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Qin M, Li S, Ma P, Lin X, Khan IM, Ding N, Zhang Y, Wang Z. An ultrasensitive dual-mode aptasensor for patulin based on the upconversion particles and G-Quadruplex-hemin DNAzyme. Talanta 2024; 279:126653. [PMID: 39098239 DOI: 10.1016/j.talanta.2024.126653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/28/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
Patulin (PAT) is a mycotoxin-produced secondary metabolite that can contaminate foods, causing toxic effects on animal and human health. Therefore, for the first time, we have constructed a "turn-on" dual-mode aptamer sensor for PAT using oleic acid-coated upconversion nanomaterials (OA-UCNPs) and G-Quadruplex-hemin DNAzyme (G4-DNAzyme) as fluorescent and colorimetry probes. The sensor employs aptamers binding to PAT as recognition elements for specific molecule detection. Mxene-Au can be used as a biological inducer to assist OA-UCNPs in controlling fluorescence intensity. In addition, colorimetric signal amplification was performed using the trivalent G4-DNAzyme to increase detection sensitivity and reduce false positives. Under optimal conditions, the dual-mode aptasensor has a detection limit of 5.3 pg mL-1 in fluorescence and 2.4 pg mL-1 in colorimetric methods, respectively, with the wider linear range and limit of detection (LOD) of the colorimetric assay. The combination aptasensor can detect PAT with high sensitivity and high specificity and has broad application prospects in the field of food safety detection.
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Affiliation(s)
- Mingwei Qin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Shuo Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Pengfei Ma
- Textile Industrial Products Testing Center of Nanjing Customs District, Wuxi Customs District PR China, Wuxi, 214100, China
| | - Xianfeng Lin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Imran Mahmood Khan
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Ning Ding
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
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2
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Lu W, Lou S, Yang B, Guo Z, Tian Z. Light-activated oxidative capacity of isoquinoline alkaloids for universal, homogeneous, reliable, colorimetric assays with DNA aptamers. Talanta 2024; 279:126667. [PMID: 39111217 DOI: 10.1016/j.talanta.2024.126667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/01/2024]
Abstract
Aptamers are good affinity receptors for bio-assays, while colorimetric method is suitable for point-of-care sensing via direct visualization. But previously aptamers often need complex re-engineering for colorimetric measurement at the cost of affinity and performance. Here isoquinoline alkaloids are found to own unique light-activated oxidative capacity, which can be specifically triggered by unmodified aptamers. This feature is universal for two alkaloids to efficiently oxidize four chromogenic substrates with obvious color changes. Based on a dye-displacement process, we have developed a novel light-activated aptamer system for the colorimetric assay of estradiol. It shows a good sensitivity with a detection limit of 326 nM, and this homogeneous assay is reliable to avoid artifacts in previous heterogeneous scheme. Besides, it is proven to be a universal design to assay other two targets. Significantly, they do not employ any aptamers re-engineering but only simply use their parental aptamers. Therefore, this light-activated oxidative capacity of isoquinoline alkaloid can serve as an ideal tool for colorimetric assay of various targets based on aptamer's specific recognition.
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Affiliation(s)
- Weiyi Lu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 410005, PR China
| | - Shuyan Lou
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 410005, PR China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 410005, PR China.
| | - Zihua Guo
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 410005, PR China
| | - Zhen Tian
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 410005, PR China
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3
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Peng JM, Liu H, Ying ZM. Rapid one-pot isothermal amplification reassembled of fluorescent RNA aptamer for SARS-CoV-2 detection. Talanta 2024; 276:126264. [PMID: 38761661 DOI: 10.1016/j.talanta.2024.126264] [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: 01/17/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The outbreak of SARS-CoV-2 poses a serious threat to human life and health. A rapid nucleic acid tests can effectively curb the spread of the disease. With the advantages of fluorescent RNA aptamers, low background and high sensitivity. A variety of fluorescent RNA aptamer sensors have been developed for the detection of nucleic acid. Here, we report a hypersensitive detection platform in which SARS-CoV-2 initiates RTF-EXPAR to amplify trigger fragments. This activation leads to the reassembled of the SRB2 fluorescent RNA aptamer, restoring its secondary structure for SR-DN binding and turn-on fluorescence. The platform completes the assay in 30 min and all reactions occur in one tube. The detection limit is as low as 116 aM. Significantly, the platform's quantitative analyses were almost identical to qPCR results in simulated tests of positive samples. In conclusion, the platform is sensitive, accurate and provides a new protocol for point-of-care testing of viruses.
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Affiliation(s)
- Jia-Min Peng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Hao Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Zhan-Ming Ying
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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4
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Yuan S, Bremmer A, Yang X, Li J, Hu Q. Splittable systems in biomedical applications. Biomater Sci 2024; 12:4103-4116. [PMID: 39012216 DOI: 10.1039/d4bm00709c] [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: 07/17/2024]
Abstract
Splittable systems have emerged as a powerful approach for the precise spatiotemporal control of biological processes. This concept relies on splitting a functional molecule into inactive fragments, which can be reassembled under specific conditions or stimuli to regain activity. Several binding pairs and orthogonal split fragments are introduced by fusing with other modalities to develop more complex and robust designs. One of the pillars of these splittable systems is modularity, which involves decoupling targeting, activation, and effector functions. Challenges, such as off-target effects and overactivation, can be addressed through precise control. This review provides an overview of the design principles, strategies, and applications of splittable systems across diverse fields including immunotherapy, gene editing, prodrug activation, biosensing, and synthetic biology.
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Affiliation(s)
- Sichen Yuan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
- Wisconsin Center for NanoBioSystems, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
| | - Alexa Bremmer
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Xicheng Yang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Jiayue Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
- Wisconsin Center for NanoBioSystems, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
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5
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Dou S, Liu M, Wang H, Zhou S, Marrazza G, Guo Y, Sun X, Darwish IA. Synthesis of dual models multivalent activatable aptamers based on HCR and RCA for ultrasensitive detection of Salmonella typhimurium. Talanta 2024; 275:126101. [PMID: 38631268 DOI: 10.1016/j.talanta.2024.126101] [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: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
Aptamers have superior structural properties and have been widely used in bacterial detection methods. However, the problem of low affinity still exists in complex sample detection. In contrast, hybridization chain reaction (HCR)-based model I and rolling circle amplification (RCA)-based model II multivalent activatable aptamers (multi-Apts) can fulfill the need for low-cost, rapid, highly sensitive and high affinity detection of S. typhimurium. In our research, two models of multi-Apts were designed. First, a monovalent activatable aptamer (mono-Apt) was constructed by fluorescence resonance energy transfer (FRET) with an S. typhimurium aptamer and its complementary chain of BHQ1. Next, the DNA scaffold was obtained by HCR and RCA, and the multi-Apts were obtained by self-assembly of the mono-Apt with a DNA scaffold. In model I, when target was presented, the complementary chain BHQ1 was released due to the binding of multi-Apts to the target and was subsequently adsorbed by UIO66. Finally, a FRET-based fluorescence detection signal was obtained. In mode II, the multi-Apts bound to the target, and the complementary chain BHQ1 was released to become the trigger chain for the next round of amplification of HCR with a fluorescence detection signal. HCR and RCA based multi-Apts were able to detect S. typhimurium as low as 2 CFU mL-1 and 1 CFU mL-1 respectively. Multi-Apts amplification strategy provides a new method for early diagnosis of pathogenic microorganisms in foods.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Shuxian Zhou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Giovanna Marrazza
- "Ugo Schiff" Chemistry Department, University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
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Wei K, Ye Z, Dong W, Zhang L, Wang W, Li J, Eltzov E, Wang S, Mao X. Generating robust aptamers for food analysis by sequence-based configuration optimization. Talanta 2024; 275:126044. [PMID: 38626500 DOI: 10.1016/j.talanta.2024.126044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.
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Affiliation(s)
- Kaiyue Wei
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ziyang Ye
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenhui Dong
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ling Zhang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenjing Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Jiao Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Sai Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China.
