidic systems for infectious diseases diagnosis is urgently required. This review highlights the mechanisms of CRISPR/Cas biosensing and cutting-edge microfluidic devices including paper, digital, and integrated wearable platforms. Strategies to simplify sample pretreatment, improve diagnostic performance, and achieve integrated detection are discussed. Current challenges and future perspectives contributing to the development of more effective CRISPR-based microfluidic diagnostic systems are also proposed.
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Affiliation(s)
- Yi Xie
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Huimin Li
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Fumin Chen
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Srisruthi Udayakumar
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Khyati Arora
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Hui Chen
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Yang Lan
- Centre for Nature‐Inspired EngineeringDepartment of Chemical EngineeringUniversity College LondonLondonWC1E 7JEUK
| | - Qinqin Hu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaonong Zhou
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaokui Guo
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Leshan Xiu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Kun Yin
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
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10
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Chen J, Liu J, Wu D, Pan R, Chen J, Wu Y, Huang M, Li G. CRISPR/Cas Precisely Regulated DNA-Templated Silver Nanocluster Fluorescence Sensor for Meat Adulteration Detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14296-14303. [PMID: 36288511 DOI: 10.1021/acs.jafc.2c04500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Meat adulteration can cause consumer fraud, food allergies, and religious issues. Rapid and sensitive detection methods are urgently demanded to supervise meat authenticity. Herein, a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas precisely regulated DNA-templated silver nanocluster (DNA-AgNC) sensor was ingeniously designed to detect meat adulteration. Specific sequence recognition of CRISPR/Cas12a allowed accurate identification of target DNA. The emerging label-free fluorescent probes, DNA-AgNCs, a class of promising fluorophores in biochemical analysis with attractive photostability and remarkably enhanced fluorescence properties, were first introduced as the substrates of CRISPR/Cas12a system, allowing a sensitive output of amplified signals through the precise regulation of the unique target DNA-activated trans-cleavage activity of Cas12a. Based on this specific recognition, efficient signal transduction of CRISPR/Cas12a, and the outstanding fluorescence properties of DNA-AgNCs, the proposed strategy achieved a satisfactory linear range from 10 pM to 1 μM with a limit of detection (LOD) as low as 1.9 pM, which can achieve sensitive detection of meat adulteration.
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Affiliation(s)
- Jiahui Chen
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jianghua Liu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, U.K
| | - Ruiyuan Pan
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jian Chen
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, 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, China
| | - Mingquan Huang
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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11
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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.
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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
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12
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Adampourezare M, Hasanzadeh M, Seidi F. Microfluidic assisted recognition of miRNAs towards point-of-care diagnosis: Technical and analytical overview towards biosensing of short stranded single non-coding oligonucleotides. Biomed Pharmacother 2022; 153:113365. [PMID: 35785705 DOI: 10.1016/j.biopha.2022.113365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/02/2022] Open
Abstract
MiRNAs are short stranded single non-coding oligonucleotides that play an important role in regulating gene expression. MiRNAs are stable in RNase enriched environments such as human body fluids and their dysregulation or abnormal abundance in human body fluids as a diagnostic biomarker has been associated with several diseases. Due to the low concentration of miRNAs, it is difficult to detect using interactive methods (ideal detection limit is femtomolar range). However, clinicians lack sensitive and reliable methods for quantifying miRNA. Microfluidic devices integrated with electrochemical, optical (fluorometric, SERs, FRET, colorimetric), electrochemiluminescence and photoelectrochemical signal readout led to development innovative diagnostic device test, can probably overcome the limitations of the traditional methods. In the present review, microfluid methods for the sensitive and selective recognition of miRNA in various biological matrices are surveyed. Also, advantages and limitation of recognition methods on the performance and efficiency of microfluidic based biosensing of miRNAs are critically investigated. Finally, the future perspectives on the diagnosis of disease based on microfluidic analysis of miRNAs are provided.
