1
|
Gu X, Tang Q, Zhu Y, Sun C, Wu L, Ji H, Wang Q, Wu L, Qin Y. Advancements of CRISPR technology in public health-related analysis. Biosens Bioelectron 2024; 261:116449. [PMID: 38850734 DOI: 10.1016/j.bios.2024.116449] [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: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Pathogens and contaminants in food and the environment present significant challenges to human health, necessitating highly sensitive and specific diagnostic methods. Traditional approaches often struggle to meet these requirements. However, the emergence of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized nucleic acid diagnostics. The present review provides a comprehensive overview of the biological sensing technology based on the CRISPR/Cas system and its potential applications in public health-related analysis. Additionally, it explores the enzymatic cleavage capabilities mediated by Cas proteins, highlighting the promising prospects of CRISPR technology in addressing bioanalysis challenges. We discuss commonly used CRISPR-Cas proteins and elaborate on their application in detecting foodborne bacteria, viruses, toxins, other chemical pollution, and drug-resistant bacteria. Furthermore, we highlight the advantages of CRISPR-based sensors in the field of public health-related analysis and propose that integrating CRISPR-Cas biosensing technology with other technologies could facilitate the development of more diverse detection platforms, thereby indicating promising prospects in this field.
Collapse
Affiliation(s)
- Xijuan Gu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, PR China
| | - Qu Tang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chenling Sun
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Lingwei Wu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Haiwei Ji
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Qi Wang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, PR China; School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| |
Collapse
|
2
|
Lim J, Son SU, Ki J, Kim S, Lee J, Jang S, Seo SB, Jang H, Kang T, Jung J, Kim E, Lim EK. Dual structure-switching aptamer-mediated signal amplification cascade for SARS-CoV-2 detection. Biosens Bioelectron 2024; 259:116375. [PMID: 38749283 DOI: 10.1016/j.bios.2024.116375] [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: 03/06/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/03/2024]
Abstract
Since the outbreak of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) at the end of 2019, the spread of the virus has posed a significant threat to public health and the global economy. This work proposed a one-step, dual-structure-switching aptamer-mediated signal amplification cascade for rapid and sensitive detection of the SARS-CoV-2 nucleocapsid protein. This system consisted of two DNA aptamers with structure-switching functionality and fuel DNA, where a cascade of strand hybridization and displacement triggered fluorescence generation and signal amplification. This aptamer-based amplification cascade required neither an amplification stage using enzymes nor pre-processing steps such as washing, viral isolation, and gene extraction. The assay could distinguish SARS-CoV-2 from other respiratory viruses and detect up to 1.0 PFU/assay of SARS-CoV-2 within 30 min at room temperature. In 35 nasopharyngeal clinical samples, the assay accurately assessed 25 positive and 10 negative clinical swab samples, which were confirmed using quantitative polymerase chain reaction. The strategy reported herein can help detect newly emerging pathogens and biomarkers of various diseases in liquid samples. In addition, the developed detection system consisting of only DNA and fluorophores can be widely integrated into liquid biopsy platforms for disease diagnosis.
Collapse
Affiliation(s)
- Jaewoo Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Medical Device Development Center, Osong Medical Innovation Foundation, 123 Osongsaengmyeong-ro, Chungcheongbuk-do, 28160, Republic of Korea
| | - Seong Uk Son
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Jisun Ki
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Changwon Hospital, Changwon, 51472, Republic of Korea
| | - Jina Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Soojin Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Seung Beom Seo
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering & Nano-bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon, 22012, Republic of Korea; Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea.
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| |
Collapse
|
3
|
Meng X, Wen K, Zhao J, Han Y, Ghandhi SA, Kaur SP, Brenner DJ, Turner HC, Amundson SA, Lin Q. Microfluidic measurement of intracellular mRNA with a molecular beacon probe towards point-of-care radiation triage. SENSORS & DIAGNOSTICS 2024; 3:1344-1352. [PMID: 39129862 PMCID: PMC11308381 DOI: 10.1039/d4sd00079j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/26/2024] [Indexed: 08/13/2024]
Abstract
In large-scale radiation exposure events, the ability to triage potential victims by the received radiation dosage is crucial. This can be evaluated by radiation-induced biological changes. Radiation-responsive mRNA is a class of biomarkers that has been explored for dose-dependency with methods such as RT-qPCR. However, these methods are challenging to implement for point-of-care devices. We have designed and used molecular beacons as probes for the measurement of radiation-induced changes of intracellular mRNA in a microfluidic device towards determining radiation dosage. Our experiments, in which fixed TK6 cells labeled with a molecular beacon specific to BAX mRNA exhibited dose-dependent fluorescence in a manner consistent with RT-qPCR analysis, demonstrate that such intracellular molecular probes can potentially be used in point-of-care radiation biodosimetry. This proof of concept could readily be extended to any RNA-based test to provide direct measurements at the bedside.
Collapse
Affiliation(s)
- Xin Meng
- Department of Mechanical Engineering, Columbia University New York NY 10027 USA
| | - Kechun Wen
- Department of Mechanical Engineering, Columbia University New York NY 10027 USA
| | - Jingyang Zhao
- Department of Mechanical Engineering, Columbia University New York NY 10027 USA
| | - Yaru Han
- Department of Mechanical Engineering, Columbia University New York NY 10027 USA
| | - Shanaz A Ghandhi
- Center for Radiological Research, Columbia University Irving Medical Center New York New York 10032 USA
| | - Salan P Kaur
- Center for Radiological Research, Columbia University Irving Medical Center New York New York 10032 USA
| | - David J Brenner
- Center for Radiological Research, Columbia University Irving Medical Center New York New York 10032 USA
| | - Helen C Turner
- Center for Radiological Research, Columbia University Irving Medical Center New York New York 10032 USA
| | - Sally A Amundson
- Center for Radiological Research, Columbia University Irving Medical Center New York New York 10032 USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University New York NY 10027 USA
| |
Collapse
|
4
|
Han C, Liu Q, Luo X, Zhao J, Zhang Z, He J, Ge F, Ding W, Luo Z, Jia C, Zhang L. Development of a CRISPR/Cas12a-mediated aptasensor for Mpox virus antigen detection. Biosens Bioelectron 2024; 257:116313. [PMID: 38688229 DOI: 10.1016/j.bios.2024.116313] [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: 10/28/2023] [Revised: 01/23/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
The emergence and rapid spread of Mpox (formerly monkeypox) have caused significant societal challenges. Adequate and appropriate diagnostics procedures are an urgent necessity. Herein, we discover a pair of aptamers through the systematic evolution of ligands by exponential enrichment (SELEX) that exhibit high affinity and bind to different sites towards the A29 protein of the Mpox virus. Subsequently, we propose a facile, sensitive, convenient CRISPR/Cas12a-mediated aptasensor for detecting the A29 antigen. The procedure employs the bivalent aptamers recognition, which induces the formation of a proximity switch probe and initiates subsequent cascade strand displacement reactions, then triggers CRISPR/Cas12a DNA trans-cleavage to achieve the sensitive detection of Mpox. Our method enables selective and ultrasensitive evaluation of the A29 protein within the range of 1 ng mL-1 to 1 μg mL-1, with a limit of detection (LOD) at 0.28 ng mL-1. Moreover, spiked A29 protein recovery exceeds 96.9%, while the detection activity remains above 91.9% after six months of storage at 4 °C. This aptasensor provides a novel avenue for exploring clinical diagnosis in cases involving Mpox as facilitating development in various analyte sensors.
Collapse
Affiliation(s)
- Cong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Qirui Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Xuantong Luo
- Tianjin Haihe High School, Tianjin, 300202, PR China
| | - Jian Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Zheng Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Jiaxuan He
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Feng Ge
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, 300071, PR China
| | - Wei Ding
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, 300071, PR China
| | - Zhaofeng Luo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Chao Jia
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China.
| | - Liyun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China.
| |
Collapse
|
5
|
Hu C, Yang S, Li S, Liu X, Liu Y, Chen Z, Chen H, Li S, He N, Cui H, Deng Y. Viral aptamer screening and aptamer-based biosensors for virus detection: A review. Int J Biol Macromol 2024; 276:133935. [PMID: 39029851 DOI: 10.1016/j.ijbiomac.2024.133935] [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: 08/12/2023] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Virus-induced infectious diseases have a detrimental effect on public health and exert significant influence on the global economy. Therefore, the rapid and accurate detection of viruses is crucial for effectively preventing and diagnosing infections. Aptamer-based detection technologies have attracted researchers' attention as promising solutions. Aptamers, small single-stranded DNA or RNA screened via systematic evolution of ligands by exponential enrichment (SELEX), possess a high affinity towards their target molecules. Numerous aptamers targeting viral marker proteins or virions have been developed and widely employed in aptamer-based biosensors (aptasensor) for virus detection. This review introduces SELEX schemes for screening aptamers and discusses distinctive SELEX strategies designed explicitly for viral targets. Furthermore, recent advances in aptamer-based biosensing methods for detecting common viruses using different virus-specific aptamers are summarized. Finally, limitations and prospects associated with developing of aptamer-based biosensors are discussed.
