1
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Wei C, Lei X, Yu S. Multiplexed Detection Strategies for Biosensors Based on the CRISPR-Cas System. ACS Synth Biol 2024; 13:1633-1646. [PMID: 38860462 DOI: 10.1021/acssynbio.4c00161] [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: 06/12/2024]
Abstract
A growing number of applications require simultaneous detection of multiplexed nucleic acid targets in a single reaction, which enables higher information density in combination with reduced assay time and cost. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-Cas system have broad applications for the detection of nucleic acids due to their strong specificity, high sensitivity, and excellent programmability. However, realizing multiplexed detection is still challenging for the CRISPR-Cas system due to the nonspecific collateral cleavage activity, limited signal reporting strategies, and possible cross-reactions. In this review, we summarize the principles, strategies, and features of multiplexed detection based on the CRISPR-Cas system and further discuss the challenges and perspective.
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Affiliation(s)
- Cong Wei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
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2
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Jin Z, Yim W, Retout M, Housel E, Zhong W, Zhou J, Strano MS, Jokerst JV. Colorimetric sensing for translational applications: from colorants to mechanisms. Chem Soc Rev 2024. [PMID: 38835195 DOI: 10.1039/d4cs00328d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Colorimetric sensing offers instant reporting via visible signals. Versus labor-intensive and instrument-dependent detection methods, colorimetric sensors present advantages including short acquisition time, high throughput screening, low cost, portability, and a user-friendly approach. These advantages have driven substantial growth in colorimetric sensors, particularly in point-of-care (POC) diagnostics. Rapid progress in nanotechnology, materials science, microfluidics technology, biomarker discovery, digital technology, and signal pattern analysis has led to a variety of colorimetric reagents and detection mechanisms, which are fundamental to advance colorimetric sensing applications. This review first summarizes the basic components (e.g., color reagents, recognition interactions, and sampling procedures) in the design of a colorimetric sensing system. It then presents the rationale design and typical examples of POC devices, e.g., lateral flow devices, microfluidic paper-based analytical devices, and wearable sensing devices. Two highlighted colorimetric formats are discussed: combinational and activatable systems based on the sensor-array and lock-and-key mechanisms, respectively. Case discussions in colorimetric assays are organized by the analyte identities. Finally, the review presents challenges and perspectives for the design and development of colorimetric detection schemes as well as applications. The goal of this review is to provide a foundational resource for developing colorimetric systems and underscoring the colorants and mechanisms that facilitate the continuing evolution of POC sensors.
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Affiliation(s)
- Zhicheng Jin
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maurice Retout
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Emily Housel
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wenbin Zhong
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jiajing Zhou
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse V Jokerst
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
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3
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Zhang Z, Liu T, Dong M, Ahamed MA, Guan W. Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1969. [PMID: 38783564 PMCID: PMC11141732 DOI: 10.1002/wnan.1969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/10/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Zhikun Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Md. Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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4
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Song X, Cao Y, Yan F. Isothermal Nucleic Acid Amplification-Based Lateral Flow Testing for the Detection of Plant Viruses. Int J Mol Sci 2024; 25:4237. [PMID: 38673821 PMCID: PMC11050433 DOI: 10.3390/ijms25084237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Isothermal nucleic acid amplification-based lateral flow testing (INAA-LFT) has emerged as a robust technique for on-site pathogen detection, providing a visible indication of pathogen nucleic acid amplification that rivals or even surpasses the sensitivity of real-time quantitative PCR. The isothermal nature of INAA-LFT ensures consistent conditions for nucleic acid amplification, establishing it as a crucial technology for rapid on-site pathogen detection. However, despite its considerable promise, the widespread application of isothermal INAA amplification-based lateral flow testing faces several challenges. This review provides an overview of the INAA-LFT procedure, highlighting its advancements in detecting plant viruses. Moreover, the review underscores the imperative of addressing the existing limitations and emphasizes ongoing research efforts dedicated to enhancing the applicability and performance of this technology in the realm of rapid on-site testing.
