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Zhang Z, Li J, Chen C, Tong Y, Liu D, Li C, Lu H, Huang L, Feng W, Sun X. Exploring T7 RNA polymerase-assisted CRISPR/Cas13a amplification for the detection of BNP via electrochemiluminescence sensing platform. Anal Chim Acta 2024; 1300:342409. [PMID: 38521567 DOI: 10.1016/j.aca.2024.342409] [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: 12/04/2023] [Revised: 01/25/2024] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Brain natriuretic peptide (BNP) is considered to be an important biomarker of heart failure (HF) attracting attention. However, its low concentration and short half-life in blood lead to a low-sensitivity detection of BNP, which is a challenge that has to be overcome. In this work, we propose a highly specific, highly sensitive T7 RNA polymerase-assisted clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a system to detect BNP via an electrochemiluminescence (ECL) sensing platform and incorporate exonuclease III (Exo III)-hairpin and dumbbell-shaped hybridization chain reaction (HCR) technologies. In this detection scheme, the ECL sensing platform possesses low background signal and high sensitivity. Firstly, the T7 promoter-initiated T7 RNA polymerase acts as a signal amplification technique to generate large amounts of RNAs that can activate CRISPR/Cas13a activity. Secondly, CRISPR/Cas13a is able to trans-cleave the surrounding trigger strand to produce DNA1. Thirdly, DNA1 is involved in the co-amplification reaction of Exo III and hairpin DNA, which subsequently triggers a dumbbell-shaped HCR technology. Eventually, a large number of Ru (II) molecules are inserted into the interstitial space of the dumbbell-shaped HCR to generate a strong ECL signal. The CRISPR/Cas13a possesses outstanding specificity for a single base and increased sensitivity. The tightly conformed dumbbell-shaped HCR provides higher sensitivity than the traditional linear HCR amplification technique. Ultimately, the clever combination of several amplification reactions enables the limit of detection (LOD) as low as 3.2 fg/mL. It showed promise for clinical sample testing, with recovery rates ranging from 98.4% to 103% in 5% human serum samples. This detection method offered a valuable tool for early HF detection, emphasizing the synergy of amplification strategies and specificity conferred by CRISPR/Cas13a technology.
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Affiliation(s)
- Zaiyong Zhang
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Jinglong Li
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Chunlin Chen
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Yuwei Tong
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Dehui Liu
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Cuizhi Li
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Huan Lu
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China.
| | - Li Huang
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Wanling Feng
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
| | - Xiaoting Sun
- Department of Cardiology, Guangzhou Eighth People's Hospital Guangzhou Medical University, Guangzhou, 510440, PR China
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Wei J, Song Z, Cui J, Gong Y, Tang Q, Zhang K, Song X, Liao X. Entropy-driven assisted T7 RNA polymerase amplification-activated CRISPR/Cas13a activity for SARS-CoV-2 detection in human pharyngeal swabs and environment by an electrochemiluminescence biosensor. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131268. [PMID: 36965355 DOI: 10.1016/j.jhazmat.2023.131268] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
In this study, we introduce an electrochemiluminescence (ECL) sensing platform based on the "Entropy-driven triggered T7 amplification-CRISPR/Cas13a system" (EDT-Cas). This platform combines a programmable entropy-driven cycling strategy, T7 RNA polymerase, and the CRISPR/Cas13a system to amplify the determination of the SARS-CoV-2 RdRp gene. The Ti3C2Tx-compliant ECL signaling molecule offers unique benefits when used with the ECL sensing platform to increase the assay sensitivity and the electrode surface modifiability. To obtain the T7 promoter, the SARS-CoV-2 RdRp gene may first initiate an entropy-driven cyclic amplification response. Then, after recognizing the T7 promoter sequence on the newly created dsDNA, T7 RNA polymerase starts transcription, resulting in the production of many single-stranded RNAs (ssRNAs), which in turn trigger the action of CRISPR/Cas13a. Finally, Cas13a/crRNA identifies the transcribed ssRNA. When it cleaves the ssRNA, many DNA reporter probes carrying -U-U- are cleaved on the electrode surface, increasing the ECL signal and allowing for the rapid and highly sensitive detection of SARS-CoV-2. With a detection limit of 7.39 aM, our method enables us to locate the SARS-CoV-2 RdRp gene in clinical samples. The detection method also demonstrates excellent repeatability and stability. The SARS-CoV-2 RdRp gene was discovered using the "Entropy-driven triggered T7 amplification-CRISPR/Cas13a system" (EDT-Cas). The developed ECL test had excellent recoveries in pharyngeal swabs and environmental samples. It is anticipated to offer an early clinical diagnosis of SARS-CoV-2 and further control the spread of the pandemic.
