1
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Naresh M, Nagaraju VS, Kollem S, Kumar J, Peddakrishna S. Non-invasive glucose prediction and classification using NIR technology with machine learning. Heliyon 2024; 10:e28720. [PMID: 38601525 PMCID: PMC11004754 DOI: 10.1016/j.heliyon.2024.e28720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
In this paper, a dual wavelength short near-infrared system is described for the detection of glucose levels. The system aims to improve the accuracy of blood glucose detection in a cost-effective and non-invasive way. The accuracy of the method is evaluated using real-time samples collected with the reference finger prick glucose device. A feed forward neural network (FFNN) regression method is employed to predict glucose levels based on the input data obtained from NIR technology. The system calculates glucose evaluation metrics and performs Surveillance error grid (SEG) analysis. The coefficient of determination R 2 and mean absolute error are observed 0.99 and 2.49 mg/dl, respectively. Additionally, the system determines the root mean square error (RMSE) as 3.02 mg/dl. It also shows that the mean absolute percentage error (MAPE) is 1.94% and mean squared error (MSE) is 9.16 ( m g / d l ) 2 for FFNN. The SEG analysis shows that the glucose values measured by the system fall within the clinically acceptable range when compared to the reference method. Finally, the system uses the multi-class classification method of the multilayer perceptron (MLP) and K-nearest neighbors (KNN) classifier to classify glucose levels with an accuracy of 99%.
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Affiliation(s)
- M. Naresh
- School of Electronics Engineering, VIT-AP University, Amaravti, Guntur, 522241, Andhra Pradesh, India
| | - V. Siva Nagaraju
- Department of ECE, Institute of Aeronautical Engineering, Dundigal, Hyderabad, 500043, Telangana, India
| | - Sreedhar Kollem
- Department of ECE, School of Engineering, SR University, Warangal, 506371, Telangana, India
| | - Jayendra Kumar
- School of Electronics Engineering, VIT-AP University, Amaravti, Guntur, 522241, Andhra Pradesh, India
| | - Samineni Peddakrishna
- School of Electronics Engineering, VIT-AP University, Amaravti, Guntur, 522241, Andhra Pradesh, India
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2
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Zhou J, Wang TY, Lan Z, Yang HJ, Ye XJ, Min R, Wang ZH, Huang Q, Cao J, Gao YE, Wang WL, Sun XL, Zhang Y. Strategy of functional nucleic acids-mediated isothermal amplification for detection of foodborne microbial contaminants: A review. Food Res Int 2023; 173:113286. [PMID: 37803599 DOI: 10.1016/j.foodres.2023.113286] [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: 04/17/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/08/2023]
Abstract
Foodborne microbial contamination (FMC) is the leading cause of food poisoning and foodborne illness. The foodborne microbial detection methods based on isothermal amplification have high sensitivity and short detection time, and functional nucleic acids (FNAs) could extend the detectable object of isothermal amplification to mycotoxins. Therefore, the strategy of FNAs-mediated isothermal amplification has been emergingly applied in biosensors for foodborne microbial contaminants detection, making biosensors more sensitive with lower cost and less dependent on nanomaterials for signal output. Here, the mechanism of six isothermal amplification technologies and their application in detecting FMC is firstly introduced. Then the strategy of FNAs-mediated isothermal amplification is systematically discussed from perspectives of FNAs' versatility including recognition elements (Aptamer, DNAzyme), programming tools (DNA tweezer, DNA walker and CRISPR-Cas) and signal units (G-quadruplex, FNAs-based nanomaterials). Finally, challenges and prospects are presented in terms of addressing the issue of nonspecific amplification reaction, developing better FNAs-based sensing elements and eliminating food matrix effects.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Teng-Yu Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhi Lan
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Han-Jie Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xing-Jian Ye
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Rui Min
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhao-Hui Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qing Huang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Cao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yu-E Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wen-Long Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Lan Sun
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yi Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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3
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Shu W, Zhang X, Tang H, Wang L, Cheng M, Xu J, Li R, Ran X. Catalytic probes based on aggregation-induced emission-active Au nanoclusters for visualizing MicroRNA in living cells and in vivo. Anal Chim Acta 2023; 1268:341372. [PMID: 37268339 DOI: 10.1016/j.aca.2023.341372] [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: 03/31/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 06/04/2023]
Abstract
Highly sensitive monitoring of cancer-related miRNAs is of great significance for tumor diagnosis. Herein, catalytic probes based on DNA-functionalized Au nanoclusters (AuNCs) were prepared in this work. The aggregation-induced emission-active Au nanoclusters showed an interesting phenomenon of aggregation induced emission (AIE) affected by the aggregation state. Leveraging this property, the AIE-active AuNCs were used to develop catalytic turn-on probes for detecting in vivo cancer-related miRNA based on a hybridization chain reaction (HCR). The target miRNA triggered the HCR and induced aggregation of AIE-active AuNCs, leading to a highly luminescent signal. The catalytic approach demonstrated a remarkable selectivity and a low detection limit in comparison to noncatalytic sensing signals. In addition, the excellent delivery the ability of MnO2 carrier made it possible to use the probes for intracellular imaging and in vivo imaging. Effective in situ visualization of miR-21 was achieved not only in living cells but also in tumors in living animals. This approach potentially offers a novel method for obtaining information for tumor diagnosis via highly sensitive cancer-related miRNA imaging in vivo.
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Affiliation(s)
- Wenhao Shu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China
| | - Xuetao Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China
| | - Hongmei Tang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China
| | - Linna Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China
| | - Manxiao Cheng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China
| | - Jingwen Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China
| | - Rong Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China.
| | - Xiang Ran
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, PR China.
