1
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Ma X, Suo T, Zhao F, Shang Z, Chen Y, Wang P, Li B. Integrating CRISPR/Cas12a with strand displacement amplification for the ultrasensitive aptasensing of cadmium(II). Anal Bioanal Chem 2023; 415:2281-2289. [PMID: 36952025 DOI: 10.1007/s00216-023-04650-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/26/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
Cadmium ion (Cd(II)) is a pernicious environmental pollutant that has been shown to contaminate agricultural lands, accumulate through the food chain, and seriously threaten human health. At present, Cd(II) monitoring is dependent on centralized instruments, necessitating the development of rapid and on-site detection platforms. Against this backdrop, the present study reports on the development of a fluorometric aptasensor designed to target Cd(II), which is achieved through the integration of strand displacement amplification (SDA) and CRISPR/Cas12a. In the absence of Cd(II), the aptamer initiates SDA, resulting in the generation of a profusion of ssDNA that activates Cas12a, leading to a substantial increase in fluorescence output. Conversely, the presence of Cd(II) curtails the SDA efficiency, culminating in a significant reduction in fluorescence output. The proposed approach has been demonstrated to enable the selective detection of Cd(II) at concentrations of 60 pM, with the performance of the aptasensor validated in real water and rice samples. The proposed platform based on aptamer-target interaction holds immense promise as a signal-amplified and precise method for the detection of Cd(II) and has the potential to transform current hazard detection practices in food samples.
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Affiliation(s)
- Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing, 100101, China
| | - Tiying Suo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
- Nanjing Jiangbei New Area Biopharmaceutical Public Platform Co., Ltd., Nanjing, 211899, China
| | - Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Zhaoyang Shang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, 211166, China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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2
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Cao S, Tang X, Chen T, Chen G. Types and Applications of Nicking Enzyme-Combined Isothermal Amplification. Int J Mol Sci 2022; 23:ijms23094620. [PMID: 35563012 PMCID: PMC9100243 DOI: 10.3390/ijms23094620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.
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Affiliation(s)
- Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
- Correspondence: (T.C.); (G.C.)
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.C.); (G.C.)
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3
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Liu X, Bu S, Wei H, Wang Z, Yu S, Li Z, Hao Z, He X, Wan J. Visual assay of Escherichia coli O157:H7 based on an isothermal strand displacement and hybrid chain reaction amplification strategy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3379-3385. [PMID: 34235517 DOI: 10.1039/d1ay00644d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Here, we describe a simple, sensitive, and enzyme-free method for visual point-of-care detection of 16S rRNA of Escherichia coli O157:H7 based on an isothermal strand displacement-hybrid chain reaction (ISD-HCR) and lateral flow strip (LFS). In this study, the secondary structure of 16S rRNA of E. coli O157:H7 was unwound by two helper oligonucleotides to expose the single-strand-specific nucleic acid sequence. The free specific sequence promoted the toehold-mediated strand displacement reaction to output a large number of FITC-labeled single-stranded DNA probes (capture probe [CP]). The 3'-end sequence of the reporter probe propagated a chain reaction of hybridization events between the two hairpin probes modified with biotin to form long nicked DNA polymers with multiple biotins (RP-HCR complexes); the free CP and RP-HCR complexes then form CP/RP-HCR complexes. The biotin-labeled double-stranded DNA CP/RP-HCR polymers then introduced numerous streptavidin (SA)-labeled gold nanoparticles (AuNPs) on the LFS. The accumulation of AuNPs produced a characteristic red band, which enabled visual detection of changes in the signal of 16S rRNA of E. coli O157:H7. The current approach could detect E. coli O157:H7 at concentrations as low as 102 CFU mL-1 without instrumentation. This approach thus provides a simple, sensitive, and low-cost tool for point-of-care detection of pathogenic bacteria, especially in resource-limited countries.
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Affiliation(s)
- Xiu Liu
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130022, China.