Collapse
Affiliation(s)
- Changchun Hu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shuting Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Shuo Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Xueying Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Yuan Liu
- Institute for Future Sciences, University of South China, Changsha, Hunan 410000, China; Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Haipo Cui
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China; Institute for Future Sciences, University of South China, Changsha, Hunan 410000, China; Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| |
Collapse
|
6
|
Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024; 53:6830-6859. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [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: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
Collapse
Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| |
Collapse
|
7
|
Liang R, Wang F, Li S, Niu Y, Sun Y, Hong S, Fan A. A sensitive gold nanoflower-based lateral flow assay coupled with gold staining technique for the detection of SARS-CoV-2 antigen. Mikrochim Acta 2024; 191:434. [PMID: 38951317 DOI: 10.1007/s00604-024-06502-1] [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: 02/06/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
An enhanced lateral flow assay (LFA) is presented for rapid and highly sensitive detection of acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antigens with gold nanoflowers (Au NFs) as signaling markers and gold enhancement to amplify the signal intensities. First, the effect of the morphology of gold nanomaterials on the sensitivity of LFA detection was investigated. The results showed that Au NFs prepared by the seed growth method showed a 5-fold higher detection sensitivity than gold nanoparticles (Au NPs) of the same particle size, which may benefit from the higher extinction coefficient and larger specific surface area of Au NFs. Under the optimized experimental conditions, the Au NFs-based LFA exhibited a detection limit (LOD) of 25 pg mL-1 for N protein using 135 nm Au NFs as the signaling probes. The signal was further amplified by using a gold enhancement strategy, and the LOD for the detection of N protein achieved was 5 pg mL-1. The established LFA also exhibited good repeatability and stability and showed applicability in the diagnosis of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Rushi Liang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, PR China
| | - Feiqian Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, PR China
| | - Shanshan Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, PR China
| | - Yajing Niu
- Beijing Pharma and Biotech Center, Beijing, 100035, PR China
| | - Yinuo Sun
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, PR China
| | - Sile Hong
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, PR China
| | - Aiping Fan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, PR China.
| |
Collapse
|
8
|
Liang R, Fan A, Wang F, Niu Y. Optical lateral flow assays in early diagnosis of SARS-CoV-2 infection. ANAL SCI 2024:10.1007/s44211-024-00596-6. [PMID: 38758251 DOI: 10.1007/s44211-024-00596-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
So far, the 2019 novel coronavirus (COVID-19) is spreading widely worldwide. The early diagnosis of infection by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is essential to provide timely treatment and prevent its further spread. Lateral flow assays (LFAs) have the advantages of rapid detection, simple operation, low cost, ease of mass production, and no need for special devices and professional operators, which make them suitable for self-testing at home. This review focuses on the early diagnosis of SARS-CoV-2 infection based on optical LFAs including colorimetric, fluorescent (FL), chemiluminescent (CL), and surface-enhanced Raman scattering (SERS) LFAs for the detection of SARS-CoV-2 antigens and nucleic acids. The types of recognition components, detection modes used for antigen detection, labels employed in different optical LFAs, and strategies to improve the detection sensitivity of LFAs were reviewed. Meanwhile, LFAs coupled with different nucleic acid amplification techniques and CRISPR-Cas systems for the detection of SARS-CoV-2 nucleic acids were summarized. We hope this review provides research mentalities for developing highly sensitive LFAs that can be used in home self-testing for the early diagnosis of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Rushi Liang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Aiping Fan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Feiqian Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yajing Niu
- Beijing Pharma and Biotech Center, Beijing, 100035, People's Republic of China.
| |
Collapse
|
9
|
Tekin YS, Kul SM, Sagdic O, Rodthongkum N, Geiss B, Ozer T. Optical biosensors for diagnosis of COVID-19: nanomaterial-enabled particle strategies for post pandemic era. Mikrochim Acta 2024; 191:320. [PMID: 38727849 PMCID: PMC11087243 DOI: 10.1007/s00604-024-06373-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
The COVID-19 pandemic underlines the need for effective strategies for controlling virus spread and ensuring sensitive detection of SARS-CoV-2. This review presents the potential of nanomaterial-enabled optical biosensors for rapid and low-cost detection of SARS-CoV-2 biomarkers, demonstrating a comprehensive analysis including colorimetric, fluorescence, surface-enhanced Raman scattering, and surface plasmon resonance detection methods. Nanomaterials including metal-based nanomaterials, metal-organic frame-based nanoparticles, nanorods, nanoporous materials, nanoshell materials, and magnetic nanoparticles employed in the production of optical biosensors are presented in detail. This review also discusses the detection principles, fabrication methods, nanomaterial synthesis, and their applications for the detection of SARS-CoV-2 in four categories: antibody-based, antigen-based, nucleic acid-based, and aptamer-based biosensors. This critical review includes reports published in the literature between the years 2021 and 2024. In addition, the review offers critical insights into optical nanobiosensors for the diagnosis of COVID-19. The integration of artificial intelligence and machine learning technologies with optical nanomaterial-enabled biosensors is proposed to improve the efficiency of optical diagnostic systems for future pandemic scenarios.
Collapse
Affiliation(s)
- Yusuf Samil Tekin
- Department of Biomedical Engineering, Graduate Education Institute, Malatya Turgut Ozal University, 44210, Battalgazi, Malatya, Turkey
| | - Seyda Mihriban Kul
- Department of Food Engineering, Faculty of Chemical-Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Osman Sagdic
- Department of Food Engineering, Faculty of Chemical-Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Nadnudda Rodthongkum
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Bangkok, 10330, Patumwan, Thailand
| | - Brian Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523-1019, USA.
| | - Tugba Ozer
- Department of Bioengineering, Faculty of Chemical-Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, 34220, Istanbul, Turkey.
| |
Collapse
|
10
|
Xiao C, Wang N, Zhao Y, Liu X, Li H, Huang A, Wang L, Lou X, Gao B, Shao N. Rapid and Sensitive Detection of Inactivated SARS-CoV-2 Virus via Fiber-Optic and Electrochemical Impedance Spectroscopy Based Aptasensors. BIOSENSORS 2024; 14:231. [PMID: 38785705 PMCID: PMC11117632 DOI: 10.3390/bios14050231] [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: 04/08/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
The development of rapid detection tools for viruses is vital for the prevention of pandemics and biothreats. Aptamers that target inactivated viruses are attractive for sensors due to their improved biosafety. Here, we evaluated a DNA aptamer (named as 6.9) that specifically binds to the inactivated SARS-CoV-2 virus with a low dissociation constant (KD = 9.6 nM) for the first time. Based on aptamer 6.9, we developed a fiber-optic evanescent wave (FOEW) biosensor. Inactivated SARS-CoV-2 and the Cy5.5-tagged short complementary strand competitively bound with the aptamer immobilized on the surface of the sensor. The detection of the inactivated SARS-CoV-2 virus was realized within six minutes with a limit of detection (LOD, S/N = 3) of 740 fg/mL. We also developed an electrochemical impedance aptasensor which exhibited an LOD of 5.1 fg/mL and high specificity. We further demonstrated that the LODs of the FOEW and electrochemical impedance aptasensors were, respectively, more than 1000 and 100,000 times lower than those of commercial colloidal gold test strips. We foresee that the facile aptamer isolation process and sensor design can be easily extended for the detection of other inactivated viruses.
Collapse
Affiliation(s)
- Can Xiao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Nan Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China; (N.W.); (X.L.)
| | - Yuechao Zhao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Xuemei Liu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Hui Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Aixue Huang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Lin Wang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China; (N.W.); (X.L.)
| | - Bo Gao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; (C.X.); (Y.Z.); (X.L.); (H.L.); (A.H.); (L.W.)
| |
Collapse
|
11
|
Kouz S, Raouafi A, Ouhibi A, Lorrain N, Essafi M, Mejri M, Raouafi N, Moadhen A, Guendouz M. Detection of SARS-CoV-2 N protein using AgNPs-modified aligned silicon nanowires BioSERS chip. RSC Adv 2024; 14:12071-12080. [PMID: 38628480 PMCID: PMC11019291 DOI: 10.1039/d4ra00267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The SARS-CoV-2 (COVID-19) pandemic had a strong impact on societies and economies worldwide and tests for high-performance detection of SARS-CoV-2 biomarkers are still needed for potential future outbreaks of the disease. In this paper, we present the different steps for the design of an aptamer-based surface-enhanced Raman scattering (BioSERS) sensing chip capable of detecting the coronavirus nucleocapsid protein (N protein) in spiked phosphate-buffered solutions and real samples of human blood serum. Optimization of the preparation steps in terms of the aptamer concentration used for the functionalization of the silver nanoparticles, time for affixing the aptamer, incubation time with target protein, and insulation of the silver active surface with cysteamine, led to a sensitive BioSERS chip, which was able to detect the N protein in the range from 1 to 75 ng mL-1 in spiked phosphate-buffered solutions with a detection limit of 1 ng mL-1 within 30 min. Furthermore, the BioSERS chip was used to detect the target protein in scarcely spiked human serum. This study demonstrates the possibility of a clinical application that can improve the detection limit and accuracy of the currently commercialized SARS-CoV-2 immunodiagnostic kit. Additionally, the system is modular and can be applied to detect other proteins by only changing the aptamer.
