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Meng M, Ma X, Yu L, Zhang X, Chen Y, Li W, Wen Q, Xu D, Chen Q, Xiong Y, Ren J. Phage-induced "one-to-many" FRET sensor for highly sensitive detection of Escherichia coli O157:H7. Biosens Bioelectron 2024; 264:116661. [PMID: 39142229 DOI: 10.1016/j.bios.2024.116661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
As a foodborne pathogen capable of causing severe illnesses, early detection of Escherichia coli O157:H7 (E. coli O157:H7) is crucial for ensuring food safety. While Förster resonance energy transfer (FRET) is an efficient and precise detection technique, there remains a need for amplification strategies to detect low concentrations of E. coli O157:H7. In this study, we presented a phage (M13)-induced "one to many" FRET platform for sensitively detecting E. coli O157:H7. The aptamers, which specifically recognize E. coli O157:H7 were attached to magnetic beads as capture probes for separating E. coli O157:H7 from food samples. The peptide O157S, which specifically targets E. coli O157:H7, and streptavidin binding peptide (SBP), which binds to streptavidin (SA), were displayed on the P3 and P8 proteins of M13, respectively, to construct the O157S-M13K07-SBP phage as a detection probe for signal output. Due to the precise distance (≈3.2 nm) between two neighboring N-terminus of P8 protein, the SA-labeled FRET donor and acceptor can be fixed at the Förster distance on the surface of O157S-M13K07-SBP via the binding of SA and SBP, inducing FRET. Moreover, the P8 protein, with ≈2700 copies, enabled multiple FRET (≈605) occurrences, amplifying FRET in each E. coli O157:H7 recognition event. The O157S-M13K07-SBP-based FRET sensor can detect E. coli O157:H7 at concentration as low as 6 CFU/mL and demonstrates excellent performance in terms of selectivity, detection time (≈3 h), accuracy, precision, practical application, and storage stability. In summary, we have developed a powerful tool for detecting various targets in food safety, environmental monitoring, and medical diagnosis.
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Affiliation(s)
- Meng Meng
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Xiaoyong Ma
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Liping Yu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Xinfang Zhang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Yanni Chen
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Wang Li
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Qian Wen
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Dong Xu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Qi Chen
- Institute of Translational Medicine, Nanchang University, Nanchang, 330031, China
| | - Ying Xiong
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China.
| | - Jiali Ren
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China.
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Ferreira da Silva L, Valle Garay A, Queiroz PF, Garcia de Resende S, Gomide M, Moreira de Oliveira IC, Souza Bernasol A, Arce A, Canet Santos L, Torres F, Silva-Pereira I, de Freitas SM, Marques Coelho C. A novel viral RNA detection method based on the combined use of trans-acting ribozymes and HCR-FRET analyses. PLoS One 2024; 19:e0310171. [PMID: 39325749 PMCID: PMC11426510 DOI: 10.1371/journal.pone.0310171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
The diagnoses of retroviruses are essential for controlling the rapid spread of pandemics. However, the real-time Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR), which has been the gold standard for identifying viruses such as SARS-CoV-2 in the early stages of infection, is associated with high costs and logistical challenges. To innovate in viral RNA detection a novel molecular approach for detecting SARS-CoV-2 viral RNA, as a proof of concept, was developed. This method combines specific viral gene analysis, trans-acting ribozymes, and Fluorescence Resonance Energy Transfer (FRET)-based hybridization of fluorescent DNA hairpins. In this molecular mechanism, SARS-CoV-2 RNA is specifically recognized and cleaved by ribozymes, releasing an initiator fragment that triggers a hybridization chain reaction (HCR) with DNA hairpins containing fluorophores, leading to a FRET process. A consensus SARS-CoV-2 RNA target sequence was identified, and specific ribozymes were designed and transcribed in vitro to cleave the viral RNA into fragments. DNA hairpins labeled with Cy3/Cy5 fluorophores were then designed and synthesized for HCR-FRET assays targeting the RNA fragment sequences resulting from ribozyme cleavage. The results demonstrated that two of the three designed ribozymes effectively cleaved the target RNA within 10 minutes. Additionally, DNA hairpins labeled with Cy3/Cy5 pairs efficiently detected target RNA specifically and triggered detectable HCR-FRET reactions. This method is versatile and can be adapted for use with other viruses. Furthermore, the design and construction of a DIY photo-fluorometer prototype enabled us to explore the development of a simple and cost-effective point-of-care detection method based on digital image analysis.
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Affiliation(s)
- Leonardo Ferreira da Silva
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Aisel Valle Garay
- Laboratory of Molecular Biophysics, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Pedro Felipe Queiroz
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Sophia Garcia de Resende
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Mayna Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Izadora Cristina Moreira de Oliveira
- Laboratory of Molecular Biophysics, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Amanda Souza Bernasol
- Laboratory of Molecular Biophysics, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Anibal Arce
- Institute for biological and medical engineering, Pontificia Universidad Católica de Chile, Santiago de Chile, Chile
| | - Liem Canet Santos
- Laboratory of Molecular Biophysics, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Fernando Torres
- Laboratory of Molecular Biology, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Ildinete Silva-Pereira
- Laboratory of Molecular Biology of Pathogenic Fungi, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Sonia Maria de Freitas
- Laboratory of Molecular Biophysics, Department of Cell Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Federal District, Brazil
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Zhang Z, Liu T, Dong M, Ahamed MA, Guan W. Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1969. [PMID: 38783564 PMCID: PMC11141732 DOI: 10.1002/wnan.1969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/10/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Zhikun Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Md. Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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4
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Wang WX, Huang S, Jiang LP. 3D walkable DNA gears for ultrasensitive detection of multiple microRNAs in lung cancer cell lysates. Talanta 2024; 270:125570. [PMID: 38142612 DOI: 10.1016/j.talanta.2023.125570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
As a tumor biomarker with therapeutic application potential, microRNA (miRNA) was crucial for the accurate and sensitive detection of early-stage tumors. Herein, a unique three dimensional (3D) DNA nanomachine (DNM) was created, which was capable detecting lung cancer-related biomarkers miRNA-21, miRNA-205 and miRNA-125b in lung cancer cell lysates with extreme sensitivity. The 3D DNM was composed of DNA scissors and three flexible walkable DNA gears modified with various species of silver nanoclusters (AgNCs). Based on the flexibility of DNA scissors and the walkability of DNA gears, neighboring DNA gears closed the distance between different species of AgNCs by walking in the presence of targets, generating fluorescence resonance energy transfer (FRET) effect and emitting different kinds of fluorescence to complete the highly sensitive detection of single targets and multiple targets. The findings demonstrated that a linear model provided an excellent match for the association between fluorescence signal and target miRNAs. For miRNA-21, miRNA-205, and miRNA-125b, the limits of detection (LODs) (signal/noise = 3) were 4.2 pmol/L (pM), 6.3 pM, and 10.2 pM, respectively. Their recoveries in A549 cell lysate samples ranged from 95.3 to 108.8 % with relative standard deviations of 1.26 %-4.88 %. Satisfactorily, the 3D DNM displayed exceptional analytical performance with high sensitivity and stability, strong specificity and reproducibility, which was triumphantly employed to identify miRNAs in tumor cell lysates, providing a workable technique in creating adaptable nanostructure for dependable bioanalysis and clinical diagnosis of cancer biomarkers.