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4
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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5
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Sun Z, Wu Y, Gao F, Li H, Wang C, Du L, Dong L, Jiang Y. In situ detection of exosomal RNAs for cancer diagnosis. Acta Biomater 2023; 155:80-98. [PMID: 36343908 DOI: 10.1016/j.actbio.2022.10.061] [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: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Exosomes are considered as biomarkers reflecting the physiological state of the human body. Studies have revealed that the expression levels of specific exosomal RNAs are closely associated with certain cancers. Thus, detection of exosomal RNA offers a new avenue for liquid biopsy of cancers. Many exosomal RNA detection methods based on various principles have been developed, and most of the methods detect the extracted RNAs after lysing exosomes. Besides complex and time-consuming extraction steps, a major drawback of this approach is the degradation of the extracted RNAs in the absence of plasma membrane and cytosol. In addition, there is considerable loss of RNAs during their extraction. In situ detection of exosomal RNAs can avoid these drawbacks, thus allowing higher diagnostic reliability. In this paper, in situ detection of exosomal RNAs was systematically reviewed from the perspectives of detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, and involved functional materials. Furthermore, the limitations and possible improvements of the current in situ detection methods for exosomal RNAs towards the clinical diagnostic application are discussed. This review aims to provide a valuable reference for the development of in situ exosomal RNA detection strategies for non-invasive diagnosis of cancers. STATEMENT OF SIGNIFICANCE: Certain RNAs have been identified as valuable biomarkers for some cancers, and sensitive detection of cancer-related RNAs is expected to achieve better diagnostic efficacy. Currently, the detection of exosomal RNAs is receiving increasing attention due to their high stability and significant concentration differences between patients and healthy individuals. In situ detection of exosomal RNAs has greater diagnostic reliability due to the avoidance of RNA degradation and loss. However, this mode is still limited by some factors such as detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, etc. This review focuses on the progress of in situ detection of exosomal RNAs and aims to promote the development of this field.
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Affiliation(s)
- Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Yanqiu Wu
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Fucheng Gao
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Hui Li
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China.
| | - Lun Dong
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan 250012, China.
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China.
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6
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Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022; 220:114922. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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7
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Kachwala MJ, Smith CW, Nandu N, Yigit MV. Recombinase amplified CRISPR enhanced chain reaction (RACECAR) for viral genome detection. NANOSCALE 2022; 14:13500-13504. [PMID: 36102688 PMCID: PMC9623498 DOI: 10.1039/d2nr03590a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We have developed a 'recombinase amplified CRISPR enhanced chain reaction' (RACECAR) assay that can detect as little as 40 copies of hepatitis B virus (HBV) genome using a benchtop spectrofluorometer. The limit of detection was determined to be 3 copies of HBV genome. The specificity of RACECAR was confirmed against hepatitis A virus (HAV). This assay can detect the genomic targets directly in serum samples without an extraction step. The 4 h-long fluorometric assay was developed by combining three tiers of isothermal amplification processes and can be repurposed for any target of choice. This highly modular reaction setup is an untapped resource that can be incorporated into the front-runners of molecular diagnostics.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
| | - Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA
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8
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Hybridization chain reaction and DNAzyme-based dual signal amplification strategy for sensitive fluorescent sensing of aflatoxin B1 by using the pivot of triplex DNA. Food Res Int 2022; 158:111538. [DOI: 10.1016/j.foodres.2022.111538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 11/22/2022]
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9
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Wang X, Lu D, Liu Y, Wang W, Ren R, Li M, Liu D, Liu Y, Liu Y, Pang G. Electrochemical Signal Amplification Strategies and Their Use in Olfactory and Taste Evaluation. BIOSENSORS 2022; 12:bios12080566. [PMID: 35892464 PMCID: PMC9394270 DOI: 10.3390/bios12080566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 05/07/2023]
Abstract
Biosensors are powerful analytical tools used to identify and detect target molecules. Electrochemical biosensors, which combine biosensing with electrochemical analysis techniques, are efficient analytical instruments that translate concentration signals into electrical signals, enabling the quantitative and qualitative analysis of target molecules. Electrochemical biosensors have been widely used in various fields of detection and analysis due to their high sensitivity, superior selectivity, quick reaction time, and inexpensive cost. However, the signal changes caused by interactions between a biological probe and a target molecule are very weak and difficult to capture directly by using detection instruments. Therefore, various signal amplification strategies have been proposed and developed to increase the accuracy and sensitivity of detection systems. This review serves as a reference for biosensor and detector research, as it introduces the research progress of electrochemical signal amplification strategies in olfactory and taste evaluation. It also discusses the latest signal amplification strategies currently being employed in electrochemical biosensors for nanomaterial development, enzyme labeling, and nucleic acid amplification techniques, and highlights the most recent work in using cell tissues as biosensitive elements.
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Affiliation(s)
- Xinqian Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
| | - Dingqiang Lu
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
- Correspondence: (D.L.); (G.P.)
| | - Yuan Liu
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (W.W.)
| | - Wenli Wang
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (W.W.)
| | - Ruijuan Ren
- Tianjin Institute for Food Safety Inspection Technology, Tianjin 300308, China;
| | - Ming Li
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
| | - Danyang Liu
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
| | - Yujiao Liu
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
| | - Yixuan Liu
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
| | - Guangchang Pang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China; (X.W.); (M.L.); (D.L.); (Y.L.); (Y.L.)
- Correspondence: (D.L.); (G.P.)
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10
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Zhao R, Yu C, Lu B, Li B. Coupling nucleic acid circuitry with the CRISPR-Cas12a system for universal and signal-on detection. RSC Adv 2022; 12:10374-10378. [PMID: 35425009 PMCID: PMC8977996 DOI: 10.1039/d2ra01332k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
We report a universal and signal-on HCR based detection platform via innovatively coupling the CRISPR-Cas12a system with HCR. By using this CRISPR-HCR pathway, we can detect different targets by only changing the crRNA. The CRISPR-HCR platform coupling with an upstream amplifier can achieve a practical sensitivity as low as ∼aM of ASFV gene in serum.