Collapse
Affiliation(s)
- Sadok Kouz
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Amal Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Awatef Ouhibi
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Nathalie Lorrain
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Makram Essafi
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Manel Mejri
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Noureddine Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Adel Moadhen
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Mohammed Guendouz
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| |
Collapse
|
12
|
Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
Collapse
Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| |
Collapse
|
13
|
Uppal GK, Poolsup S, Zaripov E, Gu Y, Berezovski MV. Comparative analysis of aptamers binding to SARS-CoV-2 N protein using capillary electrophoresis and bio-layer interferometry. Anal Bioanal Chem 2024; 416:1697-1705. [PMID: 38305861 DOI: 10.1007/s00216-024-05174-3] [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: 11/08/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Aptamers are increasingly employed in SARS-CoV-2 theragnostics in recent years. Characterization of aptamers, testing affinity and kinetic parameters (e.g., equilibrium dissociation constant (KD), kon, and koff), can be done by several methods and influenced by many factors. This study aims to characterize the binding of aptamers to SARS-CoV-2 nucleocapsid (N) protein using capillary electrophoresis (CE) and bio-layer interferometry (BLI). These two analytical methods differ by how the aptamer binds to its target protein once the aptamer, as a capture ligand, is partitioned in solution (CE) or immobilized on the biosensor (BLI). With CE, the KD values of the N-binding aptamers (tNSP1, tNSP2, and tNSP3) were determined to be 18 ± 4 nM, 45 ± 11 nM, and 32 ± 7 nM, respectively, while the KD measurements by BLI yielded 4.8 ± 0.6, 4.5 ± 0.5, and 2.9 ± 0.3 nM, respectively. CE results showed a higher KD across all aptamers tested. The differences in the steric hindrance and confirmational structures of the aptamers immobilized on the BLI biosensors versus those suspended in the CE sample solution affect the molecular interactions between aptamers and the target proteins. Moreover, the buffer composition including pH and ionic strength can influence the stability of aptamer structures, or aptamer-protein complexes. All these variables affect the binding and calculated KD. In this sense, a KD value alone is not sufficient to make comparisons between aptamers; instead, the entire experimental setup should also be considered. This is particularly important when implementing aptamers in different bioanalytical systems.
Collapse
Affiliation(s)
- Gurcharan K Uppal
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Yuxuan Gu
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| |
Collapse
|
14
|
Chen L, Yu Z, Wu Z, Zhou M, Wang Y, Yu X, Li W, Liu G, Tang Y. AptaDB: a comprehensive database integrating aptamer-target interactions. RNA (NEW YORK, N.Y.) 2024; 30:189-199. [PMID: 38164624 PMCID: PMC10870366 DOI: 10.1261/rna.079784.123] [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: 08/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Aptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine, and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration has hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB, derived from experimentally validated data manually collected from the literature, was hence developed, integrating comprehensive aptamer-related data, which include six key components: (i) experimentally validated aptamer-target interaction information, (ii) aptamer property information, (iii) structure information of aptamer, (iv) target information, (v) experimental activity information, and (vi) algorithmically calculated similar aptamers. AptaDB currently contains 1350 experimentally validated aptamer-target interactions, 1230 binding affinity constants, 1293 aptamer sequences, and more. Compared to other aptamer databases, it contains twice the number of entries found in available databases. The collection and integration of the above information categories is unique among available aptamer databases and provides a user-friendly interface. AptaDB will also be continuously updated as aptamer research evolves. We expect that AptaDB will become a powerful source for aptamer rational design and a valuable tool for aptamer screening in the future. For access to AptaDB, please visit http://lmmd.ecust.edu.cn/aptadb/.
Collapse
Affiliation(s)
- Long Chen
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Moran Zhou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xinxin Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
15
|
Dong Y, Yuan X, Zhuang K, Li Y, Luo X. Simultaneous and sensitive detection of SARS-CoV-2 proteins spike and nucleocapsid based on long-range SERS biosensor. Anal Chim Acta 2024; 1287:342070. [PMID: 38182376 DOI: 10.1016/j.aca.2023.342070] [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: 09/22/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Early diagnosis of SARS-CoV-2 infection is still critical to control COVID-19 outbreak. Traditional polymerase chain reaction, enzyme-linked immunosorbent assay or lateral flow immunoassay performed poorly on detection times, sample preparation process and accuracy. Surface-enhanced Raman scattering (SERS)-based detection has emerged as a powerful analytical technique, which overcomes the above limitations. However, due to the near-field effect of traditional substrate, it is difficult to monitor the binding event of aptamers with proteins. It is obvious that a novel SERS substrate thatsupportedextended and stronger electromagnetic fields was required to hold long-range effects and allow for binding event testing. RESULTS Driven by this challenge, we reported a long-range SERS-active substrate, which was built by inserting bowtie nanoaperture arrays in a refractive-index-symmetric environment and Au mirror surfaces, for SARS-CoV-2 protein binding event detection. Then, a double-π structure aptasensor was simply designed through the hybridization of spike (S) and nucleocapsid (N) proteins aptamers, and a corresponding complementary strand. This kind of double-π structure would dissociate when targets proteins S and N existed and led to the SERS responses decreased, which established the detection basis of our system. What's more, due to two Raman labels were involved, both proteins S and N can be sensed simultaneously. Our proposed method showed improved sensitivity with a low limit of detection for multiplex detection (1.6 × 10-16 g/mL for protein S and 1.0 × 10-16 g/mL for protein N) over a wide concentration range. SIGNIFICANCE This represents the first long-range SERS apatasensor platform for detection of S and N proteins simultaneously. Our method showed high sensitivity, selectivity, reproducibility, stability and remarkable recoveries in human in saliva and serum samples, which is particularly important for the early diagnostics of COVID as well as for future unknown coronavirus.
Collapse
Affiliation(s)
- Ying Dong
- School of Science, Xihua University, Chengdu, 610039, PR China
| | - Xue Yuan
- School of Science, Xihua University, Chengdu, 610039, PR China
| | - Kaiyi Zhuang
- School of Science, Xihua University, Chengdu, 610039, PR China
| | - Yuanyuan Li
- Shanghai Anti-Doping Laboratory, Shanghai University of Sport, Shanghai, 200438, PR China.
| | - Xiaojun Luo
- School of Science, Xihua University, Chengdu, 610039, PR China; Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu, 610039, PR China.
| |
Collapse
|
16
|
Qi L, Liu J, Liu S, Liu Y, Xiao Y, Zhang Z, Zhou W, Jiang Y, Fang X. Ultrasensitive Point-of-Care Detection of Protein Markers Using an Aptamer-CRISPR/Cas12a-Regulated Liquid Crystal Sensor (ALICS). Anal Chem 2024; 96:866-875. [PMID: 38164718 DOI: 10.1021/acs.analchem.3c04492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Despite extensive efforts, point-of-care testing (POCT) of protein markers with high sensitivity and specificity and at a low cost remains challenging. In this work, we developed an aptamer-CRISPR/Cas12a-regulated liquid crystal sensor (ALICS), which achieved ultrasensitive protein detection using a smartphone-coupled portable device. Specifically, a DNA probe that contained an aptamer sequence for the protein target and an activation sequence for the Cas12a-crRNA complex was prefixed on a substrate and was released in the presence of target. The activation sequence of the DNA probe then bound to the Cas12a-crRNA complex to activate the collateral cleavage reaction, producing a bright-to-dark optical change in a DNA-functionalized liquid crystal interface. The optical image was captured by a smartphone for quantification of the target concentration. For the two model proteins, SARS-CoV-2 nucleocapsid protein (N protein) and carcino-embryonic antigen (CEA), ALICS achieved detection limits of 0.4 and 20 pg/mL, respectively, which are higher than the typical sensitivity of the SARS-CoV-2 test and the clinical CEA test. In the clinical sample tests, ALICS also exhibited superior performances compared to those of the commercial ELISA and lateral flow test kits. Overall, ALICS represents an ultrasensitive and cost-effective platform for POCT, showing a great potential for pathogen detection and disease monitoring under resource-limited conditions.
Collapse
Affiliation(s)
- Lubin Qi
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Jie Liu
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Songlin Liu
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yang Liu
- Department of Orthopedics, Second Affiliated Hospital of Shandong First Medical University, Taian 271000, PR China
| | - Yating Xiao
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, PR China
| | - Zhen Zhang
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, PR China
| | - Wei Zhou
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yifei Jiang
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Xiaohong Fang
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, PR China
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, PR China
| |
Collapse
|
17
|
Wu SW, Chen YJ, Chang YW, Huang CY, Liu BH, Yu FY. Novel enzyme-linked aptamer-antibody sandwich assay and hybrid lateral flow strip for SARS-CoV-2 detection. J Nanobiotechnology 2024; 22:5. [PMID: 38169397 PMCID: PMC10762915 DOI: 10.1186/s12951-023-02191-9] [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: 07/02/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024] Open
Abstract
We have successfully generated oligonucleotide aptamers (Apts) and monoclonal antibodies (mAbs) targeting the recombinant nucleocapsid (N) protein of SARS-CoV-2. Apts were obtained through seven rounds of systematic evolution of ligands by exponential enrichment (SELEX), while mAbs were derived from the 6F6E11 hybridoma cell line. Leveraging these Apts and mAbs, we have successfully devised two innovative and remarkably sensitive detection techniques for the rapid identification of SARS-CoV-2 N protein in nasopharyngeal samples: the enzyme-linked aptamer-antibody sandwich assay (ELAAA) and the hybrid lateral flow strip (hybrid-LFS). ELAAA exhibited an impressive detection limit of 0.1 ng/mL, while hybrid-LFS offered a detection range of 0.1 - 0.5 ng/mL. In the evaluation using ten nasopharyngeal samples spiked with known N protein concentrations, ELAAA demonstrated an average recovery rate of 92%. Additionally, during the assessment of five nasopharyngeal samples from infected individuals and ten samples from healthy volunteers, hybrid-LFS displayed excellent sensitivity and specificity. Our study introduces a novel and efficient on-site approach for SARS-CoV-2 detection in nasopharyngeal samples. The reliable hybrid Apt-mAb strategy not only advances virus diagnostic methods but also holds promise in combating the spread of related diseases.
Collapse
Affiliation(s)
- Shih-Wei Wu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, No.1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - Ying-Ju Chen
- School of Medicine, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Rd, Taichung, 402, Taiwan
| | - Yu-Wen Chang
- Department of Biomedical Sciences, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Rd, Taichung, 402, Taiwan
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Rd, Taichung, 402, Taiwan
| | - Biing-Hui Liu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, No.1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan.
| | - Feng-Yih Yu
- Department of Biomedical Sciences, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Rd, Taichung, 402, Taiwan.
- Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec. 1, Chien Kuo N. Rd, Taichung, 402, Taiwan.
| |
Collapse
|
18
|
Cai S, Ren R, He J, Wang X, Zhang Z, Luo Z, Tan W, Korchev Y, Edel JB, Ivanov AP. Selective Single-Molecule Nanopore Detection of mpox A29 Protein Directly in Biofluids. NANO LETTERS 2023; 23:11438-11446. [PMID: 38051760 PMCID: PMC10755749 DOI: 10.1021/acs.nanolett.3c02709] [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: 07/20/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.
Collapse
Affiliation(s)
- Shenglin Cai
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Ren Ren
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Jiaxuan He
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Zheng Zhang
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Zhaofeng Luo
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of 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, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Yuri Korchev
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| |
Collapse
|
19
|
Yin B, Tang P, Wang L, Xie W, Chen X, Wang Y, Weng T, Tian R, Zhou S, Wang Z, Wang D. An aptamer-assisted nanopore strategy with a salt gradient for direct protein sensing. J Mater Chem B 2023; 11:11064-11072. [PMID: 37966856 DOI: 10.1039/d3tb01875j] [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: 11/16/2023]
Abstract
Nanopore sensing is at the forefront of the technological revolution of the protein research field and has been widely used in molecular diagnosis and molecular dynamics, as well as for various sequencing applications. However, direct protein sensing with biological nanopores is still challenging owing to the large molecular size. Here, we propose an aptamer-assisted nanopore strategy for direct protein sensing and demonstrate its proof-of-concept utilities by experiments with SARS-Cov-2 nucleocapsid protein (NP), the most abundantly expressed viral protein, that is widely used in clinical diagnosis for COVID-19. NP binds with an oligonucleotide-tailed aptamer to form a protein-DNA complex which induces a discriminative two-level pattern of current blockades. We reveal the potential molecular interaction mechanism for the characteristic blockades and identify the salt gradient condition as the dominant factor of the phenomenon. Furthermore, we achieve a high sensitivity of 10 pM for NP detection within one hour and make a preliminary exploration on clinical diagnosis. This work promises a new platform for rapid and label-free protein detection.
Collapse
Affiliation(s)
- Bohua Yin
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, Jilin, China.
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Peng Tang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Xiaohan Chen
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Rong Tian
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Shuo Zhou
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, Jilin, China.
| | - Deqiang Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, Jilin, China.
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Shang Z, Deng Z, Yi X, Yang M, Nong X, Lin M, Xia F. Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5564-5576. [PMID: 37861233 DOI: 10.1039/d3ay01618h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.
Collapse
Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Zixuan Deng
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| |
Collapse
|
22
|
Yin W, Hu J, Chen F, Zhu L, Ma Y, Wang N, Wei H, Yang H, Chou SH, He J. Combining hybrid nanoflowers with hybridization chain reaction for highly sensitive detection of SARS-CoV-2 nucleocapsid protein. Anal Chim Acta 2023; 1279:341838. [PMID: 37827653 DOI: 10.1016/j.aca.2023.341838] [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: 08/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND COVID-19 (coronavirus disease 2019) pandemic has had enormous social and economic impacts so far. The nucleocapsid protein (N protein) is highly conserved and is a key antigenic marker for the diagnosis of early SARS-CoV-2 infection. RESULTS In this study, the N protein was first captured by an aptamer (Aptamer 58) coupled to magnetic beads (MBs), which in turn were bound to another DNA sequence containing the aptamer (Aptamer 48-Initiator). After adding 5'-biotinylated hairpin DNA Amplifier 1 and Amplifier 2 with cohesive ends for complementary hybridization, the Initiator in the Aptamer 48-Initiator began to trigger the hybridization chain reaction (HCR), generating multiple biotin-labeled DNA concatamers. When incubated with synthetic streptavidin-invertase-Ca3(PO4)2 hybrid nanoflower (SICa), DNA concatamers could specifically bind to SICa through biotin-streptavidin interaction with high affinity. After adding sucrose, invertase in SICa hydrolyzed sucrose to glucose, whose concentration could be directly read with a portable glucometer, and its concentration was positively correlated with the amount of captured N protein. The method is highly sensitive with a detection limit as low as 1 pg/mL. SIGNIFICANCE We believe this study provided a practical solution for the early detection of SARS-CoV-2 infection, and offered a new method for detecting other viruses through different target proteins.
Collapse
Affiliation(s)
- Wen Yin
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Ji Hu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Chen
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nuo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430000, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430000, China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
23
|
Qi H, Xiao L, Wu J, Lv L, Hu X, Zhuang Y, Liu X, Zhao W, You F, Zhang J, Zheng L. One-step and real-time detection of Hg 2+ in brown rice flour using a biosensor integrated with AC electrothermal enrichment. Food Chem 2023; 416:135823. [PMID: 36893644 DOI: 10.1016/j.foodchem.2023.135823] [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: 11/05/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Mercury (Hg2+) is one of the most toxic heavy metals in farm products, so rapid detection of trace Hg2+ has always been sought after with high interest. Herein, we report a biosensor to specifically recognize Hg2+ in leaching solutions of brown rice flour. This sensor is simple and of low cost, with a very short assay time of 30 s. Another merit is the ultra-low limit of detection (LOD) at fM level. In addition, the specific aptamer probe realizes a good selectivity above 105: 1 against the interferences. This sensor is developed based on an aptamer-modified gold electrode array (GEA) for capacitive sensing. Alternating current electrothermal (ACET) enrichment is induced during the AC capacitance acquirement. Thus, the enrichment and detection are coupled as a single step, and pre-concentration is needless. Owing to the sensing mechanism of solid-liquid interfacial capacitance and ACET enrichment, Hg2+ level can be sensitively and rapidly reflected. Also, the sensor has a wide linear range from 1 fM to 0.1 nM and a shelf life of 15 days. This biosensor shows advantages on overall performance, enabling easy-to-operate, real-time, and large-scale Hg2+ detection in farm products.
Collapse
Affiliation(s)
- Haochen Qi
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lei Xiao
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA.
| | - Li Lv
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, China
| | - Xinyu Hu
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, China
| | - Youyi Zhuang
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, China
| | - Xiaoru Liu
- School of Engineering, Trinity College Dublin, Dublin 999015, Ireland
| | - Wenci Zhao
- School of Microelectronics, Hefei University of Technology, Hefei 230009, China
| | - Fangshuo You
- School of Microelectronics, Hefei University of Technology, Hefei 230009, China
| | - Jian Zhang
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| |
Collapse
|
24
|
Chang ZY, Alhamami FAMS, Chin KL. Aptamer-Based Strategies to Address Challenges in COVID-19 Diagnosis and Treatments. Interdiscip Perspect Infect Dis 2023; 2023:9224815. [PMID: 37554129 PMCID: PMC10406522 DOI: 10.1155/2023/9224815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Coronavirus disease (COVID-19), a highly contagious and rapidly spreading disease with significant fatality in the elderly population, has swept across the world since 2019. Since its first appearance, the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has undergone multiple mutations, with Omicron as the predominant circulating variant of concern at the moment. The gold standard for diagnosis of COVID-19 by real-time polymerase chain reaction (RT-PCR) to detect the virus is laborious and requires well-trained personnel to perform sophisticated procedures. Also, the genetic variants of SARS-CoV-2 that arise regularly could result in false-negative detection. Meanwhile, the current COVID-19 treatments such as conventional medicine, complementary and alternative medicine, passive antibody therapy, and respiratory therapy are associated with adverse effects. Thus, there is an urgent need to discover novel diagnostic and therapeutic approaches against SARS-CoV-2 and its variants. Over the past 30 years, nucleic acid-based aptamers have gained increasing attention and serve as a promising alternative to the antibodies in the diagnostic and therapeutic fields with their uniqueness of being small, nonimmunogenicity, and thermally stable. Aptamer targeting the SARS-CoV-2 structural proteins or the host receptor proteins represent a powerful tool to control COVID-19 infection. In this review, challenges faced by currently available diagnostic and therapeutic tools for COVID-19 are underscored, along with how aptamers can shed a light on the current COVID-19 pandemic, focusing on the critical factors affecting the discovery of high-affinity aptamers and their potential applications to control COVID-19 infection.
Collapse
Affiliation(s)
- Zi Yuan Chang
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | | | - Kai Ling Chin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| |
Collapse
|
25
|
Ma P, Liu J, Pang S, Zhou W, Yu H, Wang M, Dong T, Wang Y, Wang Q, Liu A. Biopanning of specific peptide for SARS-CoV-2 nucleocapsid protein and enzyme-linked immunosorbent assay-based antigen assay. Anal Chim Acta 2023; 1264:341300. [PMID: 37230729 DOI: 10.1016/j.aca.2023.341300] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide which triggered serious public health issues. The search for rapid and accurate diagnosis, effective prevention, and treatment is urgent. The nucleocapsid protein (NP) of SARS-CoV-2 is one of the main structural proteins expressed and most abundant in the virus, and is considered a diagnostic marker for the accurate and sensitive detection of SARS-CoV-2. Herein, we report the screening of specific peptides from the pIII phage library that bind to SARS-CoV-2 NP. The phage monoclone expressing cyclic peptide N1 (peptide sequence, ACGTKPTKFC, with C&C bridged by disulfide bonding) specifically recognizes SARS-CoV-2 NP. Molecular docking studies reveal that the identified peptide is bound to the "pocket" region on the SARS-CoV-2 NP N-terminal domain mainly by forming a hydrogen bonding network and through hydrophobic interaction. Peptide N1 with the C-terminal linker was synthesized as the capture probe for SARS-CoV-2 NP in ELISA. The peptide-based ELISA was capable of assaying SARS-CoV-2 NP at concentrations as low as 61 pg/mL (∼1.2 pM). Furthermore, the as-proposed method could detect the SARS-CoV-2 virus at limits as low as 50 TCID50 (median tissue culture infective dose)/mL. This study demonstrates that selected peptides are powerful biomolecular tools for SARS-CoV-2 detection, providing a new and inexpensive method of rapidly screening infections as well as rapidly diagnosing coronavirus disease 2019 patients.
