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Chen Y, Liu Z, Zhang B, Wu H, Lv X, Zhang Y, Lin Y. Biomedical Utility of Non-Enzymatic DNA Amplification Reaction: From Material Design to Diagnosis and Treatment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404641. [PMID: 39152925 DOI: 10.1002/smll.202404641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/04/2024] [Indexed: 08/19/2024]
Abstract
Nucleic acid nanotechnology has become a promising strategy for disease diagnosis and treatment, owing to remarkable programmability, precision, and biocompatibility. However, current biosensing and biotherapy approaches by nucleic acids exhibit limitations in sensitivity, specificity, versatility, and real-time monitoring. DNA amplification reactions present an advantageous strategy to enhance the performance of biosensing and biotherapy platforms. Non-enzymatic DNA amplification reaction (NEDAR), such as hybridization chain reaction and catalytic hairpin assembly, operate via strand displacement. NEDAR presents distinct advantages over traditional enzymatic DNA amplification reactions, including simplified procedures, milder reaction conditions, higher specificity, enhanced controllability, and excellent versatility. Consequently, research focusing on NEDAR-based biosensing and biotherapy has garnered significant attention. NEDAR demonstrates high efficacy in detecting multiple types of biomarkers, including nucleic acids, small molecules, and proteins, with high sensitivity and specificity, enabling the parallel detection of multiple targets. Besides, NEDAR can strengthen drug therapy, cellular behavior control, and cell encapsulation. Moreover, NEDAR holds promise for constructing assembled diagnosis-treatment nanoplatforms in the forms of pure DNA nanostructures and hybrid nanomaterials, which offer utility in disease monitoring and precise treatment. Thus, this paper aims to comprehensively elucidate the reaction mechanism of NEDAR and review the substantial advancements in NEDAR-based diagnosis and treatment over the past five years, encompassing NEDAR-based design strategies, applications, and prospects.
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Affiliation(s)
- Ye Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Bowen Zhang
- Department of Prosthodontics, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, 300041, P. R. China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, 300041, P. R. China
| | - Haoyan Wu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaoying Lv
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, 610041, P. R. China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
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Sugawara T, Oishi M. Latent Toehold-Mediated DNA Circuits Based on a Bulge-Loop Structure for Leakage Reduction and Its Application to Signal-Amplifying DNA Logic Gates. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15907-15915. [PMID: 38508218 DOI: 10.1021/acsami.3c19344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
DNA circuits based on successive toehold-mediated DNA displacement reactions, particularly entropy-driven DNA circuit (EDC) systems, have attracted considerable attention as powerful enzyme-free tools for dynamic DNA nanotechnology. However, background leakage (noise signal) often occurs when the circuit is executed nonspecifically, even in the absence of the appropriate catalyst DNA (input). This study designed and developed a new latent toehold-mediated DNA circuit (LDC) system that relies on a bulge-loop structure as a latent toehold toward leakage reduction. Furthermore, the number (size) of nucleotides (nt) in the bulge-loop is found to play a significant role in the performance (i.e., leakage, signal, and kinetics) of LDC systems. In fact, the signal rate for the LDC systems increased as the number of nt in the bulge-loop increased from 4 to 8, whereas the leakage rate of the LDC systems with bulge-loops of 7 nt or less was low, but the leakage rate of the LDC system with a bulge-loop of 8 nt increased significantly. Note that the LDC system with the optimal bulge-loop (7 nt) was capable of not only reducing the leakage but also accelerating the circuit speed without any signal loss, unlike methods of reducing the leakage by reducing the signal reported previously for the conventional EDC systems. These facts indicate that the 7 nt bulge-loop acts as a "latent" toehold for the DNA circuit system. By using the amplification function of output signals with an accelerated circuit and reduced leakage, our LDC system with a 7 nt bulge-loop could be applied directly and successfully to signal-amplifying DNA logic gates such as OR and AND gates, and thus, sufficient output signals could be obtained even with a small amount of input. These findings reveal that our LDC systems with a bulge-loop structure can replace the conventional EDC system and have enormous potential in the field of DNA nanotechnology.
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Affiliation(s)
- Taku Sugawara
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| | - Motoi Oishi
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
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Zhang L, Zhao H, Yang H, Su X. Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection. Biosens Bioelectron 2023; 239:115622. [PMID: 37611449 DOI: 10.1016/j.bios.2023.115622] [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: 05/29/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
DNA-based enzyme-free signal amplification strategies are widely employed to detect biomarkers in low abundance. To enhance signal amplification, localized DNA reaction units which increases molecular collision probability is commonly utilized. However, the current understanding of the structure-function relationships in localized DNA signal amplification probes is limited, leading to unsatisfied performance. In this study, we introduced a coarse-grained molecular model to simulate the dynamic behavior of two DNA reaction units within a DNA enzyme-free signal amplification circuit called Localized Catalytic Hairpin Assembly (LCHA). We investigated the impact of localized distance and flexibility on reaction performance. The most efficient LCHA probe guided by simulation exhibits sensitivity 28 times greater that of free CHA, with a detection limit of miR-21 reaching 16 pM, while the least effective LCHA probe demonstrated a modest improvement of only 7 times. We successfully employed the optimized probe to differentiate cancer cells from normal cells based on their miR-21 expression levels, showcasing its quantification ability. By elucidating the mechanistic insights and structure-function relationship in our work, we aim to contribute valuable information that can save users' time and reduce costs when designing localized DNA probes. With a comprehensive understanding of how the localization affects probe performance, researchers can now make more informed and efficient decisions during the design process. This work would find broad applications of DNA nanotechnology in biosensing, biocomputing, and bionic robots.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hongyang Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huixiao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Kou Q, Wang L, Zhang L, Ma L, Fu S, Su X. Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2205191. [PMID: 36287076 DOI: 10.1002/smll.202205191] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/30/2022] [Indexed: 06/16/2023]
Abstract
DNA-based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse-grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided-LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation-guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL-1 , respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.