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Affiliation(s)
- Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
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Zhang N, Li J, Liu B, Zhang D, Zhang C, Guo Y, Chu X, Wang W, Wang H, Yan X, Li Z. Signal enhancing strategies in aptasensors for the detection of small molecular contaminants by nanomaterials and nucleic acid amplification. Talanta 2022; 236:122866. [PMID: 34635248 DOI: 10.1016/j.talanta.2021.122866] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022]
Abstract
Small molecular contaminants (such as mycotoxins, antibiotics, pesticide residues, etc.) in food and environment have given rise to many biological and ecological toxicities, which has attracted worldwide attention in recent years. Meanwhile, due to the advantages of aptamers such as high specificity and stability, easy synthesis and modification, as well as low cost and immunogenicity, various aptasensors for the detection of small molecular contaminants have been flourishing. An aptasensor as a whole is composed of an aptamer-based target recognizer and a signal transducer, which are fields of concentrated research. In the practical detection applications, in order to achieve the quantitative detection of small molecular contaminants at low abundance in real samples, a large number of signal enhancing strategies have been utilized in the development of aptasensors. Recent years is a vintage period for efficient signal enhancing strategies of aptasensors by the aid of nanomaterials and nucleic acid amplification that are applied in the elements for target recognition and signal conversion. Therefore, this paper meticulously reviews the signal enhancing strategies based on nanomaterials (including the (quasi-)zero-dimensional, one-dimensional, two-dimensional and three-dimensional nanomaterials) and nucleic acid amplification (including enzyme-assisted nucleic acid amplification and enzyme-free nucleic acid amplification). Furthermore, the challenges and future trends of the abovementioned signal enhancing strategies for application are also discussed in order to inspire the practitioners in the research and development of aptasensors for small molecular contaminants.
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Affiliation(s)
- Nan Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jingrong Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Boshi Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Di Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chengyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuheng Guo
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xinhong Chu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Wenting Wang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Haixia Wang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xiaohui Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
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12
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Xia LY, Tang YN, Zhang J, Dong TY, Zhou RX. Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications. Semin Cancer Biol 2022; 86:1105-1119. [PMID: 34979273 DOI: 10.1016/j.semcancer.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.
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Affiliation(s)
- Ling-Ying Xia
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ya-Nan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Tian-Yu Dong
- College of Chemistry, Sichuan University Chengdu, Sichuan 610064, PR China
| | - Rong-Xing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China.
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13
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Wong ZW, Ng JF, New SY. Ratiometric Detection of microRNA Using Hybridization Chain Reaction and Fluorogenic Silver Nanoclusters. Chem Asian J 2021; 16:4081-4086. [PMID: 34668337 DOI: 10.1002/asia.202101145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/18/2021] [Indexed: 12/30/2022]
Abstract
miRNA (miR)-155 is a potential biomarker for breast cancers. We aimed at developing a nanosensor for miR-155 detection by integrating hybridization chain reaction (HCR) and silver nanoclusters (AgNCs). HCR serves as an enzyme-free and isothermal amplification method, whereas AgNCs provide a built-in fluorogenic detection probe that could simplify the downstream analysis. The two components were integrated by adding a nucleation sequence of AgNCs to the hairpin of HCR. The working principle was based on the influence of microenvironment towards the hosted AgNCs, whereby unfolding of hairpin upon HCR has manipulated the distance between the hosted AgNCs and cytosine-rich toehold region of hairpin. As such, the dominant emission of AgNCs changed from red to yellow in the absence and presence of miR-155, enabling a ratiometric measurement of miR with high sensitivity. The limit of detection (LOD) of our HCR-AgNCs nanosensor is 1.13 fM in buffered solution. We have also tested the assay in diluted serum samples, with comparable LOD of 1.58 fM obtained. This shows the great promise of our HCR-AgNCs nanosensor for clinical application.
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Affiliation(s)
- Zheng Wei Wong
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Jeck Fei Ng
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, No. 1 Jalan Taylor's, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Siu Yee New
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
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14
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Zhang C, Luo Z, Wu M, Ning W, Tian Z, Duan Y, Li Y. A highly sensitive fluorescence biosensor for detection of Staphylococcus aureus based on HCR-mediated three-way DNA junction nicking enzyme assisted signal amplification. Analyst 2021; 146:6528-6536. [PMID: 34569562 DOI: 10.1039/d1an01335a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sensitive and efficient monitoring of food-borne bacteria is of great importance for food safety control. Herein, a novel biosensor for highly sensitive detection of Staphylococcus aureus (S. aureus) was constructed by combining hybridization chain reaction (HCR) and nicking enzyme. Different from the upstream-downstream based circuit, the proposed biosensor integrated HCR circuit and three-way DNA junction nicking enzyme assisted signal amplification (3WJ-NEASA) into a virtuous circle of promotion. In the HCR-mediated 3WJ-NEASA sensing strategy, target DNA of S. aureus initiated the self-assembly between HCR hairpins (H1 and H2), which exposed the gap to capture molecular beacon (MB) and construct the 3WJ structure. Meanwhile, MB increased the stability of HCR nanowires and enhanced the efficiency of the HCR circuit, and thus more 3WJ-NEASA circuits were generated in HCR nanowires. Benefiting from the synergistic amplification coupling HCR and 3WJ-NEASA, this isothermal biosensor can detect as low as 6.7 pM of target DNA in one step within only 30 min. Furthermore, the HCR-mediated 3WJ-NEASA assay has been applied in the detection of S. aureus with a limit of detection (LOD) as low as 1.2 × 101 cfu mL-1, and has exhibited reliable practicability in spiked milk. It is the first time that a DNA biosensor combining HCR and 3WJ-NEASA for dual signal amplification was developed and has been adopted to the sensitive analysis of food-borne bacteria. Additionally, this strategy can serve as a universal platform for monitoring other analytes, and therefore possesses broad application prospects in food safety and environmental monitoring.
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Affiliation(s)
- Chuyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| | - Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
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15
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Hybridization chain reaction and its applications in biosensing. Talanta 2021; 234:122637. [PMID: 34364446 DOI: 10.1016/j.talanta.2021.122637] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022]
Abstract
To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.
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16
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Castle LM, Schuh DA, Reynolds EE, Furst AL. Electrochemical Sensors to Detect Bacterial Foodborne Pathogens. ACS Sens 2021; 6:1717-1730. [PMID: 33955227 DOI: 10.1021/acssensors.1c00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial foodborne pathogens cause millions of illnesses each year and disproportionately impact those in developing countries. To combat these diseases and their spread, effective monitoring of foodborne pathogens is needed. Technologies to detect these microbes must be deployable at the point-of-contamination, often in nonideal environments. Electrochemical sensors are uniquely suited for field-deployable monitoring, as they are quantitative, rapid, and do not require expensive instrumentation. When combined with the inherent recognition capabilities of biomolecules, electrochemistry is unmatched for quantitative biological measurements with minimal equipment requirements. This Review is centered on recent advances in electrochemical sensors for the detection of bacterial foodborne pathogens with a specific emphasis on field-deployable platforms, as this is a key requirement of any technology that could effectively halt the spread of foodborne diseases. Innovative electrochemical sensing strategies are highlighted that demonstrate the ability of these technologies to achieve high sensitivity and large detection ranges with rapid readout. Sensing strategies are categorized on the basis of whether they incorporate biological pretreatments or biorecognition elements, and their key advantages and disadvantages are summarized. As this class of sensors continues to mature, methods to incorporate device specificity and to detect targets from complex solutions will enable the translation of these platforms from laboratory prototypes to real-world implementation.