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Affiliation(s)
- Mina Adampourezare
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
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13
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Habimana JDD, Huang R, Muhoza B, Kalisa YN, Han X, Deng W, Li Z. Mechanistic insights of CRISPR/Cas nucleases for programmable targeting and early-stage diagnosis: A review. Biosens Bioelectron 2022; 203:114033. [DOI: 10.1016/j.bios.2022.114033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/21/2022]
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14
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Bao M, Chen Q, Xu Z, Jensen EC, Liu C, Waitkus JT, Yuan X, He Q, Qin P, Du K. Challenges and Opportunities for Clustered Regularly Interspaced Short Palindromic Repeats Based Molecular Biosensing. ACS Sens 2021; 6:2497-2522. [PMID: 34143608 DOI: 10.1021/acssensors.1c00530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, CRISPR, has recently emerged as a powerful molecular biosensing tool for nucleic acids and other biomarkers due to its unique properties such as collateral cleavage nature, room temperature reaction conditions, and high target-recognition specificity. Numerous platforms have been developed to leverage the CRISPR assay for ultrasensitive biosensing applications. However, to be considered as a new gold standard, several key challenges for CRISPR molecular biosensing must be addressed. In this paper, we briefly review the history of biosensors, followed by the current status of nucleic acid-based detection methods. We then discuss the current challenges pertaining to CRISPR-based nucleic acid detection, followed by the recent breakthroughs addressing these challenges. We focus upon future advancements required to enable rapid, simple, sensitive, specific, multiplexed, amplification-free, and shelf-stable CRISPR-based molecular biosensors.
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Affiliation(s)
- Mengdi Bao
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Qun Chen
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Zhiheng Xu
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Erik C. Jensen
- HJ Science & Technology Inc., San Leandro, California 94710, United States
| | - Changyue Liu
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Jacob T. Waitkus
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Xi Yuan
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Qian He
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Ke Du
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
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15
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Peyravian N, Malekzadeh Kebria M, Kiani J, Brouki Milan P, Mozafari M. CRISPR-Associated (CAS) Effectors Delivery via Microfluidic Cell-Deformation Chip. MATERIALS (BASEL, SWITZERLAND) 2021; 14:3164. [PMID: 34207502 PMCID: PMC8226447 DOI: 10.3390/ma14123164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Accepted: 05/30/2021] [Indexed: 12/26/2022]
Abstract
Identifying new and even more precise technologies for modifying and manipulating selectively specific genes has provided a powerful tool for characterizing gene functions in basic research and potential therapeutics for genome regulation. The rapid development of nuclease-based techniques such as CRISPR/Cas systems has revolutionized new genome engineering and medicine possibilities. Additionally, the appropriate delivery procedures regarding CRISPR/Cas systems are critical, and a large number of previous reviews have focused on the CRISPR/Cas9-12 and 13 delivery methods. Still, despite all efforts, the in vivo delivery of the CAS gene systems remains challenging. The transfection of CRISPR components can often be inefficient when applying conventional delivery tools including viral elements and chemical vectors because of the restricted packaging size and incompetency of some cell types. Therefore, physical methods such as microfluidic systems are more applicable for in vitro delivery. This review focuses on the recent advancements of microfluidic systems to deliver CRISPR/Cas systems in clinical and therapy investigations.
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Affiliation(s)
- Noshad Peyravian
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; (N.P.); (M.M.K.)
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Maziar Malekzadeh Kebria
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; (N.P.); (M.M.K.)
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Jafar Kiani
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran;
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Peiman Brouki Milan
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; (N.P.); (M.M.K.)