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Affiliation(s)
- Wen-Xin Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Shan Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China; School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
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5
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Feng T, Yan S, Huang Y. Novel Enzyme-Assisted Recycle Amplification Strategy for Tetracycline Detection Based on Oxidized Single-Walled Carbon Nanohorns. Molecules 2024; 29:1444. [PMID: 38611724 PMCID: PMC11013240 DOI: 10.3390/molecules29071444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
In this study, oxidized single-walled carbon nanohorns (oxSWCNHs) were prepared using nitric acid oxidation and subsequently combined with 3'6-carboxyfluorescein through charge transfer to prepare fluorescent probes. These oxSWCNHs were used to quench fluorogen signals at short distances and dissociate ssDNA using cryonase enzymes. We established a method for rapidly detecting tetracycline (TC) in complex samples based on the amplification of cryonase enzyme signals. After optimizing the experimental conditions, our method showed a detection limit of 5.05 ng/mL, with good specificity. This method was used to determine the TC content in complex samples, yielding a recovery rate of 90.0-103.3%. This result validated the efficacy of our method in detecting TC content within complex samples.
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Affiliation(s)
- Tingting Feng
- College of Traditional Chinese Medicine and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, China; (S.Y.); (Y.H.)
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6
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Long K, Cao G, Qiu Y, Yang N, Chen J, Yang M, Hou C, Huo D. Hybridization chain reaction circuit controller: CRISPR/Cas12a conversion amplifier for miRNA-21 sensitive detection. Talanta 2024; 266:125130. [PMID: 37657377 DOI: 10.1016/j.talanta.2023.125130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023]
Abstract
MicroRNA (miRNA) is crucial to the diagnose of various diseases. However, the accurate detection of miRNA has been challenging due to its short length and low abundance. Here, we designed a hybridization chain reaction (HCR) circuit controller to initiate the CRISPR/Cas12a conversion amplifier (HCR-Cas12a controller) for sensitive detection of miRNA-21 (miR-21). In the HCR, pre-crRNA was encapsulated in a hairpin structure until the miR-21 was present. Afterward, Cas12a fully exerted its RNase activity to self-mature pre-crRNA. Then, the trans-cleavage activity of Cas12a was initiated by activator. This results in the conversion of biological signals to fluorescent signal. During HCR-Cas12a controller, the circuit formed quickly, while the Cas12a system worked in a short time. The miR-21 was ultra-sensitively detected with the wide detection range of 1 fM - 100 nM, and the calculated limit of detection was 75.4 aM. The sensitivity was an order of magnitude lower than the standard method. The formation of HCR at room temperature does not require a thermal cycler. Additionally, Cas12a can work without the need for precise or expensive instruments. Therefore, our proposed method was suitable for low-resource settings, and provided a technical basis for sensitive detection of miRNA in low concentration range.
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Affiliation(s)
- Keyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Yue Qiu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Nannan Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Jian Chen
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China.
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
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Lin Q, Cao Y, Han G, Sun W, Weng W, Chen H, Wang H, Kong J. Programmable Clostridium perfringens Argonaute-Based, One-Pot Assay for the Multiplex Detection of miRNAs. Anal Chem 2023; 95:13401-13406. [PMID: 37565811 DOI: 10.1021/acs.analchem.3c01990] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Assays for the molecular detection of miRNAs are typically constrained by the level of multiplexing, especially in a single tube. Here, we report a general and programmable diagnostic platform by combining mesophilic Clostridium perfringens Argonaute (CpAgo) with exponential isothermal amplification (EXPAR), which is a dual-signal amplification strategy, allowing for the rapid and sensitive detection of multiple miRNAs with single-nucleotide discrimination in one pot. The CpAgo-based One-Pot (COP) assay achieved a limit of detection of 1 zM miRNA within 30 min of turnaround time and a wide concentration range. This COP assay was applied to simultaneously detect four miRNAs in a single tube from clinical serum samples, showing superior analytical performance in distinguishing colorectal cancer patients from healthy individuals. This programmable, one-pot, multiplex, rapid, and specific strategy offers great promise in scientific research and clinical applications.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, 200438 Shanghai, China
| | - Yuanwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Guobin Han
- Department of Chemistry, Fudan University, 200438 Shanghai, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Wenhao Weng
- Department of Clinical Laboratory Yangpu Hospital, Tongji University School of Medicine, 200090 Shanghai, China
| | - Hui Chen
- Department of Chemistry, Fudan University, 200438 Shanghai, China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, 200438 Shanghai, China
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Wei B, Huang B, Zhao X. An overview of biochemical technologies for the cancer biomarker miR-21 detection. ANAL SCI 2023; 39:815-827. [PMID: 36840858 DOI: 10.1007/s44211-023-00304-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023]
Abstract
In recent years, the incidence of cancer has continuously increased, in which various miRNAs have been proposed as biomarkers for the early screening of cancer patients. As a consequence, the development of accurate methods for miRNA quantification has become a major research challenge worldwide. As one of the first discovered oncogenic miRNAs, microRNA-21 (miR-21) has been highlighted for its critical role in cancers. This review describes the main techniques currently available for miR-21 detection, compares the differences of the methods and the amplification strategies, and provides an overview of the state of knowledge in the field.
