1
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Lee RC, Corsano A, Tseng CY, Laohakunakorn N, Chou LYT. Rewireable Building Blocks for Enzyme-Powered DNA Computing Networks. J Am Chem Soc 2024. [PMID: 39255470 DOI: 10.1021/jacs.4c07221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Neural networks enable the processing of large, complex data sets with applications in disease diagnosis, cell profiling, and drug discovery. Beyond electronic computers, neural networks have been implemented using programmable biomolecules such as DNA; this confers unique advantages, such as greater portability, electricity-free operation, and direct analysis of patterns of biomolecules in solution. Analogous to bottlenecks in electronic computers, the computing power of DNA-based neural networks is limited by the ability to add more computing units, i.e., neurons. This limitation exists because current architectures require many nucleic acids to model a single neuron. Each additional neuron compounds existing problems such as long assembly times, high background signal, and cross-talk between components. Here, we test three strategies to solve this limitation and improve the scalability of DNA-based neural networks: (i) enzymatic synthesis for high-purity neurons, (ii) spatial patterning of neuron clusters based on their network position, and (iii) encoding neuron connectivity on a universal single-stranded DNA backbone. We show that neurons implemented via these strategies activate quickly, with a high signal-to-background ratio and process-weighted inputs. We rewired our modular neurons to demonstrate basic neural network motifs such as cascading, fan-in, and fan-out circuits. Finally, we designed a prototype two-layer microfluidic device to automate the operation of our circuits. We envision that our proposed design will help scale DNA-based neural networks due to its modularity, simplicity of synthesis, and compatibility with various neural network architectures. This will enable portable computing power for applications in portable diagnostics, compact data storage, and autonomous decision making for lab-on-a-chips.
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Affiliation(s)
- Ryan C Lee
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| | - Ariel Corsano
- Department of Bioengineering, McGill University, 3480 University Street Room, 350 McConnell Engineering Building, Montreal, Quebec H3A 0E9, Canada
| | - Chung Yi Tseng
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| | - Nadanai Laohakunakorn
- School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, The King's Buildings, Edinburgh, Scotland EH9 3FF, U.K
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
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2
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Hu R, Guo C, Liu C, Zhang Q, Zhang X, Chen Y, Liu Y. From Lab to Home: Ultrasensitive Rapid Detection of SARS-CoV-2 with a Cascade CRISPR/Cas13a-Cas12a System Based Lateral Flow Assay. Anal Chem 2024; 96:14197-14204. [PMID: 39161182 DOI: 10.1021/acs.analchem.4c02726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Currently, CRISPR/Cas-based molecular diagnostic techniques usually rely on the introduction of nucleic acid amplification to improve their sensitivity, which is usually more time-consuming, susceptible to aerosol contamination, and therefore not suitable for at-home molecular testing. In this research, we developed an advanced CRISPR/Cas13a-Cas12a-based lateral flow assay that facilitated the ultrasensitive and rapid detection of SARS-CoV-2 RNA directly from samples, without the need for nucleic acid amplification. This method was called CRISPR LFA enabling at-home RNA testing (CLEAR). CLEAR used a novel cascade mechanism with specially designed probes that fold into hairpin structures, enabling visual detection of SARS-CoV-2 sequences down to 1 aM sensitivity levels. More importantly, CLEAR had a positive coincidence rate of 100% and a negative coincidence rate of 100% for clinical nasopharyngeal swabs from 16 patients. CLEAR was particularly suitable for at-home molecular testing, providing a low-cost, user-friendly solution that can efficiently distinguish between different SARS-CoV-2 variants. CLEAR overcame the common limitations of high sensitivity and potential contamination associated with traditional PCR-based systems, making it a promising tool for widespread public health application, especially in environments with limited access to laboratory resources.
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Affiliation(s)
- Ronghuan Hu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, People's Republic of China
| | - Chuanghao Guo
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, People's Republic of China
| | - Conghui Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, People's Republic of China
| | - Qianling Zhang
- Environmental Engineering and Graphene Composite, Research Center, College of Chemistry and Environmental, Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
| | - Xueji Zhang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, People's Republic of China
| | - Yong Chen
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
- Environmental Engineering and Graphene Composite, Research Center, College of Chemistry and Environmental, Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
| | - Yizhen Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, People's Republic of China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, People's Republic of China
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3
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Dong Y, Guo C, Wang J, Ye C, Min Q. Recent Advances in DNA Nanotechnology-Based Sensing Platforms for Rapid Virus Detection. Chembiochem 2024; 25:e202400230. [PMID: 38825565 DOI: 10.1002/cbic.202400230] [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: 03/26/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/04/2024]
Abstract
Several major viral pandemics in history have significantly impacted the public health of human beings. The COVID-19 pandemic has further underscored the critical need for early detection and screening of infected individuals. However, current detection techniques are confronted with deficiencies in sensitivity and accuracy, restricting the capability of detecting trace amounts of viruses in human bodies and in the environments. The advent of DNA nanotechnology has opened up a feasible solution for rapid and sensitive virus determination. By harnessing the designability and addressability of DNA nanostructures, a range of rapid virus sensing platforms have been proposed. This review overviewed the recent progress, application, and prospect of DNA nanotechnology-based rapid virus detection platforms. Furthermore, the challenges and developmental prospects in this field were discussed.
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Affiliation(s)
- Yuxiang Dong
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Cheng Guo
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Jialing Wang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Changqing Ye
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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4
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Sonwal S, Gupta VK, Shukla S, Umapathi R, Ghoreishian SM, Han S, Bajpai VK, Cho Y, Huh YS. Panoramic view of artificial fruit ripening agents sensing technologies and the exigency of developing smart, rapid, and portable detection devices: A review. Adv Colloid Interface Sci 2024; 331:103199. [PMID: 38909548 DOI: 10.1016/j.cis.2024.103199] [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] [Received: 12/22/2023] [Revised: 04/22/2024] [Accepted: 05/18/2024] [Indexed: 06/25/2024]
Abstract
Recently, the availability of point-of-care sensor systems has led to the rapid development of smart and portable devices for the detection of hazardous analytes. The rapid flow of artificially ripened fruits into the market is associated with an elevated risk to human life, agriculture, and the ecosystem due to the use of artificial fruit ripening agents (AFRAs). Accordingly, there is a need for the development of "Point-of-care Sensors" to detect AFRAs due to several advantages, such as simple operation, promising detection mechanism, higher selectivity and sensitivity, compact, and portable. Traditional detection approaches are time-consuming and inappropriate for on-the-spot analyses. Presented comprehensive review aimed to reveal how such technology has systematically evolved over time (through conventional, advanced, and portable smart techniques) detection detect AFRA, till date. Moreover, focuses and highlights a framework of initiatives undertaken for technological advancements in the development of smart the portable detection techniques (kits) for the onsite detection of AFRAs in fruits with in-depth discussion over sensing mechanism and analytical performance of the sensing technology. Notably, colorimetric detection methods have the greatest potential for real-time monitoring of AFRA and its residues because they are easy to assemble, have a high level of selectivity and sensitivity, and can be read by the human eye independently. This study sought to differentiate between traditional credible strategies by presenting new prospects, perceptions, and challenges related to portable devices. This review provides systematic framework of advances in portable field recognition strategies for the on-spot AFRA detection in fruits and critical information for development of new paper-based portable sensors for fruit diagnostic sectors.
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Affiliation(s)
- Sonam Sonwal
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Vivek Kumar Gupta
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Shruti Shukla
- Department of Nanotechnology, North-Eastern Hill University (NEHU), East Khasi Hills, Shillong, Meghalaya 793022, India
| | - Reddicherla Umapathi
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | | | - Soobin Han
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Vivek Kumar Bajpai
- Department of Energy and Materials Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Youngjin Cho
- Food Safety and Distribution Research Group, Korea Food Research Institute, Wanju 55365, Republic of korea.
| | - Yun Suk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea.
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5
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Wang A, Chen Z, Feng X, He G, Zhong T, Xiao Y, Yu X. Magnetic-gold nanoparticle-mediated paper-based biosensor for highly sensitive colorimetric detection of food adulteration. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134849. [PMID: 38885584 DOI: 10.1016/j.jhazmat.2024.134849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/27/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
Food adulteration presents a significant challenge due to the evasion of legal oversight and the difficulty of identification. Addressing this issue, there is an urgent need for on-site, rapid, visually based small-scale equipment, along with large-scale screening technology, to enable prompt results without providing opportunities for dishonest traders to react. Colorimetric reactions offer advantages in terms of speed, visualization, and miniaturization. However, there is a scarcity of suitable colorimetric reactions for food adulteration detection, and interference from colored food impurities and easily comparable color results affects accuracy. To overcome limitations, this study introduces a novel approach utilizing polydopamine magnetic nanoparticles to enrich DNA in food samples, effectively eliminating interfering components. By employing gold nanoparticles to generate magnetic-gold nanoparticles, a single magnetic bead achieves simultaneous enrichment, impurity removal, and detection. The use of paper-based biosensors and visualization equipment allows for the visualization and digital analysis of results, achieving a low detection limit of 4.59 nmol mL-1. The method also exhibits high accuracy and repeatability, with a RSD ranging from 1.6 % to 4.0 %. This innovative colorimetric method addresses the need for rapid, miniaturized, and large-scale detection, thus providing a solution for food adulteration challenges.
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Affiliation(s)
- Anyu Wang
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macao Special Administrative Region of China
| | - Zihan Chen
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macao Special Administrative Region of China
| | - Xiao Feng
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, China
| | - Guangyun He
- Institute of Quality Standard and Testing Technology for Agro-Products, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macao Special Administrative Region of China
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macao Special Administrative Region of China
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macao Special Administrative Region of China.
