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Tang Q, Wang J, Zhang J, Zeng H, Su Z, Zhu X, Wei J, Gong Y, Tang Q, Zhang K, Liao X. Electrochemiluminescence biosensor for MMP-2 determination using CRISPR/Cas13a and EXPAR amplification: a novel approach for anti-aging research. Mikrochim Acta 2024; 191:665. [PMID: 39397178 DOI: 10.1007/s00604-024-06707-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 09/13/2024] [Indexed: 10/15/2024]
Abstract
Matrix metalloproteinase-2 (MMP-2) plays a pivotal role in anti-aging research. Developing advanced detection platforms for MMP-2 with high specificity, sensitivity, and accessibility is crucial. This study introduces a novel electrochemiluminescence (ECL) biosensor for MMP-2 determination, leveraging the CRISPR/Cas13a system and Exponential Amplification Reaction (EXPAR). The biosensor operates by utilizing the T7 RNA polymerase to transcribe RNA from a DNA template upon MMP-2 interaction. This RNA activates Cas13a, leading to signal amplification and ECL detection. The incorporation of the "photoswitch" molecule [Ru(phen)2dppz]2+ streamlines the process by eliminating the need for extensive electrode modification and cleaning. Under optimized conditions, the biosensor achieved an impressive detection limit of 12.8 aM for MMP-2. The platform demonstrated excellent selectivity, reproducibility, and stability, making it highly suitable for detecting MMP-2 in complex biological samples. This innovative approach shows great potential for applications in molecular diagnostics and anti-aging research.
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Affiliation(s)
- Qiang Tang
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Jie Wang
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Jiayi Zhang
- West Guangxi Key Laboratory for Prevention and Treatment of High-Incidence Diseases, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Hongyu Zeng
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Zhixue Su
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Xiying Zhu
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Jihua Wei
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Yuanxun Gong
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Qianli Tang
- Guangxi Key Laboratory for Preclinical and Translational Research On Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
| | - Kai Zhang
- School of Chemistry and Materials Science, Nanjing University of Information Science and Technology, Nanjing, 210044, P. R. China.
| | - Xianjiu Liao
- West Guangxi Key Laboratory for Prevention and Treatment of High-Incidence Diseases, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
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2
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Tang Q, Huang X, Liu G, Huang H, Zhang J, Wei J, Gong Y, Tang Q, Zhang K, Liao X. Electrochemical detection of MMP-2 with enhanced sensitivity: Utilizing T7 RNA polymerase and CRISPR-Cas12a for neuronal studies. Talanta 2024; 281:126795. [PMID: 39236519 DOI: 10.1016/j.talanta.2024.126795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
This study introduces a novel electrochemical biosensor for detecting Matrix Metalloproteinase-2 (MMP-2), a key biomarker in cancer diagnostics and tissue remodeling. The biosensor is based on a dual-amplification strategy utilizing T7 RNA polymerase isothermal amplification and CRISPR-Cas12a technology. The principle involves the release of a DNA template in the presence of MMP-2, leading to RNA synthesis by T7 RNA polymerase. This RNA activates CRISPR-Cas12a, which cleaves a DNA probe on the electrode surface, resulting in a measurable electrochemical signal.The biosensor demonstrated exceptional sensitivity, with a detection limit of 2.62 fM for MMP-2. This high sensitivity was achieved through the combination of transcriptional amplification and the collateral cleavage activity of CRISPR-Cas12a, which amplifies the signal. The sensor was able to detect MMP-2 across a wide dynamic range from 2 fM to 1 nM, showing a strong linear correlation between MMP-2 concentration and the electrochemical signal. In practical applications, the biosensor accurately detected elevated levels of MMP-2 in cell culture supernatants from HepG2 liver cancer cells, distinguishing them from normal LO2 liver cells. The use of an MMP-2 inhibitor confirmed the specificity of the detection. These results underscore the biosensor's potential for clinical diagnostics, particularly in early cancer detection and monitoring of tissue remodeling activities. The biosensor's design allows for rapid, point-of-care testing without the need for complex laboratory equipment, making it a promising tool for personalized healthcare and diagnostic applications.
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Affiliation(s)
- Qiang Tang
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China
| | - Xiaoling Huang
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China
| | - Guangxing Liu
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China
| | - Hongran Huang
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China
| | - Jiayi Zhang
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Jihua Wei
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China
| | - Yuanxun Gong
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China
| | - Qianli Tang
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangx, 533000, China.
| | - Kai Zhang
- School of Chemistry and Materials Science, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Xianjiu Liao
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China.