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Affiliation(s)
- Qiaoni Kou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Lei Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Liang Ma
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, 100029, P. R. China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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Liu Q, Hou L, Zhang Y, Liu M, Jin Y, Li B. Improving efficiency of entropy-driven DNA amplification biosensing through producing two label-free signal strands in one cycle. Anal Chim Acta 2022; 1232:340484. [DOI: 10.1016/j.aca.2022.340484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/01/2022]
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Kim E, Xu J, Kim J, Chun H. Improving the robustness of a catalyzed hairpin assembly with a three-arm nanostructure for nonenzymatic signal amplification. Analyst 2022; 147:1899-1905. [DOI: 10.1039/d2an00209d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nonenzymatic and isothermal signal amplification was performed by a 3-arm structure based on a catalyzed hairpin DNA assembly (3-CHA). By suppressing the leakage pathway, the sensitivity (<30 pM LOD) and selectivity of the 3-CHA were improved.
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Affiliation(s)
- Eunjoo Kim
- Department of Biomedical Engineering, Korea University, Hana Science Hall, 145 Anamro, Seongbukgu, Seoul 02841, Korea
| | - Jiaxin Xu
- Department of Biomedical Engineering, Korea University, Hana Science Hall, 145 Anamro, Seongbukgu, Seoul 02841, Korea
| | - Jinah Kim
- Department of Biomedical Engineering, Korea University, Hana Science Hall, 145 Anamro, Seongbukgu, Seoul 02841, Korea
| | - Honggu Chun
- Department of Biomedical Engineering, Korea University, Hana Science Hall, 145 Anamro, Seongbukgu, Seoul 02841, Korea
- Institute of Precision Public Health, Korea University, Hana Science Hall, 145 Anamro, Seongbukgu, Seoul 02841, Korea
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Nasrollahpour H, Khalilzadeh B, Naseri A, Sillanpää M, Chia CH. Homogeneous Electrochemiluminescence in the Sensors Game: What Have We Learned from Past Experiments? Anal Chem 2021; 94:349-365. [PMID: 34878242 DOI: 10.1021/acs.analchem.1c03909] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hassan Nasrollahpour
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 51664-14766, Iran
| | - Balal Khalilzadeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 51664-14766, Iran
| | - Abdolhossein Naseri
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 51664-14766, Iran
| | - Mika Sillanpää
- Environmental Engineering and Management Research Group, Ton Duc Thang University, 70000 Ho Chi Minh City, Vietnam.,Faculty of Environment and Labour Safety, Ton Duc Thang University, 70000 Ho Chi Minh City, Vietnam
| | - Chin Hua Chia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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8
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Ultrasensitive electrochemical detection of microRNA based on in-situ catalytic hairpin assembly actuated DNA tetrahedral interfacial probes. Talanta 2021; 233:122600. [PMID: 34215088 DOI: 10.1016/j.talanta.2021.122600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Selective and sensitive detection of microRNA is crucial for early diagnosis and pathogenesis of disease. Here, we established a novel electrochemical biosensor for simple and accurate analysis of the tumor biomarker microRNA-141, which was based on in-situ catalytic hairpin assembly (CHA) actuated DNA tetrahedral (DTN) interfacial probes. Two hairpin structures used for CHA reaction were placed on the DTN, in which the hairpin H1 on the one vertex of DTN and hairpin H2 embedded in adjacent edge, respective. The target microRNA-141 could open the hairpin H1 and activated the in-situ CHA reaction between H1 and H2 to alter the conformational of DTN, increasing the chances of the direct interaction between methylene blue (MB) and the electrode surface, leading to an increase in the electrochemical signal. Meanwhile, the released miRNA-141 could unfold another H1, enabling the enzyme-free recycling of the target to obtain amplified electrochemical signals. Moreover, the in-situ catalytic hairpin assembly reaction on DTN could shorten the reaction time and enhance the sensitivity. The established biosensor exhibited a wide linear dynamic range of miRNA-141 from 1 fM to 100 pM with a detection limit of 0.32 fM. Besides, the approach can discriminate the target miRNA from mismatched ones with excellent selectivity and can be successfully applied in diluted serum samples, holding great potential for sensitive detection of various biomarkers clinically.
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Li S, Meng HM, Zong H, Chen J, Li J, Zhang L, Li Z. Entropy-driven amplification strategy-assisted lateral flow assay biosensor for ultrasensitive and convenient detection of nucleic acids. Analyst 2021; 146:1668-1674. [PMID: 33475625 DOI: 10.1039/d0an02273j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate, sensitive and rapid nucleic acid tests are important to implement timely treatment measures and control the spread of disease. Herein, we developed a novel portable platform for highly sensitive and specific detection of nucleic acids by integrating an entropy-driven amplification strategy into lateral flow assay (LFA) biosensor. We find that introducing an entropy-driven amplification strategy yields bright intensities on the test line of LFA stirp, which results in improved sensitivity for targeted nucleic acid detection. The developed LFA biosensor showed good reproducibility, specificity and sensitivity for target DNA and H1N1-RNA detection with a low detection limit of 1.43 pM and 2.02 pM, respectively. Its practical potential was also verified by detecting the target nucleic acid in human serum. More importantly, the design of an entropy-driven amplification strategy in this portable platform retained the convenient, rapid and low-cost characterizations of LFA biosensor due to the compact amplification principle and the elimination of enzyme use. Thus, we believe that this assay biosensor will certainly report its own position in the timely detection of nucleic acid, especially when the medical environment and resources are fewer.
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Affiliation(s)
- Shasha Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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10
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Xu H, Lin Y, Sun L, Fang X, Jia L. An integrated target recognition and polymerase primer probe for microRNA detection. Talanta 2020; 219:121302. [PMID: 32887044 DOI: 10.1016/j.talanta.2020.121302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 11/29/2022]
Abstract
Extremely sensitive and visual measurements of microRNA (miRNA) in situ for early detection and monitoring of diseases remains a major challenge. To address this issue, this work reports a rapid, highly sensitive and selective microRNA (miRNA) biosensing strategy based on isothermal circular strand-displacement polymerization (ICSDP), and miRNA imaging was performed inside cells. In this work, a double hairpin DNA probe (HP1/HP2 complex) embedded with a sensing region and polymerase primer region was designed. Briefly, after the specific binding of target miRNA with the HP1/HP2 probe, HP1/HP2 itself can function as a primer to initiate the ICSDP with the help of Klenow Fragment (KF), yielding target miRNA for new rounds of ICSDP. In this process, one target can produce multiple signal outputs (1: n), achieving low abundance of miRNA detection. Under optimized conditions, the proposed strategy showed high sensitivity with a detection limit of 5 pM within 15 min and can also easily distinguish the control miRNA from the target miRNA. This method can be further applied to image the intracellular miRNA of interest in situ inside the cancer cells.