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Affiliation(s)
- Jihua Wei
- Guangxi Key Laboratory of Basic and Translational Research of Bone and Joint Degenerative Disease, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Zichun Song
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Jiuying Cui
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Yuanxun Gong
- Guangxi Key Laboratory of Basic and Translational Research of Bone and Joint Degenerative Disease, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Qianli Tang
- Guangxi Key Laboratory of Basic and Translational Research of Bone and Joint Degenerative Disease, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Kai Zhang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China.
| | - Xinlei Song
- Maternity & Child Care Center of Dezhou, Dezhou 253000, 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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Cheng X, Xia X, Ren D, Chen Q, Xu G, Wei F, Yang J, Wang L, Hu Q, Zou J, Cen Y. Programmable CRISPR-Cas12a and self-recruiting crRNA assisted dual biosensing platform for simultaneous detection of lung cancer biomarkers hOGG1 and FEN1. Anal Chim Acta 2023; 1240:340748. [PMID: 36641157 DOI: 10.1016/j.aca.2022.340748] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Human 8-oxoguanine DNA glycosylase (hOGG1) and flap endonuclease 1 (FEN1) are recognized as potential biomarkers in lung cancer investigations. Developing analytical platforms of simultaneously targeting hOGG1 and FEN1 with high selectivity, sensitivity, especially programmability and universality is highly valuable for clinical research. Herein, we established a signal-amplified platform for simultaneously detecting hOGG1 and FEN1 on the basis of cleavage-induced ligation of DNA dumbbell probes, rolling circle transcription (RCT) and CRISPR-Cas12a. A hOGG1 cleavable site and FEN1 cleavable flap were dexterously designed at the 5' end of DNA flapped dumbbell probes (FDP) for hOGG1 and FEN1. After cleavage, the resulting nick sites with juxtaposition of 5' phosphate and 3' hydroxyl terminus could be linked to closed DNA dumbbell probes (CDP) by DNA ligase. The CDP served as a template for RCT, producing plentiful crRNA repeats to activate the trans-cleavage activity of CRISPR-Cas12a which could cleave fluorophores (TAMRA and FAM) and quenchers (BHQ2 and BHQ1) double-labeled ssDNA reporters. Then, hOGG1 and FEN1 could be detected by the recovered fluorescence signal, allowing for the highly sensitive calculated detection limits of 0.0013 and 0.0052 U/mL, respectively. Additionally, this method made it possible to evaluate the inhibitory effects, even to measure hOGG1 and FEN1 activities at the single-cell level. This novel target enzyme-initiated, circles-transcription without promoters, real-time generation, and self-assembly features of FDP-RCT-Cas12a system suppressed nonspecific background remarkably and relieved rigorous requirement of protospacer adjacent motif site. Hence, the universality of FDP-RCT-Cas12a system toward various disease-related non-nucleic acid targets which are tested without using aptamers was extremely improved.
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Affiliation(s)
- Xia Cheng
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Dandan Ren
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Lin Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
| | - Jianjun Zou
- Department of Clinical Pharmacology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, PR China.
