1
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Qin H, Chen Z, Zuo F, Cao R, Wang F, Wu H, Wang S, Xie Y, Ding S, Min X, Duan X. "DSN-mismatched CRISPR″sensor for highly selective and sensitive detection of under-expressed miR-let-7a. Anal Chim Acta 2024; 1295:342273. [PMID: 38355234 DOI: 10.1016/j.aca.2024.342273] [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: 11/16/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
Several microRNAs (miRNAs) are expressed at lower levels in specific tumors, e.g., miR-let-7a in non-small cell lung cancer (NSCLC). This makes it challenging to analyze their lower abundance versus specifically elevated miRNAs. Here, we describe a novel fluorescent biosensor for the highly selective and sensitive detection of miR-let-7a constructed by combining miRNA screening assisted by a duplex-specific nuclease (DSN) with CRISPR-Cas12a system signal amplification. We meticulously designed a mismatch in the first three to four bases at the 5'-end of the capture DNA to improve the signal-to-noise ratio of the CRISPR-Cas12a system. Within this "DSN-mismatched CRISPR" fluorescence strategy, miR-let-7a was accurately screened by DSN-assisted cleavage, and the mismatched capture DNA unbound to target miRNA could trigger the CRISPR-Cas12a system to produce a mass of trans-cleave fluorescence signals. This "turn-off" approach was suitable for detecting decreased levels of miRNAs. This approach can not only discriminate the single-base mismatched let-7 family but also reach a limit of detection at 64.17 fM as well as be quantified from 100 fM to 500 pM. The miR-let-7a levels were then measured in clinical serum samples from healthy volunteers and patients with NSCLC. This study holds promise for the development of a universal under-expressed miRNA assay for early diagnosis and treatment of cancers.
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Affiliation(s)
- Huijun Qin
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China; Department of Clinical Laboratory, Dazhou Central Hospital, Dazhou, 635000, PR China
| | - Zhuoying Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Fujiang Zuo
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Rufei Cao
- College of Basic Medicine, Zunyi Medical University, Zunyi, 563000, PR China
| | - Fangyuan Wang
- College of Basic Medicine, Zunyi Medical University, Zunyi, 563000, PR China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Shuji Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Yuanjiang Xie
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China.
| | - Xiaolei Duan
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China; College of Basic Medicine, Zunyi Medical University, Zunyi, 563000, PR China.
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2
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Anbiaee G, Khoshbin Z, Zahraee H, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Exonuclease-based aptasensors: Promising for food safety and diagnostic aims. Talanta 2023; 259:124500. [PMID: 37001398 DOI: 10.1016/j.talanta.2023.124500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023]
Abstract
As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.
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Affiliation(s)
- Ghasem Anbiaee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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3
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Norouzi S, Soltani S, Alipour E. Recent advancements in biosensor designs toward the detection of intestine cancer miRNA biomarkers. Int J Biol Macromol 2023:125509. [PMID: 37364808 DOI: 10.1016/j.ijbiomac.2023.125509] [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: 04/09/2023] [Revised: 05/28/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Cancer diagnosis and treatment have been of broad interest among scientists in the last decades due to the high death rate, widespread occurrence, and recurrence after treatment. The survival rate of cancer patients depends greatly on early detection and appropriate treatments. Therefore developing new technologies applicable to sensitive and specific methods of cancer detection is an inevitable task for cancer researchers. Abnormal miRNA expression is contributed to severe diseases such as cancers and since their expression level and type differ strictly during carcinogenesis and later metastasis and treatments, the improved detection accuracy of these miRNAs would undoubtedly lead to early diagnosis, prognosis, and targeted therapy. Biosensors are accurate and straightforward analytical devices that have had practical applications especially in the last decade. Their domain is still growing through a combination of attractive nanomaterials and amplification methods, leading to innovative biosensing platforms for the efficient detection of miRNAs as diagnostic and prognostic biomarkers. In this review, we will provide the recent developments in biosensors to detect intestine cancer miRNA biomarkers and also discuss the challenges and outcomings of this field.
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Affiliation(s)
| | - Somaieh Soltani
- Pharmacy faculty, Tabriz University of Medical Sciences, Tabriz, Iran.
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4
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Liu J, Xie G, Lv S, Xiong Q, Xu H. Recent applications of rolling circle amplification in biosensors and DNA nanotechnology. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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5
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Boonbanjong P, Treerattrakoon K, Waiwinya W, Pitikultham P, Japrung D. Isothermal Amplification Technology for Disease Diagnosis. BIOSENSORS 2022; 12:bios12090677. [PMID: 36140062 PMCID: PMC9496038 DOI: 10.3390/bios12090677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
Abstract
Isothermal amplification (IA) is a nucleic acid amplification technology (NAAT) that has contributed significantly to the healthcare system. The combination of NAAT with a suitable detection platform resulted in higher sensitivity, specificity, and rapid disease diagnosis. Traditional NAAT, such as polymerase chain reaction (PCR), is widely applied in the general healthcare system but is rarely accessed in resource-limited hospitals. Some IA methods provide a rapid, sensitive, specific, and simple method for disease diagnosis. However, not all IA techniques have been regularly used in clinical applications because different biomarkers and sample types affect either the enzyme in the IA system or sample preparation. This review focuses on the application of some IA techniques that have been applied in the medical field and have the potential for use at points of care.