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
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7
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Wang J, Chang Y, Liu M. Proximity-Dependent Activation of Split DNAzyme Kinase. Chembiochem 2024:e202400368. [PMID: 38954271 DOI: 10.1002/cbic.202400368] [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: 04/21/2024] [Revised: 06/15/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Binary (also known as split) nucleic acid enzymes have emerged as novel tools in biosensors. We report a new split strategy to split the DNAzyme kinase into two independent and non-functional fragments, denoted Dk1sub and Dk1enz. In the presence of the specific target, their free ends are brought sufficiently close to interact with each other without the formation of Watson-Crick base pairings between Dk1sub and Dk1enz, thus allowing the DNA phosphorylation reaction. We term this approach proximity-dependent activation of split DNAzyme kinase (ProxSDK). The utility of ProxSDK is demonstrated by engineering a biosensing system that is capable of measuring specific DNA-protein interactions. We envision that the approach described herein will find useful applications in biosensing, imaging, and clinical diagnosis.
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Affiliation(s)
- Jiayi Wang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT Laboratory, Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT Laboratory, Dalian University of Technology, Dalian, 116024, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT Laboratory, Dalian University of Technology, Dalian, 116024, China
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8
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Bai S, Yang Y, Sheng R, Qi Y, Jia Y, Wang X, Cui W, Zheng Y, Li H, Li J. Blood cellular membrane-coated Au/polydopamine nanoparticle-targeted NIR-II antibacterial therapy. J Colloid Interface Sci 2024; 665:855-862. [PMID: 38564949 DOI: 10.1016/j.jcis.2024.03.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Bacterial infections are the primary causes of infectious diseases in humans. In recent years, the abuse of antibiotics has led to the widespread enhancement of bacterial resistance. Concerns have been raised about the identification of a common treatment platform for bacterial infections. In this study, a composite nanomaterial was used for near-infrared II (NIR-II) photothermal antibacterial treatment. Red blood cell membrane was peeled and coated onto the surface of the Au/polydopamine nanoparticle-containing aptamer. The composite nanomaterials based on Au/polydopamine exhibit highest photothermal conversion capability. Moreover, these assembled nanoparticles can quickly enter the body's circular system with a specific capability to recognise bacteria. In vivo experiments demonstrated that the composites could kill bacteria from infected blood while significantly reducing the level of bacteria in various organs. Such assemblies offer a paradigm for the treatment of bacterial infections caused by the side effects of antibiotics.
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Affiliation(s)
- Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Rongtian Sheng
- School of Public Health, Jilin University, Changchun 130021, China
| | - Yanfei Qi
- School of Public Health, Jilin University, Changchun 130021, China
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaolong Wang
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Wei Cui
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yichen Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hong Li
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China.
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Wang X, Xu N, Zhu L, Yang H, Li C, Tian H, Xu W. Structural Antagonism-Aided Conformational Regulation Enables an Aptamer-Loop G-Quadruplex Modular Sensor of β-Lactoglobulin. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307995. [PMID: 38212277 DOI: 10.1002/smll.202307995] [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: 09/12/2023] [Revised: 12/13/2023] [Indexed: 01/13/2024]
Abstract
A simple, reliable method for identifying β-lactoglobulin (β-LG) in dairy products is needed to protect those with β-LG allergies. A common, practical strategy for target detection is designing simplified nucleic acid nanodevices by integrating functional components. This work presents a label-free modular β-LG aptasensor consisting of an aptamer-loop G-quadruplex (G4), the working conformation of which is regulated by conformational antagonism to ensure respective module functionality and the related signal transduction. The polymorphic conformations of the module-fused sequence are systematically characterized, and the cause is revealed as shifting antagonistic equilibrium. Combined with conformational folding dynamics, this helped regulate functional conformations by fine-tuning the sequences. Furthermore, the principle of specific β-LG detection by parallel G4 topology is examined as binding on the G4 aptamer loop by β-LG to reinforce the G4 topology and fluorescence. Finally, a label-free, assembly-free, succinct, and turn-on fluorescent aptasensor is established, achieving excellent sensitivity across five orders of magnitude, rapidly detecting β-LG within 22-min. This study provides a generalizable approach for the conformational regulation of module-fused G4 sequences and a reference model for creating simplified sensing devices for a variety of targets.
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Affiliation(s)
- Xinxin Wang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
- College of Life Science and Engineering, Handan University, Handan, 056005, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Ning Xu
- School of Life Science, Tsinghua University, Beijing, 100091, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - He Yang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Chen Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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10
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Wang Y, Duan H, Yalikun Y, Cheng S, Li M. Chronoamperometric interrogation of an electrochemical aptamer-based sensor with tetrahedral DNA nanostructure pendulums for continuous biomarker measurements. Anal Chim Acta 2024; 1305:342587. [PMID: 38677841 DOI: 10.1016/j.aca.2024.342587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/07/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Tetrahedral DNA nanostructure (TDN) is highly promising in developing electrochemical aptamer-based (E-AB) sensors for biomolecular detection, owing to its inherit programmability, spatial orientation and structural robustness. However, current interrogation strategies applied for TDN-based E-AB sensors, including enzyme-based amperometry, voltammetry, and electrochemical impedance spectroscopy, either require complicated probe design or suffer from limited applicability or selectivity. In this study, a TDN pendulum-empowered E-AB sensor interrogated by chronoamperometry for reagent-free and continuous monitoring of a blood clotting enzyme, thrombin, was developed. TDN pendulums with extended aptamer sequences at three vertices were immobilized on a gold electrode via a thiolated double-stranded DNA (dsDNA) at the fourth vertex, and their motion is modulated by the bonding of target thrombin to aptamers. We observed a significantly amplified signalling output on our sensor based on the TDN pendulum compared to E-AB sensors modified with linear pendulums. Moreover, our sensor achieved highly selective and rapidly responsive measurement of thrombin in both PBS and artificial urine, with a wide dynamic range from 1 pM to 10 nM. This study shows chronoamperometry-enabled continuous biomarker monitoring on a sub-second timescale with a drift-free baseline, demonstrating a novel approach to accurately detect molecular dynamics in real time.
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Affiliation(s)
- Yizhou Wang
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Haowei Duan
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yaxiaer Yalikun
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Shaokoon Cheng
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
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11
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Chovelon B, Ranganathan V, Srinivasan S, McConnell EM, Faure P, Fiore E, Ravelet C, Peyrin E, DeRosa M. Noncompetitive Determination of Small Analytes by Sandwich-Type Lateral Flow Assay Based on an Aptamer Kissing Complex. Anal Chem 2024; 96:6875-6880. [PMID: 38651263 DOI: 10.1021/acs.analchem.3c05472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Here, we present the proof-of-concept of a lateral flow assay (LFA) that is capable of detecting small-molecule targets in a noncompetitive manner by deploying a sandwich-type format based on the aptamer kissing complex (AKC) strategy. A fluorescently labeled hairpin aptamer served as the signaling agent, while a specific RNA hairpin grafted onto the strip served as the capture element. The hairpin aptamer switched from an unfolded to a folded form in the presence of the target, resulting in kissing interactions between the loops of the reporter and the capture agents. This design triggered a target-dependent fluorescent signal at the test line. The AKC-based LFA was developed for the detection of adenosine, achieving a detection limit in the micromolar range. The assay revealed the presence of the same analyte in urine. The method also proved effective with another small molecule (theophylline). We believe that the AKC-based LFA approach could overcome many of the shortcomings associated with conventional signal-off methods and competitive processes.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
- Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU-Biology and Pathology Institute, F-38041 Grenoble, France
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Velu Ranganathan
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Sathya Srinivasan
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Erin M McConnell
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
- Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU-Biology and Pathology Institute, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
| | - Maria DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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12
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Kim J, Nah Y, Kim S, Kim WJ. Transformation of nanoparticles via the transition of functional DNAs responsive to pH and vascular endothelial growth factor for photothermal anti-tumor therapy. Biomater Sci 2024; 12:1031-1041. [PMID: 38214329 DOI: 10.1039/d3bm01968c] [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: 01/13/2024]
Abstract
This study presents a novel approach for the development of DNA-functionalized gold nanoparticles (AuNPs) capable of responding to disease-specific factors and microenvironmental changes, resulting in an effective anti-tumor effect via photothermal therapy. The AuNPs are decorated with two types of DNAs, an i-motif duplex and a VEGF split aptamer, enabling recognition of changes in pH and VEGF, respectively. The formation of VEGF aptamers on the AuNPs induces their aggregation, further enhanced by VEGF ligands. The resulting changes in the optical properties of the AuNPs are detected by monitoring the absorbance. Upon irradiation with a near-infrared laser, the aggregated AuNPs generate heat due to their thermoplasmonic characteristic, leading to an anti-tumor effect. This study demonstrates the enhanced anti-tumor effect of DNA-functionalized AuNPs via photothermal therapy in both in vitro and in vivo tumor models. These findings suggest the potential utilization of such functional AuNPs for precise disease diagnosis and treatment by detecting disease-related factors in the microenvironment.