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Affiliation(s)
- Huo Xu
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China.
| | - Yongju Lin
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Lijun Sun
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Xiaojun Fang
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, and Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Lee Jia
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China; Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, and Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.
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11
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Kim DM, Yoo SM. DNA-modifying enzyme reaction-based biosensors for disease diagnostics: recent biotechnological advances and future perspectives. Crit Rev Biotechnol 2020; 40:787-803. [DOI: 10.1080/07388551.2020.1764485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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Chandrasekaran AR, Punnoose JA, Zhou L, Dey P, Dey BK, Halvorsen K. DNA nanotechnology approaches for microRNA detection and diagnosis. Nucleic Acids Res 2019; 47:10489-10505. [PMID: 31287874 PMCID: PMC6847506 DOI: 10.1093/nar/gkz580] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.
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Affiliation(s)
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Bijan K Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
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Li Q, Liu Z, Zhou D, Pan J, Liu C, Chen J. A cascade toehold-mediated strand displacement strategy for label-free and sensitive non-enzymatic recycling amplification detection of the HIV-1 gene. Analyst 2019; 144:2173-2178. [PMID: 30768078 DOI: 10.1039/c8an02340a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this work, a label-free fluorescence biosensor for simple detection of the HIV-1 gene was proposed by using toehold-mediated strand displacement reactions (TMSDRs) combined with a non-enzymatic target recycling amplification strategy. In this system, two TMSDRs were used. In the presence of the HIV-1 gene, an autocatalytic DNA machine can be activated. This leads to the generation of numerous free G-rich sequences, which can associate with a fluorescent dye N-methylmesoporphyrin IX (NMM) to yield an amplified fluorescence signal for the target detection. This sensing platform showed a high sensitivity towards the HIV-1 gene with a detection limit as low as 1.9 pM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits an excellent selectivity for the HIV-1 gene compared with other interference DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the HIV-1 gene in a real biological sample with satisfactory results, suggesting that this method is promising for simple and early clinical diagnosis of HIV infection. Thanks to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a universal platform for the detection of other genes by substituting the target-recognition element.
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Affiliation(s)
- Qiong Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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14
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Kong Y, Liu X, Liu C, Xue Q, Li X, Wang H. A dandelion-like liposomes-encoded magnetic bead probe-based toehold-mediated DNA circuit for the amplification detection of MiRNA. Analyst 2019; 144:4694-4701. [PMID: 31268436 DOI: 10.1039/c9an00887j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of facile and sensitive miRNA quantitative detection methods is a central challenge for the early diagnosis of miRNA-related diseases. Herein, we propose a strategy for a liposome-encoded magnetic bead-based DNA toehold-mediated DNA circuit for the simple and sensitive detection of miRNA based on a toehold-mediated circular strand displacement reaction (TCSDR) coupled with a personal glucometer (PGM ). In this strategy, a glucoamylase-encapsulated liposomes (GELs)-encoded magnetic bead (GELs-MB) probe is designed to integrate target binding, magnetic separation, and signal response. Upon sensing the target miRNA-21, a GELs-MB probe-based toehold-mediated circular strand displacement reaction (TCSDR) was initiated with the help of fuel-DNA, constructing a DNA circuit system, and realizing target recycling amplification and the disassembly of the liposomes. The disassembled liposomes were finally removed via magnetic separation, and the encapsulated glucoamylase was liberated to catalyze amylose hydrolysis with multiple turnovers to glucose for a PGM readout. Benefiting from target recycling amplification initiated by the toehold-mediated DNA circuit and the liposome multiple-label amplification, a small quantity of target miRNA-21 can be transformed into a large glucose signal. The strategy realized the quantification of miRNA-21 down to a level of 0.7 fM without enzymatic amplification or precise instrumentation. Moreover, the high-density GELs-MB probe allows the sensitive detection of miRNA-21 to be accomplished within 1.5 h. Furthermore, this strategy exhibits the advantages of specificity and simplicity, since a toehold-mediated strand displacement reaction, magnetic separation and portable PGM were used. Importantly, this strategy has been demonstrated to allow the high-confidence quantification of miRNA. Therefore, with the advantages of low cost, ease of use, portability, and sensitivity, the reported method holds great potential for the early diagnosis of miRNA-related diseases.
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Affiliation(s)
- Yancong Kong
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Xiaowen Liu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Chunxue Liu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Huaisheng Wang
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
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Wang Y, Lv Q, Zhang Y, Wang L, Dong Y. Probe computing model based on small molecular switch. BMC Bioinformatics 2019; 20:285. [PMID: 31182004 PMCID: PMC6557740 DOI: 10.1186/s12859-019-2767-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA has been widely used to construct the advanced logic devices. Results Herein, a molecular probe apparatus was constructed based on DNA molecular computing to perform fluorescent quenching and fluorescent signal recovery, with an ’ ON/OFF’ switching function. In this study, firstly, we program the streptavidin-mediated fluorescent quenching apparatus based on short-distance strand migration. The variation of fluorescent signal is acted as output. Then DNAzyme as a switching controller was involved to regulate the fluorescent signal increase. Finally, on this base, a cascade DNA logic gate consists of two logic AND operations was developed to enrich probe machine. Conclusion The designed probe computing model can be implemented with readout of fluorescence intensity, and exhibits great potential applications in the field of bioimaging as well as disease diagnosis.