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Affiliation(s)
- Xuemei Song
- School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo 315211, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yuhao Cao
- School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo 315211, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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5
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Ahamed MA, Khalid MAU, Dong M, Politza AJ, Zhang Z, Kshirsagar A, Liu T, Guan W. Sensitive and specific CRISPR-Cas12a assisted nanopore with RPA for Monkeypox detection. Biosens Bioelectron 2024; 246:115866. [PMID: 38029710 PMCID: PMC10842690 DOI: 10.1016/j.bios.2023.115866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
Monkeypox virus (MPXV) poses a global health emergency, necessitating rapid, simple, and accurate detection to manage its spread effectively. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technique has emerged as a promising next-generation molecular diagnostic approach. Here, we developed a highly sensitive and specific CRISPR-Cas12a assisted nanopore (SCAN) with isothermal recombinase polymerase amplification (RPA) for MPXV detection. The RPA-SCAN method offers a sensitivity unachievable with unamplified SCAN while also addressing the obstacles of PCR-SCAN for point-of-care applications. We demonstrated that size-counting of single molecules enables analysis of reaction-time dependent distribution of the cleaved reporter. Our MPXV-specific RPA assay achieved a limit of detection (LoD) of 19 copies in a 50 μL reaction system. By integrating 2 μL of RPA amplifications into a 20 μL CRISPR reaction, we attained an overall LoD of 16 copies/μL (26.56 aM) of MPXV at a 95% confidence level using the SCAN sensor. We also verified the specificity of RPA-SCAN in distinguishing MPXV from cowpox virus with 100% accuracy. These findings suggest that the isothermal RPA-SCAN device is well-suited for highly sensitive and specific Monkeypox detection. Given its electronic nature and miniaturization potential, the RPA-SCAN system paves the way for diagnosing a wide array of other infectious pathogens at the point of care.
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Affiliation(s)
- Md Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | | | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Zhikun Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA.
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6
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Feng F, Fu Q, Cao F, Yuan Y, Kong R, Ji D, Liu H. A Lateral Flow Assay Based on Streptavidin-biotin Amplification System with Recombinase Polymerase Amplification for Rapid and Quantitative Detection of Salmonella enteritidis. Chembiochem 2024; 25:e202300575. [PMID: 37963820 DOI: 10.1002/cbic.202300575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Salmonella constitutes a prevalent alimentary pathogen, instigating zoonotic afflictions. Consequently, the prompt discernment of Salmonella in sustenance is of cardinal significance. Lateral flow assays utilizing colorimetric methodologies adequately fulfill the prerequisites of point-of-care diagnostics, however, their detection threshold remains elevated, generally permitting only qualitative discernment, an impediment to the preliminary screening of nascent pathogens. In response to this conundrum, we propose a lateral flow diagnostic predicated upon a streptavidin-biotin amplification system with recombinase polymerase amplification engineered for the expeditious and quantitative discernment of Salmonella enteritidis. Trace nucleic acids within a sample undergo exponential amplification via recombinase polymerase amplification to a level discernable, constituting the initial signal amplification. Subsequently, along the test line (T-line) of the lateral flow strip, the chromatic signal undergoes augmentation by securing a greater quantity of AuNPs through the magnification capacity of the streptavidin-biotin mechanism, affecting the second signal amplification. Quantitative results are procured via smartphone capture and transferred to computer software for precise calculation of the targeted quantity. The lateral flow strip exhibits a LOD at 19.41 CFU/mL for cultured S. enteritidis. The RSD of three varying concentrations were respectively 3.74 %, 5.96 %, and 4.25 %.
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Affiliation(s)
- Fan Feng
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, 250353, China
| | - Qiang Fu
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, 250353, China
| | - Fengrong Cao
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, 250353, China
| | - Yun Yuan
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, 250353, China
| | - Ruixue Kong
- Department of Nursing, Shandong Medical College, No 5460 Erhuanan Road, Jinan, Shandong, 250002, China
| | - Dandan Ji
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, 250353, China
| | - Haiyun Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in, Universities of Shandong, Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, Shandong, 250022, China
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7
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Chang MM, Ma A, Novak EN, Barra M, Kundrod KA, Montealegre JR, Scheurer ME, Castle PE, Schmeler K, Richards-Kortum R. A novel tailed primer nucleic acid test for detection of HPV 16, 18 and 45 DNA at the point of care. Sci Rep 2023; 13:20397. [PMID: 37989845 PMCID: PMC10663460 DOI: 10.1038/s41598-023-47582-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023] Open
Abstract
Cervical cancer is a leading cause of death for women in low-resource settings despite being preventable through human papillomavirus (HPV) vaccination, early detection, and treatment of precancerous lesions. The World Health Organization recommends high-risk HPV (hrHPV) as the preferred cervical cancer screening strategy, which is difficult to implement in low-resource settings due to high costs, reliance on centralized laboratory infrastructure, and long sample-to-answer times. To help meet the need for rapid, low-cost, and decentralized cervical cancer screening, we developed tailed primer isothermal amplification and lateral flow detection assays for HPV16, HPV18, and HPV45 DNA. We translated these assays into a self-contained cartridge to achieve multiplexed detection of three hrHPV genotypes in a disposable cartridge. The developed test achieves clinically relevant limits of detection of 50-500 copies per reaction with extracted genomic DNA from HPV-positive cells. Finally, we performed sample-to-answer testing with direct lysates of HPV-negative and HPV-positive cell lines and demonstrated consistent detection of HPV16, HPV18, and HPV45 with 5000-50,000 cells/mL in < 35 min. With additional optimization to improve cartridge reliability, incorporation of additional hrHPV types, and validation with clinical samples, the assay could serve as a point-of-care HPV DNA test that improves access to cervical cancer screening in low-resource settings.