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
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4
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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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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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Singh V, Johansson P, Ekedahl E, Lin YL, Hammarsten O, Westerlund F. Quantification of single-strand DNA lesions caused by the topoisomerase II poison etoposide using single DNA molecule imaging. Biochem Biophys Res Commun 2022; 594:57-62. [DOI: 10.1016/j.bbrc.2022.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/11/2022] [Indexed: 11/02/2022]
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7
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Chen L, Liang J. A proximity ligation assay (PLA) based sensing platform for the ultrasensitive detection of P53 protein-specific SUMOylation. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Hao Q, Xu Q, Niu S, Ding C, Luo X. Anti-Fouling Magnetic Beads Combined with Signal Amplification Strategies for Ultra-Sensitive and Selective Electrochemiluminescence Detection of MicroRNAs in Complex Biological Media. Anal Chem 2021; 93:10679-10687. [PMID: 34288646 DOI: 10.1021/acs.analchem.1c02186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, an electrochemiluminescence (ECL) microRNA biosensor based on anti-fouling magnetic beads (MBs) and two signal amplification strategies was developed. The newly designed anti-fouling dendritic peptide was wrapped on the surfaces of MBs to make them resistant to nonspecific adsorption of biomolecules in complex biological samples so as to realize accurate and selective target recognition. One of the amplification strategies was achieved through nucleic acid cycle amplification based on the DNAzyme on the surfaces of MBs. Then, the output DNA generated by the nucleic acid cycle amplification program stimulated the hybrid chain reaction (HCR) process on the modified electrode surface to generate the other amplification of the ECL response. Titanium dioxide nanoneedles (TiO2 NNs), as a co-reaction accelerator of the Ru(bpy)2(cpaphen)2+ and tripropylamine (TPrA) system, were wrapped with the electrodeposited polyaniline (PANI) on the electrode surface to enhance the ECL intensity of Ru(bpy)2(cpaphen)2+. The conducting polymer PANI can not only immobilize the TiO2 NNs but also improve the conductivity of the modified electrodes. The biosensor exhibited ultra-high sensitivity and excellent selectivity toward the detection of miRNA 21, with a detection limit of 0.13 fM. More importantly, with the anti-fouling MBs as a unique separation tool, this ECL biosensor was capable of assaying targets in complex biological media such as serum and cell lysate.
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Affiliation(s)
- Qiuxia Hao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qingzhang Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Shuyan Niu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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9
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Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms. Talanta 2020; 218:121141. [PMID: 32797898 DOI: 10.1016/j.talanta.2020.121141] [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: 02/13/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.
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Singh V, Johansson P, Torchinsky D, Lin YL, Öz R, Ebenstein Y, Hammarsten O, Westerlund F. Quantifying DNA damage induced by ionizing radiation and hyperthermia using single DNA molecule imaging. Transl Oncol 2020; 13:100822. [PMID: 32652469 PMCID: PMC7350159 DOI: 10.1016/j.tranon.2020.100822] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 11/19/2022] Open
Abstract
Ionizing radiation (IR) is a common mode of cancer therapy, where DNA damage is the major reason of cell death. Here, we use an assay based on fluorescence imaging of single damaged DNA molecules isolated from radiated lymphocytes, to quantify IR induced DNA damage. The assay uses a cocktail of DNA-repair enzymes that recognizes and excises DNA lesions and then a polymerase and a ligase incorporate fluorescent nucleotides at the damage sites, resulting in a fluorescent “spot” at each site. The individual fluorescent spots can then be counted along single stretched DNA molecules and the global level of DNA damage can be quantified. Our results demonstrate that inclusion of the human apurinic/apyrimidinic endonuclease 1 (APE1) in the enzyme cocktail increases the sensitivity of the assay for detection of IR induced damage significantly. This optimized assay also allowed detection of a cooperative increase in DNA damage when IR was combined with mild hyperthermia, which is sometimes used as an adjuvant in IR therapy. Finally, we discuss how the method may be used to identify patients that are sensitive to IR and other types of DNA damaging agents.
