1
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Li H, Wang Y, Wan Y, Li M, Xu J, Wang Q, Wu D. Stimuli-responsive incremental DNA machine auto-catalyzed CRISPR-Cas12a feedback amplification permits ultrasensitive molecular diagnosis of esophageal cancer-related microRNA. Talanta 2024; 271:125675. [PMID: 38245957 DOI: 10.1016/j.talanta.2024.125675] [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: 11/28/2023] [Revised: 01/07/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Development of new diagnostic methods is essential for disease diagnosis and treatment. In this work, we present a stimuli-responsive incremental DNA machine auto-catalyzed CRISPR-Cas12a (SRI-DNA machine/CRISPR-Cas12a) feedback amplification for ultrasensitive molecular detection of miRNA-21, which is an important biomarker related closely to the initiation and development of cancers, such as esophageal cancer. Strategically, the powerful SRI-DNA machine and efficient trans-cleavage activity of the CRISPR-Cas12a system are ingeniously integrated via a rationally designed probe termed as stem-elongated functional hairpin probe (SEF-HP). The SRI-DNA machine begins with the target miRNA, the trigger of the reaction, binding complementarily to the SEF-HP, followed by autonomously performed mechanical strand replication, cleavage, and displacement circuit at multiple sites. This conversion process led to the amplified generation of numerous DNA activators that are complementary with CRISPR RNA (CrRNA). Once formed the DNA activator/CrRNA heteroduplex, the trans-cleavage activity of the CRISPR-Cas12a was activated to nonspecific cleavage of single-stranded areas of a reporter probe for fluorescence emission. Under optimal conditions, the target miRNA can be detected with a wide linear range and an excellent specificity. As a proof-of-concept, this SRI-DNA machine/CRISPR-Cas12a feedback amplification system is adaptable and scalable to higher-order artificial amplification circuits for biomarkers detection, highlighting its promising potential in early diagnosis and disease treatment.
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Affiliation(s)
- Hongxia Li
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Yi Wang
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Yu Wan
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Meimei Li
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Jianguo Xu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, PR China; Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological, Hefei University of Technology, Hefei, 230009, PR China.
| | - Qi Wang
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, PR China.
| | - Donglei Wu
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China.
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2
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Wang X, Zheng D, Wang C, Xue D, Wang Q, Xia J. Harnessing intermolecular G-quadruplex-based spatial confinement effect for accelerated activation of CRISPR/Cas12a empowers ultra-sensitive detection of PML/RARA fusion genes. Anal Chim Acta 2024; 1287:342108. [PMID: 38182385 DOI: 10.1016/j.aca.2023.342108] [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: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024]
Abstract
Accurate detection and classification of the three isoforms of PML/RARA genomic fragments are crucial for predicting disease progression, stratifying risk, and administering precise drug therapies in acute promyelocytic leukemia (APL). In this study, we have developed a highly specific nucleic acid detection platform capable of quantifying the long isoform of the three main PML-RARA isoforms at a constant temperature. This platform integrates the strengths of the CRISPR/Cas12a nuclease-based method and the rolling circle amplification (RCA) technique. Notably, the RCA-assisted CRISPR/Cas12a trans-cleavage system incorporates a spatial confinement effect by utilizing intermolecular G-quadruplex structures. This innovative design effectively enhances the local concentration of CRISPR/Cas12a, thereby accelerating its cleaving efficiency towards reporter nucleic acids and enabling the detection of PML/RARA fusion gene expression through spectroscopy. The robust detection of PML/RARA fusion gene from human serum samples validates the reliability and potential of this platform in the screening, diagnosis, and prognosis of APL cases. Our findings present an approach that holds significant potential for the further development of the robust CRISPR/Cas sensor system, offering a rapid and adaptable paradigm for APL diagnosis.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, 350000, PR China; NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian, 350000, PR China.
| | - Dan Zheng
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Chengyi Wang
- Department of Hematology & Oncology, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, Fujian, 350011, PR China
| | - Danni Xue
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Qi Wang
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Juan Xia
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China.