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4
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Zyrina NV, Antipova VN. Nonspecific Synthesis in the Reactions of Isothermal Nucleic Acid Amplification. BIOCHEMISTRY (MOSCOW) 2021; 86:887-897. [PMID: 34284713 DOI: 10.1134/s0006297921070099] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The review focuses on the main factors involved in the formation of nonspecific products in isothermal nucleic acid amplification, such as mispriming, ab initio DNA synthesis, and additional activities of DNA polymerases, and discusses approaches to prevent formation of such nonspecific products in LAMP, RPA, NASBA, RCA, SDA, LSDA, NDA, and EXPAR.
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Affiliation(s)
- Nadezhda V Zyrina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Valeriya N Antipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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5
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Xu H, Wu B, Wang J, Cao H, Yang J, Hao K, Chen S, Ye S, Shen Z. Label-free detection of cancer related gene based on target recycling and palindrome-mediated strand displacement amplification. Talanta 2020; 215:120897. [PMID: 32312442 DOI: 10.1016/j.talanta.2020.120897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
STAT3 plays an important role in regulating gene expression and is closely related with cancer. Thus, the sensitive and specific detection of the STAT3 biomarker is of great importance for disease diagnosis and therapeutics. In this study, by combining the target recycling amplification (TRA) with strand displacement amplification (SDA), we have developed a label-free and highly sensitive method for the dual-amplified detection of STAT3. The assay system consists of polymerization primer and label-free hairpin probe (HP) containing palindromic fragment and nicking site. In the presence of STAT3, the stem of the HP is opened, followed by the primer binding to initiate TRA and SDA with the help of Klenow Fragment (KF) and nickase. After multiple replication, nicking, and strand displacement, STAT3 was released and initiated the next round of reactions, generating a large number of terminal palindrome-contained fragments. Subsequently, the intermolecular hybridization between palindromic fragments occurred and the bidirectional extension by polymerase takes place, forming the dsDNAs. The double-stranded DNA products can be quantified by measuring the fluorescence intensity of SYBR Green I. The proposed strategy shows the excellent specificity and high sensitivity with a detection limit as low as 50 pM. In addition, this designed protocol can be successfully applied to detect the STAT3 in human serum, indicating great potential for the practical application in early diagnosis and prognosis.
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Affiliation(s)
- Huo Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Cancer Metastasis Alert and Prevention Center, Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, And Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, 350002, China; Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Biting Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jue Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Cancer Metastasis Alert and Prevention Center, Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, And Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, 350002, China
| | - Hongwen Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jie Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kaixuan Hao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Si Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Sheng Ye
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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6
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Lei S, Liu Z, Xu L, Zou L, Li G, Ye B. A "signal-on" electrochemical biosensor based on DNAzyme-driven bipedal DNA walkers and TdT-mediated cascade signal amplification strategy. Anal Chim Acta 2019; 1100:40-46. [PMID: 31987151 DOI: 10.1016/j.aca.2019.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022]
Abstract
In this work, a dual amplified signal enhancement approach based on coupling deoxyribozyme (DNAzyme)-driven bipedal DNA walkers (BDW) and terminal deoxynucleotidyl transferase (TdT)-mediated DNA elongation signal amplifications has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. In presence of thrombin, the BDW complex, which is comprised from the target thrombin and two DNAzyme-containing probes, can exhibit autonomous cleavage behavior on the surface of the substrate DNA (SD) modified electrode, and remove the cleaved DNA fragment from the electrode surface. Subsequently, the TdT can catalyze the elongation of the SD with free 3'-OH termini and formation of many G-quadruplex sequence replicates with the presence of 2'-deoxyaguanosine-5'-triphosphate (dGTP) and adenosine 5'-triphosphate (dATP) at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a "signal-on" and completely label-free fashion. Under optimized conditions, the response peak current was linear with the concentration of thrombin in the range from 0.5 pM to 100000 pM with detection limit of 0.31 pM. This research provides us a sustainable idea for the hyphenated multiple amplification strategies and a stable and effective method for the detection of protein biomarkers.