Collapse
Affiliation(s)
- Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Wenhao Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Yanbo Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Qiqin Wang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China.
| |
Collapse
|
26
|
Yu X, Pan B, Zhao C, Shorty D, Solano LN, Sun G, Liu R, Lam KS. Discovery of Peptidic Ligands against the SARS-CoV-2 Spike Protein and Their Use in the Development of a Highly Sensitive Personal Use Colorimetric COVID-19 Biosensor. ACS Sens 2023; 8:2159-2168. [PMID: 37253267 PMCID: PMC10255569 DOI: 10.1021/acssensors.2c02386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In addition to efficacious vaccines and antiviral therapeutics, reliable and flexible in-home personal use diagnostics for the detection of viral antigens are needed for effective control of the COVID-19 pandemic. Despite the approval of several PCR-based and affinity-based in-home COVID-19 testing kits, many of them suffer from problems such as a high false-negative rate, long waiting time, and short storage period. Using the enabling one-bead-one-compound (OBOC) combinatorial technology, several peptidic ligands with a nanomolar binding affinity toward the SARS-CoV-2 spike protein (S-protein) were successfully discovered. Taking advantage of the high surface area of porous nanofibers, immobilization of these ligands on nanofibrous membranes allows the development of personal use sensors that can achieve low nanomolar sensitivity in the detection of the S-protein in saliva. This simple biosensor employing naked-eye reading exhibits detection sensitivity comparable to some of the current FDA-approved home detection kits. Furthermore, the ligand used in the biosensor was found to detect the S-protein derived from both the original strain and the Delta variant. The workflow reported here may enable us to rapidly respond to the development of home-based biosensors against future viral outbreaks.
Collapse
Affiliation(s)
- Xingjian Yu
- Department
of Biochemistry & Molecular Medicine, University of California, Sacramento, Sacramento, California 95817, United States
- Department
of Chemistry, University of California,
Sacramento, Sacramento, California 95616, United States
| | - Bofeng Pan
- Department
of Biological and Agricultural Engineering, University of California, Davis, Davis, California 95616, United States
| | - Cunyi Zhao
- Department
of Biological and Agricultural Engineering, University of California, Davis, Davis, California 95616, United States
| | - Diedra Shorty
- Department
of Biochemistry & Molecular Medicine, University of California, Sacramento, Sacramento, California 95817, United States
- Department
of Chemistry, University of California,
Sacramento, Sacramento, California 95616, United States
| | - Lucas N. Solano
- Department
of Biochemistry & Molecular Medicine, University of California, Sacramento, Sacramento, California 95817, United States
| | - Gang Sun
- Department
of Biological and Agricultural Engineering, University of California, Davis, Davis, California 95616, United States
| | - Ruiwu Liu
- Department
of Biochemistry & Molecular Medicine, University of California, Sacramento, Sacramento, California 95817, United States
| | - Kit S. Lam
- Department
of Biochemistry & Molecular Medicine, University of California, Sacramento, Sacramento, California 95817, United States
| |
Collapse
|
27
|
Chen C, Song X, Yu Y, Wang X, Xu H, Ji W, Ma J, Zhao C, Feng S, Wang Y, Su XD, Wang W. Aptamer-based nanointerferometer enables amplification-free ultrasensitive detection and differentiation of SARS-CoV-2 variants. Anal Chim Acta 2023; 1260:341207. [PMID: 37121656 PMCID: PMC10085716 DOI: 10.1016/j.aca.2023.341207] [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: 12/01/2022] [Revised: 03/07/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023]
Abstract
The state-of-the-art SARS-CoV-2 detection methods include qRT-PCR and antibody-based lateral flow assay (LFA) point-of-care tests. Despite the high sensitivity and selectivity, qRT-PCR is slow, expensive and needs well-trained operators. On the other extreme, LFA suffers from low sensitivity albeit its fast detection speed, low detection cost and ease of use. Therefore, the continuing COVID-19 pandemic calls for a SARS-CoV-2 detection method that is rapid, convenient and cost-effective without compromise in sensitivity. Here we provide a proof-of-principle demonstration of an optimized aptamer-based nanointerferometer that enables rapid and amplification-free detection of SARS-CoV-2 spike protein-coated pseudovirus directly from human saliva with the limit of detection (LOD) of about 400 copies per mL. This LOD is on par with that of qRT-PCR, making it 1000 to 100,000-fold more sensitive than commercial LFA tests. Using various combinations of negative selections during the screens for the aptamer targeting the receptor binding domain of the spike protein of SARS-CoV-2, we isolated two aptamers that can distinguish the Omicron and Delta variants. Integrating these two aptamers with LFA strips or the nanointerferometer sensors allows both detection and differentiation of the Omicron and Delta variants which has the potential to realize rapid triage of patients infected different SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Changtian Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China; Center for Life Sciences, Beijing, 100871, China
| | - Xiaohui Song
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yuanling Yu
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China
| | - Xingwei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hua Xu
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Weiwei Ji
- College of Physics and Electronic Science, Hubei Normal University, Hubei, 435002, China
| | - Jingchen Ma
- School of Materials and Energy, Guangdong University of Technology, Guangzhou, 510006, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
| | - Silu Feng
- School of Integrated Circuits, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China; Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China.
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Wei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China; Center for Life Sciences, Beijing, 100871, China.
| |
Collapse
|
28
|
Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
Collapse
Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| |
Collapse
|
29
|
Kar SS, Dhar AK, Palei NN, Bhatt S. Small-molecule oligonucleotides as smart modality for antiviral therapy: a medicinal chemistry perspective. Future Med Chem 2023; 15:1091-1110. [PMID: 37584172 DOI: 10.4155/fmc-2023-0091] [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: 08/17/2023] Open
Abstract
Small-molecule oligonucleotides could be exploited therapeutically to silence the expression of viral infection-causing genes, and a few of them are now in clinical trials for the management of viral infections. The most challenging aspect of these oligonucleotides' therapeutic success involves their delivery. Thus medicinal chemistry strategies are inevitable to avoid degradation by serum nucleases, avoid kidney clearance and improve cellular uptake. Recently small-molecule oligonucleotide design has opened up new avenues to improve the treatment of drug-resistant viral infections, along with the development of COVID-19 medicines. This review is directed toward the recent advances in rational design, mechanism of action, structure-activity relationships and future perspective of the small-molecule oligonucleotides targeting viral infections, including COVID-19.
Collapse
Affiliation(s)
- Sidhartha S Kar
- Institute of Pharmacy & Technology, Salipur, Cuttack, Odisha, 754202, India
| | - Arghya Kusum Dhar
- School of Pharmacy, The Neotia University, Sarisa, D.H. Road, 24 Pgs (South) West Bengal, 743368, India
| | - Narahari N Palei
- Amity Institute of Pharmacy, Amity University Lucknow Campus, Uttar Pradesh, 226010, India
| | - Shvetank Bhatt
- School of Health Sciences and Technology, Dr Vishwanath Karad MIT World Peace University, Pune, Maharashtra, 411038, India
| |
Collapse
|
30
|
Neff CP, Cikara M, Geiss BJ, Thomas Caltagirone G, Liao A, Atif SM, Macdonald B, Schaden R. Nucleocapsid protein binding DNA aptamers for detection of SARS-COV-2. CURRENT RESEARCH IN BIOTECHNOLOGY 2023; 5:100132. [PMID: 37275459 PMCID: PMC10223630 DOI: 10.1016/j.crbiot.2023.100132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV-2) has infected millions of individuals and continues to be a major health concern worldwide. While reverse transcription-polymerase chain reaction remains a reliable method for detecting infections, limitations of this technology, particularly cost and the requirement of a dedicated laboratory, prevent rapid viral monitoring. Antigen tests filled this need to some extent but with limitations including sensitivity and specificity, particularly against emerging variants of concern. Here, we developed aptamers against the SARS-CoV-2 Nucleocapsid protein to complement or replace antibodies in antigen detection assays. As detection reagents in ELISA-like assays, our DNA aptamers were able to detect as low as 150 pg/mL of the protein and under 150 k copies of inactivated SARS-CoV-2 Wuhan Alpha strain in viral transport medium with little cross-reactivity to other human coronaviruses (HCoVs). Further, our aptamers were reselected against the SARS-CoV-2 Omicron variant of concern, and we found two sequences that had a more than two-fold increase in signal compared to our original aptamers when used as detection reagents against protein from the Omicron strain. These findings illustrate the use of aptamers as promising alternative detection reagents that may translate for use in current tests and our findings validate the method for the reselection of aptamers against emerging viral strains.