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3
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Gong Y, Tong D, Qiu P, Song R, Li Z, He Y, Luo Q, Tang Q, Zhang K, Liao X. A novel electrochemical biosensor for B-type natriuretic peptide detection based on CRISPR/Cas13a and chain substitution reaction. Talanta 2024; 274:125966. [PMID: 38554484 DOI: 10.1016/j.talanta.2024.125966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/01/2024]
Abstract
B-type natriuretic peptide (BNP) is a biomarker for heart failure, a serious and prevalent disease that requires rapid and accurate diagnosis. In this study, we developed a novel electrochemical biosensor for BNP detection based on CRISPR/Cas13a and chain substitution reaction. The biosensor consists of a DNA aptamer that specifically binds to BNP, a T7 RNA polymerase that amplifies the signal, a CRISPR/Cas13a system that cleaves the target RNA, and a two-dimensional DNA nanoprobe that generates an electrochemical signal. The biosensor exhibits high sensitivity, specificity, and stability, with a detection limit of 0.74 aM. The biosensor can also detect BNP in human serum samples with negligible interference, demonstrating its potential for clinical and point-of-care applications. This study presents a novel strategy for integrating CRISPR/Cas13a and chain substitution reaction into biosensor design, offering a versatile and effective platform for biomolecule detection.
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Affiliation(s)
- Yuanxun Gong
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Danlei Tong
- Graduate School, Guangxi University of Chinese Medicine, Nanning, 530001, China
| | - Ping Qiu
- Graduate School, Guangxi University of Chinese Medicine, Nanning, 530001, China
| | - Rilian Song
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Zhidan Li
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Yanlin He
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Qisheng Luo
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Qianli Tang
- Guangxi Key Laboratory for Preclinical and Translational Research on Bone and Joint Degenerative Diseases, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China; Graduate School, Guangxi University of Chinese Medicine, Nanning, 530001, China.
| | - Kai Zhang
- School of Chemistry and Materials Science, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Xianjiu Liao
- Key Laboratory of Research on Prevention and Control of High Incidence Diseases in Western Guangxi, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China.
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4
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Wang Z, Zhang R, Liu S, Zhang W, Han J, Bu H. Thermodynamic Allosteric Switch-Actuated 3D DNA Nanomachine for Ultrasensitive Electrochemical/Fluorescent Dual-Mode Biosensing of a Transcription Factor. ACS APPLIED BIO MATERIALS 2024; 7:1073-1080. [PMID: 38215043 DOI: 10.1021/acsabm.3c01018] [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] [Indexed: 01/14/2024]
Abstract
Herein, we reported an innovative thermodynamic allosteric switch-actuated 3D DNA nanomachine for selective, sensitive, and accurate electrochemical (EC)/fluorescent (FL) dual-mode biosensing of a microphthalmia-associated transcription factor (MITF). The thermodynamic allosteric switch was ingeniously customized as a hairpin probe (HP) that was in dynamic equilibrium but rapidly interconverting conformations. At the "inactive state", the MITF-binding region and the switch part were "sequestered". Upon the introduction of MITF, an MITF-HP complex promptly formed, and the equilibrium of HP thermodynamically inclined from the "inactive state" toward the "active state" conformation. Immediately, the exposed switch on HP effectively actuated the 3D DNA nanomachine and synchronously produced the restriction site for Nb.BbvCI nicking endonuclease. After the autonomous conveying of the 3D DNA nanomachine by means of the high-efficiency circularly nicking endonuclease signal amplification (NESA), not only was MB-S1 in the supernatant used for FL measurements but also MB-SP/MNs/S2 in the precipitate was adapted for EC analysis, significantly improving the utilization of output products derived from the 3D DNA nanomachine. Accordingly, benefiting from the efficient DNA nanomachine signal amplification manner and the self-calibration function of a dual-mode bioassay, the constructed biosensor exhibits superior sensitivity and accuracy for MITF determination.