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Affiliation(s)
- Jinseong Kim
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Yunyoung Nah
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Seongmin Kim
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Won Jong Kim
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- OmniaMed Co., Ltd, Pohang, Republic of Korea
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13
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Smietana M, Müller S. Stimuli-Responsive Boronate Formation to Control Nucleic Acid-Based Functional Architectures. Chempluschem 2024; 89:e202300613. [PMID: 38033190 DOI: 10.1002/cplu.202300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/02/2023]
Abstract
Boronate esters, formed by the reaction of an oligonucleotide bearing a 5'-boronic acid moiety with the 3'-terminal cis-diol of another oligonucleotide, support the assembly of functional nucleic acid architectures. Reversible formation of boronate esters occurs in templated fashion and has been shown to restore the activity of split DNA and RNA enzymes as well as a split fluorescent light-up aptamer. Apart from their suitability for the design and application of split nucleic acid enzymes and aptamers in the field of biosensing, boronate esters may have played an important role in early life as surrogates of the natural phosphodiester bond. Their formation is reversible and thus fulfills an important requirement for biological self-assembly. Here we discuss the general concept of stimuli-dependent boronate formation and its application in biomolecules with implications for future research.
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Affiliation(s)
- Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM Pôle Chimie Balard, 34095, Montpellier, France
| | - Sabine Müller
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
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14
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Chamorro A, Rossetti M, Bagheri N, Porchetta A. Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:71-106. [PMID: 38273204 DOI: 10.1007/10_2023_235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.
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Affiliation(s)
| | - Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
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15
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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16
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Zhao Y, Patel N, Sun P, Faulds K, Graham D, Liu J. Light-up split aptamers: binding thermodynamics and kinetics for sensing. Analyst 2023; 148:5612-5618. [PMID: 37819248 DOI: 10.1039/d3an01368e] [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: 10/13/2023]
Abstract
Due to their programmable structures, many aptamers can be readily split into two halves while still retaining their target binding function. While split aptamers are prevalent in the biosensor field, fundamental studies of their binding are still lacking. In this work, we took advantage of the fluorescence enhancement property of a new aptamer named OTC5 that can bind to tetracycline antibiotics to compare various split aptamers with the full-length aptamer. The split aptamers were designed to have different stem lengths. Longer stem length aptamers showed similar dissociation constants (Kd) to the full-length aptamer, while a shorter stem construct showed an 85-fold increase in Kd. Temperature-dependent fluorescence measurements confirmed the lower thermostability of split aptamers. Isothermal titration calorimetry indicated that split aptamer binding can release more heat but have an even larger entropy loss. Finally, a colorimetric biosensor using gold nanoparticles was designed by pre-assembling two thiolated aptamer halves, which can then link gold nanoparticles to give a red-to-blue color change.
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Affiliation(s)
- Yichen Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
| | - Nikesh Patel
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
- Department of Pure and Applied Chemistry, Technology and Innovation Center, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
| | - Peihuan Sun
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
| | - Karen Faulds
- Department of Pure and Applied Chemistry, Technology and Innovation Center, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
| | - Duncan Graham
- Department of Pure and Applied Chemistry, Technology and Innovation Center, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario, N2L 3G1, Canada.
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17
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Cheng W, Yao Y, Li D, Duan C, Wang Z, Xiang Y. Asymmetrically split DNAzyme-based colorimetric and electrochemical dual-modal biosensor for detection of breast cancer exosomal surface proteins. Biosens Bioelectron 2023; 238:115552. [PMID: 37542978 DOI: 10.1016/j.bios.2023.115552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023]
Abstract
Exosomal surface proteins are potentially useful for breast cancer diagnosis and awareness of risk. However, some detection techniques involving complex operations and expensive instrumentation are limited to advance to clinical applications. To solve this problem, we develop a dual-modal sensor combining naked-eye detection and electrochemical assay of exosomal surface proteins from breast cancer. Most of existing sensors rely on aptamers recognizing exosomes and generating amplified signals at the same time, which require well-designed aptamer probes to avoid difficulties in identifying exosomes. In our work, aptamers not bound by the exosomes can serve as complete templates to induce formation of G quadruplexes. The peroxidase activity of the G-quadruplex/hemin DNAzyme catalyze substrates can generate both color and electrochemical signals. The developed dual-modal sensor offers a remarkable capability to differentiate nonmetastatic, metastatic breast cancer patients, and healthy individuals through the analysis of exosomal surface proteins. The sensor's distinctive features, including its universality, simplicity, and cost-effectiveness, position it as a promising diagnostic tool in breast cancer research and clinical practice.
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Affiliation(s)
- Wenting Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Yanheng Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Zhongyun Wang
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China.
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18
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Lauzon D, Vallée-Bélisle A. Programing Chemical Communication: Allostery vs Multivalent Mechanism. J Am Chem Soc 2023; 145:18846-18854. [PMID: 37581934 DOI: 10.1021/jacs.3c04045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The emergence of life has relied on chemical communication and the ability to integrate multiple chemical inputs into a specific output. Two mechanisms are typically employed by nature to do so: allostery and multivalent activation. Although a better understanding of allostery has recently provided a variety of strategies to optimize the binding affinity, sensitivity, and specificity of molecular switches, mechanisms relying on multivalent activation remain poorly understood. As a proof of concept to compare the thermodynamic basis and design principles of both mechanisms, we have engineered a highly programmable DNA-based switch that can be triggered by either a multivalent or an allosteric DNA activator. By precisely designing the binding interface of the multivalent activator, we show that the affinity, dynamic range, and activated half-life of the molecular switch can be programed with even more versatility than when using an allosteric activator. The simplicity by which the activation properties of molecular switches can be rationally tuned using multivalent assembly suggests that it may find many applications in biosensing, drug delivery, synthetic biology, and molecular computation fields, where precise control over the transduction of binding events into a specific output is key.
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Affiliation(s)
- Dominic Lauzon
- Département de Chimie, Laboratoire de Biosenseurs et Nanomachines, Université de Montréal, Montréal QC H2V 0B3, Canada
| | - Alexis Vallée-Bélisle
- Département de Chimie, Laboratoire de Biosenseurs et Nanomachines, Université de Montréal, Montréal QC H2V 0B3, Canada
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19
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Fan Y, Li J, Amin K, Yu H, Yang H, Guo Z, Liu J. Advances in aptamers, and application of mycotoxins detection: A review. Food Res Int 2023; 170:113022. [PMID: 37316026 DOI: 10.1016/j.foodres.2023.113022] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Mycotoxin contamination in food products can easily cause serious health hazards and economic losses to human beings. How to accurately detect and effectively control mycotoxin contamination has become a global concern. Mycotoxins conventional detection techniques e.g; ELISA, HPLC, have limitations like, low sensitivity, high cost and time-consuming. Aptamer-based biosensing technology has the advantages of high sensitivity, high specificity, wide linear range, high feasibility, and non-destructiveness, which overcomes the shortcomings of conventional analysis techniques. This review summarizes the sequences of mycotoxin aptamers that have been reported so far. Based on the application of four classic POST-SELEX strategies, it also discusses the bioinformatics-assisted POST-SELEX technology in obtaining optimal aptamers. Furthermore, trends in the study of aptamer sequences and their binding mechanisms to targets is also discussed. The latest examples of aptasensor detection of mycotoxins are classified and summarized in detail. Newly developed dual-signal detection, dual-channel detection, multi-target detection and some types of single-signal detection combined with unique strategies or novel materials in recent years are focused. Finally, the challenges and prospects of aptamer sensors in the detection of mycotoxins are discussed. The development of aptamer biosensing technology provides a new approach with multiple advantages for on-site detection of mycotoxins. Although aptamer biosensing shows great development potential, still some challenges and difficulties are there in practical applications. Future research need high focus on the practical applications of aptasensors and the development of convenient and highly automated aptamers. This may lead to the transition of aptamer biosensing technology from laboratory to commercialization.