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Affiliation(s)
- Lauren M. Castle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daena A. Schuh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin E. Reynolds
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L. Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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17
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The mechanism and improvements to the isothermal amplification of nucleic acids, at a glance. Anal Biochem 2021; 631:114260. [PMID: 34023274 DOI: 10.1016/j.ab.2021.114260] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023]
Abstract
A comparative review of the most common isothermal methods is provided. In the last two decades, the challenge of using isothermal amplification systems as an alternate to the most extensive and long-standing nucleic acids-amplifying method-the polymerase chain reaction-has arisen. The main advantage of isothermal amplification is no requirement for expensive laboratory equipment for thermal cycling. Considerable efforts have been made to improve the current techniques of nucleic acid amplification and the development of new approaches based on the main drawbacks of each method. The most important and challenging goal was to achieve a low-cost, straightforward system that is rapid, specific, accurate, and sensitive.
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18
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Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing. Talanta 2021; 226:122146. [PMID: 33676697 DOI: 10.1016/j.talanta.2021.122146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.
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19
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Yu C, Wang Y, Wu R, Zhu Z, Li B. Study on the Functionalization and Signaling Efficiency of the Hybridization Chain Reaction Using Traditional and Single Molecular Characterizations. ACS APPLIED BIO MATERIALS 2021; 4:3649-3657. [PMID: 35014450 DOI: 10.1021/acsabm.1c00136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As an important enzyme-free amplifier, the hybridization chain reaction (HCR) uses an ssDNA to trigger cycled displacement interactions between substrate hairpins and finally form elongated dsDNA concatamer mixtures. In many cases, to provide a signal probe or advanced function, additional oligonucleotides (named hairpin tails) have to be extended upon classic HCR hairpin substrates, but by doing so the HCR assembly efficiency and signal-to-noise ratio (SNR) may get seriously reduced. In this Article, a rational and general model that may guide the study on HCR functionalization and signaling efficiency is provided. We rationally design a four-hairpin model HCR system (4H-HCR) in which one or more hairpin substrates are appended with additional tails as a signaling probe. After HCR assembly, two adjacent tails are supposedly integrating into a full G-quadruplex structure to provide the evidence or signal for the assembly. A systematic study has been applied to reveal the relationship between the "tail-design" with assembly efficiency and SNR. A clear design rule-set guiding the optimized assembly and signal has been provided for traditional electrophoresis and G-quadruplex-enhanced fluorescence signal. Importantly, solid-state nanopore single molecular detection has been innovatively introduced and recommended as an "antirisk" and "mutual benefit" readout to traditional G-quadruplex signaling. Nanopore detection can provide a clear signal distinguished before and after the HCR reaction, especially when the traditional G-quadruplex-enhanced signal only provides low SNR. The G-quadruplex, in turn, may enhance the nanopore signal amplitude via increasing the diameter of the HCR products.
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Affiliation(s)
- Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Zhentong Zhu
- College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu 730070, People's Republic of China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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20
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An amplified fluorescent biosensor for Ag + detection through the hybridization chain reactions. Colloids Surf B Biointerfaces 2021; 202:111686. [PMID: 33714924 DOI: 10.1016/j.colsurfb.2021.111686] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 12/17/2022]
Abstract
Ag is widely distributed in nature and it is used in almost all areas of human life. However, due to the widespread use of Ag materials, Ag+ pollution seriously threatens the human health and environment. The traditional detection methods for Ag+ suffer from disadvantages including high operational cost, complicated operating unit and instrument, and high requirements for professionals. Thus, in this study, a new type of Ag+ detection biosensor based on the hybridization signal amplification was designed to overcome these problems. Combining cytosine-Ag+-cytosine mismatch structure with the hybridization chain reaction, this biosensor converted the conventional detection signal into the nucleic acid amplification signal, which realized efficient, rapid, sensitive, and specific detection of Ag+. The limit-of-detection of this sensor reached 0.69 pM, which is much less than the maximum concentration (0.1 mg L-1, 927 nM) suggested for drinking water by the World Health Organization, and the maximum concentration (0.05 mg L-1, 464 nM) suggested by the United States Environmental Protection Agency. This method provides a promising new platform for detecting Ag+ concentrations at ultralow levels.
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21
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Salva ML, Rocca M, Hu Y, Delamarche E, Niemeyer CM. Complex Nucleic Acid Hybridization Reactions inside Capillary-Driven Microfluidic Chips. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2005476. [PMID: 33201612 DOI: 10.1002/smll.202005476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization reactions play an important role in many (bio)chemical fields, for example, for the development of portable point-of-care diagnostics, and often such applications require nucleic acid-based reaction systems that ideally run without enzymes under isothermal conditions. The use of novel capillary-driven microfluidic chips to perform two isothermal nucleic acid hybridization reactions, the simple opening of molecular beacon structures and the complex reaction cascade of a clamped-hybridization chain reaction (C-HCR), is reported here. For this purpose, reagents are arranged in a self-coalescence module (SCM) of a passive silicon microfluidic chip using inkjet spotting. The SCM occupies a footprint of ≈7 mm2 of a ≈0.4 × 2 cm2 microfluidic chip. By means of fluorophore-labeled DNA probes, the hybridization reactions can be analyzed in just ≈2 min and using only ≈3 µL of the sample. Furthermore, the SCM chip offers a variety of reagent delivery options, allowing, for example, the influence of the initiator concentration on the kinetics of C-HCR to be investigated systematically with minimal sample and time requirements. These results suggest that self-powered microfluidic chips equipped with a SCM provide a powerful platform for performing and investigating complex reaction systems.