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Affiliation(s)
- Sheng Lei
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Zi Liu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lingling Xu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Baoxian Ye
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China.
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7
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Song H, Yang Z, Jiang M, Zhang G, Gao Y, Shen Z, Wu ZS, Lou Y. Target-catalyzed hairpin structure-mediated padlock cyclization for ultrasensitive rolling circle amplification. Talanta 2019; 204:29-35. [DOI: 10.1016/j.talanta.2019.05.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/02/2019] [Accepted: 05/12/2019] [Indexed: 12/24/2022]
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8
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Fluorometric determination of the p53 cancer gene using strand displacement amplification on gold nanoparticles. Mikrochim Acta 2019; 186:517. [DOI: 10.1007/s00604-019-3609-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022]
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9
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Li J, Kong C, Liu Q, Chen Z. Colorimetric ultrasensitive detection of DNA based on the intensity of gold nanoparticles with dark-field microscopy. Analyst 2019; 143:4051-4056. [PMID: 30059077 DOI: 10.1039/c8an00825f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present an ultrasensitive colorimetric nucleic acid assay based on the intensity of gold nanoparticles (Au NPs) using dark field microscopy. In the absence of target DNA, two hairpin-like DNA strands with protruding single-stranded DNA (ssDNA) can be absorbed onto the Au NP surface via non-covalent interactions between the exposed nitrogen bases of ssDNA and Au NPs, which inhibits Au NPs from aggregating in a high concentration of salt media, while in the presence of target DNA, two hairpin DNA strands hybridize with target DNA to form double-stranded DNA (dsDNA). After hybridization chain reaction (HCR) amplification, rigid dsDNA polymers are formed, which results in serious Au NP aggregation in the salt environment. By measuring the intensity change of yellow and red dots on a dark-field image, the concentration of target DNA can be accurately quantified with a limit of detection (LOD) of 66 fM.
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Affiliation(s)
- Jingjing Li
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China.
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10
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Liu S, Xin C, Yu X, Ding Z, Liu S. A catalytic DNA circuit-programmed and enzyme-powered autonomous DNA machine for nucleic acid detection. Analyst 2019; 144:5923-5927. [DOI: 10.1039/c9an01568j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A catalytic DNA circuit-programmed and enzyme-powered autonomous DNA machine was proposed for one-step, isothermal and dual-level amplified detection of nucleic acids.
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Affiliation(s)
- Shuang Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Chen Xin
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xiaoxiao Yu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Zhenbo Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Shufeng Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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11
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Ultrasensitive assay based on a combined cascade amplification by nicking-mediated rolling circle amplification and symmetric strand-displacement amplification. Anal Chim Acta 2019; 1047:172-178. [DOI: 10.1016/j.aca.2018.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/31/2018] [Accepted: 10/03/2018] [Indexed: 01/05/2023]
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12
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Zhong W, Tang W, Fan J, Zhang J, Zhou X, Liu Y. A domain-based DNA circuit for smart single-nucleotide variant identification. Chem Commun (Camb) 2018; 54:1311-1314. [PMID: 29177325 DOI: 10.1039/c7cc07733e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, P. R. China.
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13
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Zhu C, Liu M, Li X, Zhang X, Chen J. A new electrochemical aptasensor for sensitive assay of a protein based on the dual-signaling electrochemical ratiometric method and DNA walker strategy. Chem Commun (Camb) 2018; 54:10359-10362. [PMID: 30152501 DOI: 10.1039/c8cc05829f] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, a new electrochemical aptamer-based biosensor for highly sensitive assay of thrombin has been developed based on the dual-signaling electrochemical ratiometric method and the DNA walker strategy, and shows a low detection limit of about 56 fM.