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Affiliation(s)
- Yiting Fan
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; Division of Soybean Processing, Soybean Research & Development Center, Chinese Agricultural Research System, Changchun 130118, China.
| | - Jiaxin Li
- Division of Soybean Processing, Soybean Research & Development Center, Chinese Agricultural Research System, Changchun 130118, China; Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Sciences, 32004 Ourense, Spain.
| | - Khalid Amin
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; Division of Soybean Processing, Soybean Research & Development Center, Chinese Agricultural Research System, Changchun 130118, China.
| | - Hansong Yu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; Division of Soybean Processing, Soybean Research & Development Center, Chinese Agricultural Research System, Changchun 130118, China.
| | - Huanhuan Yang
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing 163000, China; College of Life Science Chang Chun Normal University, Changchun 130032, China.
| | - Zhijun Guo
- College of Agriculture, Yanbian University, Yanji 133002, China.
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, Jilin 130118, China.
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20
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Ma J, Guan Y, Xing F, Wang Y, Li X, Yu Q, Yu X. Smartphone-based chemiluminescence detection of aflatoxin B 1 via labelled and label-free dual sensing systems. Food Chem 2023; 413:135654. [PMID: 36796268 DOI: 10.1016/j.foodchem.2023.135654] [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: 10/12/2022] [Revised: 01/24/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
To develop a sensing platform for onsite determination of AFB1 in foodstuffs, we developed smartphone-based chemiluminescence detection of AFB1 via labelled and label-free dual modes. The labelled mode was characteristic of double streptavidin-biotin mediated signal amplification, obtaining limit of detection (LOD) of 0.04 ng/mL in the linear range of 1-100 ng/mL. To reduce the complexity in the labelled system, a label-free mode based on both split aptamer and split DNAzyme was fabricated. A satisfactory LOD of 0.33 ng/mL was generated in the linear range of 1-100 ng/mL. Both labelled and label-free sensing systems achieved outstanding recovery rate in AFB1-spiked maize and peanut kernel samples. Finally, two systems were successfully integrated into smartphone-based portable device based on custom-made components and android application, achieving comparable AFB1 detection ability to a commercial microplate reader. Our systems hold huge potential for AFB1 onsite detection in food supply chain.
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Affiliation(s)
- Junning Ma
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yue Guan
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fuguo Xing
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Wang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xu Li
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiang Yu
- Qingdao Tianxiang Foods Group Co., Ltd, Qingdao 266737, China
| | - Xiaohua Yu
- Qingdao Tianxiang Foods Group Co., Ltd, Qingdao 266737, China
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21
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Lauzon D, Vallée-Bélisle A. Functional advantages of building nanosystems using multiple molecular components. Nat Chem 2023; 15:458-467. [PMID: 36759713 DOI: 10.1038/s41557-022-01127-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/15/2022] [Indexed: 02/11/2023]
Abstract
Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.
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Affiliation(s)
- D Lauzon
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - A Vallée-Bélisle
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada.
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22
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Zhang X, Du Y, Liu X, Feng R, Jia Y, Ren X, Zhang N, Liu L, Wei Q, Ju H. Enhanced anode electrochemiluminescence in split aptamer sensor for kanamycin trace monitoring. Food Chem 2023; 420:136083. [PMID: 37059023 DOI: 10.1016/j.foodchem.2023.136083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023]
Abstract
Covalently modifying electrochemiluminescence (ECL) luminophores to alter their energy levels or generate energy/electron transfer processes for improved performance is hindered by the complex design and fabrication processes. In this study, non-covalent bond self-assembly was employed to enhance the ECL property of gold nanoclusters with tryptophan (Try) and mercaptopropionic acid (MPA) as ligands (Try-MPA-gold nanoclusters). Specifically, through the molecular recognition of Try by cucurbit[7]uril, some non-radiative transition channels of the charge carriers on the surface of the Try-MPA-gold nanoclusters were restricted, resulting in a significant enhancement of the ECL intensity of the nanoclusters. Furthermore, rigid macrocyclic molecules acted on the surface of the nanoclusters through self-assembly, forming a passive barrier that improved the physical stability of the nanoclusters in the water-phase and indirectly improved their luminescent stability. As an application, cucurbit[7]uril-treated Try-MPA-gold nanoclusters (cucurbit[7]uril@Try-MPA-gold nanoclusters) were used as signal probes, and Zn-doped SnO2 nanoflowers (Zn-SnO2 NFs) with high electron mobility were used as electrode modification material to establish an ECL sensor for kanamycin (KANA) detection, utilizing split aptamers as capture probes. The advanced split aptamer sensor demonstrated excellent sensitivity analysis for KANA in complex food substrates with a recovery rate of 96.2 to 106.0%.
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Affiliation(s)
- Xiaoyue Zhang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yu Du
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Xuejing Liu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Rui Feng
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Yue Jia
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Xiang Ren
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Nuo Zhang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Lei Liu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China; Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Huangxian Ju
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China; State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210023, China
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23
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Hu Y, Li C, Hu M, Zhang Z, Fu R, Tang X, Wu T. Allosteric Nucleic Acid Enzyme: A Versatile Stimuli-Responsive Tool for Molecular Computing and Biosensing Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2300207. [PMID: 36978231 DOI: 10.1002/smll.202300207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Allostery is a naturally occurring mechanism in which effector binding induces the modulation and fine control of a related biomolecule function. Deoxyribozyme (DNAzyme) with catalytic activity and substrate recognition ability is ideal to be regulated by allosteric strategies. However, the current regulations frequently confront various obstacles, such as severe activity decay, signal leakage, and limited effectors. In this work, a rational regulation strategy for developing versatile effectors-responsive allosteric nucleic acid enzyme (ANAzyme) by introducing an allosteric domain in response to diverse effectors is established. The enzyme-like activity of this re-engineered ANAzyme can be modulated in a more predictable and fine way compared with the previous DNAzyme regulation strategies. Based on the allosteric strategy, the construction of allosterically coregulatory nanodevices and a series of basic logic gates and logic circuits are achieved, demonstrating that the proposed ANAzyme-regulated strategy showed great potential in molecular computing. Given these facts, the rational design of ANAzyme with the allosteric domain presented here can expand the available toolbox to develop a variety of stimuli-responsive allosteric DNA materials, including molecular machines, computing systems, biosensing platforms, and gene-silencing tools.