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Affiliation(s)
- Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ariel Ma
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jane Richards Montealegre
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael E Scheurer
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Xu Y, Luo J, Lai W, Da J, Yang B, Luo X, Zhan L, Fei Y, Liu L, Zha Y. Multiplex lateral flow test strip for detection of carbapenemase genes using barcoded tetrahedral DNA capture probe-based biosensing interface. Mikrochim Acta 2023; 190:360. [PMID: 37606732 DOI: 10.1007/s00604-023-05903-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023]
Abstract
Carbapenem-resistant Enterobacterales pose significant global health challenges due to their rapid spread and ability to hydrolyse various beta-lactam antibiotics. Rapid tests for these carbapenemase genes are crucial to ensure appropriate prescription administration and infection control. In this study, we developed a rapid visual nanodiagnostic platform for multiplexed detection of carbapenemase genes using a lateral flow strip. The nanodiagnostic strip was designed with separate barcoded DNA tetrahedrons for the blaKPC and blaNDM genes. These tetrahedrons were distributed on a nitrocellulose membrane at two different test lines as capture probes. When tested against a panel of carbapenemase genes, the tetrahedral probes captured single-stranded amplicons of asymmetric PCR via strand hybridisation. The amplicons acted as bridging elements, binding the DNA-modified gold nanoparticles to the test line of the strip, resulting in clear visual readouts specific to the blaKPC and blaNDM genes. By employing barcoded tetrahedrons and asymmetric PCR in conjunction with the lateral flow strip, a single diagnostic test enabled the detection of multiple carbapenemase genes. The test yielded results as low as 0.12 fM for blaKPC and 0.05 fM for blaNDM within 75 min. Furthermore, the strip effectively identified specific carbapenemase genes in clinical isolates using real-time PCR, antibody-based lateral flow systems for carbapenemase detection, and carbapenemase phenotype experiments. Thus, the strip develop has a high potential for testing blaKPC and blaNDM genes in practice.
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Affiliation(s)
- Yongjie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Jie Luo
- Department of Laboratory Medicine, Guizhou Provincial Second People's Hospital, Guiyang, 550002, Guizhou, China
| | - Wei Lai
- School of Medical Laboratory, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jingjing Da
- Renal Division, Department of Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Bin Yang
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Xiangrong Luo
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Lin Zhan
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Ying Fei
- School of Medical Laboratory, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Lin Liu
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
| | - Yan Zha
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
- Renal Division, Department of Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
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Zhu R, Jiang H, Li C, Li Y, Peng M, Wang J, Wu Q, Yan C, Bo Q, Wang J, Shen C, Qin P. CRISPR/Cas9-based point-of-care lateral flow biosensor with improved performance for rapid and robust detection of Mycoplasma pneumonia. Anal Chim Acta 2023; 1257:341175. [PMID: 37062563 DOI: 10.1016/j.aca.2023.341175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Screening of acute respiratory infections causes serious challenges in urgent point-of-care scenarios where conventional methods are impractical and alternative techniques suffer from low accuracy, poor robustness, and reliance on sophisticated instruments. As an improvement to this paradigm, we report a point-of-care lateral flow biosensor (LFB) based on the recognition property of clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (Cas9) and apply it to the detection of Mycoplasma pneumoniae (M. pneumoniae). The designed biosensor employs CRISPR/Cas9 for secondary recognition after preamplification of target gene using specific primer set, avoiding false positives caused by nontarget factors. The high amplification efficiency and low applicable temperatures of recombinase polymerase amplification brings the detection limit of the biosensor to 3 copies even at a preamplification temperature of 25 °C. Its practical application is further demonstrated with 100% accuracy by testing with 43 M. pneumoniae-infected specimens and 80 uninfected specimens. Additionally, the entire detection, including pretreatment, preamplification, CRISPR/Cas9 recognition, and visual analysis, can be completed in 30 min. Featured with the combination of CRISPR/Cas9 and LFB, the biosensor we developed herein ensures excellent convenience, accuracy, and robustness, which endows promising point-of-care screening potential for infectious pathogens.