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Affiliation(s)
- Caixia Zhu
- 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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14
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Ye X, Li Y, Wang L, Fang X, Kong J. A novel exonuclease-assisted isothermal nucleic acid amplification with ultrahigh specificity mediated by full-length Bst DNA polymerase. Chem Commun (Camb) 2018; 54:10562-10565. [PMID: 30065993 DOI: 10.1039/c8cc04577a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Here, we introduced a novel exonuclease-assisted isothermal nucleic acid amplification (Exo-NAT) utilizing the full-length Bst DNA polymerase combined with a melting curve analysis. This method achieved an ultrahigh specificity with a good detection limit (102 copies) in both singleplex and multiplex detection, which was validated by detecting three diarrhea-inducing pathogens, rotavirus A, astrovirus, and adenovirus, in 42 clinical samples.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China.
| | - Yang Li
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318, P. R. China and Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318, P. R. China
| | - Lijuan Wang
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318, P. R. China and Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318, P. R. China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China.
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China.
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15
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Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs. Anal Bioanal Chem 2018; 410:6819-6826. [PMID: 30066196 DOI: 10.1007/s00216-018-1277-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/02/2018] [Accepted: 07/16/2018] [Indexed: 01/23/2023]
Abstract
In this study, a biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) was proposed for the highly sensitive detection of cancer-related let-7a microRNA (miRNA). The sensing system consists of a padlock probe (PP), which contains a target recognition sequence and two binding sites for nicking endonuclease (NEase), and molecular beacon (MB) as reporting molecule. Upon hybridization with let-7a, the PP can be circularized by ligase. Then, the miRNA acted as polymerization primer to initiate rolling circle amplification (RCA). With the assistance of NEase, RCA products can be nicked on the cyclized PP and are displaced during the subsequent duplication process, generating numerous nicked fragments (NFs). These NFs not only induce another RCA reaction but also open the molecular beacons (MBs) via hybridization, leading to significantly amplified fluorescence signal. Under the optimized conditions, this method exhibits high sensitivity toward target miRNA let-7a with a detection limit of as low as 10 pM, a dynamic range of three orders of magnitude is achieved, and its family member is easily distinguished even with only one mismatched base. Meanwhile, it displays good recovery and satisfactory reproducibility in fetal bovine serum (FBS). Therefore, these merits endow the newly proposed N-RCA strategy with powerful implications for miRNA detection. Graphical abstract A biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) for the highly sensitive detection of cancer-related let-7a microRNA.
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16
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Qu X, Jin H, Liu Y, Sun Q. Strand Displacement Amplification Reaction on Quantum Dot-Encoded Silica Bead for Visual Detection of Multiplex MicroRNAs. Anal Chem 2018; 90:3482-3489. [DOI: 10.1021/acs.analchem.7b05235] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Haojun Jin
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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17
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Li K, Wang L, Xu X, Jiang W. Label-free molecular beacons-based cascade amplification DNA machine for sensitive detection of telomerase activity. Talanta 2017; 167:645-650. [DOI: 10.1016/j.talanta.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/24/2017] [Accepted: 03/02/2017] [Indexed: 02/07/2023]
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18
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A label-free colorimetric isothermal cascade amplification for the detection of disease-related nucleic acids based on double-hairpin molecular beacon. Anal Chim Acta 2017; 957:55-62. [DOI: 10.1016/j.aca.2016.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/10/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022]
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19
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A Biofunctional Molecular Beacon for Detecting Single Base Mutations in Cancer Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e302. [PMID: 27045206 PMCID: PMC5014519 DOI: 10.1038/mtna.2016.18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/09/2016] [Indexed: 12/22/2022]
Abstract
The development of a convenient and sensitive biosensing system to detect
specific DNA sequences is an important issue in the field of genetic disease
therapy. As a classic DNA detection technique, molecular beacon (MB) is often
used in the biosensing system. However, it has intrinsic drawbacks, including
high assay cost, complicated chemical modification, and operational complexity.