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Affiliation(s)
- Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Changjiang Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Ruolan Fu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
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24
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Zhao Y, Gao B, Chen Y, Liu J. An aptamer array for discriminating tetracycline antibiotics based on binding-enhanced intrinsic fluorescence. Analyst 2023; 148:1507-1513. [PMID: 36891736 DOI: 10.1039/d3an00154g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Tetracyclines are a class of antibiotics with a similar four-ringed structure. Due to this structural similarity, they are not easily differentiated from each other. We recently selected aptamers using oxytetracycline as a target and focused on an aptamer named OTC5, which has similar affinities for oxytetracycline (OTC), tetracycline (TC), and doxycycline (DOX). Tetracyclines exhibit an intrinsic fluorescence that is enhanced upon aptamer binding, allowing convenient binding assays and label-free detection. In this study, we analyzed the top 100 sequences from the previous selection library. Three other sequences were found to differentiate between different tetracyclines (OTC, DOX, and TC) by the selective enhancement of their intrinsic fluorescence. Among them, the OTC43 aptamer was more selective for OTC with a limit of detection (LOD) of 0.7 nM OTC, OTC22 was more selective for DOX (LOD 0.4 nM), and OTC2 was more selective for TC (0.3 nM). Using these three aptamers to form a sensor array, principal component analysis was able to discriminate between the three tetracyclines from each other and from the other molecules. This group of aptamers could be useful as probes for the detection of tetracycline antibiotics.
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Affiliation(s)
- Yichen Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Biwen Gao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Yijing Chen
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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25
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Parolo C, Idili A, Heikenfeld J, Plaxco KW. Conformational-switch biosensors as novel tools to support continuous, real-time molecular monitoring in lab-on-a-chip devices. LAB ON A CHIP 2023; 23:1339-1348. [PMID: 36655710 PMCID: PMC10799767 DOI: 10.1039/d2lc00716a] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent years have seen continued expansion of the functionality of lab on a chip (LOC) devices. Indeed LOCs now provide scientists and developers with useful and versatile platforms across a myriad of chemical and biological applications. The field still fails, however, to integrate an often important element of bench-top analytics: real-time molecular measurements that can be used to "guide" a chemical response. Here we describe the analytical techniques that could provide LOCs with such real-time molecular monitoring capabilities. It appears to us that, among the approaches that are general (i.e., that are independent of the reactive or optical properties of their targets), sensing strategies relying on binding-induced conformational change of bioreceptors are most likely to succeed in such applications.
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Affiliation(s)
- Claudio Parolo
- Barcelona Institute for Global Health, Hospital Clínic Universitat de Barcelona, 08036, Barcelona, Spain
| | - Andrea Idili
- Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy
| | - Jason Heikenfeld
- Novel Devices Laboratory, University of Cincinnati, Cincinnati, Ohio, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA.
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, USA
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26
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Mintz Hemed N, Melosh NA. An integrated perspective for the diagnosis and therapy of neurodevelopmental disorders - From an engineering point of view. Adv Drug Deliv Rev 2023; 194:114723. [PMID: 36746077 DOI: 10.1016/j.addr.2023.114723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/14/2022] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Neurodevelopmental disorders (NDDs) are complex conditions with largely unknown pathophysiology. While many NDD symptoms are familiar, the cause of these disorders remains unclear and may involve a combination of genetic, biological, psychosocial, and environmental risk factors. Current diagnosis relies heavily on behaviorally defined criteria, which may be biased by the clinical team's professional and cultural expectations, thus a push for new biological-based biomarkers for NDDs diagnosis is underway. Emerging new research technologies offer an unprecedented view into the electrical, chemical, and physiological activity in the brain and with further development in humans may provide clinically relevant diagnoses. These could also be extended to new treatment options, which can start to address the underlying physiological issues. When combined with current speech, language, occupational therapy, and pharmacological treatment these could greatly improve patient outcomes. The current review will discuss the latest technologies that are being used or may be used for NDDs diagnosis and treatment. The aim is to provide an inspiring and forward-looking view for future research in the field.
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Affiliation(s)
- Nofar Mintz Hemed
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
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27
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Irkham I, Ibrahim AU, Pwavodi PC, Al-Turjman F, Hartati YW. Smart Graphene-Based Electrochemical Nanobiosensor for Clinical Diagnosis: Review. SENSORS (BASEL, SWITZERLAND) 2023; 23:2240. [PMID: 36850837 PMCID: PMC9964617 DOI: 10.3390/s23042240] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The technological improvement in the field of physics, chemistry, electronics, nanotechnology, biology, and molecular biology has contributed to the development of various electrochemical biosensors with a broad range of applications in healthcare settings, food control and monitoring, and environmental monitoring. In the past, conventional biosensors that have employed bioreceptors, such as enzymes, antibodies, Nucleic Acid (NA), etc., and used different transduction methods such as optical, thermal, electrochemical, electrical and magnetic detection, have been developed. Yet, with all the progresses made so far, these biosensors are clouded with many challenges, such as interference with undesirable compound, low sensitivity, specificity, selectivity, and longer processing time. In order to address these challenges, there is high need for developing novel, fast, highly sensitive biosensors with high accuracy and specificity. Scientists explore these gaps by incorporating nanoparticles (NPs) and nanocomposites (NCs) to enhance the desired properties. Graphene nanostructures have emerged as one of the ideal materials for biosensing technology due to their excellent dispersity, ease of functionalization, physiochemical properties, optical properties, good electrical conductivity, etc. The Integration of the Internet of Medical Things (IoMT) in the development of biosensors has the potential to improve diagnosis and treatment of diseases through early diagnosis and on time monitoring. The outcome of this comprehensive review will be useful to understand the significant role of graphene-based electrochemical biosensor integrated with Artificial Intelligence AI and IoMT for clinical diagnostics. The review is further extended to cover open research issues and future aspects of biosensing technology for diagnosis and management of clinical diseases and performance evaluation based on Linear Range (LR) and Limit of Detection (LOD) within the ranges of Micromolar µM (10-6), Nanomolar nM (10-9), Picomolar pM (10-12), femtomolar fM (10-15), and attomolar aM (10-18).
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Affiliation(s)
- Irkham Irkham
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Bandung 40173, Indonesia
| | - Abdullahi Umar Ibrahim
- Department of Biomedical Engineering, Near East University, Mersin 10, Nicosia 99010, Turkey
| | - Pwadubashiyi Coston Pwavodi
- Department of Bioengineering/Biomedical Engineering, Faculty of Engineering, Cyprus International University, Haspolat, North Cyprus via Mersin 10, Nicosia 99010, Turkey
| | - Fadi Al-Turjman
- Research Center for AI and IoT, Faculty of Engineering, University of Kyrenia, Mersin 10, Kyrenia 99320, Turkey
- Artificial Intelligence Engineering Department, AI and Robotics Institute, Near East University, Mersin 10, Nicosia 99010, Turkey
| | - Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Bandung 40173, Indonesia
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28
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Shi L, Ma X, Xie H, Qin Y, Huang Y, Zhang Y, Sun L, Yang J, Li G. Engineering m 6A demethylation-activated DNAzyme for visually and sensitively sensing fat mass and obesity-associated protein. Biosens Bioelectron 2023; 222:115007. [PMID: 36527832 DOI: 10.1016/j.bios.2022.115007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Fat mass and obesity-associated protein (FTO) regulating the N6-methyladenine (m6A, the most pervasive epigenetic modification) levels within the nucleus has been identified as a potential biomarker for cancer diagnosis and prognosis. However, current methods for FTO detection are complicated or/and not sensitive enough for practical application. Herein, we propose a colorimetric biosensor for detecting FTO based on a delicate design of m6A demethylation-activated DNAzyme. Specifically, an m6A-blocked DNAzyme is constructed as a switch of the biosensor that can be turned on by target FTO. The decreased thermal stability resulting from substrate cleavage leads to a DNAzyme recycling to produce multiple primers. Then the rolling circle amplification (RCA) reactions can be initiated to generate G-quadruplex-DNAzymes catalyzing 2,2-azino-bis-(3-ethylben-zthiazoline-6-sulfonic acid (ABTS) oxidation which can be readily observed by the naked eye. Quantitative detection can also be achieved with a limit of detection (LOD) down to 69.9 fM, exhibiting higher sensitivity than previous reports. Therefore, this biosensor opens a simple and sensitive way to achieve visual assay of FTO via triple signal amplification. In addition, our biosensor has been successfully applied to FTO detection in clinical samples, which shows great potential in clinical molecular diagnostics.
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Affiliation(s)
- Liu Shi
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Xuemei Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Haojie Xie
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Yujia Qin
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Yue Huang
- Department of Food Science and Engineering, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, PR China
| | - Yuanyuan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Jie Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China; State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China.