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3
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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4
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Kong X, Wang J, Lv S, Wang C, Hong H, Xie P, Guo Y, Zhu N, Qin P, Sun Y, Xu J. Bidirectional motivated bimodal isothermal strand displacement amplifier with a table tennis-like movement for the ultrasensitive fluorescent and colorimetric detection of depression-related microRNA. Anal Chim Acta 2023; 1247:340894. [PMID: 36781251 DOI: 10.1016/j.aca.2023.340894] [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: 11/21/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
An increasing number of studies have highlighted the potential of microRNAs (miRNAs) as physiological indicators of major depressive disorder (MDD). Herein, we developed a bidirectional-motivated bimodal isothermal strand displacement amplifier (BB-ISDA) for the ultrasensitive fluorescent and colorimetric detection of MDD-related miRNA-132. In the BB-ISDA system, a pair of functionalized hairpin probes (HP1 and HP2) with nicking recognition sites are designed to recognize target miRNA. The recognition of target miRNA by HP1 (or HP2) generates copious numbers of nicked triggers by HP1 (or HP2)-based ISDA to recognize HP2 (or HP1) by autonomous strand polymerization, cleavage, and displacement, which in turn induces the subsequent generation of copious numbers of nicked G-quadruplex triggers by HP2 (or HP1)-based ISDA to recognize HP1 (or HP2) along a same line. After many cycles, this bidirectional motivated table-tennis-like movement amplifies the fluorescent signal from HP1 and the colorimetric signal from HP2, simultaneously. The dual-signal output pattern was cross-validated for sensing miRNA-132. Each of the detection modal shows the capability for qualitative and quantitative detection of miRNA-132 with high sensitivity and specificity. The adaptability of the bimodal mechanism was verified via the detection of target miRNA-132 from clinical human blood samples. We envision that this BB-ISDA with dual-signal output for accurate and reliable analysis of miRNA is promising for the molecular diagnosis of human mental diseases.
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Affiliation(s)
- Xiaoming Kong
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Junfeng Wang
- School of Public Health, Anhui Medical University, Hefei, 230032, Anhui, PR China
| | - Siwen Lv
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Chen Wang
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Hong Hong
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Pengyv Xie
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Yv Guo
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Nannan Zhu
- Affiliated Psychological Hospital of Anhui Medical University, Anhui Mental Health Center, Hefei Fourth People's Hospital, 316 Huangshan Road, Hefei, 230022, PR China
| | - Panzhu Qin
- School of Public Health, Anhui Medical University, Hefei, 230032, Anhui, PR China.
| | - Yan Sun
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, PR China.
| | - Jianguo Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, Anhui, PR China.
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5
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Xia J, Liu Z, Gao S, Wang Q, Xu J, Wu H. Intermolecular and Intramolecular Priming Co-directed Synergistic Multi-strand Displacement Amplification Empowers Ultrasensitive Determination of microRNAs. Anal Chem 2022; 94:16132-16141. [DOI: 10.1021/acs.analchem.2c03466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juan Xia
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Chemistry and Materials Engineering, Fuyang Normal University, Anhui Fuyang 236037, P. R. China
| | - Zhaoqiang Liu
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Shulin Gao
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Qi Wang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui, Hefei 230601, P. R. China
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Hai Wu
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Chemistry and Materials Engineering, Fuyang Normal University, Anhui Fuyang 236037, P. R. China
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6
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Sun Y, Xu YX, Wang N, Wang F, Hui CC, Cheng YW, Cui MJ, Huang QY, Xu JG, Kong XM. Time-resolved strand displacement amplification enables G-quadruplex-amplified detection of type 2 diabetes mellitus-related circulating microRNA-146a. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Zhong X, Li Y, Chang Y, Yuan R, Chai Y. A highly-efficient 3D DNAzyme motor for sensitive biosensing analysis. Talanta 2022; 250:123683. [PMID: 35777344 DOI: 10.1016/j.talanta.2022.123683] [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: 12/07/2021] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 11/19/2022]
Abstract
Herein, driven by the need of highly-efficient DNAzyme-amplified detection strategy, a novel 3D DNAzyme motor was designed as a biosensor platform for realizing sensitive detection of target DNA. The 3D DNAzyme motor was composed of target-activated DNAzyme nanowires and substrates H1-Fc that co-immobilized on Au@Fe3O4 nanoparticles (Au@Fe3O4NPS) surface, possessing high local concentration of DNA reactants and shortened distance between DNAzyme and substrates for enhancing electrochemical signal. Compared with traditional DNAzyme-powered machines, the target-activated DNAzyme nanowires of 3D DNAzyme motor had greater flexibility and more powerful cleavage capability without troublesome sequence optimization, which overcame the space limitation and simultaneously interacted with adjacent and distant substrates H1-Fc to output a large amount of cleavage products with high signal response. Therefore, on account of the above-mentioned merits of nanoparticles localization DNA design and DNAzyme nanowires, the reported 3D DNAzyme motor ingeniously overcame many defects existing in traditional DNAzyme-amplified detection strategies such as low reactants concentration, limited flexibility of DNAzyme and small DNAzyme swing range, realizing the sensitive detection of target DNA with a detection limit of 1.7 fM ranging from 5 fM to 50 nM. Impressively, the 3D DNAzyme motor here presented a new strategy to achieve effective DNAzyme signal amplification and provided a reference for the assembly of various and functional 3D DNA machines in the future.