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Affiliation(s)
- Poramin Boonbanjong
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Kiatnida Treerattrakoon
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Wassa Waiwinya
- Multidisciplinary Program of Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Piyawat Pitikultham
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
- Correspondence: ; Tel.: +66-2-117-6665
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6
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Bodulev OL, Sakharov IY. Modern Methods for Assessment of microRNAs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:425-442. [PMID: 35790375 DOI: 10.1134/s0006297922050042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.
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Affiliation(s)
- Oleg L Bodulev
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
| | - Ivan Yu Sakharov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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7
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Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
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Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
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8
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Qu H, Fan C, Chen M, Zhang X, Yan Q, Wang Y, Zhang S, Gong Z, Shi L, Li X, Liao Q, Xiang B, Zhou M, Guo C, Li G, Zeng Z, Wu X, Xiong W. Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection. J Nanobiotechnology 2021; 19:403. [PMID: 34863202 PMCID: PMC8645109 DOI: 10.1186/s12951-021-01149-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Mingjian Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xu Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
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9
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Li Y, Su R, Li H, Guo J, Hildebrandt N, Sun C. Fluorescent Aptasensors: Design Strategies and Applications in Analyzing Chemical Contamination of Food. Anal Chem 2021; 94:193-224. [PMID: 34788014 DOI: 10.1021/acs.analchem.1c04294] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Ruifang Su
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique: Réactivité et Analyse), UMR 6014, CNRS, Université de Rouen Normandie, INSA, 76821 Mont-Saint-Aignan Cedex, France
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Jiajia Guo
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055 Shenzhen, China
| | - Niko Hildebrandt
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique: Réactivité et Analyse), UMR 6014, CNRS, Université de Rouen Normandie, INSA, 76821 Mont-Saint-Aignan Cedex, France.,Université Paris-Saclay, 91190 Saint-Aubin, France.,Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
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10
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Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments. BIOSENSORS-BASEL 2021; 11:bios11100352. [PMID: 34677308 PMCID: PMC8533700 DOI: 10.3390/bios11100352] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.
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11
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Ratiometric fluorescent detection and imaging of microRNA in living cells with manganese dioxide nanosheet-active DNAzyme. Talanta 2021; 233:122518. [PMID: 34215133 DOI: 10.1016/j.talanta.2021.122518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) play an important role in multiple biological processes and can be used as biomarkers for clinical disease diagnosis, so their detection is of great importance. Here, manganese dioxide (MnO2) nanosheet acts as carrier to deliver DNAzyme probes into cells through endocytosis, where intracellular glutathione (GSH) reduces the MnO2 nanosheet to manganese ions (Mn2+) and releases the probes. The generated Mn2+ can be further used as an effective cofactor to activate the DNAzyme probe, and cleave the DNA strand into two fragments. Then, the miRNA-155 in the cells can hybridize with the cleaved fragment to cause the fluorescence signal change of the probe. The proposed proportional fluorescent method has been applied to the imaging of miRNA-155 in HeLa cells and HepG2 cells with the estimated detection limit (LOD) as 1.6 × 10-12 M. The new method can provide great help for cancer diagnosis and biological research related to miRNA.
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12
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Chen J, Jin T, Li J, Zhang X, Liu F, Tan C, Tan Y. One-Pot Simultaneous Detection of Multiple DNA and MicroRNA by Integrating the Cationic-Conjugated Polymer and Nuclease-Assisted Cyclic Amplification. ACS APPLIED BIO MATERIALS 2021. [DOI: 10.1021/acsabm.0c01362] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Junyue Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
- Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
| | - Tian Jin
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
| | - Jingfeng Li
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
| | - Xinyan Zhang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
| | - Feng Liu
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
- Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
- Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, P. R. China
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13
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Liu LQ, Yin F, Lu Y, Yan XL, Wu CC, Li X, Li C. A light-up "G-quadruplex nanostring" for label-free and selective detection of miRNA via duplex-specific nuclease mediated tandem rolling circle amplification. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 32:102339. [PMID: 33227538 DOI: 10.1016/j.nano.2020.102339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/29/2022]
Abstract
MicroRNA (miRNA) has emerged as a promising genetic marker for cancer diagnosis and therapy because its expression level is closely related to the progression of malignant diseases. Herein, a label-free and selective fluorescence platform was proposed for miRNA based on light-up "G-quadruplex nanostring" via duplex-specific nuclease (DSN) mediated tandem rolling circle amplification (RCA). First, a long DNA generated from upstream RCA was designed with the antisense sequences for miR-21 and downstream RCA primer. Upon recognizing miR-21, the resulting DNA-RNA permitted DSN digestion and triggered downstream two-way RCA, and generation of abundant "G-quadruplex nanostring" binding with ZnPPIX for label-free fluorescent responses. In our strategy, the strong preference of DSN for perfectly matched DNA/RNA ensures its excellent selectivity. The developed method generated wide linear response with LOD of 1.019 fM. Additionally, the miR-21 levels in cell extracts have been evaluated, revealing the utility of this tool for biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Qi Liu
- Department of Chemistry, Liaocheng University, Liaocheng, China
| | - Fei Yin
- Department of Chemistry, Liaocheng University, Liaocheng, China
| | - Yu Lu
- Department of Chemistry, Liaocheng University, Liaocheng, China
| | - Xi-Luan Yan
- Department of Bio-industrial Mechatronics Engineering, National Chung Hsing University, Taiwan
| | - Ching-Chou Wu
- Department of Bio-industrial Mechatronics Engineering, National Chung Hsing University, Taiwan
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, China.