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29
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Gambill L, Staubus A, Mo KW, Ameruoso A, Chappell J. A split ribozyme that links detection of a native RNA to orthogonal protein outputs. Nat Commun 2023; 14:543. [PMID: 36725852 PMCID: PMC9892565 DOI: 10.1038/s41467-023-36073-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023] Open
Abstract
Individual RNA remains a challenging signal to synthetically transduce into different types of cellular information. Here, we describe Ribozyme-ENabled Detection of RNA (RENDR), a plug-and-play strategy that uses cellular transcripts to template the assembly of split ribozymes, triggering splicing reactions that generate orthogonal protein outputs. To identify split ribozymes that require templating for splicing, we use laboratory evolution to evaluate the activities of different split variants of the Tetrahymena thermophila ribozyme. The best design delivers a 93-fold dynamic range of splicing with RENDR controlling fluorescent protein production in response to an RNA input. We further resolve a thermodynamic model to guide RENDR design, show how input signals can be transduced into diverse outputs, demonstrate portability across different bacteria, and use RENDR to detect antibiotic-resistant bacteria. This work shows how transcriptional signals can be monitored in situ and converted into different types of biochemical information using RNA synthetic biology.
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Affiliation(s)
- Lauren Gambill
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77005, USA
| | - August Staubus
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| | - Kim Wai Mo
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| | - Andrea Ameruoso
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| | - James Chappell
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77005, USA. .,Department of Biosciences, Rice University, Houston, TX, 77005, USA. .,Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
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30
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Chen J, Xu J, Xiang J, Wan T, Deng H, Li D. A multivalent activatable aptamer probe with ultralow background signal and high sensitivity for diagnosis of lung adenocarcinoma. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Qi S, Dong X, Sun Y, Zhang Y, Duan N, Wang Z. Split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive detection of 17β-estradiol. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129590. [PMID: 35872451 DOI: 10.1016/j.jhazmat.2022.129590] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
DNA walker machines, as one of the dynamic DNA nanodevices, have attracted extensive interest in the field of analysis due to their inherent superiority. Herein, we reported a split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive, specific, and high-signal-background ratio determination of 17β-estradiol (E2) in food samples. Two split probes (STWS-a and STWS-b) were rationally designed that can undergo structural reassembled to serve as walking strands (STWS) under the induction of the target. Meanwhile, an intact E6-DNAzyme region was formed and activated at the tail of STWS. The activated E6-DNAzyme then continuously drives the 3D-DNA walker for signal amplification and specific detection of E2. Under optimal conditions, the proposed DNA walker-based biosensor exhibited excellent linearity in the range of 1 pM to 50 nM with a low limit of detection (LOD) of 0.28 pM, and good precision (2.7%) for 11 replicate determinations of 1 nM of E2. Furthermore, the developed DNA walker-based biosensor achieved excellent sensitive analysis of E2 in the complex food matrix with recoveries of 95.6-106.5%. This newly proposed split aptamer-based strategy has the advantages of ultrasensitive, high signal-to-background ratio, and high stability. Noteworthy, the successful operation of the DNA walker initiated by the split aptamer expands the principles of DNA walker design and provides a universal signal amplification platform for trace analysis.
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Affiliation(s)
- Shuo Qi
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoze Dong
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuhan Sun
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China.
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32
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Zhao Y, Ong S, Chen Y, Jimmy Huang PJ, Liu J. Label-free and Dye-free Fluorescent Sensing of Tetracyclines Using a Capture-Selected DNA Aptamer. Anal Chem 2022; 94:10175-10182. [PMID: 35777074 DOI: 10.1021/acs.analchem.2c01561] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tetracyclines are a group of important antibiotics with a common four-ring scaffold. While most tetracyclines are currently used only in animals, their leaching into the environment and residues in food have caused health concerns. Aptamers are an attractive way to detect tetracyclines, and all previously reported aptamers for tetracyclines were obtained by immobilizing target molecules. In this work, we selected a few DNA aptamers by immobilizing the DNA library using oxytetracycline as the target. We obtained new aptamers with no overlapping sequences compared to the previously reported ones, and a representative sequence named OTC5 had a dissociation constant of 147 nM measured by isothermal titration calorimetry. Similar binding affinities were also observed with tetracycline and doxycycline. Because tetracyclines are fluorescent and their fluorescence intensity was enhanced by binding to the aptamers, a label-free and dye-free fluorescent biosensor was developed with a detection limit of 25 nM oxytetracycline. The sensor was able to detect targets in milk after extraction. Fluorescence polarization measurement showed that this aptamer is insensitive to sodium concentration but requires magnesium. Finally, a strand-displacement biosensor was designed, and it has a detection limit of 1.2 μM oxytetracycline.
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Affiliation(s)
- Yichen Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Steven Ong
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Yijing Chen
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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33
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Wang L, Hast K, Aggarwal T, Baci M, Hong J, Izgu EC. MicroRNA detection in biologically relevant media using a split aptamer platform. Bioorg Med Chem 2022; 69:116909. [PMID: 35779513 DOI: 10.1016/j.bmc.2022.116909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
Abstract
MicroRNA (miRNA)-based intercellular communication has been implicated in many functional and dysfunctional biological processes. This has raised interest in the potential use of miRNAs as biomarkers for diagnosis and prognosis. Though the list of clinically significant miRNA biomarkers is expanding, it remains challenging to adapt current chemical tools to investigate miRNAs in complex environments native to cells and tissues. We describe here a methodology for rapidly developing aptamer-based fluorescent biosensors that can specifically detect miRNAs in biologically relevant media (10-30% v/v), including medium collected from cultured HeLa cells, human serum, and human plasma. This methodology involves the semi-rational design of the hybridization between DNA oligonucleotides and the miRNA target to build a pool of potential aptamers, and the screening of this pool for high signal-to-background ratio and target specificity. The DNA oligonucleotides are readily available and require no chemical modification, rendering these chemical tools highly adaptable to any novel and niche miRNA target. Following this approach, we developed sensors that detect distinct oncogenic miRNA targets (miR-19b, miR-21, and miR-92a) at concentrations as low as 5 nM without amplification and are selective against single-nucleotide mutants. This work provides a systematic approach toward the development of miRNA biosensors that are easily accessible and can perform in biological environments with minimal sample handling.
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Affiliation(s)
- Liming Wang
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Kern Hast
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Melih Baci
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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34
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Abstract
The cytoskeleton is an essential component of a cell. It controls the cell shape, establishes the internal organization, and performs vital biological functions. Building synthetic cytoskeletons that mimic key features of their natural counterparts delineates a crucial step towards synthetic cells assembled from the bottom up. To this end, DNA nanotechnology represents one of the most promising routes, given the inherent sequence specificity, addressability and programmability of DNA. Here we demonstrate functional DNA-based cytoskeletons operating in microfluidic cell-sized compartments. The synthetic cytoskeletons consist of DNA tiles self-assembled into filament networks. These filaments can be rationally designed and controlled to imitate features of natural cytoskeletons, including reversible assembly and ATP-triggered polymerization, and we also explore their potential for guided vesicle transport in cell-sized confinement. Also, they possess engineerable characteristics, including assembly and disassembly powered by DNA hybridization or aptamer–target interactions and autonomous transport of gold nanoparticles. This work underpins DNA nanotechnology as a key player in building synthetic cells. ![]()
Cytoskeletons are essential components of cells that perform a variety of tasks, and artificial cytoskeletons that perform these functions are required for the bottom-up assembly of synthetic cells. Now, a multi-functional cytoskeleton mimic has been engineered from DNA, consisting of confined DNA filaments that are capable of reversible self-assembly and transport of gold nanoparticles and vesicular cargo.