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6
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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; 53:7681-7741. [PMID: 38835195 DOI: 10.1039/d4cs00328d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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7
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Zhang T, Wang Y, Teng X, Deng R, Li J. Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test. Nat Protoc 2024:10.1038/s41596-024-01022-x. [PMID: 39026122 DOI: 10.1038/s41596-024-01022-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
The evolution and mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgent concerns as they pose the risk of vaccine failure and increased viral transmission. However, affordable and scalable tools allowing rapid identification of SARS-CoV-2 variants are not readily available, which impedes diagnosis and epidemiological surveillance. Here we present a colorimetric nucleic acid assay named MARVE (multiplexed, preamplification-free, single-nucleotide-resolved viral evolution) that is convenient to perform and yields single-nucleotide resolution. The assay integrates nucleic acid strand displacement reactions with enzymatic amplification to colorimetrically sense viral RNA using a metal ion-incorporated DNA probe (TEprobe). We provide detailed guidelines to design TEprobes for discriminating single-nucleotide variations in viral RNAs, and to fabricate a test paper for the detection of SARS-CoV-2 variants of concern. Compared with other nucleic acid assays, our assay is preamplification-free, single-nucleotide-resolvable and results are visible via a color change. Besides, it is smartphone readable, multiplexed, quick and cheap ($0.30 per test). The protocol takes ~2 h to complete, from the design and preparation of the DNA probes and test papers (~1 h) to the detection of SARS-CoV-2 or its variants (30-45 min). The design of the TEprobes requires basic knowledge of molecular biology and familiarity with NUPACK or the Python programming language. The fabrication of the origami papers requires access to a wax printer using the CAD and PDF files provided or requires users to be familiar with AutoCAD to design new origami papers. The protocol is also applicable for designing assays to detect other pathogens and their variants.
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Affiliation(s)
- Ting Zhang
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, New Cornerstone Science Institute, Tsinghua University, Beijing, China
- College of Biomass Science and Engineering, Department of Respiration and Critical Care Medine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxi Wang
- College of Biomass Science and Engineering, Department of Respiration and Critical Care Medine, West China Hospital, Sichuan University, Chengdu, China
| | - Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, New Cornerstone Science Institute, Tsinghua University, Beijing, China
- Beijing Institute of Life Science and Technology, Beijing, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Department of Respiration and Critical Care Medine, West China Hospital, Sichuan University, Chengdu, China.
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, New Cornerstone Science Institute, Tsinghua University, Beijing, China.
- Beijing Institute of Life Science and Technology, Beijing, China.
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8
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Zolotareva M, Cascalheira F, Caneiras C, Bárbara C, Caetano DM, Teixeira MC. In the flow of molecular miniaturized fungal diagnosis. Trends Biotechnol 2024:S0167-7799(24)00157-4. [PMID: 38987118 DOI: 10.1016/j.tibtech.2024.06.010] [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: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.
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Affiliation(s)
- Maria Zolotareva
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Francisco Cascalheira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Cátia Caneiras
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, 2829-511 Almada, Portugal; Institute of Preventive Medicine and Public Health, Universidade de Lisboa, 1649-026 Lisboa, Portugal
| | - Cristina Bárbara
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Centro Hospitalar Universitário Lisboa Norte, 1600-190, Lisboa, Portugal
| | - Diogo Miguel Caetano
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; Department of Electrical and Computer Engineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
| | - Miguel Cacho Teixeira
- iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
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9
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Zhang YB, Arizti-Sanz J, Bradley A, Huang Y, Kosoko-Thoroddsen TSF, Sabeti PC, Myhrvold C. CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza. J Mol Diagn 2024; 26:599-612. [PMID: 38901927 DOI: 10.1016/j.jmoldx.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 06/22/2024] Open
Abstract
The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.
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Affiliation(s)
- Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts
| | - Yujia Huang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | | | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts; Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey; Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey; Department of Chemistry, Princeton University, Princeton, New Jersey.
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10
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Aminiranjbar Z, Gultakti CA, Alangari MN, Wang Y, Demir B, Koker Z, Das AK, Anantram MP, Oren EE, Hihath J. Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements. ACS Sens 2024; 9:2888-2896. [PMID: 38773960 DOI: 10.1021/acssensors.3c02734] [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: 05/24/2024]
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.
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Affiliation(s)
- Zahra Aminiranjbar
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mashari Nasser Alangari
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Department of Electrical Engineering, University of Hail, Hail 2240, Saudi Arabia
| | - Yiren Wang
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Zeynep Koker
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Arindam K Das
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
- Department of Computer Science and Electrical Engineering, Eastern Washington University, Cheney, Washington 99004,United States
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Center for Bioelectronics and Biosensors, School of Electrical, Computer, and Energy Engineering, Arizona State University, Phoenix, Arizona 85287, United States
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11
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Zhang Y, Xu S, Luo M, Chen J, Wang L, Yang F, Ye J, Liu J, He B, Weng L, Li S, Zhang D. Hairpin-Empowered Invasive Reaction Combined with Catalytic Hairpin Assembly Cascade Amplification for the Specific Detection of Single-Nucleotide Polymorphisms. Anal Chem 2024; 96:10283-10293. [PMID: 38864304 DOI: 10.1021/acs.analchem.4c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Single-nucleotide polymorphism (SNP) is widely used in the study of disease-related genes and in the genetic study of animal and plant strains. Therefore, SNP detection is crucial for biomedical diagnosis and treatment as well as for molecular design breeding of animals and plants. In this regard, this article describes a novel technique for detecting SNP using flap endonuclease 1 (FEN 1) as a specific recognition element and catalytic hairpin assembly (CHA) cascade reaction as a signal amplification strategy. The mutant target (MT) was hybridized with a biotin-modified upstream probe and hairpin-type downstream probe (DP) to form a specific three-base overlapping structure. Then, FEN 1 was employed for three-base overlapping structure-specific recognition, namely, the precise SNP site identification and the 5' flap of DP dissociation. After dissociation, the hybridized probes were magnetically separated by a streptavidin-biotin complex. Especially, the ability to establish such a hairpin-type DP provided a powerful tool that could be used to hide the cut sequence (CS) and avoid false-positive signals. The cleaved CS initiated the CHA reaction and allowed superior fluorescence signal generation. Owing to the high specificity of FEN 1 for single base recognition, only the MT could be distinguished from the wild-type target and mismatched DNA. Owing to the dual signal amplification, as low as 0.36 fM MT and 1% mutation abundance from the mixtures could be detected, respectively. Furthermore, it could accurately identify SNPs from human cancer cells, as well as soybean leaf genome extracts. This strategy paves the way for the development of more precise and sensitive tools for diagnosing early onset diseases as well as molecular design breeding tools.
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Affiliation(s)
- Yunshan Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shijie Xu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Ma Luo
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Lanyue Wang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Fang Yang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Jing Ye
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jichong Liu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Bingxiao He
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Diming Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
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12
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Kumar S, Kaushal JB, Lee HP. Sustainable Sensing with Paper Microfluidics: Applications in Health, Environment, and Food Safety. BIOSENSORS 2024; 14:300. [PMID: 38920604 PMCID: PMC11202065 DOI: 10.3390/bios14060300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024]
Abstract
This manuscript offers a concise overview of paper microfluidics, emphasizing its sustainable sensing applications in healthcare, environmental monitoring, and food safety. Researchers have developed innovative sensing platforms for detecting pathogens, pollutants, and contaminants by leveraging the paper's unique properties, such as biodegradability and affordability. These portable, low-cost sensors facilitate rapid diagnostics and on-site analysis, making them invaluable tools for resource-limited settings. This review discusses the fabrication techniques, principles, and applications of paper microfluidics, showcasing its potential to address pressing challenges and enhance human health and environmental sustainability.
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Affiliation(s)
- Sanjay Kumar
- Durham School of Architectural Engineering and Construction, University of Nebraska-Lincoln, Scott Campus, Omaha, NE 68182-0816, USA
| | - Jyoti Bala Kaushal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Heow Pueh Lee
- Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore;
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13
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Park SY, Sivakumar R, Lee NY. D-Glucose-Mediated Gold Nanoparticle Fabrication for Colorimetric Detection of Foodborne Pathogens. BIOSENSORS 2024; 14:284. [PMID: 38920588 PMCID: PMC11202049 DOI: 10.3390/bios14060284] [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: 04/20/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Gold nanoparticle (AuNP) fabrication via the oxidation of D-glucose is applied for detecting two foodborne pathogens, Enterococcus faecium (E. faecium) and Staphylococcus aureus (S. aureus). D-glucose is used as a reducing agent due to its oxidation to gluconic acid by sodium hydroxide (NaOH), resulting in the formation of AuNPs. Based on this mechanism, we develop AuNP-based colorimetric detection in conjunction with loop-mediated isothermal amplification (LAMP) for accurately identifying the infectious bacteria. Here, Au+ ions bind to the base of double-stranded DNA. In the presence of D-glucose and NaOH, the LAMP amplicon-Au+ complex maintains its bound state at 65 °C for 10 min while it is reduced to AuNPs in a dispersed form, exhibiting a red color. We aimed to pre-mix D-glucose with LAMP reagents before amplification and induce successful colorimetry without inhibiting amplification to simplify the experimental process and decrease the reaction time. Therefore, the entire process, including LAMP and colorimetric detection, is accomplished in approximately 1 h. The limit of detection of E. faecium and S. aureus is confirmed using the introduced method as 101 CFU/mL and 100 fg/μL, respectively. We expect that colorimetric detection using D-glucose-mediated AuNP synthesis offers an application for simple and immediate molecular diagnosis.
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Affiliation(s)
| | | | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea; (S.Y.P.); (R.S.)