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Affiliation(s)
- Vandana Singh
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pegah Johansson
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Dmitry Torchinsky
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Israel
| | - Yii-Lih Lin
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Robin Öz
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Israel
| | - Ola Hammarsten
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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11
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Wang G, Tian W, Liu X, Ren W, Liu C. New CRISPR-Derived microRNA Sensing Mechanism Based on Cas12a Self-Powered and Rolling Circle Transcription-Unleashed Real-Time crRNA Recruiting. Anal Chem 2020; 92:6702-6708. [DOI: 10.1021/acs.analchem.0c00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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, P. R. China
| | - Weimin Tian
- 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, P. R. 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, P. R. 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, P. R. 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, P. R. China
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12
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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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13
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Wang LJ, Lu YY, Zhang CY. Construction of a self-directed replication system for label-free and real-time sensing of repair glycosylases with zero background. Chem Sci 2020; 11:587-595. [PMID: 32206275 PMCID: PMC7069502 DOI: 10.1039/c9sc04738g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA damage and repair are involved in multiple fundamental biological processes, including metabolism, disease, and aging. Inspired by the natural repair mechanism in vivo, we demonstrate for the first time the construction of a self-directed replication system for label-free and real-time sensing of repair glycosylases with zero background. The presence of DNA glycosylase can catalyze the excision repair of the damaged base, successively autostarting the self-directed replication through recycling polymerization extension and strand-displacement DNA synthesis for the generation of exponentially amplified dsDNAs. The resultant dsDNA products can be label-free and real-time monitored with SYBR Green I as the fluorescent indicator. Owing to the high efficiency of self-directed exponential replication and the absolute zero background resulting from the efficient inhibition of nonspecific amplification induced by multiple primer-dependent amplification, this strategy exhibits high sensitivity with a detection limit of 1 × 10-8 U μL-1 in vitro and 1 cell in vivo, and it can be further used to screen inhibitors, quantify DNA glycosylase from diverse cancer cells, and even monitor various repair enzymes by simply changing the specific damaged base in the DNA template. Importantly, this assay can be performed in a label-free, real-time and isothermal manner with the involvement of only a single type of polymerase, providing a simple, robust and universal platform for repair enzyme-related biomedical research and clinical therapeutics.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86-531-86186033
| | - Ying-Ying Lu
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86-531-86186033
| | - Chun-Yang Zhang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86-531-86186033
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14
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Electrochemical lead(II) biosensor by using an ion-dependent split DNAzyme and a template-free DNA extension reaction for signal amplification. Mikrochim Acta 2019; 186:709. [PMID: 31650391 DOI: 10.1007/s00604-019-3857-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/19/2019] [Indexed: 01/08/2023]
Abstract
A voltammetric biosensor for lead(II) (Pb2+) is described that is based on signal amplification by using an ion-dependent split DNAzyme and template-free DNA extension reaction. The Pb2+-dependent split DNAzyme was assembled on gold nanoparticles (Au@Fe3O4), and this nanoprobe then was exposed to Pb2+ which causes the split-off of DNAzymes to release primers containing 3'-OH groups (S1 and S2). The template-free DNA extension reaction triggers the generation of long ssDNA nanotails, which then can bind the free redox probe N,N'-bis(2-(trimethylammonium iodide)propylene)perylene-3,4,9,10-tetracarboxyldiimide (PDA+) via electrostatic adsorption. Hence, the concentration of PDA+ in solution is reduced. Therefore, less free PDA+ can be immobilized on a glassy carbon electrode modified with electrodeposited gold nanoparticles (depAu) to produce an electrochemical signal, typically measured at ∼0.38 V (vs. SCE) for quantitation of Pb2+. The use of a Pb2+-dependent split DNAzyme avoids the usage of a proteinic enzyme. It also increases the sensitivity of the sensor which has a lower detection limit of 30 pM of Pb2+. Graphical abstract Novel electrochemical biosensor based on the amplification of ion-dependent split DNAzyme and template-free DNA extension reaction for trace detection of Pb2+.