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35
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Technique Evolutions for Microorganism Detection in Complex Samples: A Review. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid detection of microorganisms is a major challenge in the medical and industrial sectors. In a pharmaceutical laboratory, contamination of medical products may lead to severe health risks for patients, such as sepsis. In the specific case of advanced therapy medicinal products, contamination must be detected as early as possible to avoid late production stop and unnecessary costs. Unfortunately, the conventional methods used to detect microorganisms are based on time-consuming and labor-intensive approaches. Therefore, it is important to find new tools to detect microorganisms in a shorter time frame. This review sums up the current methods and represents the evolution in techniques for microorganism detection. First, there is a focus on promising ligands, such as aptamers and antimicrobial peptides, cheaper to produce and with a broader spectrum of detection. Then, we describe methods achieving low limits of detection, thanks to Raman spectroscopy or precise handling of samples through microfluids devices. The last part is dedicated to techniques in real-time, such as surface plasmon resonance, preventing the risk of contamination. Detection of pathogens in complex biological fluids remains a scientific challenge, and this review points toward important areas for future research.
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Liu D, Tang J, Xu H, Yuan K, Aryee AA, Zhang C, Meng H, Qu L, Li Z. Split-aptamer mediated regenerable temperature-sensitive electrochemical biosensor for the detection of tumour exosomes. Anal Chim Acta 2022; 1219:340027. [DOI: 10.1016/j.aca.2022.340027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/11/2022] [Accepted: 05/29/2022] [Indexed: 02/08/2023]
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Debiais M, Vasseur JJ, Smietana M. Applications of the Reversible Boronic Acids/Boronate Switch to Nucleic Acids. CHEM REC 2022; 22:e202200085. [PMID: 35641415 DOI: 10.1002/tcr.202200085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Indexed: 11/09/2022]
Abstract
Over the last decades, boron and nucleic acids chemistries have gained a lot of attention for biological, medicinal and analytical applications. Our laboratory has a long-standing interest in both chemistries and owing to the ability of boronic acids to react with cis-diol function in aqueous media we developed over the years a variety of applications ranging from molecular recognition and sensing to the development of reversible dynamic systems in which the natural phosphodiester linkage was replaced by a boronate. In this account, we summarize research results from our group from our preliminary studies on molecular recognition of ribonucleosides to the dynamic assembly of functional DNAzymes. In particular, the various parameters influencing the dynamic nature of these reversible covalent bonds able to respond to external stimuli are discussed. Finally, current challenges and opportunities for boron-based nucleic acids are also addressed.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
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Zhang LM, Gao QX, Xie BP, Chen J, Duan WJ. Highly accelerated isothermal nucleic acid amplifications by butanol dehydration: simple, more efficient, and ultrasensitive. Chem Commun (Camb) 2022; 58:5793-5796. [PMID: 35466974 DOI: 10.1039/d2cc01589g] [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
Enzyme-free isothermal amplification reactions for nucleic acid analysis usually take several hours to obtain sufficient detection sensitivity, which limits their practical applications. Herein, we report a butanol dehydration-based method to greatly improve both the efficiency and the sensitivity of nucleic acid detections by three types of enzyme-free isothermal amplification reactions. The reaction time has been shortened from 3 h to 5-20 min with higher sensitivities. Especially in the DNAzyme-based amplification, the detection limit can be lowered over 16 000-fold to 3 × 10-17 mol L-1 in 2 h compared to the normal 3 h-reaction. We demonstrate that the high amplification efficiencies are attributed to the greatly accelerated reaction rates in the extremely concentrated reaction solutions caused by the butanol dehydration. This approach enhances the potential of applications of isothermal amplification reactions in clinical rapid tests, nanostructure synthesis, etc. and is promising to expand to other types of chemical reactions.
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Affiliation(s)
- Li-Min Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Qing-Xin Gao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Bao-Ping Xie
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Jun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Wen-Jun Duan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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Tang T, Liu Y, Jiang Y. Recent Progress on Highly Selective and Sensitive Electrochemical Aptamer-based Sensors. Chem Res Chin Univ 2022; 38:866-878. [PMID: 35530120 PMCID: PMC9069955 DOI: 10.1007/s40242-022-2084-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/10/2022] [Indexed: 12/31/2022]
Abstract
Highly selective, sensitive, and stable biosensors are essential for the molecular level understanding of many physiological activities and diseases. Electrochemical aptamer-based (E-AB) sensor is an appealing platform for measurement in biological system, attributing to the combined advantages of high selectivity of the aptamer and high sensitivity of electrochemical analysis. This review summarizes the latest development of E-AB sensors, focuses on the modification strategies used in the fabrication of sensors and the sensing strategies for analytes of different sizes in biological system, and then looks forward to the challenges and prospects of the future development of electrochemical aptamer-based sensors.
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Affiliation(s)
- Tianwei Tang
- College of Chemistry, Beijing Normal University, Beijing, 100875 P. R. China
| | - Yinghuan Liu
- College of Chemistry, Beijing Normal University, Beijing, 100875 P. R. China
| | - Ying Jiang
- College of Chemistry, Beijing Normal University, Beijing, 100875 P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190 P. R. China
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40
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Ye H, Yang Z, Khan IM, Niazi S, Guo Y, Wang Z, Yang H. Split aptamer acquisition mechanisms and current application in antibiotics detection: a short review. Crit Rev Food Sci Nutr 2022; 63:9098-9110. [PMID: 35507474 DOI: 10.1080/10408398.2022.2064810] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Antibiotic contamination is becoming a prominent global issue. Therefore, sensitive, specific and simple technology is desirable the demand for antibiotics detection. Biosensors based on split aptamer has gradually attracted extensive attention for antibiotic detection due to its higher sensitivity, lower cost, false positive/negative avoidance and flexibility in sensor design. Although many of the reported split aptamers are antibiotics aptamers, the acquisition and mechanism of splitting is still unknow. In this review, six reported split aptamers in antibiotics are outlined, including Enrofloxacin, Kanamycin, Tetracycline, Tobramycin, Neomycin, Streptomycin, which have contributed to promote interest, awareness and thoughts into this emerging research field. The study introduced the pros and cons of split aptamers, summarized the assembly principle of split aptamer and discussed the intermolecular binding of antibiotic-aptamer complexes. In addition, the recent application of split aptamers in antibiotic detection are introduced. Split aptamers have a promising future in the design and development of biosensors for antibiotic detection in food and other field. The development of the antibiotic split aptamer meets many challenges including mechanism discovery, stability improvement and new biosensor development. It is believed that split aptamer could be a powerful molecular probe and plays an important role in aptamer biosensor.
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Affiliation(s)
- Hua Ye
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhixin Yang
- Department of Food Science & Technology, National University of Singapore, Singapore, Singapore
| | | | - Sobia Niazi
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yuanxin Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhouping Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hongshun Yang
- Department of Food Science & Technology, National University of Singapore, Singapore, Singapore
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41
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Yang L, Ye X, Li X, Huang Z, Chen F, Yang W, Wang Z. Colorimetric aptasensor for sensitive detection of quinclorac based on exonuclease III-assisted cyclic release of phosphorodiamidate morpholino oligomer mimic enzyme strategy. Anal Chim Acta 2022; 1207:339815. [DOI: 10.1016/j.aca.2022.339815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/01/2022]
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42
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Sun Y, Lv Y, Qi S, Zhang Y, Wang Z. Sensitive colorimetric aptasensor based on stimuli-responsive metal-organic framework nano-container and trivalent DNAzyme for zearalenone determination in food samples. Food Chem 2022; 371:131145. [PMID: 34600366 DOI: 10.1016/j.foodchem.2021.131145] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 12/17/2022]
Abstract
Zearalenone (ZEN) poses a serious threat to human and animal health. The development of sensitive determination methods for ZEN is of great significance for ensuring the quality and safety of food. Herein, based on a stimuli-responsive aptamer-functionalized metal-organic framework (MOF) nano-container and trivalent DNA peroxidase mimicking enzyme (DNAzyme), an efficient aptasensor was constructed initially for the colorimetric determination of ZEN. The proposed aptasensor only required simple operations but exhibited outstanding specificity, reproducibility, storage stability and reusability simultaneously. Under the optimal conditions, there was a good linear relationship between the changed absorbance and logarithm concentration of ZEN within 0.01-100 ng mL-1, and the limit of detection (LOD) could reach 0.36 pg mL-1. Moreover, the proposed aptasensor was reliable in quantifying ZEN in spiked food samples. The current bioassay provides a promising scheme for constructing stable, specific and rapid colorimetric platforms with potential applications in the fields of food safety.