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14
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Li X, Sun R, Pan J, Shi Z, An Z, Dai C, Lv J, Liu G, Liang H, Liu J, Lu Y, Zhang F, Liu Q. Rapid and on-site wireless immunoassay of respiratory virus aerosols via hydrogel-modulated resonators. Nat Commun 2024; 15:4035. [PMID: 38740742 PMCID: PMC11091083 DOI: 10.1038/s41467-024-48294-1] [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: 01/02/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Rapid and accurate detection of respiratory virus aerosols is highlighted for virus surveillance and infection control. Here, we report a wireless immunoassay technology for fast (within 10 min), on-site (wireless and battery-free), and sensitive (limit of detection down to fg/L) detection of virus antigens in aerosols. The wireless immunoassay leverages the immuno-responsive hydrogel-modulated radio frequency resonant sensor to capture and amplify the recognition of virus antigen, and flexible readout network to transduce the immuno bindings into electrical signals. The wireless immunoassay achieves simultaneous detection of respiratory viruses such as severe acute respiratory syndrome coronavirus 2, influenza A H1N1 virus, and respiratory syncytial virus for community infection surveillance. Direct detection of unpretreated clinical samples further demonstrates high accuracy for diagnosis of respiratory virus infection. This work provides a sensitive and accurate immunoassay technology for on-site virus detection and disease diagnosis compatible with wearable integration.
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Affiliation(s)
- Xin Li
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Taizhou Key Laboratory of Medical Devices and Advanced Materials, Research Institute of Zhejiang University-Taizhou, Taizhou, 318000, China
| | - Rujing Sun
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jingying Pan
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- School of Medicine, Zhejiang University, Hangzhou, 310027, China
| | - Zhenghan Shi
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zijian An
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Chaobo Dai
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jingjiang Lv
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Guang Liu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Biosafety III Laboratory, Life Science Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jun Liu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Taizhou Key Laboratory of Medical Devices and Advanced Materials, Research Institute of Zhejiang University-Taizhou, Taizhou, 318000, China
| | - Yanli Lu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Fenni Zhang
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Qingjun Liu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China.
- Taizhou Key Laboratory of Medical Devices and Advanced Materials, Research Institute of Zhejiang University-Taizhou, Taizhou, 318000, China.
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15
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Liu Y, Tang Y, Bao Y, Cai K, Lu B, Zhao R, Yu C, Du Y, Li B. Iso-E-Codelock: A Rebuilding-free Electrochemical Chip with a Customizable Decoding Probe for Real-Time and Portable Pathogen Diagnostics. Angew Chem Int Ed Engl 2024; 63:e202400340. [PMID: 38497899 DOI: 10.1002/anie.202400340] [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: 01/05/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/19/2024]
Abstract
In order to realize portable pathogen diagnostics with easier quantitation, digitization and integration, we develop a ready-to-use electrochemical sensing strategy (Iso-E-Codelock) for real-time detection of isothermal nucleic acid amplification. Bridged by a branched DNA as codelock, the isothermal amplicon is transduced into increased current of an electrochemical probe, holding multiple advantages of high sensitivity, high selectivity, signal-on response, "zero" background and one-pot operation. Through a self-designed portable instrument (BioAlex PHE-T), the detection can be implemented on a multichannel microchip and output real-time amplification curves just like an expensive commercial PCR machine. The microchip is a rebuilding-free and disposable component. The branch codelock probe can be customized for different targets and designs. Such high performance and flexibility have been demonstrated utilizing four virus (SARS-CoV-2, African swine fever, FluA and FluB) genes as targets, and two branch (3-way and 4-way) DNAs as codelock probes.
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Affiliation(s)
- Yichen Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yin Bao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Kaiwei Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
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16
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Xiong E, Liu P, Deng R, Zhang K, Yang R, Li J. Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro. Natl Sci Rev 2024; 11:nwae118. [PMID: 38742234 PMCID: PMC11089818 DOI: 10.1093/nsr/nwae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/16/2024] Open
Abstract
Single-nucleotide variants (SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.
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Affiliation(s)
- Erhu Xiong
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Pengfei Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Jinghong Li
- Department of Chemistry, Center for Bioanalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Institute of Life Science and Technology, Beijing 102206, China
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17
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Dong T, Ding R, Zhou R, Shen C, Sheridan W, Paez D, Zhao Z, Wu P, Li F. A Portable Nucleic Acid Testing Platform with Photosensitization, a Three-Dimensionally Printed Multipiece Chip, and Digital Color Sensing. Anal Chem 2024; 96:6628-6633. [PMID: 38626114 DOI: 10.1021/acs.analchem.3c05897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Portable nucleic acid testing (NAT) holds great promise for point-of-care disease diagnosis and field-based applications but remains difficult to achieve. Herein, we describe a portable NAT that streamlines loop-mediated isothermal amplification with photosensitization-based color development in a fully sealed 3D-printed multipiece chip. Using a smartphone accessory and an APP, we also introduce a calibration-free quantification approach via digital color sensing and library matching. With these innovative approaches, our detection platform is highly accessible, allowing for rapid and sensitive NAT without requiring sophisticated instruments and well-trained personnel. The field applicability of our NAT platform was demonstrated by detecting tuberculosis infections in clinical sputum samples and food adulteration in commercial salmon meat products.
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Affiliation(s)
- Tianyu Dong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Ruolin Ding
- National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610064, P. R. China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu 610064, P. R. China
| | - Chenlan Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu 610064, P. R. China
| | - Will Sheridan
- Nix Sensor Ltd., 286 Sanford Ave N Unit 501, Hamilton, Ontario L8L 6A1, Canada
| | - Dixon Paez
- Nix Sensor Ltd., 286 Sanford Ave N Unit 501, Hamilton, Ontario L8L 6A1, Canada
| | - Zhihe Zhao
- National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610064, P. R. China
| | - Peng Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
- Analytical & Testing Center, Sichuan University, Chengdu 610064, P. R. China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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18
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Bagheri N, Chamorro A, Idili A, Porchetta A. PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications. Angew Chem Int Ed Engl 2024; 63:e202319677. [PMID: 38284432 DOI: 10.1002/anie.202319677] [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: 12/19/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
The RNA-programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio-engineering strategies are required to achieve control over Cas12a activity. Here, we show that Toehold Switch DNA hairpins, presenting a rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used to control Cas12a in response to molecular inputs. Reconfiguring the Toehold Switch DNA from a hairpin to a duplex conformation through a strand displacement reaction provides an effective means to modulate the accessibility of the PAM, thereby controlling the binding and cleavage activities of Cas12a. Through this approach, we showcase the potential to trigger downstream Cas12a activity by leveraging proximity-based strand displacement reactions in response to target binding. By utilizing the trans-cleavage activity of Cas12a as a signal transduction method, we demonstrate the versatility of our approach for sensing applications. Our system enables rapid, one-pot detection of IgG antibodies and small molecules with high sensitivity and specificity even within complex matrices. Besides the bioanalytical applications, the switchable PAM-engineered Toehold Switches serve as programmable tools capable of regulating Cas12a-based targeting and DNA processing in response to molecular inputs and hold promise for a wide array of biotechnological applications.
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Affiliation(s)
- Neda Bagheri
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alejandro Chamorro
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Andrea Idili
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
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19
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Chen Y, He S, Lian H, Liu G, Liu B, Wei X. Microfluidic Immunosensing Platform Based on a Rolling Circle Amplification-Assisted DNA Dendrimer Probe for Portable and Sensitive Detection of Allergen-Specific IgE. Anal Chem 2024; 96:5625-5632. [PMID: 38556980 DOI: 10.1021/acs.analchem.4c00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The robust point-of-care platform for sensitive, multiplexed, and affordable detection of allergen-specific IgE (sIgE) is an urgent demand in component-resolved diagnostics. Here, we developed a microfluidic immunosensing platform based on a rolling circle amplification-assisted DNA dendrimer probe for sensitive detection of multiple sIgEs. The versatile multichannel microfluidic whole blood analytical device integrates cell filtration, recombinant antigen-modified magnetic enrichment, and DNA dendrimer probe-amplified signal transduction for portable on-chip analysis. Three sIgEs against common oyster allergens were simultaneously detected in blood samples by simple smartphone-based imaging without any pretreatment. The quantitative detection of multiple allergen-specific antibodies on the platform was achieved with limits of detection of less than 50 pg/mL, exhibiting superior sensitivity compared to most point-of-care testing. The detection results of 55 serum samples and 4 whole blood samples were 100% consistent with the ELISA results, confirming the accuracy and stability of our platform. Additionally, the reversible combination of hexahistidine6-tag and Ni-IMAC magbead was elegantly utilized on the immunosensing platform for desired reversibility. With the advantages of general applicability, high sensitivity, and reversibility, the DNA dendrimer-based microfluidic immunosensing platform provides great potential for the portable detection of immune proteins as a point-of-care platform in disease diagnostics and biological analysis.
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Affiliation(s)
- Yiyu Chen
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Shan He
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Huiting Lian
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
- Key Laboratory of Molecular Designing and Green Conversions, Huaqiao University, Xiamen 361021, China
| | - Guangming Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Bin Liu
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
- Key Laboratory of Molecular Designing and Green Conversions, Huaqiao University, Xiamen 361021, China
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, Huaqiao University, Xiamen 361021, China
| | - Xiaofeng Wei
- College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
- Key Laboratory of Molecular Designing and Green Conversions, Huaqiao University, Xiamen 361021, China
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, Huaqiao University, Xiamen 361021, China
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20
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Shi C, Yang D, Ma X, Pan L, Shao Y, Arya G, Ke Y, Zhang C, Wang F, Zuo X, Li M, Wang P. A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202320179. [PMID: 38288561 DOI: 10.1002/anie.202320179] [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: 12/28/2023] [Indexed: 02/17/2024]
Abstract
Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one-stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost-effective detection of low-abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS-CoV-2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point-of-care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics.
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Affiliation(s)
- Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuanchuan Shao
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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21
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Yang B, Wang H, Kong J, Fang X. Long-term monitoring of ultratrace nucleic acids using tetrahedral nanostructure-based NgAgo on wearable microneedles. Nat Commun 2024; 15:1936. [PMID: 38431675 PMCID: PMC10908814 DOI: 10.1038/s41467-024-46215-w] [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: 11/08/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Here, we report a tetrahedral nanostructure-based Natronobacterium gregoryi Argonaute (NgAgo) for long-term stable monitoring of ultratrace unamplified nucleic acids (cell-free DNAs and RNAs) in vivo for sepsis on wearable device. This integrated wireless wearable consists of a flexible circuit board, a microneedle biosensor, and a stretchable epidermis patch with enrichment capability. We comprehensively investigate the recognition mechanism of nucleic acids by NgAgo/guide DNA and signal transformation within the Debye distance. In vivo experiments demonstrate the suitability for real-time monitoring of cell-free DNA and RNA with a sensitivity of 0.3 fM up to 14 days. These results provide a strategy for highly sensitive molecular recognition in vivo and for on-body detection of nucleic acid.