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Oishi M, Nakatani K. Dynamically Programmed Switchable DNA Hydrogels Based on a DNA Circuit Mechanism. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900490. [PMID: 30859712 DOI: 10.1002/smll.201900490] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Biological stimuli-responsive DNA hydrogels have attracted much attention in the field of medical engineering owing to their unique phase transitions from gel to sol through cleavage of DNA cross-linking points in response to specific biomolecular inputs. In this paper, a new class of biological stimuli-responsive DNA hydrogels with a dynamically programmed DNA system that relies on a DNA circuit system through cascading toehold-mediated DNA displacement reactions is constructed, allowing the catalytic cleavage of cross-linking points and main chains in response to an appropriate DNA input. The dynamically programmed DNA hydrogels exhibit a significant sharp phase transition from gel to sol in comparison to another DNA hydrogel showing noncatalytic cleavage of cross-linking points due to synchronization of the catalytic cleavage of cross-linking points and the main chains. Further, the sol-gel phase transitions of the DNA hydrogels in response to the DNA input are easily tunable by changing the cross-linking density. Additionally, with a structure-switching aptamer, DNA hydrogels encapsulating PEGylated gold nanoparticles can be used as enzyme-free signal amplifiers for the colorimetric detection of adenosine 5'-triphosphate (ATP); this detection system provides simplicity and higher sensitivity (limit of detection: 5.6 × 10-6 m at 30 min) compared to other DNA hydrogel-based ATP detection systems.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan
| | - Kazuki Nakatani
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan
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17
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Hongxia C, Zaijun L, Ruiyi L, Guangli W, Zhiguo G. Molecular machine and gold/graphene quantum dot hybrid based dual amplification strategy for voltammetric detection of VEGF165. Mikrochim Acta 2019; 186:242. [PMID: 30877385 DOI: 10.1007/s00604-019-3336-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
Graphene quantum dots (GQDs) were prepared via pyrolysis of citric acid and glutamic acid, then reacted with chlorauric acid to form a gold/graphene quantum dot hybrid (Au/GQD), and finally connected with hairpin DNA probe 1 (H1) and thionine (Thi). The H1-Au/GQD-Thi composite is found to be a viable redox probe for electrochemical and aptamer-based determination of vascular endothelial growth factor VEGF165. A dual amplification strategy is employed based on the use of molecular machine and the Au/GQD. Each single VEGF165 molecule can bind two DNA probes via specific aptamer-target recognition to produce a molecular machine. Surface-tethered hairpin DNA 2 (H2) hybridizes with the molecular machine through proximity effect, and the prelocked toehold domain of H2 becomes exposed. This part binds to H1-Au/GQD-Thi to release the molecular machine which then moves to the neighboring H2 upon which a surface programmatic chain reaction is initiated. By continuous molecular machine travel, many H1-Au/GQD-Thi probes are present on the gold electrode surface. This implies an efficient signal amplification capability. The Au/GQD based redox probes in-situ catalyzes the redox activity of thionine and further enhances the detection signal. The aptasensor exhibits ultrahigh sensitivity and selectivity for VEGF165. The square wave voltammetric signal, best measured at -0.18 V vs. Ag/AgCl, increases linearly in the 1.0 fM to 120 pM VEGF165 concentration range, and the detection limit is 0.3 fM. Conceivably, the method may be applied to other target proteins if the corresponding high-affinity aptamers are available. Graphical abstract This study report one dual amplification strategy for ultrasensitive electrochemical detection of VEGF165 based on gold-graphene quantum dot hybrid (Au/GQD) and bipedal molecular machine (BMM) powered surface programmatic chain reaction (SPCR).
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Affiliation(s)
- Chu Hongxia
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Li Zaijun
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China.
| | - Li Ruiyi
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China.
| | - Wang Guangli
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Gu Zhiguo
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
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18
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Liu C, Zhang S, Li X, Xue Q, Jiang W. Multi-code magnetic beads based on DNAzyme-mediated double-cycling amplification for a point-of-care assay of telomerase activity. Analyst 2019; 144:4241-4249. [DOI: 10.1039/c9an00589g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of a reliable and facile telomerase activity assay with high specificity and sensitivity is a central challenge to make telomerase testing a routine part of medical care with respect to cancer.
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Affiliation(s)
- Chunxue Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Susu Zhang
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Xia Li
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
- School of Chemistry and Chemical Engineering
| | - Qingwang Xue
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
- School of Chemistry and Chemical Engineering
| | - Wei Jiang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P.R. China
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19
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Liu Q, Kang PJ, Chen ZP, Shi CX, Chen Y, Yu RQ. Highly specific and sensitive detection of microRNAs by tandem signal amplification based on duplex-specific nuclease and strand displacement. Chem Commun (Camb) 2019; 55:14210-14213. [DOI: 10.1039/c9cc06790f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A platform for microRNA detection was developed based on understanding the hydrolysis patterns of duplex-specific nuclease against probe DNAs.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Peng-Jian Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Zeng-Ping Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Cai-Xia Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Yao Chen
- Hunan Key Lab of Biomedical Materials and Devices
- College of Life Sciences and Chemistry
- Hunan University of Technology
- Zhuzhou
- P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
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20
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Hybridization-initiated exonuclease resistance strategy for simultaneous detection of multiple microRNAs. Talanta 2018; 190:248-254. [DOI: 10.1016/j.talanta.2018.07.070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/16/2018] [Accepted: 07/22/2018] [Indexed: 01/15/2023]
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21
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Wei K, Zhao J, Qin Y, Li S, Huang Y, Zhao S. A novel multiplex signal amplification strategy based on microchip electrophoresis platform for the improved separation and detection of microRNAs. Talanta 2018; 189:437-441. [DOI: 10.1016/j.talanta.2018.07.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 01/18/2023]
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22
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Hu P, Li M, Wei X, Yang B, Li Y, Li CY, Du J. Cooperative Toehold: A Mechanism To Activate DNA Strand Displacement and Construct Biosensors. Anal Chem 2018; 90:9751-9760. [PMID: 30040891 DOI: 10.1021/acs.analchem.8b01202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Toehold-mediated DNA strand displacement has proven powerful in the construction of various DNA circuits, DNA machines, and biosensors. So far, many new toehold activation mechanisms have been developed to achieve programmed DNA strand displacement behaviors. However, almost all those toeholds are inflexible via either a covalently attached manner or a complementary hybridization strategy, which limit the versatility of DNA devices. To solve this problem, we developed a new toehold, named "cooperative toehold", to activate DNA strand displacement. On the basis of a base stacking mechanism, the cooperative toehold is comprised of two moieties with completely independent DNA sequences between each other. The cooperative toehold enabled one to continuously tune the rate of DNA strand displacement, as well as more sophisticated strand displacement reactions. The cooperative toehold has also been employed as a universal signal translator for biosensors to qualitatively determine RNA and ATP. Moreover, as a novel specific PCR monitoring system, cooperative toehold-mediated DNA strand displacement can detect the pUC18 plasmid in genomic DNA samples with an aM detection limit.