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Affiliation(s)
- Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Rongrong Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Shuning Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Wen Zhang
- School of Chemical Engineering, Xi'an University, Xi'an 710065, China
| | - Jing Han
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Huaiyu Bu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
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5
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Guo Z, Tan X, Yuan H, Zhang L, Wu J, Yang Z, Qu K, Wan Y. Bis-enzyme cascade CRISPR-Cas12a platform for miRNA detection. Talanta 2023; 252:123837. [DOI: 10.1016/j.talanta.2022.123837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/23/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
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6
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Ratiometric detection of transcription factor based on Europium(III) complex-doped silicon nanoparticles and a G-quadruplex-selective Iridium(III) complex. Anal Chim Acta 2022; 1209:339855. [DOI: 10.1016/j.aca.2022.339855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
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7
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Zhang K, Fan Z, Huang Y, Ding Y, Xie M. A strategy combining 3D-DNA Walker and CRISPR-Cas12a trans-cleavage activity applied to MXene based electrochemiluminescent sensor for SARS-CoV-2 RdRp gene detection. Talanta 2022; 236:122868. [PMID: 34635250 PMCID: PMC8429000 DOI: 10.1016/j.talanta.2021.122868] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022]
Abstract
Early diagnosis and timely management of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are the keys to preventing the spread of the epidemic and controlling new infection clues. Therefore, strengthening the surveillance of the epidemic and timely screening and confirming SARS-CoV-2 infection is the primary task. In this work, we first proposed the idea of activating CRISPR-Cas12a activity using double-stranded DNA amplified by a three-dimensional (3D) DNA walker. We applied it to the design of an electrochemiluminescent (ECL) biosensor to detect the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) gene. We first activated the cleavage activity of CRISPR-Cas12a by amplifying the target DNA into a segment of double-stranded DNA through the amplification effect of a 3D DNA walker. At the same time, we designed an MXene based ECL material: PEI-Ru@Ti3C2@AuNPs, and constructed an ECL biosensor to detect the RdRp gene based on this ECL material as a framework. Activated CRISPR-Cas12a cleaves the single-stranded DNA on the surface of this sensor and causes the ferrocene modified at one end of the DNA to move away from the electrode surface, increasing the ECL signal. The extent of the change in electrochemiluminescence reflects the concentration of the gene to be measured. Using this system, we detected the SARS-CoV-2 RdRp gene with a detection limit of 12.8 aM. This strategy contributes to the rapid and convenient detection of SARS-CoV-2-associated nucleic acids and promotes the clinical application of ECL biosensors based on CRISPR-Cas12a and novel composite materials.
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Affiliation(s)
- Kai Zhang
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China.
| | - Zhenqiang Fan
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Yue Huang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Yuedi Ding
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Minhao Xie
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China.
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8
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Woo J, Kim JH, Kim S, Park KS. Promoter engineering improves transcription efficiency in biomolecular assays. Chem Commun (Camb) 2021; 57:1619-1622. [PMID: 33458724 DOI: 10.1039/d0cc07797f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We identified a novel 12 bp promoter that significantly increased transcription efficiency. Unlike the standard 20 bp promoter, which contains both recognition and initiation regions, the new promoter contains only a recognition region and is more suitable for diagnostic applications due to its smaller size. This promoter effectively produced different light-up RNA aptamers via transcription. Moreover, we used the promoter to analyze RNase H activity and achieved a detection limit of 0.009 U mL-1, which was significantly better than that achieved via previous methods. We propose that the new promoter may serve as a key component in various diagnostic applications.
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Affiliation(s)
- Jisu Woo
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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9
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Li B, Xie S, Xia A, Suo T, Huang H, Zhang X, Chen Y, Zhou X. Recent advance in the sensing of biomarker transcription factors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116039] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Wang G, Fan W, Ren W, Liu X, Liu C. High-sensitive sensing of plant microRNA by integrating click chemistry with an unusual on-bead poly(T)-promoted transcription amplification. Anal Chim Acta 2020; 1111:16-22. [PMID: 32312392 DOI: 10.1016/j.aca.2020.03.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/12/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) act as pivotal regulators in plants. Therefore, sensing strategies with high specificity and high sensitivity are desired for plant miRNA analysis in order to unveil the exact biofunctions of miRNAs. Toward this goal, a fluorescent assay is developed based on a two-step signal amplification strategy. In the first step, target miRNA-templated cycling click nucleic acid ligation is employed for target recognition and amplification, the product of which can bind to magnetic microbeads (MBs) and introduce the T7 promoter sequence to the surface. In the second step, the poly(T) containing transcription template partially hybridizes with the T7 promoter sequence on the ligated strand and then regulates the on-bead transcription in a cycling manner with the participation of T7 RNA polymerase. Surprisingly, different from other reported templates, the poly(T) template improves the transcription efficiency to an unexpectedly high level by releasing ultra-long RNA chains in the reaction system. Finally, the RNA intercalating dye, RiboGreen, is utilized to specifically light up the as-produced RNA chains for low-background signal readout. Benefiting from the elaborate design, the detection limit of plant miRNA is down to ∼0.1 amol. This strategy provides a highly specific and highly sensitive platform for plant miRNA detection, which promises potential in the practical applications of miRNA-related biofunctions.