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Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Haonan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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22
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Kim KH, Ryu E, Khaleel ZH, Seo SE, Kim L, Kim YH, Park HG, Kwon OS. Plasmonic digital PCR for discriminative detection of SARS-CoV-2 variants. Biosens Bioelectron 2024; 246:115859. [PMID: 38011776 DOI: 10.1016/j.bios.2023.115859] [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] [Received: 10/30/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
We developed a novel strategy for discriminative detection of SARS-CoV-2 variants based on the plasmonic photothermal effect of gold nanofilms and digital polymerase chain reaction (dPCR) technology. This method consists of the gold nanofilm-based dPCR chip fabrication for ultrafast heating and cooling cycles by the plasmonic photothermal effect, the LED quencher immobilization through the interfacing compound on the surface of the gold nanofilm to prevent photoquenching of PCR signaling dye, and the discriminative detection of the variant viruses from the COVID-19 clinical samples by photothermal cycles with fabricated dPCR chips and a portable plasmonic PCR device. Compared to conventional sequencing or RT-qPCR-based variant detection methods, this technology can be effectively applied to point-of-care testing by enabling ultrafast quantitative analysis with a small device. With this method, we successfully detected the delta variant and the omicron variant with a high sensitivity of 10 copies from COVID-19 patients' clinical samples within 25 min, including reverse transcription. This method can be applied universally to rapid and accurate point-of-care testing for various pandemic viruses as well as the coronavirus.
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Affiliation(s)
- Kyung Ho Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eunsu Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Zinah Hilal Khaleel
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sung Eun Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Lina Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Oh Seok Kwon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
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23
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Kong D, Zhang S, Guo M, Li S, Wang Q, Gou J, Wu Y, Chen Y, Yang Y, Dai C, Tian Z, Wee ATS, Liu Y, Wei D. Ultra-Fast Single-Nucleotide-Variation Detection Enabled by Argonaute-Mediated Transistor Platform. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307366. [PMID: 37805919 DOI: 10.1002/adma.202307366] [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: 07/24/2023] [Revised: 10/03/2023] [Indexed: 10/09/2023]
Abstract
"Test-and-go" single-nucleotide variation (SNV) detection within several minutes remains challenging, especially in low-abundance samples, since existing methods face a trade-off between sensitivity and testing speed. Sensitive detection usually relies on complex and time-consuming nucleic acid amplification or sequencing. Here, a graphene field-effect transistor (GFET) platform mediated by Argonaute protein that enables rapid, sensitive, and specific SNV detection is developed. The Argonaute protein provides a nanoscale binding channel to preorganize the DNA probe, accelerating target binding and rapidly recognizing SNVs with single-nucleotide resolution in unamplified tumor-associated microRNA, circulating tumor DNA, virus RNA, and reverse transcribed cDNA when a mismatch occurs in the seed region. An integrated microchip simultaneously detects multiple SNVs in agreement with sequencing results within 5 min, achieving the fastest SNV detection in a "test-and-go" manner without the requirement of nucleic acid extraction, reverse transcription, and amplification.
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Affiliation(s)
- Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Shen Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200433, P. R. China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Qiang Wang
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Jian Gou
- Department of Physics, National University of Singapore, Singapore, 117542, Singapore
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yuetong Yang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore, Singapore, 117542, Singapore
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
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24
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Li D, Sun C, Zhuang P, Mei X. Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods. Talanta 2024; 266:124937. [PMID: 37481886 DOI: 10.1016/j.talanta.2023.124937] [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] [Received: 03/08/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.
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Affiliation(s)
- Dan Li
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co., Ltd., Shenyang, China
| | - Pengfei Zhuang
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Key Laboratory of Medical Tissue Engineering of Liaoning Province, Jinzhou Medical University, Jinzhou, Liaoning, China.
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25
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Ma T, Peng L, Ran Q, Zeng Y, Liang F. Toward the Development of Simplified Lateral Flow Assays Using Hydrogels as the Universal Control Line. ACS APPLIED BIO MATERIALS 2023; 6:5685-5694. [PMID: 38035477 DOI: 10.1021/acsabm.3c00817] [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: 12/02/2023]
Abstract
Lateral flow assays (LFA) have been widely utilized as point-of-care testing devices in diverse fields. However, it is imperative to preprint costly bioreceptors onto the lateral flow nitrocellulose membrane at the control line. The complex manufacturing process and relatively limited detection capabilities of LFA have impeded their utilization in more challenging fields. Here, we propose a novel and simple strategy to simplify the manufacture of LFA while simultaneously improving the sensitivity by modifying the hydrogel line (HL). In our study, it was observed that the sensitivity of commercial LFA strips could be enhanced by 2-5-fold by incorporating an extra HL. Particularly, a universal control line was developed to accommodate multiple LFA detection modes by substituting the conventional antibody control line with a hydrogel control line (HCL). As a proof of concept, the HCL performance could be associated with the slowdown and interception effect toward fluid, which are dependent on the permeation and hydrophilicity of the hydrogel with varying concentrations in the nitrocellulose membrane. This new design builds the foundation to enhance the sensitivity and develop the simplified LFA sensing platform without additional complicated processes.
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Affiliation(s)
- Tao Ma
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Linlin Peng
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Qinying Ran
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Yan Zeng
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
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26
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Hao L, Li X, Liang H, Lei W, Yang W, Zhang B. Biosensors based on potent miniprotein binder for sensitive testing of SARS-CoV‑2 variants of concern. Mikrochim Acta 2023; 191:38. [PMID: 38110824 DOI: 10.1007/s00604-023-06113-2] [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: 09/07/2023] [Accepted: 11/21/2023] [Indexed: 12/20/2023]
Abstract
The miniprotein binder TRI2-2 was employed as an antibody alternative to build a single antibody-coupled TRI2-2 based gold nanoparticle-based lateral flow immunoassay (AT-GLFIA) biosensor. The biosensor provides high specificity and affinity binding between TRI2-2 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) spike antigen receptor binding domain (S-RBD). It also enables rapid testing of wild-type (WT), B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) SARS-CoV-2 S-RBD and is at least ~ 16-fold more sensitive than conventional antibody pair-based GLFIA (AP-GLFIA). Besides, we developed a wireless micro-electrochemical assay (WMECA) biosensor based on the TRI2-2, which demonstrates an excellent VOCs testing capability at the pg mL-1 level. Overall, our results demonstrate that integrating miniprotein binders into conventional immunoassay systems is a promising design for improving the testing capabilities of such systems without hard-to-obtain antibody pair, complex reporter design, laborious signal amplification strategies, or specific instrumentation.
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Affiliation(s)
- Liangwen Hao
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Xue Li
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Hongying Liang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Wenjing Lei
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Weitao Yang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Bingbo Zhang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai, 200065, China.
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27
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Lee S, Bi L, Chen H, Lin D, Mei R, Wu Y, Chen L, Joo SW, Choo J. Recent advances in point-of-care testing of COVID-19. Chem Soc Rev 2023; 52:8500-8530. [PMID: 37999922 DOI: 10.1039/d3cs00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Advances in microfluidic device miniaturization and system integration contribute to the development of portable, handheld, and smartphone-compatible devices. These advancements in diagnostics have the potential to revolutionize the approach to detect and respond to future pandemics. Accordingly, herein, recent advances in point-of-care testing (POCT) of coronavirus disease 2019 (COVID-19) using various microdevices, including lateral flow assay strips, vertical flow assay strips, microfluidic channels, and paper-based microfluidic devices, are reviewed. However, visual determination of the diagnostic results using only microdevices leads to many false-negative results due to the limited detection sensitivities of these devices. Several POCT systems comprising microdevices integrated with portable optical readers have been developed to address this issue. Since the outbreak of COVID-19, effective POCT strategies for COVID-19 based on optical detection methods have been established. They can be categorized into fluorescence, surface-enhanced Raman scattering, surface plasmon resonance spectroscopy, and wearable sensing. We introduced next-generation pandemic sensing methods incorporating artificial intelligence that can be used to meet global health needs in the future. Additionally, we have discussed appropriate responses of various testing devices to emerging infectious diseases and prospective preventive measures for the post-pandemic era. We believe that this review will be helpful for preparing for future infectious disease outbreaks.
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Affiliation(s)
- Sungwoon Lee
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea.
| | - Liyan Bi
- School of Special Education and Rehabilitation, Binzhou Medical University, Yantai, 264003, China
| | - Hao Chen
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Dong Lin
- School of Pharmacy, Bianzhou Medical University, Yantai, 264003, China
| | - Rongchao Mei
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Yantai 264003, China
| | - Yixuan Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Yantai 264003, China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Yantai 264003, China
- School of Pharmacy, Bianzhou Medical University, Yantai, 264003, China
| | - Sang-Woo Joo
- Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul 06978, South Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea.