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Affiliation(s)
- Pan Hu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Mengmeng Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Xijiao Wei
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Ye Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Chun-Yan Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Jun Du
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
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23
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Wu C, Liu X, Zheng Y, He W, Yang G, Wu P, Cai C. Fluorescence activation imaging of localization, distribution, and level of miRNA in various organelles inside cells. Talanta 2018; 186:406-412. [DOI: 10.1016/j.talanta.2018.04.080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 01/11/2023]
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24
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Target-programmed and autonomous proximity binding aptasensor for amplified electronic detection of thrombin. Biosens Bioelectron 2018; 117:743-747. [PMID: 30014949 DOI: 10.1016/j.bios.2018.06.069] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/13/2018] [Accepted: 06/29/2018] [Indexed: 11/22/2022]
Abstract
The development of sensitive and simple approaches capable of monitoring trace amounts of protein biomarkers is appealing for disease diagnosis and treatment. Towards this end, we have developed an electrochemical sensing platform for sensitive and simple detection of protein biomarkers by using thrombin as the model target molecules via a target-programmed proximity binding amplification approach. The binding of thrombin to the aptamer sequences in the partial dsDNA duplex probes induces the release of the ssDNA trigger strands, which catalyze subsequent assembly formation of many methylene blue (MB)-tagged proximate DNA motifs with the presence of the DNA fuel strands through cascaded toehold-mediated strand displacement reactions. Due to the proximity-binding effect, these MB-tagged proximate DNA motifs anneal with the capture probes on the sensor surface with significantly enhanced stability against the corresponding single component counterpart, thereby pulling the MB tags close to the sensor surface and generating substantially amplified signal responses for sensitive determination of thrombin down to 23.6 pM. In addition, such aptasensor can specifically discriminate thrombin from other interference proteins, and can also be utilized to monitor thrombin in diluted serum samples, demonstrating its great potential for sensitive determination of proteins for early disease diagnosis.
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25
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Toehold-mediated strand displacement reaction triggered by nicked DNAzymes substrate for amplified electrochemical detection of lead ion. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.04.083] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Zhang K, Zhang N, Zhang L, Wang H, Shi H, Liu Q. Label-free impedimetric sensing platform for microRNA-21 based on ZrO 2-reduced graphene oxide nanohybrids coupled with catalytic hairpin assembly amplification. RSC Adv 2018; 8:16146-16151. [PMID: 35542230 PMCID: PMC9080249 DOI: 10.1039/c8ra02453g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/16/2018] [Indexed: 12/14/2022] Open
Abstract
Herein, a sensitive electrochemical impedance sensor was constructed based on ZrO2-reduced graphene oxide (RGO)-modified electrode coupled with the catalytic hairpin assembly signal amplification strategy. Electrochemical impedance spectroscopy (EIS) was used to detect microRNA (miRNA) using the change in electron transfer resistance (ΔR et) originated from nucleic acid hybridization on the electrode surface. MiRNA-21 was used as a model to verify this strategy. The results indicated that ΔR et exhibited a good linear relationship with the concentration of miRNA-21 in the range from 1.0 × 10-14 mol L-1 to 1.0 × 10-10 mol L-1 with a detection limit of 4.3 × 10-15 mol L-1 (S/N = 3). Additionally, this sensor exhibited good selectivity, and it could be applied to detect miRNA-21 in human serum samples and measure the expression levels of miRNA-21 in human breast cancer cell lines (MCF-7); thus, this sensor has great potential in cancer diagnosis.
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Affiliation(s)
- Keying Zhang
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical-Engineering, Suzhou University Suzhou Anhui 234000 People's Republic of China
| | - Na Zhang
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical-Engineering, Suzhou University Suzhou Anhui 234000 People's Republic of China
| | - Li Zhang
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical-Engineering, Suzhou University Suzhou Anhui 234000 People's Republic of China
| | - Hongyan Wang
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical-Engineering, Suzhou University Suzhou Anhui 234000 People's Republic of China
| | - Hongwei Shi
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical-Engineering, Suzhou University Suzhou Anhui 234000 People's Republic of China
| | - Qiao Liu
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical-Engineering, Suzhou University Suzhou Anhui 234000 People's Republic of China
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27
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Oishi M. Comparative Study of DNA Circuit System-Based Proportional and Exponential Amplification Strategies for Enzyme-Free and Rapid Detection of miRNA at Room Temperature. ACS OMEGA 2018; 3:3321-3329. [PMID: 30023866 PMCID: PMC6044704 DOI: 10.1021/acsomega.7b01866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/14/2018] [Indexed: 05/24/2023]
Abstract
Because circulating microRNAs (miRNAs) have been recognized as a new class of blood-based biomarkers for various diseases, a significant challenge has been the development of point-of-care testing (POCT) systems based on detection of circulating miRNAs directly from serum. A promising approach to POCT systems is considered to be the development of enzyme-free and isothermal detection systems. Here, two types of DNA circuit system based on proportional and exponential amplification strategies were constructed using double-stranded DNA-modified magnetic beads (dsDNA-MBs) and their performances for detection of miRNA were studied comparatively. Both proportional and exponential amplification DNA circuit systems enabled the detection of target miRNA (miR-141) at room temperature without the need for additional enzymes because miR-141 acted as a catalyst for successive toehold-mediated DNA displacement reactions. A significant increase in the noise fluorescence signal was observed for the exponential amplification DNA circuit system because of the leakage (undesired DNA displacement reaction) revealed by the kinetic study on each DNA displacement reaction. Nevertheless, the exponential amplification DNA circuit system showed a lower limit of detection (LOD: 46 pM) and shorter assay time (15 min) compared to those of the proportional amplification DNA circuit system (LOD: 103 pM at 180 min). It is most likely that the exponential amplification DNA circuit system enabled amplification of both the signals and target miR-141, whereas the proportional amplification DNA circuit system enabled amplification of the signals alone. In addition, the exponential amplification DNA circuit system was able to discriminate between mismatched base sequences in miR-200 family members and specifically detect miR-141 even in the presence of serum. These findings are important for the rational design for POCT systems.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science,
