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Shi SS, Li XJ, Ma RN, Shang L, Zhang W, Zhao HQ, Jia LP, Wang HS. A novel dual-signal output strategy for POCT of CEA based on a smartphone electrochemical aptasensing platform. Mikrochim Acta 2024; 191:407. [PMID: 38898338 DOI: 10.1007/s00604-024-06493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
A smartphone-based electrochemical aptasensing platform was developed for the point-of-care testing (POCT) of carcinoembryonic antigen (CEA) based on the ferrocene (Fc) and PdPt@PCN-224 dual-signal labeled strategy. The prepared PdPt@PCN-224 nanocomposite showed a strong catalytic property for the reduction of H2O2. Phosphate group-labeled aptamer could capture PdPt@PCN-224 by Zr-O-P bonds to form PdPt@PCN-224-P-Apt. Therefore, a dual signal labeled probe was formed by the hybridization between Fc-DNA and PdPt@PCN-224-P-Apt. The presence of CEA forced PdPt@PCN-224-P-Apt to leave the electrode surface due to the specific affinity, leading to the decrease of the reduction current of H2O2. At the same time, the Fc-DNA strand changed to hairpin structure, which made Fc closer to the electrode and resulted in the increase of the oxidation current of Fc. Thus, CEA can be accurately determined through both signals: the decrease of H2O2 reduction current and the increase of Fc oxidation current, which could avoid the false positive signal. Under the optimal conditions, the prepared aptasensor exhibited a wide linear range from 1 pg·mL-1 to 100 ng·mL-1 and low detection limits of 0.98 pg·mL-1 and 0.27 pg·mL-1 with Fc and PdPt@PCN-224 as signal labels, respectively. The aptasensor developed in this study has successfully demonstrated its capability to detect CEA in real human serum samples. These findings suggest that the proposed sensing platform will hold great potential for clinical tumor diagnosis and monitoring.
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Affiliation(s)
- Shan-Shan Shi
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, People's Republic of China
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China
| | - Xiao-Jian Li
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China
| | - Rong-Na Ma
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China
| | - Lei Shang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China
| | - Wei Zhang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China
| | - Huai-Qing Zhao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, People's Republic of China.
| | - Li-Ping Jia
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China.
| | - Huai-Sheng Wang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, People's Republic of China.
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2
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Chen Y, Wang X, Luo S, Dai C, Wu Y, Zhao J, Liu W, Kong D, Yang Y, Geng L, Liu Y, Wei D. Electrically Oriented Antibodies on Transistor for Monitoring Several Copies of Methylated DNA. Anal Chem 2024; 96:8300-8307. [PMID: 38747393 DOI: 10.1021/acs.analchem.3c04670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
An antibody transistor is a promising biosensing platform for the diagnosis and monitoring of various diseases. Nevertheless, the low concentration and short half-life of biomarkers require biodetection at the trace-molecule level, which remains a challenge for existing antibody transistors. Herein, we demonstrate a graphene field-effect transistor (gFET) with electrically oriented antibody probes (EOA-gFET) for monitoring several copies of methylated DNA. The electric field confines the orientation of antibody probes on graphene and diminishes the distance between graphene and methylated DNAs captured by antibodies, generating more induced charges on graphene and amplifying the electric signal. EOA-gFET realizes a limit of detection (LoD) of ∼0.12 copy μL-1, reaching the lowest LoD reported before. EOA-gFET shows a distinguishable signal for liver cancer clinical serum samples within ∼6 min, which proves its potential as a powerful tool for disease screening and diagnosis.
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Affiliation(s)
- Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Shi Luo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Junhong Zhao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Wentao Liu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Yuetong Yang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Li Geng
- Department of Special Treatment, Eastern Hepatobiliary Surgery Hospital, Shanghai, 200438, China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
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3
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Liu H, Li C, Wang L, Fang L, Huang H, Deng J, Hu Y, Li M, Ran X, Li L, Zheng J. Photoelectrochemical sensor based on AuNPs@WO 3@TpPa-1-COF for quantification of DNA methylation levels. Mikrochim Acta 2024; 191:167. [PMID: 38418644 DOI: 10.1007/s00604-024-06235-1] [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: 09/19/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
A "signal-off" photoelectrochemical (PEC) sensing platform has been designed for the ultrasensitive detection of DNA methylation levels and multiple methylated sites. The platform employs tungsten trioxide and TpPa-1-COF loaded by gold nanoparticle (AuNPs@WO3@TpPa-1-COF) composite material as the photoactive component and p-type reduced graphene (rGO) as an efficient quencher. The PEC signal of AuNPs@WO3@TpPa-1-COF composite is effectively quenched in the presence of p-type rGO, because p-type rGO can compete with AuNPs@WO3@TpPa-1-COF to deplete light energy and electron donors. In addition, a hybrid strand reaction (HCR) amplification strategy fixes more target DNA and then combines with rGO-modified anti-5-methylcytosine antibody to facilitate ultrasensitive DNA methylation detection. Under optimal conditions, DNA methylation can be measured within a linear concentration range of 10-14 to 10-8 M, with an exceptionally low detection limit of 0.19 fM (S/N = 3). At the same time, the platform can conduct quantitative determination of multi-site methylation, with the linear equation △I = 44.19LogA + 61.43, and the maximum number of methylation sites is 5. The sensor demonstrates high sensitivity, excellent selectivity, and satisfactory stability. Furthermore, the proposed signal-off PEC strategy was successfully employed to detect DNA methylation in spiked human serum samples, with recoveries ranging from 93.17 to 107.28% and relative standard deviation (RSD) ranging from 1.15 to 5.49%.