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Peng X, Mei X, Yang J, Liu J, Li Y. Ultrasensitive Hybridization Chain Reaction-Assisted Multisite Exonuclease III Amplification Strategy Combined with a Direct Quantitative Fluorescence Lateral Flow Technique for Multiple Bacterial 16S rRNA Detection. Anal Chem 2023; 95:5807-5814. [PMID: 36946074 DOI: 10.1021/acs.analchem.3c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Accurate and in-time detection of bacteria conduces to preventing their rapid spread around the environment, while a nucleic acid test (NAT) is a powerful tool for early diagnosis of pathogens. Herein, we propose a hybridization chain reaction (HCR)-mediated multisite exonuclease III (Exo-III) amplification strategy (HCR/Exo-III amplifier) to achieve the one-pot and ultrasensitive isothermal amplification of bacterial 16S rRNA and a portable fluorescence detection device (PFD) to directly read signals in a lateral flow assay (LFA). In detail, the target-initiated HCR products present multiple binding sites for triggering the Exo-III amplifier that produces numerous target amplicons. Following that, the target amplicons travel up on the strip and bridge between the DNA-CdTe/CdS probes and the capture DNA to form a positive fluorescence line. After that, the strip is inserted into the PFD to accomplish the fluorescence signal reading. The constructed HCR/Exo-III amplifier-based PFD-LFA implemented the simultaneous and specific detection of three bacteria with a detection limit of a few tenths of fM for synthetic 16S rRNA fragments and dozens of CFU/mL for Staphylococcus aureus, Listeria monocytogenes, and Salmonella typhimurium in pure cultures. The sensing platform features isothermal amplification, convenient operation, and good economy, displaying great potential for on-site testing toward multiple nucleic acid analytes.
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Affiliation(s)
- Xin Peng
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Xuecui Mei
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiao Yang
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiang Liu
- School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Yingchun Li
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
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11
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Liu H, Cao T, Chen H, Zhang J, Li W, Zhang Y, Liu H. Two-color lateral flow nucleic acid assay combined with double-tailed recombinase polymerase amplification for simultaneous detection of chicken and duck adulteration in mutton. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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12
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Ma Y, Ma X, Bu L, Shan J, Liu D, Zhang L, Qi X, Chu Y, Wu H, Zou B, Zhou G. Flap Endonuclease-Induced Steric Hindrance Change Enables the Construction of Multiplex and Versatile Lateral Flow Strips for DNA Detection. Anal Chem 2022; 94:14725-14733. [PMID: 36223239 DOI: 10.1021/acs.analchem.2c03143] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A lateral flow strip (LFS) is an ideal tool for point-of-care testing (POCT), but traditional LFSs cannot be used for multiplex detection. Herein, a multiplex and versatile LFS based on flap endonuclease 1 (FEN1)-induced steric hindrance change (FISH-LFS) is proposed. In this method, multiplex PCR coupled with cascade invasive reactions was employed to yield single-stranded flaps, which were target-specific but independent of target sequences. Then, the amplicons were applied for FISH-LFS, and the single-stranded flaps would be efficiently captured by the complementary LFS-probes at different test lines. As flaps were cleaved from the specially designed hairpin probes, competition among flaps and hairpin probes would occur in capturing the probes at test lines. We enabled the hairpin probes to flow through the test lines while the flaps to stay at the test lines by making use of the difference in steric hindrance between hairpin probes and flaps. The assay is able to detect as low as two copies of blood pathogens (HBV, HCV, and HIV), to pick up as low as 0.1% mutants from wild-type gDNA, and to genotype 200 copies of SARS-CoV-2 variants α and β within 75 min at a conventional PCR engine. As the method is free of dye, a portable PCR engine could be used for a cost-effective multiplex detection on site. Results using an ultrafast mobile PCR system for FISH-LFS showed that as fast as 30 min was achieved for detecting three pathogens (HBV, HCV, and HIV) in blood, very suitable for POCT of pathogen screening. The method is convenient in operation, simple in instrumentation, specific in genotyping, and very easy in setting up multiplex POCT assays.