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Affiliation(s)
- Buyun Wei
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Biao Huang
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xueqin Zhao
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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Zhao Y, Lv X, Peng Z, Zhao K, Zhou D, Deng Y. Microfluidic Chip Integrated with Hydrogel Microparticles and CdS Cation Interfacial Exchange for the Sensitive Determination of miRNA. ANAL LETT 2023. [DOI: 10.1080/00032719.2023.2180803] [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]
Affiliation(s)
- Yimeng Zhao
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Zhao Peng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kexin Zhao
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Di Zhou
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
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10
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Wang W, Ge Q, Zhao X. Enzyme-free isothermal amplification strategy for the detection of tumor-associated biomarkers: A review. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Kaur A, Mahmoud R, Megalathan A, Pettit S, Dhakal S. Multiplexed smFRET Nucleic Acid Sensing Using DNA Nanotweezers. BIOSENSORS 2023; 13:119. [PMID: 36671954 PMCID: PMC9856376 DOI: 10.3390/bios13010119] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The multiplexed detection of disease biomarkers is part of an ongoing effort toward improving the quality of diagnostic testing, reducing the cost of analysis, and accelerating the treatment processes. Although significant efforts have been made to develop more sensitive and rapid multiplexed screening methods, such as microarrays and electrochemical sensors, their limitations include their intricate sensing designs and semi-quantitative detection capabilities. Alternatively, fluorescence resonance energy transfer (FRET)-based single-molecule counting offers great potential for both the sensitive and quantitative detection of various biomarkers. However, current FRET-based multiplexed sensing typically requires the use of multiple excitation sources and/or FRET pairs, which complicates labeling schemes and the post-analysis of data. We present a nanotweezer (NT)-based sensing strategy that employs a single FRET pair and is capable of detecting multiple targets. Using DNA mimics of miRNA biomarkers specific to triple-negative breast cancer (TNBC), we demonstrated that the developed sensors are sensitive down to the low picomolar range (≤10 pM) and can discriminate between targets with a single-base mismatch. These simple hybridization-based sensors hold great promise for the sensitive detection of a wider spectrum of nucleic acid biomarkers.
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12
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Feng Y, Chen T, Rao Q, Xie X, Zhang L, Lv Y. Time-Resolved Persistent Luminescence Encoding for Multiplexed Severe Acute Respiratory Syndrome Coronavirus 2 Detection. Anal Chem 2022; 94:16967-16974. [DOI: 10.1021/acs.analchem.2c04788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yang Feng
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan610064, China
| | - Tingyan Chen
- College of Mathematics, Sichuan University, Chengdu, Sichuan610064, China
| | - Qianli Rao
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan610064, China
| | - Xiaobo Xie
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan610064, China
| | - Lichun Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan610064, China
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, China
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13
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Zhan J, Liu Z, Liu R, Zhu JJ, Zhang J. Near-Infrared-Light-Mediated DNA-Logic Nanomachine for Bioorthogonal Cascade Imaging of Endogenous Interconnected MicroRNAs and Metal Ions. Anal Chem 2022; 94:16622-16631. [DOI: 10.1021/acs.analchem.2c02577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jiayin Zhan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zheng Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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14
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Contact Lens Wear Induces Alterations of Lactoferrin Functionality in Human Tears. Pharmaceutics 2022; 14:pharmaceutics14102188. [PMID: 36297623 PMCID: PMC9612143 DOI: 10.3390/pharmaceutics14102188] [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: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
The tear film is a complex matrix composed of several molecular classes, from small metal ions to macromolecules. Contact lens (CL) wear can affect the protein homeostasis of the tear film, by accumulating deposits on the CL surface and/or altering their structural and functional properties. This work investigates the effect of CL wear on lactoferrin (Lf), one of the most abundant tear proteins, known as an unspecific biomarker of inflammation. Tears from eight volunteers were collected and analyzed after alternated periods of CL wear and without CL. The experimental approach is to probe Lf into unprocessed human tears by the peculiar fluorescence emission originating from complex formation of Lf with terbium (Tb3+) at the iron-binding sites. The experimental data indicate that CL wear does not significantly affect the total amount of Lf. On the other hand, Lf affinity for Tb3+ is reduced upon CL wear, suggesting relevant changes in Lf structure and possible alterations of protein functionality. Future studies based on this approach will help define CL features (material, lens-care solution, wearing time, etc.) with minimal effects on tear protein activity, in order to obtain more biocompatible and comfortable devices.
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15
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Wei W, Dai W, Yang F, Lu H, Zhang K, Xing Y, Meng X, Zhou L, Zhang Y, Yang Q, Cheng Y, Dong H. Spatially Resolved, Error-Robust Multiplexed MicroRNA Profiling in Single Living Cells. Angew Chem Int Ed Engl 2022; 61:e202116909. [PMID: 35194913 DOI: 10.1002/anie.202116909] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Indexed: 12/11/2022]
Abstract
Simultaneous imaging of multiple microRNAs (miRNAs) in individual living cells is challenging due to the lack of spectrally distinct encoded fluorophores and non-cytotoxic methods. We describe a multiplexed error-robust combinatorial fluorescent label-encoding method, termed fluorophores encoded error-corrected labels (FluoELs), enabling multiplexed miRNA imaging in living cells with error-correcting capability. The FluoELs comprise proportional dual fluorophores for encoding and a constant quantitative single fluorophore for error-corrected quantification. Both are embedded in 260 nm core-shell silica nanoparticles modified with molecular beacon detection probes. The FluoELs are low cytotoxic and could accurately quantify and spatially resolve nine breast-cancer-related miRNAs and evaluate their coordination. The FluoELs enabled a single-cell analysis platform to evaluate miRNA expression profiles and the molecular mechanisms underlying miRNA-associated diseases.
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Affiliation(s)
- Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Huiting Lu
- Department of Chemistry, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Kai Zhang
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yi Xing
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Yiyi Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Qiqi Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China.,Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, 3688, Nanhai Road, Shenzhen, 518060, Guangdong, China
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16
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Wei W, Dai W, Yang F, Lu H, Zhang K, Xing Y, Meng X, Zhou L, Zhang Y, Yang Q, Cheng Y, Dong H. Spatially Resolved, Error‐Robust Multiplexed MicroRNA Profiling in Single Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Huiting Lu
- Department of Chemistry School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road Beijing 100083 China
| | - Kai Zhang
- College of Materials Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
| | - Yi Xing
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yiyi Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Qiqi Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Marshall Laboratory of Biomedical Engineering Research Center for Biosensor and Nanotheranostic School of Biomedical Engineering Health Science Center Shenzhen University 3688, Nanhai Road Shenzhen 518060, Guangdong China
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17
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Qiu X, Xu J, Cardoso Dos Santos M, Hildebrandt N. Multiplexed Biosensing and Bioimaging Using Lanthanide-Based Time-Gated Förster Resonance Energy Transfer. Acc Chem Res 2022; 55:551-564. [PMID: 35084817 DOI: 10.1021/acs.accounts.1c00691] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The necessity to scrutinize more and more biological molecules and interactions both in solution and on the cellular level has led to an increasing demand for sensitive and specific multiplexed diagnostic analysis. Photoluminescence (PL) detection is ideally suited for multiplexed biosensing and bioimaging because it is rapid and sensitive and there is an almost unlimited choice of fluorophores that provide a large versatility of photophysical properties, including PL intensities, spectra, and lifetimes.The most frequently used technique to detect multiple parameters from a single sample is spectral (or color) multiplexing with different fluorophores, such as organic dyes, fluorescent proteins, quantum dots, or lanthanide nanoparticles and complexes. In conventional PL biosensing approaches, each fluorophore requires a distinct detection channel and excitation wavelength. This drawback can be overcome by Förster resonance energy transfer (FRET) from lanthanide donors to other fluorophore acceptors. The lanthanides' multiple and spectrally narrow emission bands over a broad spectral range can overlap with several different acceptors at once, thereby allowing FRET from one donor to multiple acceptors. The lanthanides' extremely long PL lifetimes provide two important features. First, time-gated (TG) detection allows for efficient suppression of background fluorescence from the biological environment or directly excited acceptors. Second, temporal multiplexing, for which the PL lifetimes are adjusted by the interaction with the FRET acceptor, can be used to determine specific biomolecules and/or their conformation via distinct PL decays. The high signal-to-background ratios, reproducible and precise ratiometric and homogeneous (washing-free) sensing formats, and higher-order multiplexing capabilities of lanthanide-based TG-FRET have resulted in significant advances in the analysis of biomolecular recognition. Applications range from fundamental analysis of biomolecular interactions and conformations to high-throughput and point-of-care in vitro diagnostics and DNA sequencing to advanced optical encoding, using both liquid and solid samples and in situ, in vitro, and in vivo detection with high sensitivity and selectivity.In this Account, we discuss recent advances in lanthanide-based TG-FRET for the development and application of advanced immunoassays, nucleic acid sensing, and fluorescence imaging. In addition to the different spectral and temporal multiplexing approaches, we highlight the importance of the careful design and combination of different biological, organic, and inorganic molecules and nanomaterials for an adjustable FRET donor-acceptor distance that determines the ultimate performance of the diagnostic assays and conformational sensors in their physiological environment. We conclude by sharing our vision on how progress in the development of new sensing concepts, material combinations, and instrumentation can further advance TG-FRET multiplexing and accelerate its translation into routine clinical practice and the investigation of challenging biological systems.