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Affiliation(s)
- Gaoting Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
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11
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Liu F, Yang M, Song W, Luo X, Tang R, Duan Z, Kang W, Xie S, Liu Q, Lei C, Huang Y, Nie Z, Yao S. Target-activated transcription for the amplified sensing of protease biomarkers. Chem Sci 2020; 11:2993-2998. [PMID: 34122801 PMCID: PMC8157538 DOI: 10.1039/c9sc04692e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/09/2020] [Indexed: 12/21/2022] Open
Abstract
Signal amplification is an effective way to achieve sensitive analysis of biomarkers, exhibiting great promise in biomedical research and clinical diagnosis. Inspired by the transcription process, here we present a versatile strategy that enables effective amplification of proteolysis into nucleic acid signal outputs in a homogeneous system. In this strategy, a protease-activatable T7 RNA polymerase is engineered as the signal amplifier and achieves 3 orders of magnitude amplification in signal gain. The versatility of this strategy has been demonstrated by the development of sensitive and selective assays for protease biomarkers, such as matrix metalloproteinase-2 (MMP-2) and thrombin, with sub-picomole sensitivity, which is 4.3 × 103-fold lower than that of the standard peptide-based method. Moreover, the proposed assay has been further applied in the detection of MMP-2 secreted by cancer cells, as well as in the assessment of MMP-2 levels in osteosarcoma tissue samples, providing a general approach for the monitoring of protease biomarkers in clinical diagnosis.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Min Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Wenlu Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Rui Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Zhixi Duan
- Department of Orthopedics, The Second Xiangya Hospital, Central South University Changsha 410011 Hunan P. R. China
| | - Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Qingqing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 P. R. China
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12
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Determination of the concentration of transcription factor by using exonuclease III-aided amplification and gold nanoparticle mediated fluorescence intensity: A new method for gene transcription related enzyme detection. Anal Chim Acta 2020; 1104:132-139. [PMID: 32106944 DOI: 10.1016/j.aca.2019.12.076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 12/31/2019] [Indexed: 01/20/2023]
Abstract
Herein, we report a new probe for the determination of the concentration of NF-κB p50, one kind of DNA-binding transcription factors (TFs), by using Exonuclease III (Exo III)-aided amplification and gold nanoparticle mediated fluorescence intensity. Since TFs play critical roles in various biological processes, the detection of TFs can provide a lot of useful biological information for studding gene expression regulation related disease. In our system, in the presence of transcription factor, Exo III based amplification reaction was trigged. This enzymatic digestion results in the release of intermediate DNA and ultimately liberating the fluorophore (which, separated from the quencher of AuNP and BHQ2, now fluoresces). The released intermediate DNA then hybridizes with another strand3, whence the cycle starts anew. So, the fluorescence intensity reflects the NF-κB p50 concentration with a detection limit of 1.32 pM. Importantly, this method might be further extended to selectively detect various dsDNA-binding proteins by simply changing the binding-site sequences of strand1/strand2 duplex probes.
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13
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Zang M, Su H, Lu L, Li F. A split G-quadruplex-specific dinuclear Ir(III) complex for label-free luminescent detection of transcription factor. Talanta 2019; 202:259-266. [DOI: 10.1016/j.talanta.2019.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 12/29/2022]
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14
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Zhang K, Huang W, Huang Y, Wang K, Zhu X, Xie M. Determination of the activity of uracil-DNA glycosylase by using two-tailed reverse transcription PCR and gold nanoparticle-mediated silver nanocluster fluorescence: a new method for gene therapy-related enzyme detection. Mikrochim Acta 2019; 186:181. [PMID: 30771014 DOI: 10.1007/s00604-019-3307-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/04/2019] [Indexed: 12/28/2022]
Abstract
The authors present a fluorometric method for ultrasensitive determination of the activity of uracil-DNA glycosylase (UDG). It is based on the use of two-tailed reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and an entropy-driven reaction. The assay involves the following steps: (1) UDG-driven uracil excision repair, (2) two-tailed RT-qPCR-mediated amplification, (3) RNA polymerase-aided amplification, and (4) DNA-modified silver nanoclusters (AgNCs) as a transducer to produce a fluorescent signal. UDG enables uracil to be removed from U·A pairs in DNA1 and produces a depurinated/depyrimidinated site that is readily cleaved by endonuclease IV (Endo IV). The cleaved DNA contains the T7 RNA polymerase primer for the T7 RNA polymerase amplification which produces a large number of microRNA sequences. Subsequent two-tailed RT-qPCR leads to the formation of a prolonged DNA termed DNA3. The prolonged part of DNA3 is then hybridized with an added DNA4/DNA5 duplex, where DNA5 is labeled with gold nanoparticles (AuNPs), and DNA 4 is labeled with AgNCs. The AuNPs quench the fluorescence of the AgNCs. The duplex has a toehold to hybridize the prolong part of DNA3. This results in the formation of a DNA5/DNA3 duplex due to strand displacement (by replacing the DNA4 in the DNA4/DNA5 duplex). DNA4 is released and moves away from the AuNPs. This results in restored AgNC fluorescence, best measured at excitation/emission wavelengths of 575/635 nm. The method has a detection limit as low as 0.1 mU mL-1 of UDG activity (3σ criterion) with a range of 0.001-0.01 U mL-1. It was used to measure UDG activity in cell lysates. Conceivably, it may be used to screen for UDG inhibitors such as Ugi. Graphical abstract Schematic presentation of the two-tailed RT-qPCR assay platform for ultrasensitive detection of uracil-DNA glycosylase (UDG). Two-tailed RT-qPCR-mediated amplification and RNA polymerase-aided amplification are utilized for signal amplification. DNA-modified silver nanoclusters (AgNCs) are used as a transducer to produce a fluorescent signal.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China.