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Affiliation(s)
- Huamin Liu
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Chenghong Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lina Wang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jun Deng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Yue Hu
- Emergency Department, 2, Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Mimi Li
- Emergency Department, 2, Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xiaoping Ran
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lulu Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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4
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Zhang H, Wu S, Song Z, Fang L, Wang HB. Tannic acid-accelerated fenton chemical reaction amplification for fluorescent biosensing: The proof-of-concept towards ultrasensitive detection of DNA methylation. Talanta 2023; 265:124811. [PMID: 37327662 DOI: 10.1016/j.talanta.2023.124811] [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: 04/01/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
As a promising biomarker, the level of methylated DNA usually changes in the early stage of the cancer. Ultrasensitive detection of the changes of methylated DNA offers possibility for early diagnosis of cancer. In this work, a tannic acid-accelerated Fenton chemical reaction amplification was firstly proposed for the construction of ultrasensitive fluorescent assay. Tannic acid was used as reductant to accelerate Fenton reaction procedure through the conversion of Fe3+/Fe2+, generating hydroxyl radicals (·OH) continuously. The produced ·OH oxidized massive non-fluorescent terephthalic acid (TA) to fluorescent-emitting hydroxy terephthalic acid (TAOH). In this way, the fluorescent signal could be greatly enhanced and the sensitivity was improved almost 116 times. The proposed signal amplification strategy was further applied to detect of DNA methylation with the assistance of liposome encapsulated with tannic-Fe3+ complexes. The methylated DNA was firstly captured through the hybridization with its complementary DNA that were pre-modified in the 96-well plate via the combination between streptavidin (SA) and biotin. Then, 5 mC antibody on the surface of liposomes specially recognized and combined with methylation sites, which brought large amount of tannic-Fe3+ complexes to participate Fenton reaction. The fluorescence of generated TAOH was depended on the concentration of methylated DNA. The assay showed good analytical performance for methylated DNA with a limit of detection (LOD) of 1.4 fM. It's believed that tannic acid-accelerated Fenton chemical reaction amplification strategy provides a promising platform for ultrasensitive fluorescent detection of low abundant biomarkers.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Henan Province Key Laboratory of Utilization of Non-metallic Mineral in the South of Henan, Xinyang Normal University, Xinyang, 464000, PR China; State Key Laboratory of Chemo/Biosensing Ad Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Sifei Wu
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Henan Province Key Laboratory of Utilization of Non-metallic Mineral in the South of Henan, Xinyang Normal University, Xinyang, 464000, PR China
| | - Zhixiao Song
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Henan Province Key Laboratory of Utilization of Non-metallic Mineral in the South of Henan, Xinyang Normal University, Xinyang, 464000, PR China
| | - Linxia Fang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Henan Province Key Laboratory of Utilization of Non-metallic Mineral in the South of Henan, Xinyang Normal University, Xinyang, 464000, PR China
| | - Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Henan Province Key Laboratory of Utilization of Non-metallic Mineral in the South of Henan, Xinyang Normal University, Xinyang, 464000, PR China
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5
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Zhang H, Wu S, Xing Z, Wang HB. ALP-assisted chemical redox cycling signal amplification for ultrasensitive fluorescence detection of DNA methylation. Analyst 2023; 148:5753-5761. [PMID: 37842979 DOI: 10.1039/d3an01383a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Affinity assays allow direct detection of DNA methylation events without requiring a special sequence. However, the signal amplification of these methods heavily depends on nanocatalysts and bioenzymes, making them suffer from low sensitivity. In this work, alkaline phosphatase (ALP)-assisted chemical redox cycling was employed to amplify the sensitivity of fluorescence affinity assays for DNA methylation detection using Ru@SiO2@MnO2 nanocomposites as fluorescent probes. In the ALP-assisted chemical redox cycling reaction system, ALP hydrolyzed 2-phosphate-L-ascorbic acid trisodium salt (AAP) to produce AA, which could reduce MnO2 nanosheets to form Mn2+, making the fluorescence recovery of Ru@SiO2 nanoparticles possible. Meanwhile, AA was oxidized to dehydroascorbic acid (DHA), which was re-reduced by tris(2-carboxyethyl) phosphine (TCEP) to trigger a redox cycling reaction. The constantly generated AA could etch large amounts of MnO2 nanosheets and greatly recover Ru@SiO2 fluorescence, amplifying the signal of the fluorescence assay. Employing the proposed ALP-assisted chemical redox cycling signal amplification strategy, a sensitive affinity assay for DNA methylation detection was achieved using ALP encapsulated liposomes that were linked with the 5mC antibody (Ab) to bind with methylated sites. A detection limit down to 2.9 fM was obtained for DNA methylation detection and a DNA methylation level as low as 0.1% could be distinguished, which was superior to conventional affinity assays. Moreover, the affinity assays could detect DNA methylation more specifically and directly, implying their great potential for the analysis of tumor-specific genes in liquid biopsy.