Collapse
Affiliation(s)
- Charles P Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mile Cikara
- Precision Medicine Architects, LLC, PO Box 148, Wellington, CO 80549, United States
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Albert Liao
- Aptagen, LLC, 250 North Main Street, Jacobus, PA 17407, USA
| | - Shaikh M Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bradley Macdonald
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Richard Schaden
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| |
Collapse
|
31
|
Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
Collapse
Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| |
Collapse
|
32
|
Xing W, Li Q, Han C, Sun D, Zhang Z, Fang X, Guo Y, Ge F, Ding W, Luo Z, Zhang L. Customization of aptamer to develop CRISPR/Cas12a-derived ultrasensitive biosensor. Talanta 2023; 256:124312. [PMID: 36738621 DOI: 10.1016/j.talanta.2023.124312] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
The CRISPR/Cas systems have provided wide biosensing applications. Particularly, the aptamer-involved CRISPR/Cas sensor system powerfully expanded to non-nucleic-acid targets. However, tailoring the sequence of the aptamer to explore the relationship between affinity and the activation of CRISPR/Cas12a trans-cleavage activity has not been reported yet. Herein, we developed a series of new aptamers toward the spike protein 1(S1) of SARS-CoV-2. Surface plasmon resonance measurements showed that the affinity of these aptamers to S1 was at the nM level. Subsequently, a "SET" effect (Sequence Essential Trans-cleavage activity) is discovered for the activation of CRISPR/Cas12a trans-cleavage activity. That is, an aptamer, as the activator, sequence needs to be tailored to activate CRISPR/Cas12a efficiently. A balance should be reached between affinity and activation ability. On the one hand, high affinity ensures target recognition performance, and on the other hand, activation can achieve adequate amplification and output of recognition signals. The optimized sequence (with 27 nucleotides, for short 27-nt) not only recognizes the target with a high affinity and specificity but also can trigger the CRISPR/Cas12a trans-cleavage activity efficiently, showing an excellent detection performance in electrochemical biosensors. The detection limit for SARS-CoV-2 S1 can be low at 1.5 pg mL-1. The new CRISPR/Cas12a-derived aptasensor also displays a remarkable ability to detect Beta, Delta, and Omicron variants but is selective toward other kinds of proteins. Above all, it is robust for point-of-care testing (POCT) in complex biological fluids, such as saliva, urine, and serum, and provides a universal and scalable detecting platform. Our results provide new insights into aptamer development and a different strategy for COVID-19 antigen detection and biosensor development.
Collapse
Affiliation(s)
- Wenping Xing
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300350, PR China
| | - Qian Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300350, PR China
| | - Cong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Dongdong Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Zheng Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Xiaona Fang
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Feng Ge
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, 300071, PR China
| | - Wei Ding
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, 300071, PR China
| | - Zhaofeng Luo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Liyun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China.
| |
Collapse
|
33
|
Karuppaiah G, Vashist A, Nair M, Veerapandian M, Manickam P. Emerging trends in point-of-care biosensing strategies for molecular architectures and antibodies of SARS-CoV-2. BIOSENSORS AND BIOELECTRONICS: X 2023; 13:100324. [PMID: 36844889 PMCID: PMC9941073 DOI: 10.1016/j.biosx.2023.100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/01/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023]
Abstract
COVID-19, a highly contagious viral infection caused by the occurrence of severe acute respiratory syndrome coronavirus (SARS-CoV-2), has turned out to be a viral pandemic then ravaged many countries worldwide. In the recent years, point-of-care (POC) biosensors combined with state-of-the-art bioreceptors, and transducing systems enabled the development of novel diagnostic tools for rapid and reliable detection of biomarkers associated with SARS-CoV-2. The present review thoroughly summarises and discusses various biosensing strategies developed for probing SARS-CoV-2 molecular architectures (viral genome, S Protein, M protein, E protein, N protein and non-structural proteins) and antibodies as a potential diagnostic tool for COVID-19. This review discusses the various structural components of SARS-CoV-2, their binding regions and the bioreceptors used for recognizing the structural components. The various types of clinical specimens investigated for rapid and POC detection of SARS-CoV-2 is also highlighted. The importance of nanotechnology and artificial intelligence (AI) approaches in improving the biosensor performance for real-time and reagent-free monitoring the biomarkers of SARS-CoV-2 is also summarized. This review also encompasses existing practical challenges and prospects for developing new POC biosensors for clinical monitoring of COVID-19.
Collapse
Affiliation(s)
- Gopi Karuppaiah
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi, 630 003, Tamil Nadu, India
| | - Arti Vashist
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Madhavan Nair
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Murugan Veerapandian
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi, 630 003, Tamil Nadu, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201 002, Uttar Pradesh, India
| | - Pandiaraj Manickam
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi, 630 003, Tamil Nadu, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201 002, Uttar Pradesh, India
| |
Collapse
|
34
|
Salahandish R, Hyun JE, Haghayegh F, Tabrizi HO, Moossavi S, Khetani S, Ayala-Charca G, Berenger BM, Niu YD, Ghafar-Zadeh E, Nezhad AS. CoVSense: Ultrasensitive Nucleocapsid Antigen Immunosensor for Rapid Clinical Detection of Wildtype and Variant SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206615. [PMID: 36995043 DOI: 10.1002/advs.202206615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/31/2023] [Indexed: 05/27/2023]
Abstract
The widespread accessibility of commercial/clinically-viable electrochemical diagnostic systems for rapid quantification of viral proteins demands translational/preclinical investigations. Here, Covid-Sense (CoVSense) antigen testing platform; an all-in-one electrochemical nano-immunosensor for sample-to-result, self-validated, and accurate quantification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N)-proteins in clinical examinations is developed. The platform's sensing strips benefit from a highly-sensitive, nanostructured surface, created through the incorporation of carboxyl-functionalized graphene nanosheets, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) conductive polymers, enhancing the overall conductivity of the system. The nanoengineered surface chemistry allows for compatible direct assembly of bioreceptor molecules. CoVSense offers an inexpensive (<$2 kit) and fast/digital response (<10 min), measured using a customized hand-held reader (<$25), enabling data-driven outbreak management. The sensor shows 95% clinical sensitivity and 100% specificity (Ct<25), and overall sensitivity of 91% for combined symptomatic/asymptomatic cohort with wildtype SARS-CoV-2 or B.1.1.7 variant (N = 105, nasal/throat samples). The sensor correlates the N-protein levels to viral load, detecting high Ct values of ≈35, with no sample preparation steps, while outperforming the commercial rapid antigen tests. The current translational technology fills the gap in the workflow of rapid, point-of-care, and accurate diagnosis of COVID-19.
Collapse
Affiliation(s)
- Razieh Salahandish
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Laboratory of Advanced Biotechnologies for Health Assessments (LAB-HA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Jae Eun Hyun
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Fatemeh Haghayegh
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hamed Osouli Tabrizi
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Shirin Moossavi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, T2N 1N4, Canada
- International Microbiome Centre, Cumming School of Medicine, Health Sciences Centre, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Sultan Khetani
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Giancarlo Ayala-Charca
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Byron M Berenger
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3330 Hospital Drive, Calgary, AB, T2N 4W4, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yan Dong Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Amir Sanati Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, T2N 1N4, Canada
| |
Collapse
|
35
|
Sen P, Zhang Z, Li P, Adhikari BR, Guo T, Gu J, MacIntosh AR, van der Kuur C, Li Y, Soleymani L. Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater. ACS Sens 2023; 8:1558-1567. [PMID: 36926840 PMCID: PMC10042147 DOI: 10.1021/acssensors.2c02655] [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: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.
Collapse
Affiliation(s)
- Payel Sen
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Phoebe Li
- Department of Physics, McMaster
University, Hamilton L8S 4K1, Canada
| | - Bal Ram Adhikari
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Tianyi Guo
- Forsee Instruments, Ltd.,
Hamilton L8P0A1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
| | | | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
- School of Biomedical Engineering, McMaster
University, Hamilton L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease
Research, McMaster University, Hamilton L8S 4K1,
Canada
| | - Leyla Soleymani
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
- School of Biomedical Engineering, McMaster
University, Hamilton L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease
Research, McMaster University, Hamilton L8S 4K1,
Canada
| |
Collapse
|
36
|
Gao S, Yang G, Zhang X, Shi R, Chen R, Zhang X, Peng Y, Yang H, Lu Y, Song C. β-Cyclodextrin Polymer-Based Fluorescence Enhancement Strategy via Host-Guest Interaction for Sensitive Assay of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24087174. [PMID: 37108336 PMCID: PMC10139410 DOI: 10.3390/ijms24087174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/01/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Nucleocapsid protein (N protein) is an appropriate target for early determination of viral antigen-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have found that β-cyclodextrin polymer (β-CDP) has shown a significant fluorescence enhancement effect for fluorophore pyrene via host-guest interaction. Herein, we developed a sensitive and selective N protein-sensing method that combined the host-guest interaction fluorescence enhancement strategy with high recognition of aptamer. The DNA aptamer of N protein modified with pyrene at its 3' terminal was designed as the sensing probe. The added exonuclease I (Exo I) could digest the probe, and the obtained free pyrene as a guest could easily enter into the hydrophobic cavity of host β-CDP, thus inducing outstanding luminescent enhancement. While in the presence of N protein, the probe could combine with it to form a complex owing to the high affinity between the aptamer and the target, which prevented the digestion of Exo I. The steric hindrance of the complex prevented pyrene from entering the cavity of β-CDP, resulting in a tiny fluorescence change. N protein has been selectively analyzed with a low detection limit (11.27 nM) through the detection of the fluorescence intensity. Moreover, the sensing of spiked N protein from human serum and throat swabs samples of three volunteers has been achieved. These results indicated that our proposed method has broad application prospects for early diagnosis of coronavirus disease 2019.