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15
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Chen X, Liu Y, Xu L, Wang Y, Li R, Sun P, Lin Z, Yang H. Jungle on the Electrode: A Target-Induced Enzyme-Free and Label-Free Biosensor. Anal Chem 2019; 91:13712-13719. [PMID: 31588727 DOI: 10.1021/acs.analchem.9b03004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xian Chen
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
| | - Yaoze Liu
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
| | - Liming Xu
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
| | - Yang Wang
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
| | - Rui Li
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
| | - Pengming Sun
- Fujian Provincial Maternity and Children’s Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, People’s Republic of China
| | - Zhenyu Lin
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
| | - Huanghao Yang
- College of Chemistry, Fuzhou University, Fuzhou 350116, People’s Republic of China
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16
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Hairpin probes based click polymerization for label-free electrochemical detection of human T-lymphotropic virus types II. Anal Chim Acta 2019; 1059:86-93. [DOI: 10.1016/j.aca.2019.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/05/2019] [Accepted: 01/14/2019] [Indexed: 11/24/2022]
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17
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Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis. Biosens Bioelectron 2019; 129:164-174. [PMID: 30708263 DOI: 10.1016/j.bios.2019.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/09/2018] [Accepted: 01/03/2019] [Indexed: 01/12/2023]
Abstract
Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.
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18
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Wang LJ, Wang HX, Jiang L, Zhang CY. Development of an in Vitro Autocatalytic Self-Replication System for Biosensing Application. ACS Sens 2018; 3:2675-2683. [PMID: 30460848 DOI: 10.1021/acssensors.8b01171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular self-replication is a fundamental function of all living organisms with the capability of templating and catalyzing its own synthesis, and it plays important roles in prebiotic chemical evolution and effective synthetic machineries. However, the construction of the self-replication system in vitro remains a great challenge and its application for biosensing is rare. Here, we demonstrate for the first time the construction of an in vitro enzymatic nucleic acid self-replication system and its application for amplified sensing of human 8-oxoguanine DNA glycosylase (hOGG1) based on autocatalytic self-replication-driven cascaded recycling amplification. In this strategy, hOGG1 excises 8-oxoguanine (8-oxoG) to unfold the hairpin substrate, activating the autonomous biocatalytic process with molecular beacons (MBs) as both the fuels for producing nucleic acid templates and the generators for signal output, leading to the continuous replication of biocatalytic nucleic acid templates and the repeated cleavage of MBs for an enhanced fluorescence signal. This strategy exhibits an extremely low detection limit of 4.3 × 10-7 U/μL and a large dynamic range of 5 orders of magnitude from 1 × 10-6 to 0.05 U/μL. Importantly, it can be applied for the detection of enzyme kinetic parameters, the screening of hOGG1 inhibitors, and the quantification of hOGG1 activity in even 1 single lung cancer cell, providing a new approach for biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Hou-xiu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Longhe Jiang
- Wendeng Orthopaedic Hospital of Shandong, Wendeng 264400, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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19
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Wang LJ, Han X, Li CC, Zhang CY. Single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification for sensitive and specific detection of DNA methyltransferase. Chem Sci 2018; 9:6053-6061. [PMID: 30079218 PMCID: PMC6053742 DOI: 10.1039/c8sc02215a] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/17/2018] [Indexed: 01/09/2023] Open
Abstract
Specific and sensitive detection of DNA MTase activity can be achieved by a single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification approach.