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28
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Zhou L, Vestri A, Marchesano V, Rippa M, Sagnelli D, Picazio G, Fusco G, Han J, Zhou J, Petti L. The Label-Free Detection and Identification of SARS-CoV-2 Using Surface-Enhanced Raman Spectroscopy and Principal Component Analysis. BIOSENSORS 2023; 13:1014. [PMID: 38131774 PMCID: PMC10741931 DOI: 10.3390/bios13121014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/24/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
The World Health Organization (WHO) declared in a May 2023 announcement that the COVID-19 illness is no longer categorized as a Public Health Emergency of International Concern (PHEIC); nevertheless, it is still considered an actual threat to world health, social welfare and economic stability. Consequently, the development of a convenient, reliable and affordable approach for detecting and identifying SARS-CoV-2 and its emerging new variants is crucial. The fingerprint and signal amplification characteristics of surface-enhanced Raman spectroscopy (SERS) could serve as an assay scheme for SARS-CoV-2. Here, we report a machine learning-based label-free SERS technique for the rapid and accurate detection and identification of SARS-CoV-2. The SERS spectra collected from samples of four types of coronaviruses on gold nanoparticles film, fabricated using a Langmuir-Blodgett self-assembly, can provide more spectroscopic signatures of the viruses and exhibit low limits of detection (<100 TCID50/mL or even <10 TCID50/mL). Furthermore, the key Raman bands of the SERS spectra were systematically captured by principal component analysis (PCA), which effectively distinguished SARS-CoV-2 and its variant from other coronaviruses. These results demonstrate that the combined use of SERS technology and PCA analysis has great potential for the rapid analysis and discrimination of multiple viruses and even newly emerging viruses without the need for a virus-specific probe.
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Affiliation(s)
- Lu Zhou
- Institute of Applied Sciences and Intelligent Systems of CNR, 80072 Pozzuoli, Italy; (L.Z.); (A.V.); (V.M.); (M.R.); (D.S.)
- Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China;
| | - Ambra Vestri
- Institute of Applied Sciences and Intelligent Systems of CNR, 80072 Pozzuoli, Italy; (L.Z.); (A.V.); (V.M.); (M.R.); (D.S.)
| | - Valentina Marchesano
- Institute of Applied Sciences and Intelligent Systems of CNR, 80072 Pozzuoli, Italy; (L.Z.); (A.V.); (V.M.); (M.R.); (D.S.)
| | - Massimo Rippa
- Institute of Applied Sciences and Intelligent Systems of CNR, 80072 Pozzuoli, Italy; (L.Z.); (A.V.); (V.M.); (M.R.); (D.S.)
| | - Domenico Sagnelli
- Institute of Applied Sciences and Intelligent Systems of CNR, 80072 Pozzuoli, Italy; (L.Z.); (A.V.); (V.M.); (M.R.); (D.S.)
| | - Gerardo Picazio
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (G.P.); (G.F.)
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (G.P.); (G.F.)
| | - Jiaguang Han
- Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China;
| | - Jun Zhou
- Department of Microelectronic Science and Engineering, School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Lucia Petti
- Institute of Applied Sciences and Intelligent Systems of CNR, 80072 Pozzuoli, Italy; (L.Z.); (A.V.); (V.M.); (M.R.); (D.S.)
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29
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Wang F, Ma X, Ye J, Shi C, Chen Y, Yu Z, Li T, Yang D, Li M, Wang P. Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement. Anal Chem 2023; 95:17699-17707. [PMID: 37971750 DOI: 10.1021/acs.analchem.3c03548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Detection of viral infections (e.g., SARS-CoV-2) with high precision is critical to disease control and treatment. There is an urgent need to develop point-of-care detection methods to complement the gold standard laboratory-based PCR assay with comparable sensitivity and specificity. Herein, we developed a method termed mCAD to achieve ultraspecific point-of-care detection of SARS-CoV-2 RNA while maintaining high sensitivity by programming multiplex rolling circle amplification and toehold-mediated strand displacement reactions. RCA offers sufficient amplification of RNA targets for subsequent detection. Most importantly, a multilayer of detection specificity is implemented into mCAD via sequence-specific hybridization of nucleic acids across serial steps of this protocol to fully eliminate potential false-positive detections. Using mCAD, we demonstrated a highly specific, sensitive, and convenient visual detection of SARS-CoV-2 RNA from both synthetic and clinical samples, exhibiting performance comparable to qPCR. We envision that mCAD will find its broad applications in clinical prospects for nucleic acid detections readily beyond SARS-CoV-2 RNA.
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Affiliation(s)
- Fukai Wang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200233, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jing Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yun Chen
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhicai Yu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tianming Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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30
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Fu Y, Liu Y, Song W, Yang D, Wu W, Lin J, Yang X, Zeng J, Rong L, Xia J, Lei H, Yang R, Zhang M, Liao Y. Early monitoring-to-warning Internet of Things system for emerging infectious diseases via networking of light-triggered point-of-care testing devices. EXPLORATION (BEIJING, CHINA) 2023; 3:20230028. [PMID: 38264687 PMCID: PMC10742204 DOI: 10.1002/exp.20230028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/31/2023] [Indexed: 01/25/2024]
Abstract
Early monitoring and warning arrangements are effective ways to distinguish infectious agents and control the spread of epidemic diseases. Current testing technologies, which cannot achieve rapid detection in the field, have a risk of slowing down the response time to the disease. In addition, there is still no epidemic surveillance system, implementing prevention and control measures is slow and inefficient. Motivated by these clinical needs, a sample-to-answer genetic diagnosis platform based on light-controlled capillary modified with a photocleavable linker is first developed, which could perform nucleic acid separation and release by light irradiation in less than 30 seconds. Then, on site polymerase chain reaction was performed in a handheld closed-loop convective system. Test reports are available within 20 min. Because this method is portable, rapid, and easy to operate, it has great potential for point-of-care testing. Additionally, through multiple device networking, a real-time artificial intelligence monitoring system for pathogens was developed on a cloud server. Through data reception, analysis, and visualization, the system can send early warning signals for disease control and prevention. Thus, anti-epidemic measures can be implemented effectively, and deploying and running this system can improve the capabilities for the prevention and control of infectious diseases.
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Affiliation(s)
- Yu Fu
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
- Longgang District Central Hospital of ShenzhenShenzhenChina
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Yan Liu
- Institute for Health Innovation and TechnologyNational University of SingaporeSingaporeSingapore
| | - Wenlu Song
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
| | - Delong Yang
- Department of Burn Surgerythe First People's Hospital of FoshanFoshanChina
| | - Wenjie Wu
- Department of Burn and Plastic SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Jingyan Lin
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Xiongtiao Yang
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Jian Zeng
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Lingzhi Rong
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Jiaojiao Xia
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Hongyi Lei
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Ronghua Yang
- Department of Burn and Plastic SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Mingxia Zhang
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
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31
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Liu Y, Yang Y, Wang G, Wang D, Shao PL, Tang J, He T, Zheng J, Hu R, Liu Y, Xu Z, Niu D, Lv J, Yang J, Xiao H, Wu S, He S, Tang Z, Liu Y, Tang M, Jiang X, Yuan J, Dai H, Zhang B. Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device. Nat Biomed Eng 2023; 7:1636-1648. [PMID: 37735541 DOI: 10.1038/s41551-023-01092-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.
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Affiliation(s)
- Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dou Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Pan-Lin Shao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jintao Zheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuang He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhongrong Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yan Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | | | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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32
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Yan H, Wen Y, Tian Z, Hart N, Han S, Hughes SJ, Zeng Y. A one-pot isothermal Cas12-based assay for the sensitive detection of microRNAs. Nat Biomed Eng 2023; 7:1583-1601. [PMID: 37106152 PMCID: PMC11108682 DOI: 10.1038/s41551-023-01033-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 03/29/2023] [Indexed: 04/29/2023]
Abstract
The use of microRNAs as clinical cancer biomarkers is hindered by the absence of accurate, fast and inexpensive assays for their detection in biofluids. Here we report a one-step and one-pot isothermal assay that leverages rolling-circle amplification and the endonuclease Cas12a for the accurate detection of specific miRNAs. The assay exploits the cis-cleavage activity of Cas12a to enable exponential rolling-circle amplification of target sequences and its trans-cleavage activity for their detection and for signal amplification. In plasma from patients with pancreatic ductal adenocarcinoma, the assay detected the miRNAs miR-21, miR-196a, miR-451a and miR-1246 in extracellular vesicles at single-digit femtomolar concentrations with single-nucleotide specificity. The assay is rapid (sample-to-answer times ranged from 20 min to 3 h), does not require specialized instrumentation and is compatible with a smartphone-based fluorescence detection and with the lateral-flow format for visual readouts. Simple assays for the detection of miRNAs in blood may aid the development of miRNAs as biomarkers for the diagnosis and prognosis of cancers.
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Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Yunjie Wen
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Nathan Hart
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Song Han
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Steven J Hughes
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA.
- University of Florida Health Cancer Center, Gainesville, FL, USA.
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33
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Huang Z, Wang W, Wang Y, Wang H, Pang Y, Yuan Q, Tan J, Tan W. Electrochemical Detection of Viral Nucleic Acids by DNA Nanolock-Based Porous Electrode Device. Anal Chem 2023; 95:16668-16676. [PMID: 37910393 DOI: 10.1021/acs.analchem.3c03168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Developing rapid, sensitive, and facile nucleic acid detection technologies is of paramount importance for preventing and controlling infectious diseases. Benefiting from the advantages such as rapid response, low cost, and simple operation, electrochemical impedance spectroscopy holds great promise for point-of-care nucleic acid detection. However, the sensitivity of electrochemical impedance spectroscopy for low molecular weight nucleic acids testing is still limited. This work presents a DNA nanolock-based porous electrode to improve the sensitivity of electrochemical impedance spectroscopy. Once the target nucleic acids are recognized by the DNA probes, the pore-attached DNA nanolock caused remarkable impedance amplification by blocking the nanopores. Taking SARS-CoV-2 nucleic acid as a model analyte, the detection limit of the porous electrode was as low as 0.03 fM for both SARS-CoV-2 RNA and DNA. The integration of a porous electrode with a wireless communicating unit generates a portable detection device that could be applied to direct SARS-CoV-2 nucleic acid testing in saliva samples. The portable device could effectively distinguish the COVID-19 positive and negative samples, showing a sensitivity of 100% and a specificity of 93%. Owing to its rapid, ultrasensitive, specific, and portable features, the as-designed DNA nanolock and porous electrode-based portable device holds great promise as a point-of-care platform for real-time screening of COVID-19 and other epidemics.