In this study, we developed a simple and cost-effective label-free
multifunctional MB (LMMB) by integrating elements of polymerization primer,
template, target recognition, and G-quadruplex into one entity to detect target
DNA. The core technique was accomplished by introducing a G-hairpin that
features fragments of both G-quadruplex and target DNA recognition in the
G-hairpin stem. Hybridization between LMMB and target DNA triggered
conformational change between the G-hairpin and the common C-hairpin, resulting
in significant SYBR-green signal amplification. The hybridization continues to
the isothermal circular strand-displacement polymerization and accumulation of
the double-stranded fragments, causing the uninterrupted extension of the LMMB
without a need of chemical modification and other assistant DNA sequences. The
novel and programmable LMMB could detect target DNA with sensitivity at 250
pmol/l with a linear range from 2 to 100 nmol/l and the relative standard
deviation of 7.98%. The LMMB could sense a single base mutation from the normal
DNA, and polymerase chain reaction (PCR) amplicons of the mutant-type cell line
from the wild-type one. The total time required for preparation and assaying was
only 25 minutes. Apparently, the LMMB shows great potential for detecting DNA
and its mutations in biosamples, and therefore it opens up a new prospect for
genetic disease therapy.
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20
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Sun X, Wang L, Zhao M, Zhao C, Liu S. An autocatalytic DNA machine with autonomous target recycling and cascade circular exponential amplification for one-pot, isothermal and ultrasensitive nucleic acid detection. Chem Commun (Camb) 2016; 52:11108-11. [DOI: 10.1039/c6cc06643g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An autonomous target recycling and cascade circular exponential amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.
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Affiliation(s)
- Xinya Sun
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - 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
- Qingdao 266042
| | - Mingsha Zhao
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Changzhi Zhao
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - 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
- Qingdao 266042
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21
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Yang C, Dou B, Yang J, Yuan R, Xiang Y. Cross-triggered and cascaded recycling amplification for ultrasensitive electrochemical sensing of the mutant human p53 gene. Chem Commun (Camb) 2016; 52:8707-10. [DOI: 10.1039/c6cc04587a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cross-triggered and cascaded recycling amplification enables the highly sensitive electrochemical detection of the mutant p53 gene in human serum.
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Affiliation(s)
- Cuiyun Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Jianmei Yang
- 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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22
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[G3T]5/Tb3+ based DNA biosensor with target DNA-triggered autocatalytic multi-cycle-amplification and magnetic nanoparticles assisted-background-lowered. Biosens Bioelectron 2015; 74:931-8. [DOI: 10.1016/j.bios.2015.07.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/13/2015] [Accepted: 07/23/2015] [Indexed: 11/18/2022]
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23
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Dong H, Wu ZS, Xu J, Ma J, Zhang H, Wang J, Shen W, Xie J, Jia L. Novel multifunction-integrated molecular beacon for the amplification detection of DNA hybridization based on primer/template-free isothermal polymerization. Biosens Bioelectron 2015; 72:182-90. [DOI: 10.1016/j.bios.2015.04.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/10/2023]
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24
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Liu S, Wei W, Liu T, Wang L. Catalytic Hairpin Assembly-Programmed DNA Three-Way Junction for Enzyme-Free and Amplified Electrochemical Detection of Target DNA. Chem Asian J 2015; 10:1903-8. [DOI: 10.1002/asia.201500675] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Indexed: 01/02/2023]
Affiliation(s)
- 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 Rd. Zhengzhou, Qingdao Shandong 266042 China
| | - Wenji Wei
- 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 Rd. Zhengzhou, Qingdao Shandong 266042 China
| | - Tao 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 Rd. 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 Rd. Zhengzhou, Qingdao Shandong 266042 China
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25
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Xiong E, Zhang X, Liu Y, Zhou J, Yu P, Li X, Chen J. Ultrasensitive Electrochemical Detection of Nucleic Acids Based on the Dual-Signaling Electrochemical Ratiometric Method and Exonuclease III-Assisted Target Recycling Amplification Strategy. Anal Chem 2015; 87:7291-6. [DOI: 10.1021/acs.analchem.5b01402] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Erhu Xiong
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xiaohua Zhang
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yunqing Liu
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jiawan Zhou
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Peng Yu
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xiaoyu Li
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jinhua Chen
- 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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26
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Yan L, Liu K, Sintim HO. Convenient detection of HPV virus in a clinical sample using concurrent rolling circle and junction probe amplifications. Chem Commun (Camb) 2015; 50:7147-9. [PMID: 24852020 DOI: 10.1039/c4cc02532f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein we show that two isothermal amplification strategies, rolling circle amplification and junction probe strategy, can be used in tandem in the same tube under isothermal conditions to detect HPV16 in clinical cervical swabs. It was discovered that the prior treatment of the clinical sample with a cocktail of restriction endonucleases (REAses) to digest the genomic DNA facilitated the isothermal detection assay.