DNA methylation is a predominant epigenetic modification that plays crucial roles in various cellular processes. DNA methyltransferase (MTase) is responsible for DNA methylation, and its dysregulation may induce aberrant methylation patterns that are closely related to cancers. Conventional methods for DNA MTase assay are usually cumbersome and laborious with poor sensitivity. Alternatively, some signal amplification strategies are employed to improve the sensitivity, but they suffer from poor specificity and consequently limited sensitivity due to the nonspecific amplification. Herein, we develop for the first time a new fluorescence method to specifically and sensitively detect DNA MTase activity on the basis of single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification. In the presence of DNA MTase, the hairpin substrate is methylated and cleaved by endonuclease Dpn I, releasing a 24-nt cleavage product. The 24-nt cleavage product may function as a primer and adjacently hybridize with the ligation probes (LP1 and LP2) to form the template (LP1–LP2) for strand displacement amplification (SDA), initiating the single-ribonucleotide repair-mediated cyclic ligation-dependent SDA to produce a large number of reporter probes. The reporter probe can subsequently hybridize with the signal probe that is modified with FAM and BHQ1 to form a stable double-stranded DNA (dsDNA) duplex with a ribonucleotide mismatch. Ribonuclease HII (RNase HII) can excise the single ribonucleotide, resulting in the cyclic cleavage of signal probes and the generation of an enhanced fluorescence signal. Taking advantage of the high specificity of RNase HII-catalyzed single-ribonucleotide excision and the high amplification efficiency of cyclic ligation-dependent SDA, this assay exhibits the highest sensitivity reported so far with a detection limit of 4.8 × 10–6 U mL–1 and a large dynamic range of 5 orders of magnitude. Moreover, this method can be used for the discrimination of Dam MTase from other DNA MTases, the accurate quantification of Dam MTase activity in E. coli cells, and the screening of Dam MTase inhibitors, providing a new paradigm for biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Xiao Han
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Chen-Chen Li
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Chun-Yang Zhang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
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20
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Wang LJ, Ren M, Liang L, Zhang CY. Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses. Chem Sci 2018; 9:4942-4949. [PMID: 29938021 PMCID: PMC5994793 DOI: 10.1039/c8sc01641k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.
Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Ming Ren
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Li Liang
- Department of Tumor Chemotherapy and Radiation Sickness , Peking University Third Hospital , Beijing 100191 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
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21
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Enzyme-free homogeneous electrochemical biosensor for DNA assay using toehold-triggered strand displacement reaction coupled with host-guest recognition of Fe 3O 4@SiO 2@β-CD nanocomposites. Biosens Bioelectron 2018; 114:37-43. [PMID: 29775857 DOI: 10.1016/j.bios.2018.04.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 12/31/2022]
Abstract
Taking advantages of the toehold-triggered strand displacement reaction (TSDR) and host-guest interaction of β-cyclodextrin (β-CD), a facile enzyme-free and homogeneous electrochemical sensing strategy was designed for the sensitive assay of target DNA using Fe3O4@SiO2@β-CD nanocomposites and ferrocene-labeled hairpin DNA (H-1) as the capture and electrochemical probes, respectively. Upon addition of target molecule, the initiated TSDR process induced the conformational change of H-1, and subsequently stimulated the dynamic assembly of assist probes (A-1 and A-2) to generate H-1:A-1:A-2 duplex along with the release of target sequence. The released target could drive the next TSDR recycling and finally result in the formation of numerous DNA duplex. After the molecular recognition of Fe3O4@SiO2@β-CD nanocomposites, a large number of duplex were easily separated from the supernatant solution under an external magnetic field, which led to a decreased H-1 concentration in residual solution, concomitant with a remarkable reduction of peak current. Under the optimized conditions, wide linear range (1-5000 pM), low detection limit (0.3 pM), desirable reproducibility, good selectivity, and satisfactory practical analysis were obtained by the combination of the superior recognition capability of β-CD, TSDR-induced signal amplification, and homogeneous electroanalytical method. The proposed detection strategy could offer a universal approach for the monitoring of various biological analytes via the rational design of probe sequences.