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Affiliation(s)
- Marie L Salva
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG-1), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
- IBM Research Europe, Säumerstrasse 4, Ruschlikon, 8803, Switzerland
| | - Marco Rocca
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG-1), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
- IBM Research Europe, Säumerstrasse 4, Ruschlikon, 8803, Switzerland
| | - Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG-1), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
| | | | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG-1), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
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22
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Yin C, Zhao Q, Yue A, Du W, Liu D, Zhao J, Zhang Y, Wang M. Colorimetric Detection of Class A Soybean Saponins by G-Quadruplex-Based Hybridization Chain Reaction. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2020; 2020:8813239. [PMID: 33204574 PMCID: PMC7661121 DOI: 10.1155/2020/8813239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Soybean saponin is one of the important secondary metabolites in seeds, which has various beneficial physiological functions to human health. GmSg-1 gene is the key enzyme gene for synthesizing class A saponins. It is of great significance to realize the visual and rapid detection of class A saponins at the genetic level. The hybridization chain reaction (HCR) was employed to the visual detection of GmSg-1 gene, which was implemented by changing the length of the target fragment to 92 bp and using the hairpin probes we designed to detect the GmSg-1 a and GmSg-1 b genes. The best condition of HCR reaction is hemin (1.2 μM), Triton X-100 (0.002%), ABTS (3.8 μM), and H2O2 (1.5 mM). It was found that HCR has high specificity for GmSg-1 gene and could be applied to the visual detection of different soybean cultivars containing Aa type, Ab type, and Aa/Ab type saponins, which could provide technical reference and theoretical basis for molecular breeding of soybean and development of functional soybean products.
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Affiliation(s)
- Congcong Yin
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Qiaoling Zhao
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Aiqin Yue
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Weijun Du
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Dingbin Liu
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jinzhong Zhao
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Yongpo Zhang
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Min Wang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
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23
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Zhang C, Chen J, Sun R, Huang Z, Luo Z, Zhou C, Wu M, Duan Y, Li Y. The Recent Development of Hybridization Chain Reaction Strategies in Biosensors. ACS Sens 2020; 5:2977-3000. [PMID: 32945653 DOI: 10.1021/acssensors.0c01453] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.
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Affiliation(s)
- Chuyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Chen
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Rui Sun
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Zhijun Huang
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
| | - Chen Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
- Research Center of Analytical Instrumentation, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
- Provincial Key Laboratory for Food Safety Monitoring and Risk Assessment of Sichuan, Chengdu 610041, China
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24
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Ang YS, Bando T, Sugiyama H, Yung LYL. Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide. Chembiochem 2020; 21:2912-2915. [PMID: 32458592 DOI: 10.1002/cbic.202000245] [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: 04/21/2020] [Revised: 05/20/2020] [Indexed: 11/12/2022]
Abstract
We used N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamide as an exogenous agent to modulate the formation of DNA assemblies at specific double-stranded sequences. The concept was demonstrated on the hybridization chain reaction that forms linear DNA. Through a series of melting curve analyses, we demonstrated that the binding of Py-Im polyamide positively influenced both the HCR initiation and elongation steps. In particular, Py-Im polyamide was found to drastically stabilize the DNA duplex such that its thermal stability approached that of an equivalent hairpin structure. Also, the polyamide served as an anchor between hairpin pairs in the HCR assembly, thus improving the originally weak interstrand stability. We hope that these proof-of-concept results can inspire future use of Py-Im polyamide as a molecular tool to modulate the formation of DNA assemblies.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo,-ku, Kyoto, 606-8501, Japan
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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25
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Zhang Q, Hao T, Hu D, Guo Z, Wang S, Hu Y. RNA aptamer-driven ECL biosensing for tracing histone acetylation based on nano-prism substrate and cascade DNA amplification strategy. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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26
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Fractal SERS nanoprobes for multiplexed quantitative gene profiling. Biosens Bioelectron 2020; 156:112130. [DOI: 10.1016/j.bios.2020.112130] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
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27
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Lv MM, Fan SF, Wang QL, Lv QY, Song X, Cui HF. An enzyme-free electrochemical sandwich DNA assay based on the use of hybridization chain reaction and gold nanoparticles: application to the determination of the DNA of Helicobacter pylori. Mikrochim Acta 2019; 187:73. [PMID: 31863213 DOI: 10.1007/s00604-019-3999-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/03/2019] [Indexed: 01/27/2023]
Abstract
An ultrasensitive enzyme-free electrochemical sandwich DNA biosensor is described for the detection of ssDNA oligonucleotides. A DNA sequence derived from the genom of Helicobacter pylori was selected as a model target DNA. The DNA assay was realized through catching target DNA on capture DNA immobilized gold electrode; then labeling the target DNA with reporter DNA (rpDNA) and initiator DNA (iDNA) co-modified gold nanoparticles (AuNPs). The high density of iDNAs serves as one of the amplification strategies. The iDNA triggers hybridization chain reaction (HCR) between two hairpins. This leads to the formation of a long dsDNA concatamer strand and represents one amplification strategy. The electrochemical probe [Ru(NH3)5L]2+, where L stands for 3-(2-phenanthren-9-ylvinyl)pyridine, intercalated into dsDNA chain. Multiple probe molecules intercalate into one dsDNA chain, serving as one amplification strategy. The electrode was subjected to differential pulse voltammetry for signal acquisition, and the oxidation peak current at -0.28 V was recorded. On each AuNP, 240 iDNA and 25 rpDNA molecules were immobilized. Successful execution of HCR at the DNA-modified AuNPs was confirmed by gel electrophoresis and hydrodynamic diameter measurements. Introduction of HCR significantly enhances the DNA detection signal intensity. The assay has two linear ranges of different slopes, one from 0.01 fM to 0.5 fM; and one from 1 fM to 100 fM. The detection limit is as low as 0.68 aM. Single mismatch DNA can be differentiated from the fully complementary DNA. Conceivably, this highly sensitive and selective assay provides a general method for detection of various kinds of DNA. Graphical abstractSchematic representation of the detection and the amplification principles of the electrochemical sandwich DNA assay. Purple curl: Captured DNA; Green curl: Reporter DNA; Orange curl: HCR initiator DNA; Yellow solid-circle: Gold nanoparticle; H1 and H2: Two hairpin DNA; [Ru(NH3)5L]2+: Signal probe.
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Affiliation(s)
- Man-Man Lv
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Shuang-Fei Fan
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Qiong-Lin Wang
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Qi-Yan Lv
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Xiaojie Song
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China.
| | - Hui-Fang Cui
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China.