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Affiliation(s)
- Lei Yan
- Changzhou Fangyuan Pharmaceutical Co., Ltd., 108 Hehaixi Road, Xinbei District, Changzhou, Jiangsu 213022, China.
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27
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Wu ZK, Zhou DM, Wu Z, Chu X, Yu RQ, Jiang JH. Single-base mismatch discrimination by T7 exonuclease with target cyclic amplification detection. Chem Commun (Camb) 2015; 51:2954-6. [DOI: 10.1039/c4cc09984b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
T7 exonuclease is reported for the first time to have high specificity in discriminating single-base mismatch.
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Affiliation(s)
- Zhen-Kun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Dian-Ming Zhou
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Zhan Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
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28
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Liu S, Gong H, Sun X, Liu T, Wang L. A programmable Y-shaped junction scaffold-mediated modular and cascade amplification strategy for the one-step, isothermal and ultrasensitive detection of target DNA. Chem Commun (Camb) 2015; 51:17756-9. [DOI: 10.1039/c5cc07659e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.
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Affiliation(s)
- 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
- Qingdao 266042
| | - Hongwei Gong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xinya Sun
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Tao Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - 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
- Qingdao 266042
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29
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Liu S, Liu T, Wang L. Label-free, isothermal and ultrasensitive electrochemical detection of DNA and DNA 3′-phosphatase using a cascade enzymatic cleavage strategy. Chem Commun (Camb) 2015; 51:176-9. [DOI: 10.1039/c4cc08140d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free, isothermal and cascade enzymatic cleavage strategy was developed for the ultrasensitive electrochemical detection of DNA and DNA 3′-phosphatase.
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Affiliation(s)
- 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
- Qingdao 266042
| | - Tao Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - 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
- Qingdao 266042
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30
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Xue Q, Lv Y, Zhang Y, Xu S, Li R, Yue Q, Li H, Wang L, Gu X, Zhang S, Liu J. Ultrasensitive fluorescence detection of nucleic acids using exonuclease III-induced cascade two-stage isothermal amplification-mediated zinc (II)-protoporphyrin IX/G-quadruplex supramolecular fluorescent nanotags. Biosens Bioelectron 2014; 61:351-6. [DOI: 10.1016/j.bios.2014.05.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/08/2014] [Accepted: 05/22/2014] [Indexed: 12/13/2022]
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31
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He P, Qiao W, Liu L, Zhang S. A highly sensitive surface plasmon resonance sensor for the detection of DNA and cancer cells by a target-triggered multiple signal amplification strategy. Chem Commun (Camb) 2014; 50:10718-21. [DOI: 10.1039/c4cc04776a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A SPR bioassay was developed for the detection of DNA and Ramos cells by combining the target-triggered isothermal exponential amplification with MNP-based RCA.
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Affiliation(s)
- Peng He
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, P. R. China
| | - Wenping Qiao
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, P. R. China
| | - Lijun Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, P. R. China
| | - Shusheng Zhang
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005, P. R. China
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32
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Li H, Wu Z, Qiu L, Liu J, Wang C, Shen G, Yu R. Ultrasensitive label-free amplified colorimetric detection of p53 based on G-quadruplex MBzymes. Biosens Bioelectron 2013; 50:180-5. [DOI: 10.1016/j.bios.2013.06.041] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 11/27/2022]
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