Faculty of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
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28
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Park Y, Lee CY, Kang S, Kim H, Park KS, Park HG. Universal, colorimetric microRNA detection strategy based on target-catalyzed toehold-mediated strand displacement reaction. NANOTECHNOLOGY 2018; 29:085501. [PMID: 29269591 DOI: 10.1088/1361-6528/aaa3a3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, we developed a novel, label-free, and enzyme-free strategy for the colorimetric detection of microRNA (miRNA), which relies on a target-catalyzed toehold-mediated strand displacement (TMSD) reaction. The system employs a detection probe that specifically binds to the target miRNA and sequentially releases a catalyst strand (CS) intended to trigger the subsequent TMSD reaction. Thus, the presence of target miRNA releases the CS that mediates the formation of an active G-quadruplex DNAzyme which is initially caged and inactivated by a blocker strand. In addition, a fuel strand that is supplemented for the recycling of the CS promotes another TMSD reaction, consequently generating a large number of active G-quadruplex DNAzymes. As a result, a distinct colorimetric signal is produced by the ABTS oxidation promoted by the peroxidase mimicking activity of the released G-quadruplex DNAzymes. Based on this novel strategy, we successfully detected miR-141, a promising biomarker for human prostate cancer, with high selectivity. The diagnostic capability of this system was also demonstrated by reliably determining target miR-141 in human serum, showing its great potential towards real clinical applications. Importantly, the proposed approach is composed of separate target recognition and signal transduction modules. Thus, it could be extended to analyze different target miRNAs by simply redesigning the detection probe while keeping the same signal transduction module as a universal signal amplification unit, which was successfully demonstrated by analyzing another target miRNA, let-7d.
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Affiliation(s)
- Yeonkyung Park
- Department of Chemical and Biomolecular Engineering (BK21+Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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29
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Li JJ, Li WN, Du WF, Lv MM, Wu ZK, Jiang JH. Target induced reconstruction of DNAzymatic amplifier nanomachines in living cells for concurrent imaging and gene silencing. Chem Commun (Camb) 2018; 54:10626-10629. [DOI: 10.1039/c8cc05832f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel DNAzymatic amplifier nanomachine that enables the functions of concurrent mRNA imaging and gene silencing in living cells has been reported.
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Affiliation(s)
- Jun-Jie Li
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Wan-Ning Li
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Wen-Fang Du
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Meng-Mei Lv
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Zhen-Kun Wu
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
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30
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Zou M, Li D, Yuan R, Xiang Y. A target-responsive autonomous aptamer machine biosensor for enzyme-free and sensitive detection of protein biomarkers. J Mater Chem B 2018; 6:4146-4150. [DOI: 10.1039/c8tb00610e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Target-triggered operation of an aptamer machine leads to amplified and highly sensitive detection of protein biomarkers.
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Affiliation(s)
- Mengqi Zou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering, Southwest University
- Chongqing 400715
- P. R. China
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering, Southwest University
- Chongqing 400715
- P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering, Southwest University
- Chongqing 400715
- P. R. China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering, Southwest University
- Chongqing 400715
- P. R. China
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31
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Liu J, Du P, Zhang J, Shen H, Lei J. Sensitive detection of intracellular microRNA based on a flowerlike vector with catalytic hairpin assembly. Chem Commun (Camb) 2018; 54:2550-2553. [DOI: 10.1039/c7cc09579a] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A flowerlike nanovector with horn-shaped tips is developed for in situ detection of intracellular microRNA with multiple signal outputs.
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Affiliation(s)
- Jintong Liu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Ping Du
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jing Zhang
- School of Petrochemical Engineering
- School of Food Science and Technology
- Changzhou University
- Changzhou 213164
- China
| | - Hong Shen
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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32
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Ou M, Huang J, Yang X, He X, Quan K, Yang Y, Xie N, Li J, Wang K. Live-Cell MicroRNA Imaging through MnO2
Nanosheet-Mediated DD-A Hybridization Chain Reaction. Chembiochem 2017; 19:147-152. [DOI: 10.1002/cbic.201700573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Min Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Ke Quan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Yanjing Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
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33
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Highly sensitive surface plasmon resonance biosensor for the detection of HIV-related DNA based on dynamic and structural DNA nanodevices. Biosens Bioelectron 2017; 100:228-234. [PMID: 28918231 DOI: 10.1016/j.bios.2017.08.042] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/09/2017] [Accepted: 08/17/2017] [Indexed: 01/23/2023]
Abstract
Early detection, diagnosis and treatment of human immune deficiency virus (HIV) infection is the key to reduce acquired immunodeficiency syndrome (AIDS) mortality. In our research, an innovative surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of HIV-related DNA based on entropy-driven strand displacement reactions (ESDRs) and double-layer DNA tetrahedrons (DDTs). ESDRs as enzyme-free and label-free signal amplification circuit can be specifically triggered by target DNA, leading to the cyclic utilization of target DNA and the formation of plentiful double-stranded DNA (dsDNA) products. Subsequently, the dsDNA products bind to the immobilized hairpin capture probes and further combine with DDTs nanostructures. Due to the high efficiency of ESDRs and large molecular weight of DDTs, the SPR response signal was enhanced dramatically. The proposed SPR biosensor could detect target DNA sensitively and specifically in a linear range from 1pM to 150nM with a detection limit of 48fM. In addition, the whole detecting process can be accomplished in 60min with high accuracy and duplicability. In particular, the developed SPR biosensor was successfully used to analyze target DNA in complex biological sample, indicating that the developed strategy is promising for rapid and early clinical diagnosis of HIV infection.