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28
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Zhu L, Miao M, Shao X, Du Z, Huang K, Luo Y, Xu W. A Universal Electrochemical Biosensor Using Nick-HCR Nanostructure as Molecular Gate of Nanochannel for Detecting Chromium(III) Ions and MicroRNA. Anal Chem 2019; 91:14992-14999. [DOI: 10.1021/acs.analchem.9b03489] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Longjiao Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Miao Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Xiangli Shao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Zaihui Du
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
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29
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Liu X, Zou M, Li D, Yuan R, Xiang Y. Hairpin/DNA ring ternary probes for highly sensitive detection and selective discrimination of microRNA among family members. Anal Chim Acta 2019; 1076:138-143. [DOI: 10.1016/j.aca.2019.05.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/19/2019] [Accepted: 05/13/2019] [Indexed: 12/25/2022]
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30
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Fluorometric determination of microRNA by using target-triggered cascade signal amplification and DNA-templated silver nanoclusters. Mikrochim Acta 2019; 186:669. [DOI: 10.1007/s00604-019-3789-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022]
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31
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Xiao G, Chen B, He M, Li X, Hu B. A highly sensitive assay of DNA based on inductively coupled plasma mass spectrometry detection with gold nanoparticle amplification and isothermal circular strand-displacement polymerization reaction. Talanta 2019; 202:207-213. [DOI: 10.1016/j.talanta.2019.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 01/14/2023]
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32
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Iwe IA, Li Z, Huang J. A dual-cycling fluorescence scheme for ultrasensitive DNA detection through signal amplification and target regeneration. Analyst 2019; 144:2649-2655. [PMID: 30843550 DOI: 10.1039/c9an00075e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, we propose an ultrasensitive fluorescence strategy for DNA detection. This method utilizes a molecular beacon (MB), a hairpin probe (HP), and an enzyme to trigger dual-cycling reactions (cycles I and II). In cycle I, the target is repeatedly used to amplify the fluorescence emission through hybridizations with the MB and cleavage reactions achieved by the enzyme. In cycle II, hybridization reactions between the HP and a segment of the MB continuously regenerate the target to trigger more cycle I reactions, leading to an enhanced fluorescent signal. The detection limit of the method is determined to be as low as 50 fM within 45 min, which is 2 to 3 orders of magnitude lower than that of the conventional fluorescence strategies. The method also shows a high selectivity over mismatched and random DNA sequences. The signal amplification mechanism of the strategy offers insights into constructing efficient and ultrasensitive biosensors for various applications.
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Affiliation(s)
- Idorenyin A Iwe
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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33
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Wu R, Zhu Z, Xu X, Yu C, Li B. An investigation of solid-state nanopores on label-free metal-ion signalling via the transition of RNA-cleavage DNAzyme and the hybridization chain reaction. NANOSCALE 2019; 11:10339-10347. [PMID: 31107481 DOI: 10.1039/c9nr01666j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances have proven solid-state nanopores as a powerful analysis platform that enables label-free and separation-free single-molecule analysis. However, the relatively low resolution still limits its application because many chemicals or targets with small sizes could not be recognized in a label-free condition. In this paper, we provide a possible solution that uses solid-state nanopores for small species signaling via the transition of huge DNA assembly products. DNAzyme responding to metal ions and the hybridization chain reaction (HCR) generating nanopore-detectable dsDNA concatamers are used as the transition model set. By the two-step DNAzyme-HCR transition, Pb2+ that was too tiny to be sensed was successfully recognized by the nanopore. The whole process happened in a completely homogeneous solution without any chemical modification. During condition optimization, we also discussed one possible application challenge that may affect the HCR signal-background distinction. Solid-state nanopores provide a potential solution to this challenge due to its ability to profile product length or even 3D structure information.
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Affiliation(s)
- Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
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34
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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35
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Fang X, Zheng Y, Duan Y, Liu Y, Zhong W. Recent Advances in Design of Fluorescence-Based Assays for High-Throughput Screening. Anal Chem 2019; 91:482-504. [PMID: 30481456 PMCID: PMC7262998 DOI: 10.1021/acs.analchem.8b05303] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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36
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Tang S, Li Y, Zhu A, Yao Y, Sun J, Zheng F, Lin Z, Shen W. A triple-amplification strategy based on the formation of peroxidase-like two-dimensional DNA/Fe3O4 networks initiated by the hybridization chain reaction for highly sensitive detection of microRNA. Chem Commun (Camb) 2019; 55:8386-8389. [DOI: 10.1039/c9cc03194d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxidase-like two-dimensional DNA/Fe3O4 networks were constructed by the hybridization chain reaction and applied to detect microRNA down to the aM level.
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Affiliation(s)
- Sheng Tang
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Yana Li
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Anni Zhu
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Yao Yao
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Jun Sun
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Fenfen Zheng
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Zixia Lin
- Testing Center
- Yangzhou University
- Yangzhou 225000
- P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
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37
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Xu W, Zhu L, Shao X, Huang K, Luo Y. An electrochemical biosensor based on nucleic acids enzyme and nanochannels for detecting copper (II) ion. Biosens Bioelectron 2018; 120:168-174. [DOI: 10.1016/j.bios.2018.08.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022]
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38
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A cascade autocatalytic strand displacement amplification and hybridization chain reaction event for label-free and ultrasensitive electrochemical nucleic acid biosensing. Biosens Bioelectron 2018; 113:1-8. [DOI: 10.1016/j.bios.2018.04.046] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/03/2018] [Accepted: 04/18/2018] [Indexed: 12/29/2022]
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39
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Choi HMT, Schwarzkopf M, Fornace ME, Acharya A, Artavanis G, Stegmaier J, Cunha A, Pierce NA. Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 2018; 145:dev165753. [PMID: 29945988 PMCID: PMC6031405 DOI: 10.1242/dev.165753] [Citation(s) in RCA: 619] [Impact Index Per Article: 103.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/02/2018] [Indexed: 12/17/2022]
Abstract
In situ hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed multi-decade challenges that impeded imaging of mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution and versatility. Here, with third-generation in situ HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that reagents will not generate amplified background even if they bind non-specifically within the sample. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of a higher signal-to-background ratio with the convenience of using unoptimized probe sets for new targets and organisms. In situ HCR v3.0 enables three multiplexed quantitative analysis modes: (1) qHCR imaging - analog mRNA relative quantitation with subcellular resolution in the anatomical context of whole-mount vertebrate embryos; (2) qHCR flow cytometry - analog mRNA relative quantitation for high-throughput expression profiling of mammalian and bacterial cells; and (3) dHCR imaging - digital mRNA absolute quantitation via single-molecule imaging in thick autofluorescent samples.