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Affiliation(s)
- Yuhan Sun
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yan Lv
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shuo Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China.
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43
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Arshavsky‐Graham S, Heuer C, Jiang X, Segal E. Aptasensors versus immunosensors-Which will prevail? Eng Life Sci 2022; 22:319-333. [PMID: 35382545 PMCID: PMC8961048 DOI: 10.1002/elsc.202100148] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.
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Affiliation(s)
- Sofia Arshavsky‐Graham
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Christopher Heuer
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Xin Jiang
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Ester Segal
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
- Russell Berrie Nanotechnology InstituteTechnion ‐ Israel Institute of TechnologyHaifaIsrael
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44
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Peng P, Liu C, Li Z, Xue Z, Mao P, Hu J, Xu F, Yao C, You M. Emerging ELISA Derived Technologies for in vitro Diagnostics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Xun K, Sun Y, Zhang Q, Wen N, Wang Z, Qiu L, Tan W. Aptamer-Based Analysis and Manipulation of the Protein Activity in Living Cells. Anal Chem 2022; 94:4352-4358. [PMID: 35230816 DOI: 10.1021/acs.analchem.1c05104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Directly analyzing and precisely manipulating the activity of target proteins without altering their natural structure and expression would be essential to decoding many protein-dominant cellular processes. To meet this goal, we used streptavidin as the carrier to develop an aptamer-based nanoplatform for monitoring the activation process of specific proteins in living cells. Our results showed that this nanoplatform could efficiently enter the cellular cytoplasm and specifically report the presence of RelA in the activated state. Meanwhile, with incorporation of a photoresponsive module, this aptamer-based nanoplatform was able to manipulate the nuclear translocation behavior of active RelA, enabling control over related downstream signaling events.
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Affiliation(s)
- Kanyu Xun
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
| | - Yue Sun
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
| | - Qiang Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
| | - Nachuan Wen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China.,NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410000, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
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46
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Yan X, Chen H, Du G, Guo Q, Yuan Y, Yue T. Recent trends in fluorescent aptasensors for mycotoxin detection in food: Principles, constituted elements, types, and applications. FOOD FRONTIERS 2022. [DOI: 10.1002/fft2.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Xiaohai Yan
- College of Food Science and Engineering Northwest A&F University Yangling 712100 China
- Laboratory of Quality and Safety Risk Assessment for Agro‐products (Yangling) Ministry of Agriculture Yangling 712100 China
| | - Hong Chen
- College of Food Science and Engineering Northwest A&F University Yangling 712100 China
- Laboratory of Quality and Safety Risk Assessment for Agro‐products (Yangling) Ministry of Agriculture Yangling 712100 China
| | - Gengan Du
- College of Food Science and Engineering Northwest A&F University Yangling 712100 China
- Laboratory of Quality and Safety Risk Assessment for Agro‐products (Yangling) Ministry of Agriculture Yangling 712100 China
| | - Qi Guo
- College of Food Science and Engineering Northwest A&F University Yangling 712100 China
- Laboratory of Quality and Safety Risk Assessment for Agro‐products (Yangling) Ministry of Agriculture Yangling 712100 China
| | - Yahong Yuan
- College of Food Science and Engineering Northwest A&F University Yangling 712100 China
- Laboratory of Quality and Safety Risk Assessment for Agro‐products (Yangling) Ministry of Agriculture Yangling 712100 China
| | - Tianli Yue
- College of Food Science and Engineering Northwest A&F University Yangling 712100 China
- Laboratory of Quality and Safety Risk Assessment for Agro‐products (Yangling) Ministry of Agriculture Yangling 712100 China
- College of Food Science and Technology Northwest University Xi’ an 710000 China
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Roueinfar M, Templeton HN, Sheng JA, Hong KL. An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031114. [PMID: 35164379 PMCID: PMC8839139 DOI: 10.3390/molecules27031114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is best known for its role in genomic editing. It has also demonstrated great potential in nucleic acid biosensing. However, the specificity limitation in CRISPR/Cas has created a hurdle for its advancement. More recently, nucleic acid aptamers known for their high affinity and specificity properties for their targets have been integrated into CRISPR/Cas systems. This review article gives a brief overview of the aptamer and CRISPR/Cas technology and provides an updated summary and discussion on how the two distinctive nucleic acid technologies are being integrated into modern diagnostic and therapeutic applications
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Affiliation(s)
- Mina Roueinfar
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
| | - Hayley N. Templeton
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Julietta A. Sheng
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Ka Lok Hong
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, Notre Dame of Maryland University, 4701 North Charles Street, Baltimore, MD 21210, USA
- Correspondence: ; Tel.: +1-410-532-5044
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Kapadia JB, Kharma N, Davis AN, Kamel N, Perreault J. Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes. RNA (NEW YORK, N.Y.) 2022; 28:263-273. [PMID: 34862273 PMCID: PMC8906547 DOI: 10.1261/rna.078823.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5'-end, while the other strand is labeled with a quencher at its 3'-end. These two DNA strands are perfectly complementary, but with a 3'-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is proportional to the amount of detached cleaved-off RNAs, displacing the DNA quencher strand. This method can replace or complement radio-hazardous unstable 32P as a method of measurement of the product release from ribozyme cleavage reactions; it also eliminates the need for polyacrylamide gels, for the same purpose. Critically, this method allows to distinguish between the total amount of cleaved ribozymes and the amount of detached fragments, resulting from that cleavage reaction.
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Affiliation(s)
- Jay Bhakti Kapadia
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada H7V 1B7
| | - Nawwaf Kharma
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
- Centre for Applied Synthetic Biology (CASB), Concordia University, Montreal, Quebec, Canada H4B 1R6
| | - Alen Nellikulam Davis
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
| | - Nicolas Kamel
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec, Canada H3G 1M8
| | - Jonathan Perreault
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada H7V 1B7
- Centre for Applied Synthetic Biology (CASB), Concordia University, Montreal, Quebec, Canada H4B 1R6
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Qi X, Zhao Y, Su H, Wang L, Li L, Ma R, Yan X, Sun J, Wang S, Mao X. A label-free colorimetric aptasensor based on split aptamers-chitosan oligosaccharide-AuNPs nanocomposites for sensitive and selective detection of kanamycin. Talanta 2022; 238:123032. [PMID: 34857350 DOI: 10.1016/j.talanta.2021.123032] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/09/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022]
Abstract
Herein, the split aptamers, chitosan oligosaccharide, and AuNPs were combined as nanocomposites that present different formations to develop a label-free colorimetric aptasensor for rapid detection of small molecules. Kanamycin was chosen as a model target. Computational studies were performed to assist in the design of orientated immobilization of the split aptamers onto the AuNPs surface. Chitosan oligosaccharide was initially applied as an aggregation inducer of AuNPs, and chitopentaose was screened as the optimal. Under optimized conditions, the proposed aptasensor showed high sensitivity and selectivity, with a limit of detection of 20.58 nM, a linear range of 25-800 nM, and good recoveries of 98.49-104.9% and 85.69-107.0% when employed to detect kanamycin in tap water and milk samples, respectively. Only 55 min was needed for the whole assay. More importantly, this study can serve as a novel and robust reference for the aptasensing detection of other small molecules.
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Affiliation(s)
- Xiaoyan Qi
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Yinglin Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Haipeng Su
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Lele Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Ling Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Rui Ma
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Xiaochen Yan
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Sai Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China.
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
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50
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Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal. Biosens Bioelectron 2022; 197:113739. [PMID: 34781175 PMCID: PMC8553638 DOI: 10.1016/j.bios.2021.113739] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023]
Abstract
The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.
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