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Liu JL, Tang ZL, Zhuo Y, Chai YQ, Yuan R. Ternary Electrochemiluminescence System Based on Rubrene Microrods as Luminophore and Pt Nanomaterials as Coreaction Accelerator for Ultrasensitive Detection of MicroRNA from Cancer Cells. Anal Chem 2017; 89:9108-9115. [DOI: 10.1021/acs.analchem.7b01812] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jia-Li Liu
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Zhi-Ling Tang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ying Zhuo
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ya-Qin Chai
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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35
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Feng QM, Guo YH, Xu JJ, Chen HY. Self-Assembled DNA Tetrahedral Scaffolds for the Construction of Electrochemiluminescence Biosensor with Programmable DNA Cyclic Amplification. ACS APPLIED MATERIALS & INTERFACES 2017; 9:17637-17644. [PMID: 28471159 DOI: 10.1021/acsami.7b04553] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A novel DNA tetrahedron-structured electrochemiluminescence (ECL) platform for bioanalysis with programmable DNA cyclic amplification was developed. In this work, glucose oxidase (GOD) was labeled to a DNA sequence (S) as functional conjugation (GOD-S), which could hybridize with other DNA sequences (L and P) to form GOD-S:L:P probe. In the presence of target DNA and a help DNA (A), the programmable DNA cyclic amplification was activated and released GOD-S via toehold-mediated strand displacement. Then, the obtained GOD-S was further immobilized on the DNA tetrahedral scaffolds with a pendant capture DNA and Ru(bpy)32+-conjugated silica nanoparticles (RuSi NPs) decorated on the electrode surface. Thus, the amount of GOD-S assembled on the electrode surface depended on the concentration of target DNA and GOD could catalyze glucose to generate H2O2 in situ. The ECL signal of Ru(bpy)32+-TPrA system was quenched by the presence of H2O2. By integrating the programmable DNA cyclic amplification and in situ generating H2O2 as Ru(bpy)32+ ECL quencher, a sensitive DNA tetrahedron-structured ECL sensing platform was proposed for DNA detection. Under optimized conditions, this biosensor showed a wide linear range from 100 aM to 10 pM with a detection limit of 40 aM, indicating a promising application in DNA analysis. Furthermore, by labeling GOD to different recognition elements, the proposed strategy could be used for the detection of various targets. Thus, this programmable cascade amplification strategy not only retains the high selectivity and good capturing efficiency of tetrahedral-decorated electrode surface but also provides potential applications in the construction of ECL biosensor.
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Affiliation(s)
- Qiu-Mei Feng
- School of Chemistry and Chemical Engineering, Jiangsu Normal University , Xuzhou 221116, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Yue-Hua Guo
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
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Li Z, Lin Z, Wu X, Chen H, Chai Y, Yuan R. Highly Efficient Electrochemiluminescence Resonance Energy Transfer System in One Nanostructure: Its Application for Ultrasensitive Detection of MicroRNA in Cancer Cells. Anal Chem 2017; 89:6029-6035. [DOI: 10.1021/acs.analchem.7b00616] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhaoyang Li
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Zongfan Lin
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Xiaoyu Wu
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Haotian Chen
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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Yang J, Dou B, Yuan R, Xiang Y. Aptamer/Protein Proximity Binding-Triggered Molecular Machine for Amplified Electrochemical Sensing of Thrombin. Anal Chem 2017; 89:5138-5143. [PMID: 28393515 DOI: 10.1021/acs.analchem.7b00827] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA). Subsequent toehold-mediated strand displacement by the MB-DNA leads to the release and recycling of the aptamer/protein complexes and the function of the molecular machine. Eventually, a large number of MB-DNA strands are captured by the sensor surface, generating drastically amplified electrochemical responses from the MB tags for sensitive detection of thrombin. Our signal amplified sensor is completely enzyme-free and shows a dynamic range from 5 pM to 1 nM with a detection limit of 1.7 pM. Such sensor also has a high specificity for thrombin assay in serum samples. By changing the affinity probe pairs, the developed sensor can be readily expanded as a more general platform for sensitive detection of different types of proteins.
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Affiliation(s)
- Jianmei Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, 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, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
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38
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Wen ZB, Liang WB, Zhuo Y, Xiong CY, Zheng YN, Yuan R, Chai YQ. An efficient target–intermediate recycling amplification strategy for ultrasensitive fluorescence assay of intracellular lead ions. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc04104g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An ultrasensitive fluorescence assay for intracellular Pb2+ determination was proposed through target–intermediate recycling amplification based on metal-assisted DNAzyme catalysis and strand displacement reactions.
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Affiliation(s)
- Zhi-Bin Wen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Wen-Bin Liang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Cheng-Yi Xiong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ying-Ning Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ya-Qin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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39
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Park KW, Batule BS, Kang KS, Park KS, Park HG. Rapid and ultrasensitive detection of microRNA by target-assisted isothermal exponential amplification coupled with poly (thymine)-templated fluorescent copper nanoparticles. NANOTECHNOLOGY 2016; 27:425502. [PMID: 27622680 DOI: 10.1088/0957-4484/27/42/425502] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We devised a novel method for rapid and ultrasensitive detection of target microRNA (miRNA) by employing target-assisted isothermal exponential amplification (TAIEA) combined with poly (thymine)-templated fluorescent copper nanoparticles (CuNPs) as signaling probes. The target miRNA hybridizes to the unimolecular template DNA and works as a primer for the extension reaction to form double-stranded product, which consequently generates two nicking endonuclease recognition sites. By simultaneous nicking and displacement reactions, exponential amplification generates many poly (thymine) strands as final products, which are employed for the synthesis of fluorescent CuNPs. Based on the fluorescent signal from CuNPs, target miRNA is detected as low as 0.27 fM around 1 h of total analysis time. The diagnostic capability of this system has been successfully demonstrated by reliably detecting target miRNA from different cell lysates, showing its great potential towards real clinical applications.