| | - Chenzhong Li
- Department of Bio-industrial Mechatronics Engineering, National Chung Hsing University, Taiwan
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14
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Wu Y, Cui S, Li Q, Zhang R, Song Z, Gao Y, Chen W, Xing D. Recent advances in duplex-specific nuclease-based signal amplification strategies for microRNA detection. Biosens Bioelectron 2020; 165:112449. [DOI: 10.1016/j.bios.2020.112449] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/12/2020] [Indexed: 02/06/2023]
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15
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Tang Z, Huang J, He H, Ma C, Wang K. Contributing to liquid biopsy: Optical and electrochemical methods in cancer biomarker analysis. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213317] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Huang Y, Wang C, Huo Q, Song Y, Du G, Wang L, Yang X, Chen X. A time-resolved luminescence aptasensor of ofloxacin based on rolling circle amplification and magnetic separation. Anal Bioanal Chem 2020; 412:4555-4563. [PMID: 32472145 DOI: 10.1007/s00216-020-02708-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 01/05/2023]
Abstract
A novel sensitive, competitive, and time-resolved luminescence sensor for the detection of ofloxacin (OFL) was developed in this study. The sensor used OFL-specific aptamer as a recognition molecule and rolling circle amplification (RCA) as a signal amplification tool. In this way, the time-resolved luminescence can not only avoid background noise from sample, but also provide robust luminescence for detection. Besides, the separation and enrichment of target veterinary drug can be conducted assisted by magnetic treatment. Under optimal conditions, the logarithmic correlation between the concentration of OFL and the luminescence intensity was found to be linear in the range of 5 × 10-11-5 × 10-8 mol L-1 (R2 = 0.9988), with a detection limit (LOD) of 32.1 pmol L-1. Furthermore, this method was applied to the determination of OFL in chicken and pork samples, exhibiting good recovery (72.5-100%) and repeatability (RSD < 10.0%). These results confirm that this novel established method has good application potential for the detection of OFL in food samples.
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Affiliation(s)
- Yukun Huang
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China.
- Key Laboratory of Food Non-Thermal Processing, Engineering Technology Research Center of Food Non-Thermal Processing, Yibin Xihua University Research Institute, Yibin, 644004, China.
| | - Chong Wang
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Qiuyu Huo
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Yaning Song
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Gang Du
- Sichuan Institute for Food and Drug Control, Chengdu, 611731, China
| | - Lijun Wang
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Xiao Yang
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Xianggui Chen
- School of Food and Biological Engineering, Xihua University, Chengdu, 610039, China.
- Key Laboratory of Food Non-Thermal Processing, Engineering Technology Research Center of Food Non-Thermal Processing, Yibin Xihua University Research Institute, Yibin, 644004, China.
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17
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Emerging isothermal amplification technologies for microRNA biosensing: Applications to liquid biopsies. Mol Aspects Med 2020; 72:100832. [DOI: 10.1016/j.mam.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 02/07/2023]
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18
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Quantum dot nanoconjugates for immuno-detection of circulating cell-free miRNAs. Talanta 2020; 208:120486. [PMID: 31816728 DOI: 10.1016/j.talanta.2019.120486] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/16/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022]
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19
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Zhou H, Duan S, Huang J, He F. An ultrasensitive electrochemical biosensor for Pseudomonas aeruginosa assay based on a rolling circle amplification-assisted multipedal DNA walker. Chem Commun (Camb) 2020; 56:6273-6276. [DOI: 10.1039/d0cc01619e] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An ultrasensitive electrochemical biosensor was developed based on RCA and multipedal DNA walking strategy for the assay of 16S rRNA gene, and it has great application potential in food safety, environmental monitoring, and disease diagnosis.
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Affiliation(s)
- Huang Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Shaoyun Duan
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Ji Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
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