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Affiliation(s)
- Xue Qiu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingyue Xu
- nanofret.com, Laboratoire COBRA, Université de Rouen Normandie, Normandie Université, CNRS, INSA Rouen, 76000 Rouen, France
| | - Marcelina Cardoso Dos Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Niko Hildebrandt
- nanofret.com, Laboratoire COBRA, Université de Rouen Normandie, Normandie Université, CNRS, INSA Rouen, 76000 Rouen, France
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Université Paris-Saclay, 91405 Orsay Cedex, France
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18
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Liu S, Xiang K, Wang C, Zhang Y, Fan GC, Wang W, Han H. DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects. ACS Sens 2022; 7:3-20. [PMID: 34989231 DOI: 10.1021/acssensors.1c01647] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.
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Affiliation(s)
- Shanshan Liu
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Kaikai Xiang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Chunyan Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Yutian Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Gao-Chao Fan
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, Shandong, People’s Republic of China
| | - Wenjing Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, People’s Republic of China
| | - Heyou Han
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
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19
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Wang BX, Xu W, Yang Z, Wu Y, Pi F. An Overview on Recent Progress of the Hydrogels: From Material Resources, Properties to Functional Applications. Macromol Rapid Commun 2022; 43:e2100785. [PMID: 35075726 DOI: 10.1002/marc.202100785] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/04/2022] [Indexed: 11/06/2022]
Abstract
Hydrogels, as the most typical elastomer materials with three-dimensional network structures, have attracted wide attention owing to their outstanding features in fields of sensitive stimulus response, low surface friction coefficient, good flexibility and bio-compatibility. Because of numerous fresh polymer materials (or polymerization monomers), hydrogels with various structure diversities and excellent properties are emerging, and the development of hydrogels is very vigorous over the past decade. This review focuses on state-of-the-art advances, systematically reviews the recent progress on construction of novel hydrogels utilized several kinds of typical polymerization monomers, and explores the main chemical and physical cross-linking methods to develop the diversity of hydrogels. Following the aspects mentioned above, the classification and emerging applications of hydrogels, such as pH response, ionic response, electrical response, thermal response, biomolecular response, and gas response, are extensively summarized. Finally, we have done this review with the promises and challenges for the future evolution of hydrogels and their biological applications. cross-linking methods; functional applications; hydrogels; material resources This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ben-Xin Wang
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Wei Xu
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Zhuchuang Yang
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Yangkuan Wu
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Fuwei Pi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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20
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A Novel Colorimetric Nano Aptasensor for Ultrasensitive Detection of Aflatoxin B1 Based on the Exonuclease III-Assisted Signal Amplification Approach. Foods 2021; 10:foods10112568. [PMID: 34828849 PMCID: PMC8625208 DOI: 10.3390/foods10112568] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 12/25/2022] Open
Abstract
The detection of aflatoxin B1 (AFB1) has recently garnered much attention on the issue of food safety. In this study, a novel and sensitive aptasensor towards AFB1 is proposed using an Exonuclease III (Exo III)-integrated signal amplification strategy. This reported sensing strategy is regulated by aptamer-functionalized nanobeads that can target AFB1; furthermore, complementary DNA (cDNA) strands can lock the immobilized aptamer strands, preventing the signal amplification function of Exo III in the absence of AFB1. The presence of AFB1 triggers the displacement of cDNA, which will then activate the Exo III-integrated signal amplification procedure, resulting in the generation of a guanine (G)-rich sequence to form a G-4/hemin DNAzyme, which can catalyze the substrate of ABTS to produce a green color. Using this method, a practical detection limit of 0.0032 ng/mL and a dynamic range of detection from 0.0032 to 50 ng/mL were obtained. Additionally, the practical application of the established sensing method for AFB1 in complex matrices was demonstrated through recovery experiments. The recovery rate and relative standard deviations (RSD) in three kinds of cereal samples ranged from 93.83% to 111.58%, and 0.82% to 7.20%, respectively, which were comparable with or better than previously reported methods.
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21
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Sun G, Xie Y, Sun L, Zhang H. Lanthanide upconversion and downshifting luminescence for biomolecules detection. NANOSCALE HORIZONS 2021; 6:766-780. [PMID: 34569585 DOI: 10.1039/d1nh00299f] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomolecules play critical roles in biological activities and are closely related to various disease conditions. The reliable, selective and sensitive detection of biomolecules holds much promise for specific and rapid biosensing. In recent years, luminescent lanthanide probes have been widely used for monitoring the activity of biomolecules owing to their long luminescence lifetimes and line-like emission which allow time-resolved and ratiometric analyses. In this review article, we concentrate on recent advances in the detection of biomolecule activities based on lanthanide luminescent systems, including upconversion luminescent nanoparticles, lanthanide-metal organic frameworks, and lanthanide organic complexes. We also introduce the latest remarkable accomplishments of lanthanide probes in the design principles and sensing mechanisms, as well as the forthcoming challenges and perspectives for practical achievements.