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Affiliation(s)
- Xia Zhong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yunrui Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yuanyuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
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8
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Sun F, Zhang J, Ge L, Liu S, Zhu T, Wang Y, Wang J, Li H. Linear poly-thymine probe-based coupling of autocatalytic target recycling with nonlinear DNA assembly for label-free detection of microRNAs. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Wang J, Sun J, Zhang J, Shen C, Zhang X, Xu J. Engineered G-Quadruplex-Embedded Self-Quenching Probes Regulate Single Probe-Based Multiplex Isothermal Amplification to Light Road Lamp Probes for Sensitized Determination of microRNAs. Anal Chem 2022; 94:4437-4445. [PMID: 35234452 DOI: 10.1021/acs.analchem.1c05402] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Design of oligonucleotide probe-based isothermal amplification with the ability to identify miRNA biomarkers is crucial for molecular diagnostics. In this work, we engineered a miRNA-21-responsive G-quadruplex-embedded self-quenching probe (GE-SQP) that can regulate single probe-based multiplex amplifications. The free GE-SQP is tightly locked in a quenching state with no active G-quadruplexes. Introduction of target miRNA to hybridize with GE-SQP would induce a multiplex isothermal amplification to significantly build a lot of one-bulb-contained road lamp probe (OC-RLP) and two-bulb-contained road lamp probe (TC-RLP) using G-quadruplex as the lamp bulb. When lightened by thioflavin T (ThT), beams of fluorescence were emitted to show the presented miRNA-21. Specially, the whole amplification is only a one probe-involved one-step reaction without any wasted species. The mix-to-detection and all-in amplification behavior allows the sensing system a maximally maintained operation simplicity and high assay performance. In such a way, the detection range of miRNA-21 is from 1 fM to 1 nM with a limit of detection of 0.86 fM. The practicability was demonstrated by determining miRNA-21 from serum samples with acceptable results. We expect that this method can open a new avenue for exploring advanced biosensors with improved analytical performances.
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Affiliation(s)
- Jie Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Jiayin Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Jing Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Chenlin Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Xinlei Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jianguo Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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10
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Lin L, Zhang Y, Wei Q, Lin H, Li X, Yu ME, Wang J, Huang Z, Xue D. Structure and function encoding of a bidirectional activatable synergetic DNA machine for speeded and ultrasensitive determination of microRNAs. Talanta 2022; 238:123037. [PMID: 34857317 DOI: 10.1016/j.talanta.2021.123037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
This work describes the unique design of a bidirectional activatable synergetic DNA machine (BAS-DNA machine) for speeded and ultrasensitive determination of microRNA-21 (miR-21), a well-known biomarker for biomedical research and early diagnosis of lung cancer. The BAS-DNA machine is composed by a pair of track strands (Track 1 and Track 2) encoding with two regions in the opposite direction for miR-21 recognition. Introduction of miR-21 can hybridize either with Track 1 or with Track 2 to activate the BAS-DNA machine with a synergistic effect for speeded amplifying the fluorescence signal. Moreover, compared with common DNA machine with only one switch for exogenous target recognition, the BAS-DNA machine with two switches for miR-21 binding allows the speeded and strong operation of the autonomous strand scission, replication, and displacement on Track 1 and Track 2 simultaneously. This behavior makes the BAS-DNA machine powerful for ultrasensitive, specific, and fast screening of miR-21 even from real biological samples, and the fluorescence signal was found to be linear from 1 pM to 10 nM with a detection limit of 703.6 fM. We envision this BAS-DNA machine with its superior assay performance will provide a new avenue for simple, sensitive, and affordable biomedical assays.
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Affiliation(s)
- Lan Lin
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yingying Zhang
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital/Shandong Lung Cancer Institute, Shandong, China
| | - Qiongying Wei
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Hongguang Lin
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xiaoping Li
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mei-E Yu
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jie Wang
- School of Pharmacy, Anhui Medical University, Hefei, 230031, China.
| | - Zhenghui Huang
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China.
| | - Dan Xue
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China; Department of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China.
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11
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Zhang Q, Han Y, Li CC, Zou X, Ma F, Zhang CY. Construction of a dual-functional dumbbell probe-based fluorescent biosensor for cascade amplification detection of miRNAs in lung cancer cells and tissues. Chem Commun (Camb) 2022; 58:5538-5541. [DOI: 10.1039/d2cc01341j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a dual-functional dumbbell probe-based fluorescent biosensor for cascade amplification detection of miRNAs in lung cancer cells and tissues by integrating primer exchange reaction (PER) with CRISPR-Cas12a system. This...