Collapse
Affiliation(s)
- Shanshan Gao
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Gege Yang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Xiaohui Zhang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Rui Shi
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Rongrong Chen
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Yuancheng Peng
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Hua Yang
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Ying Lu
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Chunxia Song
- Department of Applied Chemistry, School of Science, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| |
Collapse
|
37
|
Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19. Trends Biotechnol 2023; 41:528-544. [PMID: 35995601 PMCID: PMC9340053 DOI: 10.1016/j.tibtech.2022.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, remains among the main causes of global mortality. Although antigen/antibody-based immunoassays and neutralizing antibodies targeting SARS-CoV-2 have been successfully developed over the past 2 years, they are often inefficient and unreliable for emerging SARS-CoV-2 variants. Novel approaches against SARS-CoV-2 and its variants are therefore urgently needed. Aptamers have been developed for the detection and inhibition of several different viruses such as HIV, influenza viruses, Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV. Aptamers targeting SARS-CoV-2 represent a promising tool in the fight against COVID-19, which is of paramount importance for the current and any future pandemics. This review presents recent advances and future trends in the development of aptamer-based approaches for SARS-CoV-2 diagnosis and treatment.
Collapse
|
38
|
Han C, Xing W, Li W, Fang X, Zhao J, Ge F, Ding W, Qu P, Luo Z, Zhang L. Aptamers dimerization inspired biomimetic clamp assay towards impedimetric SARS-CoV-2 antigen detection. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 380:133387. [PMID: 36694572 PMCID: PMC9851723 DOI: 10.1016/j.snb.2023.133387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Antigen-detecting rapid diagnostic testing (Ag-RDT) has contributed to containing the spread of SARS-CoV-2 variants of concern (VOCs). In this study, we proposed a biomimetic clamp assay for impedimetric SARS-CoV-2 nucleocapsid protein (Np) detection. The DNA biomimetic clamp (DNA-BC) is formed by a pair of Np aptamers connected via a T20 spacer. The 5'- terminal of the DNA-BC is phosphate-modified and then anchored on the surface of the screen-printed gold electrode, which has been pre-coated with Au@UiO-66-NH2. The integrated DNA-material sensing biochip is fabricated through the strong Zr-O-P bonds to form a clamp-type impedimetric aptasensor. It is demonstrated that the aptasensor could achieve Np detection in one step within 11 min and shows pronounced sensitivity with a detection limit of 0.31 pg mL-1. Above all, the aptasensor displays great specificity and stability under physiological conditions as well as various water environments. It is a potentially promising strategy to exploit reliable Ag-RDT products to confront the ongoing epidemic.
Collapse
Affiliation(s)
- Cong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Wenping Xing
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Wenjin Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Xiaona Fang
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jian Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Feng Ge
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin 300071, China
| | - Wei Ding
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin 300071, China
| | - Pengpeng Qu
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin 300071, China
| | - Zhaofeng Luo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Liyun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300350, China
| |
Collapse
|
39
|
Zhu J, Zhao X, Mao J, Na N, Ouyang J. Single-Molecule Evaluation of the SARS-CoV-2 Nucleocapsid Protein Using Gold Particle-in-a-Frame Nanostructures Enhanced Fluorescent Assay. Anal Chem 2023; 95:5267-5274. [PMID: 36912606 PMCID: PMC10022750 DOI: 10.1021/acs.analchem.2c05191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/01/2023] [Indexed: 03/14/2023]
Abstract
Ultrasensitive evaluation of low-abundance analytes, particularly with limits approaching a single molecule, is a key challenge in the design of an assay for profiling severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen. Herein, we report an aptamer claw strategy for directly evaluating the SARS-CoV-2 antigen based on gold particle-in-a-frame nanostructures (Au PIAFs). Au PIAF was used as a metal-enhanced fluorescence material. The assay integrated with a microplate reader achieved a sensitivity of 44 fg·mL-1 in under 3 min and accurately detected the SARS-CoV-2 nucleocapsid protein (N protein) in human saliva samples. When our assay is combined with a single-molecule counting platform, the limit of detection can be as low as 0.84 ag·mL-1. This rapid and ultrasensitive assay holds promise as a tool for screening SARS-CoV-2 and other contagious viruses.
Collapse
Affiliation(s)
- Jiale Zhu
- Key Laboratory of Theoretical and Computational
Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal
University, Beijing 100875, China
| | - Xuan Zhao
- Key Laboratory of Theoretical and Computational
Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal
University, Beijing 100875, China
| | - Jinpeng Mao
- Department of Chemistry, Tsinghua
University, Beijing 100084, China
| | - Na Na
- Key Laboratory of Theoretical and Computational
Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal
University, Beijing 100875, China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational
Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal
University, Beijing 100875, China
| |
Collapse
|
40
|
Zhao L, Li C, Kang X, Li Y. A visual detection strategy for SARS-CoV-2 based on dual targets-triggering DNA walker. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 379:133252. [PMID: 36590306 PMCID: PMC9792190 DOI: 10.1016/j.snb.2022.133252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2, a highly transmissible and mutagenic virus, made huge threats to global public health. The detection strategies, which are free from testing site requirements, and the reagents and instruments are portable, are vital for early screening and play a significant role in curbing the spread. This work proposed a silver-coated glass slide (SCGS)/DNA walker based on a dual targets-triggering mechanism, enzyme-catalyzed amplification, and smartphone data analysis, which build a portable visual detection strategy for the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) gene. By this method, the detection was reflected by the ultraviolet absorbance changes and visible color changes to the naked eye which was analyzed by Red-Green-Blue (RGB) data analysis via smartphone within 30 min, simplifying the detection process and shortening the detection time. Meanwhile, the dual targets-triggering mechanism and dual signal amplification strategy ensured detection specificity and sensitivity. Further, the practicability was verified by the detection of the real sample which provided this method an application potential in SARS-CoV-2 rapid detection.
Collapse
Affiliation(s)
- Liting Zhao
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ciling Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xinhuang Kang
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yubin Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang 524088, China
- Research Center for Coastal Environmental Protection and Ecological Resilience, Guangdong Ocean University, Zhanjiang 524088, China
- Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| |
Collapse
|
41
|
Poolsup S, Zaripov E, Hüttmann N, Minic Z, Artyushenko PV, Shchugoreva IA, Tomilin FN, Kichkailo AS, Berezovski MV. Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:731-743. [PMID: 36816615 PMCID: PMC9927813 DOI: 10.1016/j.omtn.2023.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6-3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.
Collapse
Affiliation(s)
- Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Polina V Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Irina A Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Felix N Tomilin
- Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia.,Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia
| | - Anna S Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.,John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| |
Collapse
|
42
|
Chen J, Li Y, Liu Z. Functional nucleic acids as potent therapeutics against SARS-CoV-2 infection. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101249. [PMID: 36714073 PMCID: PMC9869493 DOI: 10.1016/j.xcrp.2023.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The COVID-19 pandemic has posed a severe threat to human life and the global economy. Although conventional treatments, including vaccines, antibodies, and small-molecule inhibitors, have been broadly developed, they usually fall behind the constant mutation of SARS-CoV-2, due to the long screening process and high production cost. Functional nucleic acid (FNA)-based therapeutics are a newly emerging promising means against COVID-19, considering their timely adaption to different mutants and easy design for broad-spectrum virus inhibition. In this review, we survey typical FNA-related therapeutics against SARS-CoV-2 infection, including aptamers, aptamer-integrated DNA frameworks, functional RNA, and CRISPR-Cas technology. We first introduce the pathogenesis, transmission, and evolution of SARS-CoV-2, then analyze the existing therapeutic and prophylactic strategies, including their pros and cons. Subsequently, the FNAs are recommended as potent alternative therapeutics from their screening process and controllable engineering to effective neutralization. Finally, we put forward the remaining challenges of the existing field and sketch out the future development directions.
Collapse
Affiliation(s)
- Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
43
|
Wang D, Zhang J, huang Z, Yang Y, Fu T, Yang Y, Lyu Y, Jiang J, Qiu L, Cao Z, Zhang X, You Q, Lin Y, Zhao Z, Tan W. Robust Covalent Aptamer Strategy Enables Sensitive Detection and Enhanced Inhibition of SARS-CoV-2 Proteins. ACS CENTRAL SCIENCE 2023; 9:72-83. [PMID: 36712483 PMCID: PMC9881204 DOI: 10.1021/acscentsci.2c01263] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Indexed: 06/18/2023]
Abstract
Aptamer-based detection and therapy have made substantial progress with cost control and easy modification. However, the conformation lability of an aptamer typically causes the dissociation of aptamer-target complexes during harsh washes and other environmental stresses, resulting in only moderate detection sensitivity and a decreasing therapeutic effect. Herein, we report a robust covalent aptamer strategy to sensitively detect nucleocapsid protein and potently neutralize spike protein receptor binding domain (RBD), two of the most important proteins of SARS-CoV-2, after testing different cross-link electrophilic groups via integrating the specificity and efficiency. Covalent aptamers can specifically convert aptamer-protein complexes from the dynamic equilibrium state to stable and irreversible covalent complexes even in harsh environments. Covalent aptamer-based ELISA detection of nucleocapsid protein can surpass the gold standard, antibody-based sandwich ELISA. Further, covalent aptamer performs enhanced functional inhibition to RBD protein even in a blood vessel-mimicking flowing circulation system. The robust covalent aptamer-based strategy is expected to inspire more applications in accurate molecular modification, disease biomarker discovery, and other theranostic fields.