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mozafari
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
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16
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Dubrovsky M, Blevins M, Boriskina SV, Vermeulen D. High contrast cleavage detection. OPTICS LETTERS 2021; 46:2593-2596. [PMID: 34061064 DOI: 10.1364/ol.424858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/27/2021] [Indexed: 05/22/2023]
Abstract
Photonic biosensors that use optical resonances to amplify signals from refractive index changes offer high sensitivity, real-time readout, and scalable, low-cost fabrication. However, when used with classic affinity assays, they struggle with noise from nonspecific binding and are limited by the low refractive index and small size of target biological molecules. In this Letter, we evaluate the performance of an integrated microring photonic biosensor using the high contrast cleavage detection (HCCD) mechanism, which we recently introduced. The HCCD sensors make use of dramatic optical signal amplification caused by the cleavage of large numbers of high-contrast nanoparticle reporters instead of the adsorption of labeled or unlabeled low-index biological molecules. We evaluate the advantages of the HCCD detection mechanism over conventional target-capture detection techniques with the same label and the same sensor platform, using an example of a silicon ring resonator as an optical transducer decorated with silicon nanoparticles as high-contrast reporters. In the practical realization of this detection scheme, detection specificity and signal amplification can be achieved via collateral nucleic acid cleavage caused by enzymes such as CRISPR Cas12a and Cas13 after binding to a target DNA/RNA sequence in solution.
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17
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Liu R, He Y, Lan T, Zhang J. Installing CRISPR-Cas12a sensors in a portable glucose meter for point-of-care detection of analytes. Analyst 2021; 146:3114-3120. [PMID: 33999055 DOI: 10.1039/d1an00008j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Integrating CRISPR-Cas12a sensors with a portable glucose meter (PGM) was developed based on the target-induced activation of the collateral cleavage activity of Cas12a. Considering the portability, low cost and facile incorporation of the PGM system with suitable Cas12a sensors to recognize many targets, the CRISPR/Cas12a-PGM system demonstrated here paves a way to further broaden the POC applications of CRISPR-based diagnostics.
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Affiliation(s)
- Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
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18
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Zhou X, Cao H, Zeng Y. Microfluidic circulating reactor system for sensitive and automated duplex-specific nuclease-mediated microRNA detection. Talanta 2021; 232:122396. [PMID: 34074392 DOI: 10.1016/j.talanta.2021.122396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022]
Abstract
Duplex-specific nuclease signal amplification (DSNSA) is a promising microRNA (miRNA) quantification strategy. However, existing DSNSA based miRNA detection methods suffer from costly chemical consumptions and require laborious multi-step sample pretreatment that are prone to sample loss and contamination, including total RNA extraction and enrichment. To address these problems, herein we devised a pneumatically automated microfluidic reactor device that integrates both analyte extraction/enrichment and DSNSA-mediated miRNA detection in one streamlined analysis workflow. Two flow circulation strategies were investigated to determine the effects of flow conditions on the kinetics of on-chip DSNSA reaction in a bead-packed microreactor. With the optimized workflow, we demonstrated rapid, robust on-chip detection of miR-21 with a limit-of-detection of 35 amol, while greatly reducing the consumption of DSN enzyme to 0.1 U per assay. Therefore, this microfluidic system provides a useful tool for many applications, including clinical diagnosis.
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Affiliation(s)
- Xin Zhou
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Hongmei Cao
- Department of Chemistry, University of Kansas, Lawrence, KS, 66045, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA; University of Florida Health Cancer Center, Gainesville, FL, 32610, USA.
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19
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Shi Y, Fu X, Yin Y, Peng F, Yin X, Ke G, Zhang X. CRISPR-Cas12a System for Biosensing and Gene Regulation. Chem Asian J 2021; 16:857-867. [PMID: 33638271 DOI: 10.1002/asia.202100043] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising technology in the biological world. As one of the CRISPR-associated (Cas) proteins, Cas12a is an RNA-guided nuclease in the type V CRISPR-Cas system, which has been a robust tool for gene editing. In addition, due to the discovery of target-binding-induced indiscriminate single-stranded DNase activity of Cas12a, CRISPR-Cas12a also exhibits great promise in biosensing. This minireview not only gives a brief introduction to the mechanism of CRISPR-Cas12a but also highlights the recent developments and applications in biosensing and gene regulation. Finally, future prospects of the CRISPR-Cas12a system are also discussed. We expect this minireview will inspire innovative work on the CRISPR-Cas12a system by making full use of its features and advantages.
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Affiliation(s)
- Yuyan Shi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xiaoyi Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yao Yin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Fangqi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xia Yin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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