| | - Wanting Huang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China
| | - Yue Huang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Ke Wang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China
| | - Xue Zhu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China
| | - Minhao Xie
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, Jiangsu, China.
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15
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Wang M, Tang Y, Chen Y, Cao Y, Chen G. Catalytic hairpin assembly-programmed formation of clickable nucleic acids for electrochemical detection of liver cancer related short gene. Anal Chim Acta 2019; 1045:77-84. [DOI: 10.1016/j.aca.2018.08.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
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16
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Tian Y, Zhang S, Wang L, Liu S. A Modular Nanoswitch for Mix-and-Detect Protein Assay Based on Binding-Induced Cascade Dissociation of Kissing Complex. Chembiochem 2018; 19:716-722. [PMID: 29356232 DOI: 10.1002/cbic.201700649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Indexed: 01/26/2023]
Abstract
A new modular nanoswitch was described for versatile, rapid (within 1 h), homogeneous, and sensitive protein detection. The system employs two hairpins (HP1 and HP2) that can be reciprocally recognized through the apical loop-loop interaction. HP2 possesses a conformation-switching stem-loop structure, with appended single-stranded tails on each end, which can hybridize with the recognition-element-conjugated DNA strands to construct a protein-responsive HP2 scaffold. It works according to a simple mix-and-detect assay format, with the first formation of a kissing complex between HP1 and HP2 scaffolds for fluorescence quenching, and then cascade propagation from steric strain through protein binding to the dissociation of the kissing complex for fluorescence recovery. The detection universality of such a modular nanoswitch was demonstrated by using three multivalent proteins, including anti-digoxigenin (Anti-Dig) antibody, streptavidin, and thrombin, with detection limits of 0.33, 0.17, and 0.5 nm, respectively.
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Affiliation(s)
- Yishen Tian
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Shanshan Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
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17
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Yu H, Zhang W, Lv S, Han J, Xie G, Chen S. A one-step structure-switching electrochemical sensor for transcription factor detection enhanced with synergistic catalysis of PtNi@MIL-101 and Exo III-assisted cycling amplification. Chem Commun (Camb) 2018; 54:11901-11904. [DOI: 10.1039/c8cc06468g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a new type of PtNi@MIL-101 electrocatalyst and Exo III-assisted cycling amplification for one-step electrochemical detection of NF-κB p50.
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Affiliation(s)
- Hua Yu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry & Materials Science
- Northwest University
- Xi’an
- P. R. China
| | - Wen Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry & Materials Science
- Northwest University
- Xi’an
- P. R. China
| | - Sicheng Lv
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry & Materials Science
- Northwest University
- Xi’an
- P. R. China
| | - Jing Han
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry & Materials Science
- Northwest University
- Xi’an
- P. R. China
| | - Gang Xie
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry & Materials Science
- Northwest University
- Xi’an
- P. R. China
| | - Sanping Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry & Materials Science
- Northwest University
- Xi’an
- P. R. China
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18
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Lu L, Su H, Li F. Ultrasensitive Homogeneous Electrochemical Detection of Transcription Factor by Coupled Isothermal Cleavage Reaction and Cycling Amplification Based on Exonuclease III. Anal Chem 2017; 89:8328-8334. [DOI: 10.1021/acs.analchem.7b01538] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Lihua Lu
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Huijuan Su
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Feng Li
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
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