Collapse
Affiliation(s)
- Dan Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- LIMES
Chemical Biology Unit, Universität
Bonn, 53121 Bonn, Germany
| | - Jing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhiyong huang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yuhang Yang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ting Fu
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yu Yang
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifan Lyu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jianhui Jiang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Liping Qiu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zehui Cao
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qimin You
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Ustar
Biotechnologies (Hangzhou) Ltd., Hangzhou, Zhejiang 310053, China
| | - Yuankui Lin
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Ustar
Biotechnologies (Hangzhou) Ltd., Hangzhou, Zhejiang 310053, China
| | - Zilong Zhao
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
44
|
Luo Z, Cheng Y, He L, Feng Y, Tian Y, Chen Z, Feng Y, Li Y, Xie W, Huang W, Meng J, Li Y, He F, Wang X, Duan Y. T-Shaped Aptamer-Based LSPR Biosensor Using Ω-Shaped Fiber Optic for Rapid Detection of SARS-CoV-2. Anal Chem 2023; 95:1599-1607. [PMID: 36580626 PMCID: PMC9843628 DOI: 10.1021/acs.analchem.2c04709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2, especially the variant strains, is rapidly spreading around the world. Rapid detection methods for the virus are crucial for controlling the COVID-19 epidemic. Herein, a localized surface plasmonic resonance (LSPR) biosensor based on Ω-shaped fiber optic (Ω-FO) was developed for dual assays of SARS-CoV-2 monitoring. Due to its strong ability to control the orientation and density, a new T-shaped aptamer exhibits enhanced binding affinity toward N proteins. After being combined on the fiber optic surface, the T-shaped aptamer sensitively captured N proteins of SARS-CoV-2 for a direct assay. Further, core-shell structured gold/silver nanoparticles functionalized with a T-shaped aptamer (apt-Ag@AuNPs) can amplify the signal of N protein detection for a sandwich assay. The real-time analytical feature of the dual assays endows time-dependent sensitivity enhancement behavior, which provides a guideline to save analytical time. With those characteristics, the LSPR biosensor has been successfully used to rapidly identify 39 healthy volunteers and 39 COVID-19 patients infected with the ancestral or variant SARS-CoV-2. With the help of simple pretreatment, we obtain a true negative rate of 100% and a true positive rate of 92.3% with a short analysis time of 45 min using the direct assay. Further, the LSPR biosensor could also broaden the detection application range to the surface of cold-chain foods using a sandwich assay. Thus, the LSPR biosensor based on Ω-FO was demonstrated to have broad application potential to detect SARS-CoV-2 rapidly.
Collapse
Affiliation(s)
- Zewei Luo
- Research
Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yue Cheng
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Lu He
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yanting Feng
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yonghui Tian
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Zhenhua Chen
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Yaqiang Feng
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yongxin Li
- West
China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Wenjun Xie
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Weiwei Huang
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Jiantong Meng
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Yu Li
- Research
Center of Analytical Instrumentation, Key Laboratory of Bio-resource
and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Fan He
- School
of Physics, Northwest University, Xi’an 710069, China
| | - Xu Wang
- Research
Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| | - Yixiang Duan
- Research
Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| |
Collapse
|
45
|
Juhas M. COVID-19. BRIEF LESSONS IN MICROBIOLOGY 2023:123-133. [DOI: 10.1007/978-3-031-29544-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
46
|
Kulabhusan PK, Pishva P, Çapkın E, Tambe P, Yüce M. Aptamer-based Emerging Tools for Viral Biomarker Detection: A Focus on SARS-CoV-2. Curr Med Chem 2023; 30:910-934. [PMID: 35156569 DOI: 10.2174/1568009622666220214101059] [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: 06/22/2021] [Revised: 11/11/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
Viral infections can cause fatal illnesses to humans as well as animals. Early detection of viruses is therefore crucial to provide effective treatment to patients. Recently, the Covid-19 pandemic has undoubtedly given an alarming call to develop rapid and sensitive detection platforms. The viral diagnostic tools need to be fast, affordable, and easy to operate with high sensitivity and specificity equivalent or superior to the currently used diagnostic methods. The present detection methods include direct detection of viral antigens or measuring the response of antibodies to viral infections. However, the sensitivity and quantification of the virus are still a significant challenge. Detection tools employing synthetic binding molecules like aptamers may provide several advantages over the conventional methods that use antibodies in the assay format. Aptamers are highly stable and tailorable molecules and are therefore ideal for detection and chemical sensing applications. This review article discusses various advances made in aptamer-based viral detection platforms, including electrochemical, optical, and colorimetric methods to detect viruses, specifically SARS-Cov-2. Considering the several advantages, aptamers could be game-changing in designing high-throughput biosensors for viruses and other biomedical applications in the future.
Collapse
Affiliation(s)
- Prabir Kumar Kulabhusan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Parsa Pishva
- Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, 34956, Turkey
| | - Eda Çapkın
- Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, 34956, Turkey
| | - Prajakta Tambe
- Wellcome-- Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Meral Yüce
- Sabanci University, SUNUM Nanotechnology Research, and Application Centre, Istanbul, 34956, Turkey
| |
Collapse
|
47
|
Lou B, Liu Y, Shi M, Chen J, Li K, Tan Y, Chen L, Wu Y, Wang T, Liu X, Jiang T, Peng D, Liu Z. Aptamer-based biosensors for virus protein detection. Trends Analyt Chem 2022; 157:116738. [PMID: 35874498 PMCID: PMC9293409 DOI: 10.1016/j.trac.2022.116738] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/23/2022] [Accepted: 07/13/2022] [Indexed: 02/07/2023]
Abstract
Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.
Collapse
Affiliation(s)
- Beibei Lou
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Meilin Shi
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, PR China
| | - Jun Chen
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Liwei Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Dongming Peng
- Department of Medicinal Chemistry, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China.,Molecular Imaging Research Center of Central South University, Changsha, 410008, Hunan, PR China
| |
Collapse
|
48
|
Discovery and translation of functional nucleic acids for clinically diagnosing infectious diseases: Opportunities and challenges. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
49
|
Liu X, Bai L, Cao X, Wu F, Yin T, Lu W. Rapid determination of SARS-CoV-2 nucleocapsid proteins based on 2D/2D MXene/P–BiOCl/Ru(bpy) 32+ heterojunction composites to enhance electrochemiluminescence performance. Anal Chim Acta 2022; 1234:340522. [PMID: 36328721 PMCID: PMC9575274 DOI: 10.1016/j.aca.2022.340522] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/29/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
Abstract
At the end of 2019, the novel coronavirus disease 2019 (COVID-19), a cluster of atypical pneumonia caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been known as a highly contagious disease. Herein, we report the MXene/P–BiOCl/Ru(bpy)32+ heterojunction composite to construct an electrochemiluminescence (ECL) immunosensor for SARS-CoV-2 nucleocapsid protein (CoVNP) determination. Two-dimensional (2D) material ultrathin phosphorus-doped bismuth oxychloride (P–BiOCl) is exploited and first applied in ECL. 2D architectures MXene not only act as “soft substrate” to improve the properties of P–BiOCl, but also synergistically work with P–BiOCl. Owing to the inimitable set of bulk and interfacial properties, intrinsic high electrochemical conductivity, hydrophilicity and good biocompatible of 2D/2D MXene/P–BiOCl/Ru(bpy)32+, this as-exploited heterojunction composite is an efficient signal amplifier and co-reaction accelerator in the presence of tri-n-propylamine (TPA) as a coreactant. The proposed MXene/P–BiOCl/Ru(bpy)32+-TPA system exhibits a high and stable ECL signal and achieves ECL emission quenching for “signal on-off” recognition of CoVNP. Fascinatingly, the constructed ECL biosensor towards CoVNP allows a wide linear concentration range from 1 fg/mL to 10 ng/mL and a low limit of detection (LOD) of 0.49 fg/mL (S/N = 3). Furthermore, this presented strategy sheds light on designing a highly efficient ECL nanostructure through the combination of 2D MXene architectures with 2D semiconductor materials in the field of nanomedicine. This ECL biosensor can successfully detect CoVNP in human serum, which can promote the prosperity and development of diagnostic methods of SARS-CoV-2.
Collapse
Affiliation(s)
- Xuebo Liu
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Liwei Bai
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, China
| | - Feng Wu
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tao Yin
- College of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, China
| | - Wenbo Lu
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, 030031, China,Corresponding author
| |
Collapse
|
50
|
Zhang X, Zhang X, Xu A, Yu M, Xu Y, Xu Y, Wang C, Yang G, Song C, Wu X, Lu Y. Aptamer-Gated Mesoporous Silica Nanoparticles for N Protein Triggered Release of Remdesivir and Treatment of Novel Coronavirus (2019-nCoV). BIOSENSORS 2022; 12:950. [PMID: 36354459 PMCID: PMC9688528 DOI: 10.3390/bios12110950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Since the 2019-nCoV outbreak was first reported, hundreds of millions of people all over the world have been infected. There is no doubt that improving the cure rate of 2019-nCoV is one of the most effective means to deal with the current serious epidemic. At present, Remdesivir (RDV) has been clinically proven to be effective in the treatment of SARS-CoV-2. However, the uncertain side effects make it important to reduce the use of drugs while ensuring the self-healing effect. We report an approach here with targeted therapy for the treatment of SARS-CoV-2 and other coronaviruses illness. In this study, mesoporous silica was used as the carrier of RDV, the nucleocapsid protein (N protein) aptamer was hybridized with the complementary chain, and the double-stranded DNA was combined with gold nanoparticles as the gates of mesoporous silica pores. When the RDV-loaded mesoporous silica is incubated with the N protein, aptamer with gold nanoparticles dissociate from the complementary DNA oligonucleotide on the mesoporous silica surface and bind to the N protein. The releasing of RDV was determined by detecting the UV-vis absorption peak of RDV in the solution. These results show that the RDV delivery system designed in this work has potential clinical application for the treatment of 2019-nCoV.
Collapse
Affiliation(s)
- Xiaohui Zhang
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Aoqiong Xu
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Mengdi Yu
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Yu Xu
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Ying Xu
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Chao Wang
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Gege Yang
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Chunxia Song
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- Key Laboratory of Agri-Food Safety of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Ying Lu
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei 230036, China
| |
Collapse
|