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Affiliation(s)
- Zhongnan Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Wenjie Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yingfei Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Han Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yimin Pang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
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34
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Ren R, Cai S, Fang X, Wang X, Zhang Z, Damiani M, Hudlerova C, Rosa A, Hope J, Cook NJ, Gorelkin P, Erofeev A, Novak P, Badhan A, Crone M, Freemont P, Taylor GP, Tang L, Edwards C, Shevchuk A, Cherepanov P, Luo Z, Tan W, Korchev Y, Ivanov AP, Edel JB. Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes. Nat Commun 2023; 14:7362. [PMID: 37963924 PMCID: PMC10646045 DOI: 10.1038/s41467-023-43004-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.
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Affiliation(s)
- Ren Ren
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Xiaoyi Wang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Zheng Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Micol Damiani
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Charlotte Hudlerova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Annachiara Rosa
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Wolfson Education Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Joshua Hope
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Peter Gorelkin
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Alexander Erofeev
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Pavel Novak
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Anjna Badhan
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Paul Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Graham P Taylor
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, 310027, Hangzhou, China
| | - Christopher Edwards
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Andrew Shevchuk
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Peter Cherepanov
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
| | - Yuri Korchev
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
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Zhu Y, Zheng X, Zhou S, Xiao W, Sun X, Zhou J, Qian F, Zhang T, Sheng Y, Hu J. A dual amplification-based CRISPR/Cas12a biosensor for sensitive detection of miRNA in prostate cancer. Anal Chim Acta 2023; 1279:341769. [PMID: 37827669 DOI: 10.1016/j.aca.2023.341769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 10/14/2023]
Abstract
MicroRNA (miRNA) has gained significant attention as a potential biomarker for cancer clinics, and there is an urgent need for developing sensing strategies with high selectivity, sensitivity, and low background. In vitro diagnosis based on Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated protein (CRISPR/Cas) technology could simplify the detection procedure, improve sensitivity and selectivity, and has broad application prospects as the next-generation molecular diagnosis technology. We propose a novel dual signal amplification strategy, called CENTER, which integrates the CRISPR/Cas12a system, an entropy-driven DNA signaling network, and strand displacement amplification to achieve ultrasensitive detection of miR-141, a potential marker for prostate cancer. The experimental results demonstrate that CENTER can distinguish single nucleotide mutations, and the strategy exhibits a good linear calibration curve ranging from 100 aM to 1 pM. Due to dual signal amplification, the detection limit is as low as 34 aM. We proposed a method for identifying miR-141 expressed in human serum and successfully distinguished between prostate cancer patients (n = 20) and healthy individuals (n = 15) with an impressive accuracy of 94%. Overall, CENTER shows great promise for the detection of miRNA.
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Affiliation(s)
- Yuqing Zhu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xiaohe Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shujun Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Wenjing Xiao
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xiaorui Sun
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Jianming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Feiyang Qian
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Tenghua Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Yan Sheng
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Jiaming Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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36
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Xu X, Deng Y, Ding J, Zheng X, Wang C, Wang D, Liu L, Gu H, Peiris M, Poon LLM, Zhang T. Wastewater genomic sequencing for SARS-CoV-2 variants surveillance in wastewater-based epidemiology applications. WATER RESEARCH 2023; 244:120444. [PMID: 37579567 DOI: 10.1016/j.watres.2023.120444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been widely used as a complementary approach to SARS-CoV-2 clinical surveillance. Wastewater genomic sequencing could provide valuable information on the genomic diversity of SARS-CoV-2 in the surveyed population. However, reliable detection and quantification of variants or mutations remain challenging. In this study, we used mock wastewater samples created by spiking SARS-CoV-2 variant standard RNA into wastewater RNA to evaluate the impacts of sequencing throughput on various aspects such as genome coverage, mutation detection, and SARS-CoV-2 variant deconvolution. We found that wastewater datasets with sequencing throughput greater than 0.5 Gb yielded reliable results in genomic analysis. In addition, using in silico mock datasets, we evaluated the performance of the adopted pipeline for variant deconvolution. By sequencing 86 wastewater samples covering more than 6 million people over 7 months, we presented two use cases of wastewater genomic sequencing for surveying COVID-19 in Hong Kong in WBE applications, including the replacement of Delta variants by Omicron variants, and the prevalence and development trends of three Omicron sublineages. Importantly, the wastewater genomic sequencing data were able to reveal the variant trends 16 days before the clinical data did. By investigating mutations of the spike (S) gene of the SARS-CoV-2 virus, we also showed the potential of wastewater genomic sequencing in identifying novel mutations and unique alleles. Overall, our study demonstrated the crucial role of wastewater genomic surveillance in providing valuable insights into the emergence and monitoring of new SARS-CoV-2 variants and laid a solid foundation for the development of genomic analysis methodologies for WBE of other novel emerging viruses in the future.
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Affiliation(s)
- Xiaoqing Xu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu Deng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiahui Ding
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiawan Zheng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Haogao Gu
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Malik Peiris
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Leo L M Poon
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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37
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Jiang W, Aman R, Ali Z, Rao GS, Mahfouz M. PNA-Pdx: Versatile Peptide Nucleic Acid-Based Detection of Nucleic Acids and SNPs. Anal Chem 2023; 95:14209-14218. [PMID: 37696750 PMCID: PMC10535012 DOI: 10.1021/acs.analchem.3c01809] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Monitoring diseases caused by pathogens or by mutations in DNA sequences requires accurate, rapid, and sensitive tools to detect specific nucleic acid sequences. Here, we describe a new peptide nucleic acid (PNA)-based nucleic acid detection toolkit, termed PNA-powered diagnostics (PNA-Pdx). PNA-Pdx employs PNA probes that bind specifically to a target and are then detected in lateral flow assays. This can precisely detect a specific pathogen or genotype genomic sequence. PNA probes can also be designed to invade double-stranded DNAs (dsDNAs) to produce single-stranded DNAs for precise CRISPR-Cas12b-based detection of genomic SNPs without requiring the protospacer-adjacent motif (PAM), as Cas12b requires PAM sequences only for dsDNA targets. PNA-Pdx identified target nucleic acid sequences at concentrations as low as 2 copies/μL and precisely detected the SARS-CoV-2 genome in clinical samples in 40 min. Furthermore, the specific dsDNA invasion by the PNA coupled with CRISPR-Cas12b precisely detected genomic SNPs without PAM restriction. Overall, PNA-Pdx provides a novel toolkit for nucleic acid and SNP detection as well as highlights the benefits of engineering PNA probes for detecting nucleic acids.
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Affiliation(s)
- Wenjun Jiang
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gundra S. Rao
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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38
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Huang D, Deng H, Zhou J, Wang GA, Lei Q, Guo C, Peng W, Liang P, Shen C, Ying B, Li W, Li F. Mismatch-Guided Deoxyribonucleic Acid Assembly Enables Ultrasensitive and Multiplex Detection of Low-Allele-Fraction Variants in Clinical Samples. J Am Chem Soc 2023; 145:20412-20421. [PMID: 37651106 DOI: 10.1021/jacs.3c05879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Somatic mutations are important signatures in clinical cancer treatment. However, accurate detection of rare somatic mutations with low variant-allele frequencies (VAFs) in clinical samples is challenging because of the interference caused by high concentrations of wild-type (WT) sequences. Here, we report a post amplification SNV-specific DNA assembly (PANDA) technology that eliminates the high concentration pressure caused by WT through a mismatch-guided DNA assembly and enables the ultrasensitive detection of cancer mutations with VAFs as low as 0.1%. Because it generates an assembly product that only exposes a single-stranded domain with the minimal length for signal readout and thus eliminates possible interferences from secondary structures and cross-interactions among sequences, PANDA is highly versatile and expandable for multiplex testing. With ultrahigh sensitivity, PANDA enabled the quantitative analysis of EGFR mutations in cell-free DNA of 68 clinical plasma samples and four pleuroperitoneal fluid samples, with test results highly consistent with NGS deep sequencing. Compared to digital PCR, PANDA returned fewer false negatives and ambiguous cases of clinical tests. Meanwhile, it also offers much lower upfront instrumental and operational costs. The multiplexity was demonstrated by developing a 3-plex PANDA for the simultaneous analysis of three EGFR mutations in 54 pairs of tumor and the adjacent noncancerous tissue samples collected from lung cancer patients. Because of the ultrahigh sensitivity, multiplexity, and simplicity, we anticipate that PANDA will find wide applications for analyzing clinically important rare mutations in diverse devastating diseases.
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Affiliation(s)
- Dan Huang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610061, P. R. China
| | - Hui Deng
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Guan A Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610061, P. R. China
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Chen Guo
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610061, P. R. China
| | - Wanting Peng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610061, P. R. China
| | - Peng Liang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Chenlan Shen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610061, P. R. China
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
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39
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Feng E, Zheng T, He X, Chen J, Gu Q, He X, Hu F, Li J, Tian Y. Plasmon-Induced Charge Transfer-Enhanced Raman Scattering on a Semiconductor: Toward Amplification-Free Quantification of SARS-CoV-2. Angew Chem Int Ed Engl 2023; 62:e202309249. [PMID: 37555368 DOI: 10.1002/anie.202309249] [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] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
Semiconductors demonstrate great potentials as chemical mechanism-based surface-enhanced Raman scattering (SERS) substrates in determination of biological species in complex living systems with high selectivity. However, low sensitivity is the bottleneck for their practical applications, compared with that of noble metal-based Raman enhancement ascribed to electromagnetic mechanism. Herein, a novel Cu2 O nanoarray with free carrier density of 1.78×1021 cm-3 comparable to that of noble metals was self-assembled, creating a record in enhancement factor (EF) of 3.19×1010 among semiconductor substrates. The significant EF was mainly attributed to plasmon-induced hot electron transfer (PIHET) in semiconductor which was never reported before. This Cu2 O nanoarray was subsequently developed as a highly sensitive and selective SERS chip for non-enzyme and amplification-free SARS-CoV-2 RNA quantification with a detection limit down to 60 copies/mL within 5 min. This unique Cu2 O nanoarray demonstrated the significant Raman enhancement through PIHET process, enabling rapid and sensitive point-of-care testing of emerging virus variants.