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Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Li Bu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Jingwen Shan
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Danni Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Likun Zhang
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Haiping Wu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.,School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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13
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Nature-inspired nanozymes as signal markers for in-situ signal amplification strategy: A portable dual-colorimetric immunochromatographic analysis based on smartphone. Biosens Bioelectron 2022; 210:114289. [DOI: 10.1016/j.bios.2022.114289] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 02/02/2023]
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14
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Jin X, Fu R, Du W, Shan X, Mao Z, Deng A, Lin X, Su Y, Yang H, Lv W, Zhong H, Huang G. Rapid, Highly Sensitive, and Label-Free Pathogen Assay System Using a Solid-Phase Self-Interference Recombinase Polymerase Amplification Chip and Hyperspectral Interferometry. Anal Chem 2022; 94:2926-2933. [PMID: 35107980 DOI: 10.1021/acs.analchem.1c04858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recombinase polymerase amplification (RPA) is a useful pathogen identification method. Several label-free detection methods for RPA amplicons have been developed in recent years. However, these methods still lack sensitivity, specificity, efficiency, or simplicity. In this study, we propose a rapid, highly sensitive, and label-free pathogen assay system based on a solid-phase self-interference RPA chip (SiSA-chip) and hyperspectral interferometry. The SiSA-chips amplify and capture RPA amplicons on the chips, rather than irrelevant amplicons such as primer dimers, and the SiSA-chips are then analysed by hyperspectral interferometry. Optical length increases of SiSA-chips are used to demonstrate RPA detection results, with a limit of detection of 1.90 nm. This assay system can detect as few as six copies of the target 18S rRNA gene of Plasmodium falciparum within 20 min, with a good linear relationship between the detection results and the concentration of target genes (R2 = 0.9903). Single nucleotide polymorphism (SNP) genotyping of the dhfr gene of Plasmodium falciparum is also possible using the SiSA-chip, with as little as 1% of mutant gene distinguished from wild-type loci (m/wt). This system offers a high-efficiency (20 min), high-sensitivity (6 copies/reaction), high-specificity (1% m/wt), and low-cost (∼1/50 of fluorescence assays for RPA) diagnosis method for pathogen DNA identification. Therefore, this system is promising for fast identification of pathogens to help diagnose infectious diseases, including SNP genotyping.
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Affiliation(s)
- Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rongxin Fu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenli Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohui Shan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zeyin Mao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Anni Deng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Lin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ya Su
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Han Yang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hao Zhong
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.,National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
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15
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. Recombinase Polymerase Amplification Assay with and without Nuclease-Dependent-Labeled Oligonucleotide Probe. Int J Mol Sci 2021; 22:11885. [PMID: 34769313 PMCID: PMC8584857 DOI: 10.3390/ijms222111885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 01/18/2023] Open
Abstract
The combination of recombinase polymerase amplification (RPA) and lateral flow test (LFT) is a strong diagnostic tool for rapid pathogen detection in resource-limited conditions. Here, we compared two methods generating labeled RPA amplicons following their detection by LFT: (1) the basic one with primers modified with different tags at the terminals and (2) the nuclease-dependent one with the primers and labeled oligonucleotide probe for nuclease digestion that was recommended for the high specificity of the assay. Using both methods, we developed an RPA-LFT assay for the detection of worldwide distributed phytopathogen-alfalfa mosaic virus (AMV). A forward primer modified with fluorescein and a reverse primer with biotin and fluorescein-labeled oligonucleotide probe were designed and verified by RPA. Both labeling approaches and their related assays were characterized using the in vitro-transcribed mRNA of AMV and reverse transcription reaction. The results demonstrated that the RPA-LFT assay based on primers-labeling detected 103 copies of RNA in reaction during 30 min and had a half-maximal binding concentration 22 times lower than probe-dependent RPA-LFT. The developed RPA-LFT was successfully applied for the detection of AMV-infected plants. The results can be the main reason for choosing simple labeling with primers for RPA-LFT for the detection of other pathogens.
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Affiliation(s)
| | | | | | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.I.); (I.V.S.); (A.V.Z.)
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