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Affiliation(s)
- Guotao Sun
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China.
| | - Yao Xie
- Research Center of Nano Science and Technology, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Lining Sun
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China.
- Research Center of Nano Science and Technology, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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22
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Duan Y, Glazier R, Bazrafshan A, Hu Y, Rashid SA, Petrich BG, Ke Y, Salaita K. Mechanically Triggered Hybridization Chain Reaction. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yuxin Duan
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | | | - Yuesong Hu
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Sk Aysha Rashid
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | | | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Khalid Salaita
- Department of Chemistry Emory University Atlanta GA 30322 USA
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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23
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Duan Y, Glazier R, Bazrafshan A, Hu Y, Rashid SA, Petrich BG, Ke Y, Salaita K. Mechanically Triggered Hybridization Chain Reaction. Angew Chem Int Ed Engl 2021; 60:19974-19981. [PMID: 34242462 PMCID: PMC8390435 DOI: 10.1002/anie.202107660] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Indexed: 01/16/2023]
Abstract
Cells transmit piconewton forces to receptors to mediate processes such as migration and immune recognition. A major challenge in quantifying such forces is the sparsity of cell mechanical events. Accordingly, molecular tension is typically quantified with high resolution fluorescence microscopy, which hinders widespread adoption and application. Here, we report a mechanically triggered hybridization chain reaction (mechano-HCR) that allows chemical amplification of mechanical events. The amplification is triggered when a cell receptor mechanically denatures a duplex revealing a cryptic initiator to activate the HCR reaction in situ. Importantly, mechano-HCR enables direct readout of pN forces using a plate reader. We leverage this capability and measured mechano-IC50 for aspirin, Y-27632, and eptifibatide. Given that cell mechanical phenotypes are of clinical importance, mechano-HCR may offer a convenient route for drug discovery, personalized medicine, and disease diagnosis.
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Affiliation(s)
- Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | | | - Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Sk Aysha Rashid
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Brian G Petrich
- Department of Pediatrics, Emory University, Atlanta, GA, 30322, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
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24
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Kim J, Shim JS, Han BH, Kim HJ, Park J, Cho IJ, Kang SG, Kang JY, Bong KW, Choi N. Hydrogel-based hybridization chain reaction (HCR) for detection of urinary exosomal miRNAs as a diagnostic tool of prostate cancer. Biosens Bioelectron 2021; 192:113504. [PMID: 34298498 DOI: 10.1016/j.bios.2021.113504] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022]
Abstract
Although urinary exosomal microRNAs (miRNAs) have recently emerged as potential biomarkers, clinical applications are still limited due to their low concentration in small volumes of clinical samples. Therefore, the development of a non-invasive, specific diagnostic tool, along with profiling exosomal miRNA markers from urine, remains a significant challenge. Here, we present hydrogel-based hybridization chain reaction (HCR) for multiplex signal amplification to detect urinary exosomal miRNAs from human clinical samples. We succeeded in identifying small amounts (~amol) of exosomal miRNAs from 600 μL of urine with up to ~35-fold amplification and enhanced detection limits by over an order of magnitude for two miRNA biomarker candidates, hsa-miR-6090 and hsa-miR-3665. Furthermore, we proposed ratiometric analysis without requiring normalization to a reference miRNA and validated the clinical diagnostic potential toward differentiating prostate cancer patients from healthy controls. Our hydrogel-based HCR could serve as a new diagnostic platform for a non-invasive liquid biopsy before burdensome tissue biopsy of various diseases, including prostate cancer screening, complementing the PSA test.
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Affiliation(s)
- Junbeom Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, South Korea
| | - Ji Sung Shim
- Department of Urology, Korea University College of Medicine, Seoul, 02841, South Korea
| | - Bo Hoon Han
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; School of Mechanical Engineering, Korea University, Seoul, 02841, South Korea
| | - Hye Jin Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Jaesung Park
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea; School of Interdisciplinary Bioscience and Bioengineering. Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Il-Joo Cho
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, South Korea; School of Electrical and Electronics Engineering, Yonsei University, Seoul, 03722, South Korea; Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, South Korea
| | - Sung Gu Kang
- Department of Urology, Korea University College of Medicine, Seoul, 02841, South Korea
| | - Ji Yoon Kang
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, South Korea
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, South Korea.
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, South Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, South Korea.
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25
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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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26
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Xu J, Qiu X, Hildebrandt N. When Nanoworlds Collide: Implementing DNA Amplification, Nanoparticles, Molecules, and FRET into a Single MicroRNA Biosensor. NANO LETTERS 2021; 21:4802-4808. [PMID: 34041910 DOI: 10.1021/acs.nanolett.1c01351] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Isothermal nucleic acid amplification strategies have been combined with nanotechnology for advanced biosensing, material design, and biomedical applications. However, merging phenomena and materials of different nanoscales with the aim of exploiting all their benefits at once has remained a challenging endeavor. Here, we exemplify the various problems one can encounter when combining the nanodimensions of lanthanide complexes (∼2 nm), Förster resonance energy transfer (FRET, ∼5 nm), quantum dots (QDs, ∼20 nm), and rolling circle amplification (RCA, ∼250 nm) into a single microRNA biosensor and how these challenges can be overcome. Six different approaches, including simple FRET-RCA, enzyme-digesting FRET-RCA, and FRET-hyperbranched-RCA were investigated. We demonstrated specific miR-21 detection with 80 fM limit of detection and multiplexing capability with FRET from a Tb complex to different QDs. The detailed view on the various complex multi-nanodimensional assay systems elucidated the limited clinical translation of such sophisticated multicomponent nanobiosensors.
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Affiliation(s)
- Jingyue Xu
- nanofret.com, Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Xue Qiu
- School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Niko Hildebrandt
- nanofret.com, Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
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27
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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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28
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Feng H, Liu L, Chen Y, Shu W, Huang Y, Zhang B, Wu T, Jin Z, Chen Y. A compact fiber-integrated optofluidic platform for highly specific microRNA Förster resonance energy transfer detection. Analyst 2021; 146:4454-4460. [PMID: 33982715 DOI: 10.1039/d1an00324k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) have attracted extensive interest as promising biomarkers for the profiling of diseases. However, quantitative measurement of miRNAs presents a significant challenge in biochemical studies. In this work, we developed an innovative optofluidic platform to perform a rapid, simple, quantitative and high-specificity miRNA assay using the Förster resonance energy transfer (FRET) principle. A novel three-way junction FRET probe was proposed to enable rapid and enzyme-free miRNA detection. Using this platform, we performed one-step, amplification-free miRNA detection with simple device operation and achieved miRNA identification at a low concentration. The detection system could achieve high specificity for discrimination of three-base mismatches, and the sample volume was significantly reduced, favorable for low-level miRNA detection in material-limited samples. The establishment of a compact, low-cost, highly sensitive and selective miRNA analysis platform provides a valuable tool for point-of-care diagnosis.