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Affiliation(s)
- Harry M T Choi
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Maayan Schwarzkopf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark E Fornace
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Aneesh Acharya
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Georgios Artavanis
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Johannes Stegmaier
- Center for Advanced Methods in Biological Image Analysis, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
- Institute for Automation & Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe 76344, Germany
- Institute of Imaging & Computer Vision, RWTH Aachen University, Aachen 52074, Germany
| | - Alexandre Cunha
- Center for Advanced Methods in Biological Image Analysis, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
- Center for Data-Driven Discovery, California Institute of Technology, Pasadena, CA 91125, USA
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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40
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Shi C, Wang Y, Zhang M, Ma C. DNA Self-assembly Catalyzed by Artificial Agents. Sci Rep 2017; 7:6818. [PMID: 28754968 PMCID: PMC5533707 DOI: 10.1038/s41598-017-07210-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/27/2017] [Indexed: 11/08/2022] Open
Abstract
Nucleic acids have been shown to be versatile molecules and engineered to produce various nanostructures. However, the poor rate of these uncatalyzed nucleic acid reactions has restricted the development and applications. Herein, we reported a novel finding that DNA self-assembly could be nonenzymatically catalyzed by artificial agents with an increasing dissociation rate constant K2. The catalytic role of several artificial agents in DNA self-assembly was verified by real-time fluorescent detection or agarose gel electrophoresis. We found that 20% PEG 200 could significantly catalyze DNA self-assembly and increase the reaction efficiency, such as linear hybridization chain reaction (HCR) and exponential hairpin assembly (EHA). Therefore, we foresee that a fast and efficient DNA self-assembly in structural DNA nanotechnology will be desirable.
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Affiliation(s)
- Chao Shi
- College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Yifan Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China
| | - Menghua Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China
| | - Cuiping Ma
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China.
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41
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Zhao M, Chen AY, Huang D, Chai YQ, Zhuo Y, Yuan R. MoS 2 Quantum Dots as New Electrochemiluminescence Emitters for Ultrasensitive Bioanalysis of Lipopolysaccharide. Anal Chem 2017; 89:8335-8342. [PMID: 28702989 DOI: 10.1021/acs.analchem.7b01558] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cd-based semiconductor quantum dots (QDs) with size-tunable luminescence and high quantum yield have become the most promising electrochemiluminescence (ECL) emitters. However, their unavoidable biotoxicity limited their applications in bioassays. Here, the nontoxic and economical MoS2 QDs prepared by chemical exfoliation from the bulk MoS2 were first investigated as new ECL emitters, and then the possible luminescence mechanism of MoS2 QDs was studied using ECL-potential curves and differential pulse voltammetry (DPV) methods in detail. With MoS2 QDs as the ECL emitters and triethylamine (TEA) as the efficient coreactant, a practical and label-free aptasensor for lipopolysaccharide (LPS) detection was constructed based on aptamer recognition-driven target-cycling synchronized rolling circle amplification. Comparing to conventional stepwise reactions, this target-cycling synchronized rolling circle amplification achieved more efficient signal amplification and simpler operation. The developed assay for LPS detection demonstrated a wide linear range of 0.1 fg/mL to 50 ng/mL with limit of detection down to 0.07 fg/mL. It is worth mentioning that MoS2 QDs with stable ECL emission exhibited a great application potential in ECL bioanalysis and imaging as a new type of excellent emitter candidates.
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Affiliation(s)
- Min Zhao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, China
| | - An-Yi Chen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, China
| | - Dan Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, China
| | - Ya-Qin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, China
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, China
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42
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Zhu L, Shao X, Luo Y, Huang K, Xu W. Two-Way Gold Nanoparticle Label-Free Sensing of Specific Sequence and Small Molecule Targets Using Switchable Concatemers. ACS Chem Biol 2017; 12:1373-1380. [PMID: 28211680 DOI: 10.1021/acschembio.7b00060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A two-way colorimetric biosensor based on unmodified gold nanoparticles (GNPs) and a switchable double-stranded DNA (dsDNA) concatemer have been demonstrated. Two hairpin probes (H1 and H2) were first designed that provided the fuels to assemble the dsDNA concatemers via hybridization chain reaction (HCR). A functional hairpin (FH) was rationally designed to recognize the target sequences. All the hairpins contained a single-stranded DNA (ssDNA) loop and sticky end to prevent GNPs from salt-induced aggregation. In the presence of target sequence, the capture probe blocked in the FH recognizes the target to form a duplex DNA, which causes the release of the initiator probe by FH conformational change. This process then starts the alternate-opening of H1 and H2 through HCR, and dsDNA concatemers grow from the target sequence. As a result, unmodified GNPs undergo salt-induced aggregation because the formed dsDNA concatemers are stiffer and provide less stabilization. A light purple-to-blue color variation was observed in the bulk solution, termed the light-off sensing way. Furthermore, H1 ingeniously inserted an aptamer sequence to generate dsDNA concatemers with multiple small molecule binding sites. In the presence of small molecule targets, concatemers can be disassembled into mixtures with ssDNA sticky ends. A blue-to-purple reverse color variation was observed due to the regeneration of the ssDNA, termed the light-on way. The two-way biosensor can detect both nucleic acids and small molecule targets with one sensing device. This switchable sensing element is label-free, enzyme-free, and sophisticated-instrumentation-free. The detection limits of both targets were below nanomolar.