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12
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Xu J, Li Z, Li Y, Lu Y, Wang J. Activation of palindromes on a degradable modular grafting probe enables ultrasensitive detection of microRNAs. Chem Commun (Camb) 2021; 57:5941-5944. [PMID: 34018521 DOI: 10.1039/d1cc01150b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work describes a single-stranded degradable modular grafting probe for analyzing microRNA-21. In the system, the exonuclease activity of phi29 polymerase restrains the SYBR Green I/ssDNA induced background. The palindrome activation caused remarkable target fluorescence. The detection limit was achieved as 0.26 fM, showing potential in biochemical analysis.
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Affiliation(s)
- Jianguo Xu
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Zhi Li
- College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Yumei Li
- College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Yusheng Lu
- College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Jie Wang
- College of Chemistry, Fuzhou University, Fuzhou 350002, China. and School of Pharmacy, Anhui Medical University, Hefei 230031, China
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13
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Periodically programmed building and collapse of DNA networks enables an ultrahigh signal amplification effect for ultrasensitive nucleic acids analysis. Anal Chim Acta 2021; 1150:338221. [PMID: 33583542 DOI: 10.1016/j.aca.2021.338221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 11/21/2022]
Abstract
ANALYSIS of molecular species is needed for applications in diagnosis of infections and genetic diseases. Herein, we demonstrate a target DNA-responsive ultrahigh fluorescence signal-on DNA amplification system via periodically programmed building and collapse of DNA networks. In this system, a pair of oligonucleotides of padlock probe (PP) and palindromic hairpin probe (PHP) are utilized. The presence of target DNA firstly hybridizes with PP, allowing the occurrence of rolling circle amplification (RCA) to produce RCA products with tandem repeats in abundance to bind and unfold numbers of PHPs. The conformational change of PHPs enables the building of DNA networks via the intermolecular palindrome pairing, but then makes the DNA networks collapsed via the palindrome-induced strand displacement polymerization. The displaced RCA products are dynamically reused to undergo periodically programmed multiple rounds of DNA network building and collapse. Depend on the bidirectional DNA assembly and disassembly, a strikingly amplified fluorescence can be collected to ultrasensitive and specific detection of target DNA. The practicability has been demonstrated by evaluating target-spiked human serum, saliva, and urine samples with acceptable recoveries and reproducibility. Therefore, this newly explored method opens a promising avenue for the detection of nucleic acids with low abundance in biochemical analysis and diseases diagnosis.
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14
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Amplified collection of binary G-quadruplex on a binary C-rich functionalized palindromic hairpin probe for label-free detection of a molecular cancer biomarker of microRNA. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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A simple, one-pot and ultrasensitive DNA sensor via Exo III-Assisted target recycling and 3D DNA walker cascade amplification. Anal Chim Acta 2020; 1147:15-22. [PMID: 33485573 DOI: 10.1016/j.aca.2020.12.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 11/20/2022]
Abstract
Rapid, sensitive, and user-friendly nucleic acid detection is of growing importance in early clinical diagnosis. Here, we construct a simple, one-pot and ultrasensitive DNA sensor via exonuclease III (Exo III)-assisted target recycling amplification (ERA) combined with 3D DNA walker cascade amplification. In the presence of single-stranded DNA target, the ERA process is activated to generate numerous walker strands (WS). Thereafter, Exo III-powered WSs autonomously move along magnetic bead (MB)-based 3D track to release numerous AgNCs into the supernatant as an amplified signal output. This biosensor had a low detection limit of 18 fM and an analytical range of 40 fM to 1 pM. Furthermore, the practical application potential of this biosensor was also confirmed by the spiking experiments of p53 into human serum and urine samples.
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A molecular device: A DNA molecular lock driven by the nicking enzymes. Comput Struct Biotechnol J 2020; 18:2107-2116. [PMID: 32913580 PMCID: PMC7451616 DOI: 10.1016/j.csbj.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.
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Wang L, Jiang MH, Chai YQ, Yuan R, Zhuo Y. Intense electrochemiluminescence from an organic microcrystal accelerated H2O2-free luminol system for microRNA detection. Chem Commun (Camb) 2020; 56:9000-9003. [DOI: 10.1039/d0cc02207a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 9,10-diphenylanthracene microcrystals (DPA MCs) was developed as a novel coreactant accelerator for H2O2-free luminol system, which was attributed to the efficiently catalysis towards dissolved O2 for more reactive oxygen species generation.
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Affiliation(s)
- Li Wang
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Ming-Hui Jiang
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Ya-Qin Chai
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Ruo Yuan
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Ying Zhuo
- Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
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