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Affiliation(s)
- Hongtao Feng
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Lin Liu
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yi Chen
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Weiliang Shu
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yuqing Huang
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Baoyue Zhang
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Tianzhun Wu
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Zongwen Jin
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yan Chen
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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29
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Wang G, Guo Y, Liu Y, Zhou W, Wang G. Algorithm-Assisted Detection and Imaging of microRNAs in Living Cancer Cells via the Disassembly of Plasmonic Core-Satellite Probes Coupled with Strand Displacement Amplification. ACS Sens 2021; 6:958-966. [PMID: 33445872 DOI: 10.1021/acssensors.0c02136] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acute detection and high-resolution imaging of microRNAs (miRNAs) in living cancer cells have attracted great attention in clinical diagnosis and therapy. However, current methods suffer from low detection sensitivity or heavy dependence on expensive and sophisticated spectrometers. Herein, a novel algorithm-assisted system of detecting and imaging miRNAs in living cancer cells was developed via the disassembly of plasmonic core-satellite probes coupled with strand displacement amplification (SDA). The target miRNAs in the system could trigger the disassembly of plasmonic core-satellite probes, leading to the color change in the scattering light of the probes, which could be captured by dark-field microscopy (DFM). The concentration of the target miRNAs was obtained by analyzing the dark-field image based on the proposed algorithm with a detection limit of 2 pM for miRNA-21. Thus, the performance in terms of simplicity and sensitivity of the system compared with one of the conventional spectrophotometers was well presented, which could inspire more clinical applications of inexpensive, intelligent, and rapid screening of cancer cells. The application software based on the proposed algorithm running on the Android platform was also developed, demonstrating the potential of remote diagnosis.
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Affiliation(s)
- Ganglin Wang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Yanbin Guo
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Yingbin Liu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Weihang Zhou
- Wuhan National High Magnetic Field Center and School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Guoping Wang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
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30
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Shandilya R, Ranjan S, Khare S, Bhargava A, Goryacheva IY, Mishra PK. Point-of-care diagnostics approaches for detection of lung cancer-associated circulating miRNAs. Drug Discov Today 2021; 26:1501-1509. [PMID: 33647439 DOI: 10.1016/j.drudis.2021.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
Circulating cell-free miRNAs (ccf-miRs) have gained significant interest as biomarkers for lung cancer (LC) diagnosis. However, the clinical application of ccf-miRs is mainly limited by time, cost, and expertise-related problems of existing detection strategies. Recently, the development of different point-of-care (POC) approaches offers useful on-site platforms, because these technologies have important features such as portability, rapid turnaround time, minimal sample requirement, and cost-effectiveness. In this review, we discuss different POC approaches for detecting ccf-miRs and highlight the utility of incorporating nanomaterials for enhanced biorecognition and signal transduction, further improving their diagnostic applicability in LC settings.
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Affiliation(s)
- Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Shashi Ranjan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Surbhi Khare
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Irina Yu Goryacheva
- Department of General and Inorganic Chemistry, Institute of Chemistry, Saratov State University, Saratov, Russia
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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31
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Jet T, Gines G, Rondelez Y, Taly V. Advances in multiplexed techniques for the detection and quantification of microRNAs. Chem Soc Rev 2021; 50:4141-4161. [PMID: 33538706 DOI: 10.1039/d0cs00609b] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.
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Affiliation(s)
- Thomas Jet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, CNRS SNC5096, Equipe Labellisée Ligue Nationale Contre le Cancer, F-75006 Paris, France.
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32
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Francés-Soriano L, Leino M, Dos Santos MC, Kovacs D, Borbas KE, Söderberg O, Hildebrandt N. In Situ Rolling Circle Amplification Förster Resonance Energy Transfer (RCA-FRET) for Washing-Free Real-Time Single-Protein Imaging. Anal Chem 2021; 93:1842-1850. [PMID: 33356162 DOI: 10.1021/acs.analchem.0c04828] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescence signal enhancement via isothermal nucleic acid amplification is an important approach for sensitive imaging of intra- or extracellular nucleic acid or protein biomarkers. Rolling circle amplification (RCA) is frequently applied for fluorescence in situ imaging but faces limitations concerning multiplexing, dynamic range, and the required multiple washing steps before imaging. Here, we show that Förster resonance energy transfer (FRET) between fluorescent dyes and between lanthanide (Ln) complexes and dyes that hybridize to β-actin-specific RCA products in HaCaT cells can afford washing-free imaging of single β-actin proteins. Proximity-dependent FRET could be monitored directly after or during (real-time monitoring) dye or Ln DNA probe incubation and could efficiently distinguish between photoluminescence from β-actin-specific RCA and DNA probes freely diffusing in solution or nonspecifically attached to cells. Moreover, time-gated FRET imaging with the Ln-dye FRET pairs efficiently suppressed sample autofluorescence and improved the signal-to-background ratio. Our results present an important proof of concept of RCA-FRET imaging with a strong potential to advance in situ RCA toward easier sample preparation, higher-order multiplexing, autofluorescence-free detection, and increased dynamic range by real-time monitoring of in situ RCA.
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Affiliation(s)
- Laura Francés-Soriano
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, 75124 Uppsala, Sweden
| | - Marcelina Cardoso Dos Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Daniel Kovacs
- Department of Chemistry, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - K Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, 75124 Uppsala, Sweden
| | - Niko Hildebrandt
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
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33
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Borum RM, Jokerst JV. Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging. Biomater Sci 2021; 9:347-366. [PMID: 32734995 PMCID: PMC7855509 DOI: 10.1039/d0bm00931h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.
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Affiliation(s)
- Raina M Borum
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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34
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Xu M, Lin L, Li N, Jiang X, Li J, Gong L, Zhuang J. Nanoscale assembly line composed of dual DNA-machines enabling sensitive microRNA detection using upconversion nanoparticles probes. J Pharm Biomed Anal 2020; 195:113842. [PMID: 33358621 DOI: 10.1016/j.jpba.2020.113842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
DNA machines are smart artificial devices that perform well-organized DNA hybridization reactions or nanoscale mechanical movements. Herein, a nanoscale assembly line composing of dual DNA machines is meticulously designed by coupling a catalytic hairpin assembly (CHA)-based machine with a 3D DNA walker machine. Equipped with upconversion nanoparticles (UCNPs) as signal tags, the dual DNA machines-based assembly line (DDMAL) can efficiently amplify the fluorescent signal of target recognition event, enabling sensitive detection of microRNA (miRNA). In detail, once activated by target miRNA-21, the CHA machine is initiated to constantly produce a single-stranded DNA (named binding DNA) via the strand displacement reaction. The binding DNA as a trigger factor can initiate the DNA walker machine by linking a walking strand DNA with an anchor strand DNA immobilized on the surface of magnetic beads (MBs). The movement of walking strand on the surface of MBs is then driven by Mn2+-dependent DNAzyme formed through the hybridization of walking strand with a UCNPs-linked substrate strand. The DNAzyme-catalyzed cleavage of substrate strand is accompanied by the release of numerous UCNPs from MBs. By measuring the fluorescent signal of released UCNPs after the magnetic separation, target miRNA-21 can be detected by the DDMAL system in a linear range from 1.0 fM to 10 nM, with a limit of detection (LOD) of 0.62 fM (3σ). Moreover, the practicability of DDMAL system was demonstrated by using it to evaluate the expression levels of miRNA-21 in cell lines and assay miRNA-21 in human serum.