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22
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Gai P, Gu C, Li H, Sun X, Li F. Ultrasensitive Ratiometric Homogeneous Electrochemical MicroRNA Biosensing via Target-Triggered Ru(III) Release and Redox Recycling. Anal Chem 2017; 89:12293-12298. [DOI: 10.1021/acs.analchem.7b03268] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Panpan Gai
- College of Chemistry and Pharmaceutical
Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Chengcheng Gu
- College of Chemistry and Pharmaceutical
Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Haiyin Li
- College of Chemistry and Pharmaceutical
Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Xinzhi Sun
- College of Chemistry and Pharmaceutical
Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical
Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
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23
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Li XY, Du YC, Zhang YP, Kong DM. Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Sci Rep 2017; 7:6263. [PMID: 28740223 PMCID: PMC5524717 DOI: 10.1038/s41598-017-06594-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/14/2017] [Indexed: 12/31/2022] Open
Abstract
An exonucleolytic digestion-assisted exponential rolling circle amplification (RCA) strategy was developed for sensitive and sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Herein, Phi29 DNA polymerase plays two important roles as exonuclease and polymerase. Long-stranded genomic DNAs can be broken into small DNA fragments after ultrasonication. The fragments that contain target DNA, hybridize with a linear padlock probe to trigger the formation of a circular RCA template. The tails protruding from the 3'-end of the target DNA sequences are then digested by the 3' → 5' exonuclease activity of Phi29 DNA polymerase even if they fold into a double-stranded structure. The digested DNA fragments can then initiate subsequent RCA reaction. RCA products, which are designed to fold into G-quadruplex structures, exponentially accumulate when appropriate nicking endonuclease recognition sites are introduced rationally into the RCA template. This method is demonstrated to work well for real genomic DNA detection using human pathogen Cryptococcus neoformans as a model. In addition, this work has two other important discoveries: First, the presence of a 3'-tail can protect the RCA primer from degradation by Phi29 DNA polymerase. Second, 3' → 5' exonucleolytic activity of Phi29 DNA polymerase can work for both single- and double-stranded DNA.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P.R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Yi-Chen Du
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Yu-Peng Zhang
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P.R. China.
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300071, P.R. China.
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24
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Zhang K, Wang K, Zhu X, Xu F, Xie M. Sensitive detection of microRNA in complex biological samples by using two stages DSN-assisted target recycling signal amplification method. Biosens Bioelectron 2017; 87:358-364. [DOI: 10.1016/j.bios.2016.08.081] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/19/2022]
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25
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He Z, Wei J, Gan C, Liu W, Liu Y. A rolling circle amplification signal-enhanced immunosensor for ultrasensitive microcystin-LR detection based on a magnetic graphene-functionalized electrode. RSC Adv 2017. [DOI: 10.1039/c7ra07696g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Construction of a rolling circle amplification signal-enhanced immunosensor for ultrasensitive microcystin-LR detection by using a magnetic graphene functionalized electrode.
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Affiliation(s)
- Zuyu He
- Department of Applied Chemistry
- College of Materials & Energy
- South China Agricultural University
- Guangzhou 510642
- China
| | - Jie Wei
- Department of Applied Chemistry
- College of Materials & Energy
- South China Agricultural University
- Guangzhou 510642
- China
| | - Cuifen Gan
- Department of Applied Chemistry
- College of Materials & Energy
- South China Agricultural University
- Guangzhou 510642
- China
| | - Weipeng Liu
- Department of Applied Chemistry
- College of Materials & Energy
- South China Agricultural University
- Guangzhou 510642
- China
| | - Yingju Liu
- Department of Applied Chemistry
- College of Materials & Energy
- South China Agricultural University
- Guangzhou 510642
- China
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26
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Wang H, Zuo Z, Ren L, Yuan R, Li Q, Ding S, Luo R. Ultrasensitive electrochemical biosensing strategy for microRNA-21 detection based on homogeneous target-initiated transcription amplification. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.10.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Trifunctional molecular beacon-mediated quadratic amplification for highly sensitive and rapid detection of mercury(II) ion with tunable dynamic range. Biosens Bioelectron 2016; 86:892-898. [DOI: 10.1016/j.bios.2016.07.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/18/2016] [Accepted: 07/27/2016] [Indexed: 11/20/2022]
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28
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Li Z, Lau C, Lu J. Effect of the Concentration Difference between Magnesium Ions and Total Ribonucleotide Triphosphates in Governing the Specificity of T7 RNA Polymerase-Based Rolling Circle Transcription for Quantitative Detection. Anal Chem 2016; 88:6078-83. [PMID: 27167591 DOI: 10.1021/acs.analchem.6b01460] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
T7 RNA polymerase-based rolling circle transcription (RCT) is a more powerful tool than universal runoff transcription and traditional DNA polymerase-based rolling circle amplification (RCA). However, RCT is rarely employed in quantitative detection due to its poor specificity for small single-stranded DNA (ssDNA), which can be transcribed efficiently by T7 RNA polymerase even without a promoter. Herein we show that the concentration difference between Mg(2+) and total ribonucleotide triphosphates (rNTPs) radically governs the specificity of T7 RNA polymerase. Only when the total rNTP concentration is 9 mM greater than the Mg(2+) concentration can T7 RNA polymerase transcribe ssDNA specifically and efficiently. This knowledge improves our traditional understanding of T7 RNA polymerase and makes convenient application of RCT in quantitative detection possible. Subsequently, an RCT-based label-free chemiluminescence method for microRNA detection was designed to test the capability of this sensing platform. Using this simple method, microRNA as low as 20 amol could be quantitatively detected. The results reveal that the developed sensing platform holds great potential for further applications in the quantitative detection of a variety of targets.