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Affiliation(s)
- Longjiao Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiangli Shao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlung Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
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43
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Fozooni T, Ravan H, Sasan H. Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging. Appl Biochem Biotechnol 2017; 183:1224-1253. [DOI: 10.1007/s12010-017-2494-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022]
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44
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Ultrasensitive colorimetric detection of circulating tumor DNA using hybridization chain reaction and the pivot of triplex DNA. Sci Rep 2017; 7:44212. [PMID: 28276503 PMCID: PMC5343571 DOI: 10.1038/srep44212] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/03/2017] [Indexed: 12/31/2022] Open
Abstract
This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA. Nevertheless, in the absence of ctDNA, no HCR happens. Thus, no triplex DNA and G-Quadruplex structure is formed, producing a negligible background. The colorimetric sensing platform is successfully applied in complex biological environments such as human blood plasma for ctDNA detection, with a detection limit corresponding to 0.1 pM. This study unambiguously uses triplex DNA forming as the pivot to integrate nucleic acid amplification and DNAzymes for producing a highly sensitive signal with low background.
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Zou L, Li R, Zhang M, Luo Y, Zhou N, Wang J, Ling L. A colorimetric sensing platform based upon recognizing hybridization chain reaction products with oligonucleotide modified gold nanoparticles through triplex formation. NANOSCALE 2017; 9:1986-1992. [PMID: 28106202 DOI: 10.1039/c6nr09089c] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel colorimetric sensing strategy for biomolecule assay has been developed, which integrates the signal amplification of the hybridization chain reaction (HCR) with the assembly of gold nanoparticles (AuNPs) through triplex formation. In the presence of targets, the HCR process can be triggered, the HCR products are specifically recognized by triplex-forming oligonucleotide (TFO) functionalized AuNPs, accompanying the aggregation of AuNPs and a dramatic absorbance change at 522 nm. In addition, the DNA hairpin probes can form rigid triplex structures with TFO-functionalized AuNPs in the absence of targets, resulting in a negligible background signal. By taking advantage of this new biosensor platform, a broad range of targets, involving nucleic acids, small molecules and proteins, have been successfully determined with high sensitivity and selectivity, which may hold great potential for practical application.
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Affiliation(s)
- Li Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Ruimin Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Manjun Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Yanwei Luo
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Nian Zhou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Jing Wang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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46
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Bao B, Zhu J, Gong L, Chen J, Pan Y, Wang L. Sensitive DNA detection using cascade amplification strategy based on conjugated polyelectrolytes and hybridization chain reaction. RSC Adv 2017. [DOI: 10.1039/c6ra25882d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel cascade amplification strategy that combines the molecular wire effects of CPEs with the signal amplification capability of the HCR has been developed for sensitive DNA detection.
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Affiliation(s)
- Biqing Bao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Jin Zhu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Lina Gong
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Jia Chen
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yanrui Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
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47
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Bi S, Yue S, Zhang S. Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 2017; 46:4281-4298. [DOI: 10.1039/c7cs00055c] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Makers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- P. R. China
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48
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Yin Y, Shi L, Chu Z, Jin W. A highly sensitive electrochemical IFN-γ aptasensor based on a hierarchical graphene/AuNPs electrode interface with a dual enzyme-assisted amplification strategy. RSC Adv 2017. [DOI: 10.1039/c7ra07817j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A new signal-on electrochemical aptasensor for IFN-γ assay is constructed on a hierarchical graphene/AuNPs modified electrode coupled with a dual enzyme-assisted signal amplification strategy.
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Affiliation(s)
- Yu Yin
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang 212003
- P. R. China
| | - Lei Shi
- State Key Laboratory of Lake Science and Environment
- Nanjing Institute of Geography and Limnology
- Chinese Academy of Sciences
- Nanjing 210008
- P. R. China
| | - Zhenyu Chu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Chemical Engineering
- Nanjing Tech University
- Nanjing 210009
- P. R. China
| | - Wanqin Jin
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Chemical Engineering
- Nanjing Tech University
- Nanjing 210009
- P. R. China
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Bi S, Yue S, Wu Q, Ye J. Triggered and catalyzed self-assembly of hyperbranched DNA structures for logic operations and homogeneous CRET biosensing of microRNA. Chem Commun (Camb) 2016; 52:5455-8. [PMID: 27010350 DOI: 10.1039/c6cc01308b] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Toehold-mediated strand displacement-based nanocircuits are developed by integrating catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR), which achieves self-assembly of hyperbranched DNA structures and is readily utilized as an enzyme-free amplifier for homogeneous CRET detection of microRNA with high sensitivity and selectivity.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao 266071, P. R. China.
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao 266071, P. R. China.
| | - Qiang Wu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Shandong Provincial Key Laboratory for Fishery Resources and Eco-environment, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, P. R. China
| | - Jiayan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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Wang Y, Jiang LP, Zhou S, Bi S, Zhu JJ. DNA Polymerase-Directed Hairpin Assembly for Targeted Drug Delivery and Amplified Biosensing. ACS APPLIED MATERIALS & INTERFACES 2016; 8:26532-26540. [PMID: 27690212 DOI: 10.1021/acsami.6b08597] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Due to the predictable conformation and programmable Watson-Crick base-pairing interactions, DNA has proven to be an attractive material to construct various nanostructures. Herein, we demonstrate a simple model of DNA polymerase-directed hairpin assembly (PDHA) to construct DNA nanoassemblies for versatile applications in biomedicine and biosensing. The system consists of only two hairpins, an initiator and a DNA polymerase. Upon addition of aptamer-linked initiator, the inert stems of the two hairpins are activated alternately under the direction of DNA polymerase, which thus grows into aptamer-tethered DNA nanoassemblies (AptNAs). Moreover, through incorporating fluorophores and drug-loading sites into the AptNAs, we have constructed multifunctional DNA nanoassemblies for targeted cancer therapy with high drug payloads and good biocompatibility. Interestingly, using the as-prepared AptNAs as building blocks, DNA nanohydrogels are self-assembled after centrifugation driven by liquid crystallization and dense packaging of DNA duplexes. Taking advantage of easy preparation and high loading capacity, the PDHAs are readily extended to the fabrication of a label-free biosensing platform, achieving amplified electrochemical detection of microRNA-21 (miR-21) with a detection limit as low as 0.75 fM and a dynamic range of 8 orders of magnitude. This biosensor also demonstrates excellent specificity to discriminate the target miR-21 from the control microRNAs and even the one-base mismatched one and further performs well in analyzing miR-21 in MCF-7 tumor cells.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
| | - Shiwei Zhou
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
| | - Sai Bi
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Qingdao University , Qingdao 266071, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
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