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Affiliation(s)
- Enduo Feng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
| | - Tingting Zheng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
| | - Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
| | - Qingyi Gu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, North Zhongshan Road 3663, 200062, Shanghai, China
| | - Xiao He
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, North Zhongshan Road 3663, 200062, Shanghai, China
| | - Fanghao Hu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, 100084, Beijing, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, 100084, Beijing, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
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40
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Aloraij Y, Suaifan GARY, Shibl A, Al-Kattan K, Zourob MM. Development of Rapid Aptamer-Based Screening Assay for the Detection of Covid-19 Variants. ACS OMEGA 2023; 8:32877-32883. [PMID: 37720766 PMCID: PMC10500687 DOI: 10.1021/acsomega.3c04137] [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: 06/11/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
Abstract
The development of a colorimetric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection assay with the WHO published ASSURED criteria is reported, in which the biosensor should have the following characteristics of (i) being affordable for low-income communities, (ii) sensitive, (iii) specific, (iv) user-friendly to be used by non-skilled personnel, (v) rapid and robust, (vi) equipment-free, and (vii) delivered to the end-users as a simple and easy to use point-of-care tool. Early viral infection detection prevents virus spread and controls the epidemic. We herein report the development of a colorimetric assay in which SARS-COV-2 variants can be detected by colorimetric observation of color on the sensing cotton swab surface. Using the developed biosensor assay, it is possible to discriminate between the various SARS-CoV-2 variants with a LOD of 100 ng/mL within 4 min including sample preconcentration and incubation step. The results illustrated the development of a SARS-CoV-2 colorimetric biosensor that can be mass produced, with low-reagent cost, and can be read-out visually in the field by nonskilled personnel.
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Affiliation(s)
- Yumna
M. Aloraij
- Department
of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi
Rd, Riyadh 11533, Saudi Arabia
| | - Ghadeer A. R. Y. Suaifan
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Atef Shibl
- College
of Medicine, Alfaisal University, Al Zahrawi Street, Al Maather, Al
Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Khaled Al-Kattan
- College
of Medicine, Alfaisal University, Al Zahrawi Street, Al Maather, Al
Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Mohammed M. Zourob
- Department
of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi
Rd, Riyadh 11533, Saudi Arabia
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41
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Luo Y, Zhou M, Wang L, Fan C, Xu T, Zhang X. Programmable-Modulated Ultrasonic Transducer Array for Contactless Detection of Viral RNAs. SMALL METHODS 2023; 7:e2300592. [PMID: 37401195 DOI: 10.1002/smtd.202300592] [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: 05/08/2023] [Revised: 06/13/2023] [Indexed: 07/05/2023]
Abstract
The current polymerase chain reactions-based nucleic acid tests for large-scale infectious disease diagnosis are always lab-dependent and generate large amounts of highly infectious plastic waste. Direct non-linear acoustic driven of microdroplets provide an ideal platform for contactless spatial and temporal manipulation of liquid samples. Here, a strategy to programmable-manipulate microdroplets using potential pressure well for contactless trace detection is conceptualized and designed. On such contactless modulation platform, up to seventy-two piezoelectric transducers are precisely self-focusing single-axis arranged and controlled, which can generate dynamic pressure nodes for effectively contact-free manipulating microdroplets without vessel contamination. In addition, the patterned microdroplet array can act as contactless microreactor and allow multiple trace samples (1-5 µL) biochemical analysis, and the ultrasonic vortex can also accelerate non-equilibrium chemical reactions such as recombinase polymerase amplification (RPA). The results of fluorescence detection indicated that such programmable modulated microdroplet achieved contactless trace nucleic acid detection with a sensitivity of 0.21 copy µL-1 in only 6-14 min, which is 30.3-43.3% shorter than the conventional RPA approach. Such a programmable containerless microdroplet platform can be used for toxic, hazardous, or infectious samples sensing, opening up new avenues for developing future fully automated detection systems.
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Affiliation(s)
- Yong Luo
- School of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Mengyun Zhou
- School of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
| | - Lirong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Chuan Fan
- Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Tailin Xu
- School of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
| | - Xueji Zhang
- School of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
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42
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Zhang Y, Song Y, Weng Z, Yang J, Avery L, Dieckhaus KD, Lai RY, Gao X, Zhang Y. A point-of-care microfluidic biosensing system for rapid and ultrasensitive nucleic acid detection from clinical samples. LAB ON A CHIP 2023; 23:3862-3873. [PMID: 37539483 DOI: 10.1039/d3lc00372h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Rapid and ultrasensitive point-of-care RNA detection plays a critical role in the diagnosis and management of various infectious diseases. The gold-standard detection method of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is ultrasensitive and accurate yet limited by the lengthy turnaround time (1-2 days). On the other hand, an antigen test offers rapid at-home detection (typically ~15 min) but suffers from low sensitivity and high false-negative rates. An ideal point-of-care diagnostic device would combine the merits of PCR-level sensitivity and rapid sample-to-result workflow comparable to antigen testing. However, the existing detection platforms typically possess superior sensitivity or rapid sample-to-result time, but not both. This paper reports a point-of-care microfluidic device that offers ultrasensitive yet rapid detection of viral RNA from clinical samples. The device consists of a microfluidic chip for precisely manipulating small volumes of samples, a miniaturized heater for viral lysis and ribonuclease inactivation, a Cas13a-electrochemical sensor for target preamplification-free and ultrasensitive RNA detection, and a smartphone-compatible potentiostat for data acquisition. As demonstrations, the devices achieve the detection of heat-inactivated SARS-CoV-2 samples with a limit of detection down to 10 aM within 25 minutes, which is comparable to the sensitivity of RT-PCR and rapidness of an antigen test. The platform also successfully distinguishes all nine positive unprocessed clinical SARS-CoV-2 nasopharyngeal swab samples from four negative samples within 25 minutes of sample-to-result time. Together, this device provides a point-of-care solution that can be deployed in diverse settings beyond laboratory environments for rapid and accurate detection of RNA from clinical samples. The device can potentially be expandable to detect other viral targets, such as human immunodeficiency virus self-testing and Zika virus, where rapid and ultrasensitive point-of-care detection is required.
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Affiliation(s)
- Yuxuan Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Yang Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Zhengyan Weng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005, USA
| | - Lori Avery
- Department of Pathology and Laboratory Medicine, UConn Health, Farmington, CT 06030, USA
| | - Kevin D Dieckhaus
- Division of Infectious Diseases, Department of Medicine, UConn Health, Farmington, CT 06030, USA
| | - Rebecca Y Lai
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Yi Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
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43
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Li J, Zhang Y, Wang X, Zhang S, Tan Q, Hu B, Xu Q, Li H. Engineering Entropy-Driven Nanomachine-Mediated Morphological Evolution of Anisotropic Silver Triangular Nanoplates for Colorimetric and Photothermal Biosensing. Anal Chem 2023; 95:12032-12038. [PMID: 37542454 DOI: 10.1021/acs.analchem.3c01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
A DNA/RNA biosensor capable of single nucleotide variation (SNV) resolution is highly desirable for drug design and disease diagnosis. To meet the point-of-care demand, rapid, cost-effective, and accurate SNV detection is of great significance but still suffers from a challenge. In this work, a unique nonenzymatic dual-modal (multicolorimetric and photothermal) visualization DNA biosensor is first proposed for SNV identification on the basis of an entropy-driven nanomachine with double output DNAs and coordination etching of anisotropic silver triangular nanoplates (Ag TNPs). When the target initiates the DNA nanomachine, the liberated multiple output DNAs can be utilized as a bridge to produce a superparamagnetic sandwich complex. The incoming poly-C DNA can coordinate and etch highly active Ag+ ions at the tips of Ag TNPs, causing a shift in the plasmon peak of Ag TNPs from 808 to 613 nm. The more target DNAs are introduced, the more output DNAs are released and thus the more Ag+ ions are etched. The noticeable color changes of anisotropic Ag TNPs can be differentiated by "naked eye" and accurate temperature reading. The programmable DNA nanotechnology and magnetic extraction grant the high specificity. Also, the SNV detection results can be self-verified by the two-signal readouts. Moreover, the dual-modal biosensor has the advantages of portability, cost-effectiveness, and simplicity. Particularly, the exclusive entropy-driven amplifier liberates double output DNAs to bridge more poly-C DNAs, enabling the dual-modal visualization DNA biosensor with improved sensitivity.
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Affiliation(s)
- Jing Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Yansong Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Xin Wang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Shenlong Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Qingqing Tan
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Bingtao Hu
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Qin Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, P. R. China
| | - Hongbo Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
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44
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AbdElFatah T, Jalali M, Yedire SG, I Hosseini I, Del Real Mata C, Khan H, Hamidi SV, Jeanne O, Siavash Moakhar R, McLean M, Patel D, Wang Z, McKay G, Yousefi M, Nguyen D, Vidal SM, Liang C, Mahshid S. Nanoplasmonic amplification in microfluidics enables accelerated colorimetric quantification of nucleic acid biomarkers from pathogens. NATURE NANOTECHNOLOGY 2023; 18:922-932. [PMID: 37264088 DOI: 10.1038/s41565-023-01384-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Deployment of nucleic acid amplification assays for diagnosing pathogens in point-of-care settings is a challenge due to lengthy preparatory steps. We present a molecular diagnostic platform that integrates a fabless plasmonic nano-surface into an autonomous microfluidic cartridge. The plasmonic 'hot' electron injection in confined space yields a ninefold kinetic acceleration of RNA/DNA amplification at single nucleotide resolution by one-step isothermal loop-mediated and rolling circle amplification reactions. Sequential flow actuation with nanoplasmonic accelerated microfluidic colorimetry and in conjugation with machine learning-assisted analysis (using our 'QolorEX' device) offers an automated diagnostic platform for multiplexed amplification. The versatility of QolorEX is demonstrated by detecting respiratory viruses: SARS-CoV-2 and its variants at the single nucleotide polymorphism level, H1N1 influenza A, and bacteria. For COVID-19 saliva samples, with an accuracy of 95% on par with quantitative polymerase chain reaction and a sample-to-answer time of 13 minutes, QolorEX is expected to advance the monitoring and rapid diagnosis of pathogens.