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Affiliation(s)
- Zhiyan Li
- School of Pharmacy, Fudan University , 826 Zhangheng Road, Shanghai 201203, China
| | - Choiwan Lau
- School of Pharmacy, Fudan University , 826 Zhangheng Road, Shanghai 201203, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University , 826 Zhangheng Road, Shanghai 201203, China
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Yuan R, Ding S, Yan Y, Zhang Y, Zhang Y, Cheng W. A facile and pragmatic electrochemical biosensing strategy for ultrasensitive detection of DNA in real sample based on defective T junction induced transcription amplification. Biosens Bioelectron 2016; 77:19-25. [DOI: 10.1016/j.bios.2015.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/25/2015] [Accepted: 09/04/2015] [Indexed: 11/30/2022]
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30
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Yan Y, Ding S, Zhao D, Yuan R, Zhang Y, Cheng W. Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification. Sci Rep 2016; 6:18810. [PMID: 26729209 PMCID: PMC4700466 DOI: 10.1038/srep18810] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/25/2015] [Indexed: 01/17/2023] Open
Abstract
Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.
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Affiliation(s)
- Yurong Yan
- The center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.,Key Laboratory of Laboratory Medical Diagnostics (Ministry of Education of China), Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Shijia Ding
- Key Laboratory of Laboratory Medical Diagnostics (Ministry of Education of China), Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Dan Zhao
- Key Laboratory of Laboratory Medical Diagnostics (Ministry of Education of China), Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Rui Yuan
- Key Laboratory of Laboratory Medical Diagnostics (Ministry of Education of China), Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yuhong Zhang
- The center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Wei Cheng
- The center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
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31
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Yin BC, Wu S, Ma JL, Ye BC. A novel molecular beacon-based method for isothermal detection of sequence-specific DNA via T7 RNA polymerase-aided target regeneration. Biosens Bioelectron 2015; 68:365-370. [DOI: 10.1016/j.bios.2015.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
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32
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Liang D, You W, Yu Y, Geng Y, Lv F, Zhang B. A cascade signal amplification strategy for ultrasensitive colorimetric detection of BRCA1 gene. RSC Adv 2015. [DOI: 10.1039/c5ra01766a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Schematic illustration of a colorimetric biosensor for breast cancer1 gene detection based on DNAzyme assistant DNA recycling and rolling circle amplification.
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Affiliation(s)
- Dong Liang
- The People's Hospital of Zhengzhou University (Henan Provincial People's Hospital)
- Zhengzhou
- PR China
| | - Wei You
- The People's Hospital of Zhengzhou University (Henan Provincial People's Hospital)
- Zhengzhou
- PR China
| | - Yang Yu
- The People's Hospital of Zhengzhou University (Henan Provincial People's Hospital)
- Zhengzhou
- PR China
| | - Yao Geng
- School of Food and Biological Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- PR China
| | - Feng Lv
- The People's Hospital of Zhengzhou University (Henan Provincial People's Hospital)
- Zhengzhou
- PR China
| | - Bin Zhang
- The People's Hospital of Zhengzhou University (Henan Provincial People's Hospital)
- Zhengzhou
- PR China
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