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Affiliation(s)
- Mingdi Xu
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China.
| | - Lang Lin
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Ning Li
- The Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, School of Pharmacy, Fujian Medical University, Fuzhou, 350122, PR China
| | - Xiaoyu Jiang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Jingling Li
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Lingzhu Gong
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, PR China
| | - Junyang Zhuang
- The Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, School of Pharmacy, Fujian Medical University, Fuzhou, 350122, PR China.
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35
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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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36
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Wang D, Chai Y, Yuan Y, Yuan R. Simple and Regulable DNA Dimer Nanodevice to Arrange Cascade Enzymes for Sensitive Electrochemical Biosensing. Anal Chem 2020; 92:14197-14202. [DOI: 10.1021/acs.analchem.0c03396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ding Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yali Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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37
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Yang Z, Peng X, Yang P, Zhuo Y, Chai YQ, Liang W, Yuan R. A Janus 3D DNA nanomachine for simultaneous and sensitive fluorescence detection and imaging of dual microRNAs in cancer cells. Chem Sci 2020; 11:8482-8488. [PMID: 34123108 PMCID: PMC8163441 DOI: 10.1039/d0sc02850a] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Herein, a Janus three-dimensional (3D) DNA nanomachine was constructed for the simultaneous and sensitive fluorescence detection and imaging of dual microRNAs (miRNAs) in cancer cells, which could effectively eliminate signal interference in a homogeneous nanoparticle-based 3D DNA nanostructure caused by the proximity of the two different signal probes to achieve accurate co-location in the same position of living cancer cells. In this system, the Janus nanoparticles were synthesized as the carrier for immobilizing two different oligonucleotides on two different functionalized hemispheres of the nanoparticles to form a Janus 3D DNA nanostructure, which could convert trace amounts of miRNA-21 and miRNA-155 targets into massive FAM and Cy5-labeled duplexes to induce two remarkable fluorescence emissions by the catalytic hairpin assembly (CHA) and 3D DNA walker cascade nucleic acid amplification strategy, realizing sensitive detection and imaging of miRNA targets in cancer cells. Impressively, in comparison with current miRNA imaging methods based on nanoparticle assemblies, the proposed strategy could efficiently eliminate “false positive” results obtained in single type miRNA detection and distinctly increase the immobilization concentration of two different signal probes using Janus nanoparticles as the carrier to further enhance fluorescence intensity, resulting in accurate co-location in the same position of living cells. Meanwhile, the proposed fluorescence imaging technology makes it possible to visualize low concentrations of miRNAs with tiny change associated with some cancers, which could significantly improve the accuracy and precision compared to those of the conventional fluorescence in situ hybridization (FISH) approach. Therefore, it could serve as persuasive evidence for supplying accurate information to better understand biological processes and investigate mechanisms of various biomolecules and subcellular organelles, resulting in the further validation of their function in tumor proliferation and differentiation. This strategy provided an innovative approach to design new generations of nanomachines with ultimate applications in bioanalysis and clinical diagnoses. A Janus three-dimensional DNA nanomachine was constructed for the simultaneous and sensitive fluorescent detection and imaging of dual microRNAs in the cancer cells.![]()
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Affiliation(s)
- Zezhou Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Xin Peng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Wenbin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
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38
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Xu J, Guo J, Golob-Schwarzl N, Haybaeck J, Qiu X, Hildebrandt N. Single-Measurement Multiplexed Quantification of MicroRNAs from Human Tissue Using Catalytic Hairpin Assembly and Förster Resonance Energy Transfer. ACS Sens 2020; 5:1768-1776. [PMID: 32438801 DOI: 10.1021/acssensors.0c00432] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Absolute quantification of microRNAs (miRNAs) or other nucleic acid biomarkers is an important requirement for molecular and clinical biosensing. Emerging technologies with beneficial features concerning simplicity and multiplexing present an attractive route for advancing diagnostic tools toward rapid and low-cost bioanalysis. However, the actual translation into the clinic by miRNA quantification in human samples is often missing. Here, we show that implementing time-gated Förster resonance energy transfer (TG-FRET) into a catalytic hairpin assembly (CHA) can be used for the simultaneous quantification of two miRNAs with a single measurement from total RNA extracts of human tissues. A single terbium-dye FRET pair was conjugated at two specific distances within target-specific CHA hairpin probes, such that each miRNA resulted in distinct amplified photoluminescence (PL) decays that could be distinguished and quantified by TG PL intensity detection. Enzyme-free amplification in a separation-free assay format and the absence of autofluorescence background allowed for simple, specific, and sensitive detection of miR-21 and miR-20a with limits of detection down to 1.8 pM (250 amol). Reliable duplexed quantification of both miRNAs at low picomolar concentrations was confirmed by analyzing total RNA extracts from different colon and rectum tissues with single- and dual-target CHA-TG-FRET and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for comparison. These simple and multiplexed nucleic acid biomarker assays present a capable method for clinical diagnostics and biomolecular research.