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Affiliation(s)
- Tamer AbdElFatah
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Mahsa Jalali
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | | | - Imman I Hosseini
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | | | - Haleema Khan
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Seyed Vahid Hamidi
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Olivia Jeanne
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | | | - Myles McLean
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research and McGill Centre for Viral Diseases, Jewish General Hospital, Montreal, Quebec, Canada
| | - Dhanesh Patel
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Zhen Wang
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research and McGill Centre for Viral Diseases, Jewish General Hospital, Montreal, Quebec, Canada
| | - Geoffrey McKay
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Mitra Yousefi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Dao Nguyen
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Chen Liang
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research and McGill Centre for Viral Diseases, Jewish General Hospital, Montreal, Quebec, Canada
| | - Sara Mahshid
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada.
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
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45
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Sai J, Zhou L, Jiang L, Xue D, Pei R, Liu A, Xu L. Dual Signal Amplification by Urease Catalysis and Silver Nanoparticles for Ultrasensitive Colorimetric Detection of Nucleic Acids. Anal Chem 2023. [PMID: 37464726 DOI: 10.1021/acs.analchem.3c01483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Signal amplification techniques are highly desirable for the analysis of low-level targets that are closely related with diseases and the monitoring of important biological processes. However, it is still challenging to achieve this goal in a facile and economical way. Herein, we developed a novel dual signal amplification strategy by combining urease catalysis with the release of Ag+ from silver nanoparticles (AgNPs). This strategy was used for quantifying a DNA sequence (HIV-1) related with human immunodeficiency virus (HIV). DNA target HIV-1 hybridizes with the capture DNA probe on magnetic beads and the reporter DNA probe on AgNPs, forming a sandwich complex. The captured AgNPs are then transformed into numerous Ag+ ions that inactivate numerous ureases. Without catalytic production of ammonia from urea, the substrate solution shows a low pH 5.8 that will increase otherwise. The pH change is monitored by a pH indicator (phenol red), which allows for colorimetric detection. The proposed approach is sensitive, easy to use, economic, and universal, exhibiting a low detection limit of 9.7 fM (i.e., 1.94 attomoles) and a dynamic linear range of 4 orders for HIV-1 sequence detection.
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Affiliation(s)
- Jialin Sai
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Lu Zhou
- Department of Neurology, Affiliated Taizhou Hospital of Wenzhou Medical University, Linhai 317000, China
| | - Lin Jiang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Dongguo Xue
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Lijun Xu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
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46
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Yang H, Ledesma-Amaro R, Gao H, Ren Y, Deng R. CRISPR-based biosensors for pathogenic biosafety. Biosens Bioelectron 2023; 228:115189. [PMID: 36893718 DOI: 10.1016/j.bios.2023.115189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Pathogenic biosafety is a worldwide concern. Tools for analyzing pathogenic biosafety, that are precise, rapid and field-deployable, are highly demanded. Recently developed biotechnological tools, especially those utilizing CRISPR/Cas systems which can couple with nanotechnologies, have enormous potential to achieve point-of-care (POC) testing for pathogen infection. In this review, we first introduce the working principle of class II CRISPR/Cas system for detecting nucleic acid and non-nucleic acid biomarkers, and highlight the molecular assays that leverage CRISPR technologies for POC detection. We summarize the application of CRISPR tools in detecting pathogens, including pathogenic bacteria, viruses, fungi and parasites and their variants, and highlight the profiling of pathogens' genotypes or phenotypes, such as the viability, and drug-resistance. In addition, we discuss the challenges and opportunities of CRISPR-based biosensors in pathogenic biosafety analysis.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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Lee S, Kim S, Yoon DS, Park JS, Woo H, Lee D, Cho SY, Park C, Yoo YK, Lee KB, Lee JH. Sample-to-answer platform for the clinical evaluation of COVID-19 using a deep learning-assisted smartphone-based assay. Nat Commun 2023; 14:2361. [PMID: 37095107 PMCID: PMC10124933 DOI: 10.1038/s41467-023-38104-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/14/2023] [Indexed: 04/26/2023] Open
Abstract
Since many lateral flow assays (LFA) are tested daily, the improvement in accuracy can greatly impact individual patient care and public health. However, current self-testing for COVID-19 detection suffers from low accuracy, mainly due to the LFA sensitivity and reading ambiguities. Here, we present deep learning-assisted smartphone-based LFA (SMARTAI-LFA) diagnostics to provide accurate decisions with higher sensitivity. Combining clinical data learning and two-step algorithms enables a cradle-free on-site assay with higher accuracy than the untrained individuals and human experts via blind tests of clinical data (n = 1500). We acquired 98% accuracy across 135 smartphone application-based clinical tests with different users/smartphones. Furthermore, with more low-titer tests, we observed that the accuracy of SMARTAI-LFA was maintained at over 99% while there was a significant decrease in human accuracy, indicating the reliable performance of SMARTAI-LFA. We envision a smartphone-based SMARTAI-LFA that allows continuously enhanced performance by adding clinical tests and satisfies the new criterion for digitalized real-time diagnostics.
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Affiliation(s)
- Seungmin Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Sunmok Kim
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
- Astrion Inc, Seoul, 02841, Republic of Korea
| | - Jeong Soo Park
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Hyowon Woo
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Dongho Lee
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yong Kyoung Yoo
- Department of Electronic Engineering, Catholic Kwandong University, 24, Beomil-ro 579 beon-gil, Gangneung-si, Gangwon-do, 25601, Republic of Korea.
| | - Ki-Baek Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea.
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea.
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Jiang K, Wu J, Kim JE, An S, Nam JM, Peng YK, Lee JH. Plasmonic Cross-Linking Colorimetric PCR for Simple and Sensitive Nucleic Acid Detection. NANO LETTERS 2023; 23:3897-3903. [PMID: 37083438 DOI: 10.1021/acs.nanolett.3c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Simple, low-cost, and accurate nucleic acid assay platforms hold great promise for point-of-care (POC) pathogen detection, disease surveillance, and control. Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a powerful and efficient nucleic acid amplification technique, but it lacks a simple and convenient analysis method for POC applications. Herein, we propose a novel plasmonic cross-linking colorimetric PCR (PPT-ccPCR) assay by integrating plasmonic magnetic nanoparticle (PMN)-based PPT-PCR with gold nanoparticle (AuNP)-based cross-linking colorimetry. AuNPs form assembled structures with the PMNs in the presence of amplicons and collect in a magnetic field, resulting in color changes to the supernatant. Target DNA with concentrations as low as 5 copies/μL can be visually detected within 40 min. The achieved limit of detection was 1.8 copies/μL based on the absorption signals. This simple and sensitive strategy needs no expensive instrumentation and demonstrates high potential for POC detection while enabling further applications in clinical diagnostics.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sujin An
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
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Trinh KTL, Do HDK, Lee NY. Recent Advances in Molecular and Immunological Diagnostic Platform for Virus Detection: A Review. BIOSENSORS 2023; 13:bios13040490. [PMID: 37185566 PMCID: PMC10137144 DOI: 10.3390/bios13040490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing coronavirus disease (COVID-19) outbreak and a rising demand for the development of accurate, timely, and cost-effective diagnostic tests for SARS-CoV-2 as well as other viral infections in general. Currently, traditional virus screening methods such as plate culturing and real-time PCR are considered the gold standard with accurate and sensitive results. However, these methods still require sophisticated equipment, trained personnel, and a long analysis time. Alternatively, with the integration of microfluidic and biosensor technologies, microfluidic-based biosensors offer the ability to perform sample preparation and simultaneous detection of many analyses in one platform. High sensitivity, accuracy, portability, low cost, high throughput, and real-time detection can be achieved using a single platform. This review presents recent advances in microfluidic-based biosensors from many works to demonstrate the advantages of merging the two technologies for sensing viruses. Different platforms for virus detection are classified into two main sections: immunoassays and molecular assays. Moreover, available commercial sensing tests are analyzed.
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Affiliation(s)
- Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 70000, Vietnam
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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50
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Sun C, Wang T. Organic thin-film transistors and related devices in life and health monitoring. NANO RESEARCH 2023:1-19. [PMID: 37359073 PMCID: PMC10102697 DOI: 10.1007/s12274-023-5606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/28/2023]
Abstract
The early determination of disease-related biomarkers can significantly improve the survival rate of patients. Thus, a series of explorations for new diagnosis technologies, such as optical and electrochemical methods, have been devoted to life and health monitoring. Organic thin-film transistor (OTFT), as a state-of-the-art nano-sensing technology, has attracted significant attention from construction to application owing to the merits of being label-free, low-cost, facial, and rapid detection with multi-parameter responses. Nevertheless, interference from non-specific adsorption is inevitable in complex biological samples such as body liquid and exhaled gas, so the reliability and accuracy of the biosensor need to be further improved while ensuring sensitivity, selectivity, and stability. Herein, we overviewed the composition, mechanism, and construction strategies of OTFTs for the practical determination of disease-related biomarkers in both body fluids and exhaled gas. The results show that the realization of bio-inspired applications will come true with the rapid development of high-effective OTFTs and related devices. Electronic Supplementary Material Supplementary material is available in the online version of this article at 10.1007/s12274-023-5606-1.
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Affiliation(s)
- Chenfang Sun
- Tianjin Key Laboratory of Drug Targeting and Bioimaging, Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, 300384 China
| | - Tie Wang
- Tianjin Key Laboratory of Drug Targeting and Bioimaging, Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, 300384 China
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