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Affiliation(s)
- Kwan Woo Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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40
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Bi S, Yue S, Wu Q, Ye J. Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing. Biosens Bioelectron 2016; 83:281-6. [DOI: 10.1016/j.bios.2016.04.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/16/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022]
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41
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Zheng YN, Liang WB, Xiong CY, Yuan YL, Chai YQ, Yuan R. Self-Enhanced Ultrasensitive Photoelectrochemical Biosensor Based on Nanocapsule Packaging Both Donor-Acceptor-Type Photoactive Material and Its Sensitizer. Anal Chem 2016; 88:8698-705. [PMID: 27513736 DOI: 10.1021/acs.analchem.6b01984] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, a self-enhanced ultrasensitive photoelectrochemical (PEC) biosensor was established based on a functionalized nanocapsule packaging both donor-acceptor-type photoactive material and its sensitizer. The functionalized nanocapsule with self-enhanced PEC responses was achieved first by packaging both the donor-acceptor-type photoactive material (poly{4,8-bis[5-(2-ethylhexyl)thiophen-2-yl]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophene-4,6-diyl}, PTB7-Th) and its sensitizer (nano-C60, fullerene) in poly(ethylene glycol) (PEG) to form a nanocapsule, which significantly enhanced PEC signal and stability of the PEC biosensor. Moreover, a quadratic enzymes-assisted target recycling amplification strategy was introduced to the system for ultrasensitive determination. Compared with other established PEC biosensors, our proposed self-enhanced approach showed higher effectivity, accuracy, sensitivity, and convenience without any addition of coreactant or sensitizers into the testing electrolyte for photocurrent amplification and performed excellent analytical properties for microRNA estimation down to femtomole level with microRNA-141 as a model. Additionally, the proposed PEC biosensor was employed for estimation of microRNA in different cancer cells and pharmacodynamic evaluation in cancer cells. This self-enhanced PEC strategy has laid the foundation for fabrication of simple, effective, and ultrasensitive PEC diagnostic devices, leading to the possibility for early diagnosis, timely stage estimation, and accurate prognosis judgment of disease.
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Affiliation(s)
- Ying-Ning Zheng
- 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
| | - Wen-Bin Liang
- 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.,Department of Clinical Biochemistry, Laboratory Sciences, Southwest Hospital, Third Military Medical University , 30 Gaotanyan Street, Shapingba District, Chongqing 400038, People's Republic of China
| | - Cheng-Yi Xiong
- 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
| | - Ya-Li 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
| | - Ya-Qin 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
| | - 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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42
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Zhou W, Li D, Chai Y, Yuan R, Xiang Y. RNA responsive and catalytic self-assembly of DNA nanostructures for highly sensitive fluorescence detection of microRNA from cancer cells. Chem Commun (Camb) 2016; 51:16494-7. [PMID: 26411332 DOI: 10.1039/c5cc06429e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic self-assembly of DNA nanostructures triggered by microRNA 21 (miR-21) is achieved through isothermal toe-hold strand displacement reactions. The miR-21 is autonomously recycled during the self-assembly process, which makes the generation of the DNA nanostructures proceed in a catalytic fashion. The miR-21-triggered self-assembly of DNA nanostructures can also serve as a remarkable signal amplification platform to achieve ultrasensitive detection of miR-21 from as low as 10 MCF-7 human breast cancer cells.
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Affiliation(s)
- Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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43
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Electrochemical determination of microRNAs based on isothermal strand-displacement polymerase reaction coupled with multienzyme functionalized magnetic micro-carriers. Biosens Bioelectron 2016; 80:344-351. [DOI: 10.1016/j.bios.2015.12.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/09/2015] [Accepted: 12/20/2015] [Indexed: 01/08/2023]
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44
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Cai S, Chen M, Liu M, He W, Liu Z, Wu D, Xia Y, Yang H, Chen J. A signal amplification electrochemical aptasensor for the detection of breast cancer cell via free-running DNA walker. Biosens Bioelectron 2016; 85:184-189. [PMID: 27176917 DOI: 10.1016/j.bios.2016.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/16/2016] [Accepted: 05/02/2016] [Indexed: 12/24/2022]
Abstract
Herein, a signal magnification electrochemical aptasensor for the detection of breast cancer cell via free-running DNA walker is constructed. Theoretically, just one DNA walker, released by target cell-responsive reaction, can automatically cleave all D-RNA (a chimeric DNA/RNA oligonucleotide with a cleavage point rArU) anchored on electrode into shorter produces, giving rise to considerably detectable signal finally. Under the optimal conditions, the electrochemical signal decreased linearly with the concentration of MCF-7 cell. The linear range is from 0 to 500 cells mL(-1) with a detection limit of 47 cellsmL(-1). In a word, this approach may have advantages over traditional reported DNA machines for bioassay, particularly in terms of ease of operation, cost efficiency, free of labeling and of complex track design, which may hold great potential for wide application.
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Affiliation(s)
- Shuxian Cai
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Mei Chen
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Mengmeng Liu
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Wenhui He
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Zhijing Liu
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Dongzhi Wu
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Yaokun Xia
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China
| | - Huanghao Yang
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian Province 350002, PR China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350108, PR China.
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Peng Y, Li X, Yuan R, Xiang Y. Steric hindrance inhibition of strand displacement for homogeneous and signal-on fluorescence detection of human serum antibodies. Chem Commun (Camb) 2016; 52:12586-12589. [DOI: 10.1039/c6cc06893f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Steric hindrance inhibition of strand displacement enables homogeneous and signal-on fluorescence detection of human serum antibodies.
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Affiliation(s)
- Ying Peng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Xin Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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46
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Du W, Lv M, Li J, Yu R, Jiang J. A ligation-based loop-mediated isothermal amplification (ligation-LAMP) strategy for highly selective microRNA detection. Chem Commun (Camb) 2016; 52:12721-12724. [DOI: 10.1039/c6cc06160e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel ligation-based loop-mediated isothermal amplification (ligation-LAMP) method has been developed for sensitive and selective detection of microRNA.
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Affiliation(s)
- Wenfang Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Mengmei Lv
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Junjie Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
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