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Affiliation(s)
- Jingyue Xu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
- nanofret.com, Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
| | - Jiajia Guo
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Nicole Golob-Schwarzl
- Department of Dermatology and Venerology, Medical University of Graz, A-8010 Graz, Austria
| | - Johannes Haybaeck
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, A-8010 Graz, Austria
- Department of Pathology, Neuropathology, and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Xue Qiu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
- School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao Shandong, China
| | - Niko Hildebrandt
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
- nanofret.com, Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
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39
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Emerging isothermal amplification technologies for microRNA biosensing: Applications to liquid biopsies. Mol Aspects Med 2020; 72:100832. [DOI: 10.1016/j.mam.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 02/07/2023]
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40
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Zhao H, Wang M, Xiong X, Liu Y, Chen X. Simultaneous fluorescent detection of multiplexed miRNA of liver cancer based on DNA tetrahedron nanotags. Talanta 2020; 210:120677. [DOI: 10.1016/j.talanta.2019.120677] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 02/08/2023]
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41
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Tao G, Lai T, Xu X, Ma Y, Wu X, Pei X, Liu F, Li N. Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification. Anal Chem 2020; 92:3697-3706. [PMID: 32037812 DOI: 10.1021/acs.analchem.9b04823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For multiplexed detection, it is important yet challenging to simultaneously meet the requirement of sensitivity, throughput, and implementation convenience for practical applications. Using the detection of DNAs and miRNAs for illustration, we present a colocalized particle counting platform that can realize the separation-free multiplexed detection of 6 nucleic acid targets with a zeptomole sensitivity and a dynamic range of up to 5 orders of magnitude. The presence of target induces the formation of a sandwich nanostructure via hybridization; thus, there is an occurrence of colocalization of two microbeads with two different colors. The sequence specific coding is realized by an arbitrary combination of two fluorescence channels with different emitting colors. The platform presents robustness in detecting multiple nucleic acid targets with a minimal cross talk and matrix effect as well as the ability to distinguish the specific miRNA from members of the same family. The results of simultaneous detection of 3 miRNAs in 3 different cell lines present straight consistency with that of the standard qRT-PCR. This platform can be adapted to other multiplexing designs such as the "turn-off" mode, in which the proportion of colocalized microbeads is decreased due to the strand-displacement reaction initiated by the specific target. This separation-free platform offers the possibility to achieve the on-site multiplexed detection with compatibility to different experimental designs and extensibility to other signal sources for enumeration.
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Affiliation(s)
- Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tiancheng Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xu
- Environmental Metrology Center, National Institute of Metrology, Beijing 100029, China
| | - Yurou Ma
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xi Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaojing Pei
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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42
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Advances in oligonucleotide-based detection coupled with fluorescence resonance energy transfer. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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43
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44
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Sensitive colorimetric determination of microRNA let-7a through rolling circle amplification and a peroxidase-mimicking system composed of trimeric G-triplex and hemin DNAzyme. Mikrochim Acta 2020; 187:139. [DOI: 10.1007/s00604-019-4093-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/22/2019] [Indexed: 01/07/2023]
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45
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Shen Z, He L, Wang W, Tan L, Gan N. Highly sensitive and simultaneous detection of microRNAs in serum using stir-bar assisted magnetic DNA nanospheres-encoded probes. Biosens Bioelectron 2019; 148:111831. [PMID: 31706172 DOI: 10.1016/j.bios.2019.111831] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/17/2022]
Abstract
There are critical interests in the detection of microRNA (miRNA) because it can be a blood-borne biomarker, but analytical strategies are still limited by its small size, high sequence homology among family members and low abundance. In this work, three-dimensional magnetic DNA nanospheres were synthesized and immobilized on a gold stir-bar as encoded probes for miRNA capture and signal amplification. Electrochemical tags-labeled DNAs were immobilized on gold coated magnetic nanospheres via a hyperbranched hybridization chain reaction (HHCR). Subsequently, the magnetic DNA nanospheres were immobilized on the gold stir-bar as encoded probes. Target miRNAs were captured on the surface of the stir-bar by replacing the magnetic DNA nanospheres-encoded probes, and the probes were magnetically enriched for highly sensitive and selective electrochemical detection. The gold stir-bar assisted magnetic DNA nanospheres-encoded probes possess dual functions: They are as a nanocarrier to increase the loading amounts of HHCR products, and they are also a platform for efficient electrochemical signal amplification via magnetic enrichment. The method was successfully applied for the detection of miRNA21 and miRNA155 in a wide linear range of 5 fM to 2 nM, and with detection limits of 1.5 fM and 1.8 fM, respectively. The preliminary application of the method suggests that it has great potential in the detection of miRNAs in serum samples.
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Affiliation(s)
- Zhipeng Shen
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Liyong He
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Wenhai Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Lei Tan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China.
| | - Ning Gan
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
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46
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Ma X, Li H, Qiao S, Huang C, Liu Q, Shen X, Geng Y, Xu W, Sun C. A simple and rapid sensing strategy based on structure-switching signaling aptamers for the sensitive detection of chloramphenicol. Food Chem 2019; 302:125359. [PMID: 31442702 DOI: 10.1016/j.foodchem.2019.125359] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 01/06/2023]
Abstract
A simple and rapid sensing strategy was proposed for chloramphenicol (CAP) detection based on structure-switching signaling aptamers. In this protocol, the aptamer can bind to both the fluorophore (FAM)-labeled complementary strand and the quencher (BHQ1)-labeled complementary strand, thus leading to the effective quenching of FAM fluorescence by BHQ1. However, when CAP is present, the structure switch is reversed because the aptamer recognizes CAP, resulting in fluorescence recovery. Such a fluorescence-sensing platform can monitor CAP within a good linear range (1-100 ng/mL), with a detection limit of 0.70 ng/mL. Cross-reactivity with other common antibiotics is negligible, indicating the excellent selectivity of the strategy. Moreover, as the aptamers are not modified, this method is simple and low-cost. The present work reveals a new direction for detecting CAP or other target compounds without prior knowledge of the secondary or tertiary structures of the aptamer.
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Affiliation(s)
- Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Hongxia Li
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, China
| | - Shangna Qiao
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Chujun Huang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Qiuli Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Xu Shen
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yongxing Geng
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, 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 and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China.
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47
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Qiu X, Hildebrandt N. A clinical role for Förster resonance energy transfer in molecular diagnostics of disease. Expert Rev Mol Diagn 2019; 19:767-771. [DOI: 10.1080/14737159.2019.1649144] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, France
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48
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Chen C, Corry B, Huang L, Hildebrandt N. FRET-Modulated Multihybrid Nanoparticles for Brightness-Equalized Single-Wavelength Barcoding. J Am Chem Soc 2019; 141:11123-11141. [DOI: 10.1021/jacs.9b03383] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chi Chen
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Ben Corry
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Liang Huang
- College of Chemical Engineering, Zhejiang University of Technology, 310014, Hangzhou, People’s Republic of China
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
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49
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Yang W, Shen Y, Zhang D, Li C, Yuan R, Xu W. Programmed Dual-Functional DNA Tweezer for Simultaneous and Recognizable Fluorescence Detection of microRNA and Protein. Anal Chem 2019; 91:7782-7789. [DOI: 10.1021/acs.analchem.9b01266] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wenting Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yu Shen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Danyang Zhang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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50
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Xu Z, Chang Y, Chai Y, Wang H, Yuan R. Ultrasensitive Electrochemiluminescence Biosensor for Speedy Detection of microRNA Based on a DNA Rolling Machine and Target Recycling. Anal Chem 2019; 91:4883-4888. [DOI: 10.1021/acs.analchem.9b00728] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ziqi Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yuanyuan Chang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Haijun Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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