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Sifei Wu
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Zhenhua Xing
- Xinyang Branch, Henan Boiler and Pressure Vessel Inspection Technology Research Institute, Xinyang 464000, PR China
| | - Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
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6
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Li S, Zhang H, Zhu M, Kuang Z, Li X, Xu F, Miao S, Zhang Z, Lou X, Li H, Xia F. Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives. Chem Rev 2023. [PMID: 37262362 DOI: 10.1021/acs.chemrev.1c00759] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.
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Affiliation(s)
- Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hongyuan Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Man Zhu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhujun Kuang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xun Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Siyuan Miao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zishuo Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Bao J, Ding K, Zhu Y. An electrochemical biosensor for detecting DNA methylation based on AuNPs/rGO/g-C 3N 4 nanocomposite. Anal Biochem 2023; 673:115180. [PMID: 37146956 DOI: 10.1016/j.ab.2023.115180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/07/2023]
Abstract
DNA methylation as a ubiquitously regulation is closely associated with cell proliferation and differentiation. Growing data shows that aberrant methylation contributes to disease incidence, especially in tumorigenesis. The approach for identifying DNA methylation usually depends on treatment of sodium bisulfite, which is time-consuming and conversion-insufficient. Here, with a special biosensor, we establish an alternative approach for detecting DNA methylation. The biosensor is consisted of two parts, which are gold electrode and nanocomposite (AuNPs/rGO/g-C3N4). Nanocomposite was fabricated by three components, which are gold nanoparticles (AuNPs), reduced graphene oxide (rGO) and graphite carbon nitride (g-C3N4). For methylated DNA detection, the target DNA was captured by probe DNA immobilized on the gold electrode surface through thiolating process and subjected to hybrid with anti-methylated cytosine conjugated to nanocomposite. When the methylated cytosines in target DNA were recognized by anti-methylated cytosine, a change of electrochemical signals will be observed. With different size of target DNAs, the concentration and methylation level were tested. It is shown that in short size methylated DNA fragment, the linear range and LOD of concentration is 10-7M-10-15M and 0.74 fM respectively; in longer size methylated DNA, the linear range of methylation proportion and LOD of copy number is 3%-84% and 103 respectively. Also, this approach has a high sensitivity and specificity as well as anti-disturbing ability.
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Affiliation(s)
- Junming Bao
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Kejian Ding
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China.
| | - Yunfeng Zhu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China.
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Liu Y, Wang X, Li Y, Wu H. An all-in-one strategy for bisulfite-free DNA methylation detection by temperature-programmed enzymatic reactions. Anal Chim Acta 2023; 1251:341001. [PMID: 36925290 DOI: 10.1016/j.aca.2023.341001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
The fragmentation and low concentration of cell-free DNA (cfDNA) pose higher challenges for the cfDNA methylation detection technologies. Conventional bisulfite conversion-based methods are inadequate for cfDNA methylation analysis due to cumbersome operation and exacerbating cfDNA degradation. Herein, we proposed temperature-programmed enzymatic reactions for cfDNA methylation analysis in a single tube. Endonuclease was used to mildly recognize DNA methylation to avoid the degradation of cfDNA. And two stages of amplification reactions significantly improved the detection sensitivity for GC-rich sequence. With vimentin as the target, the detection sensitivity was 10 copies of methylated DNA. Meanwhile, the proposed method can accurately quantify the methylation level of target sequence from 1000-fold of unmethylated DNA background. Further, the methylated vimentin gene in 20 clinical plasma samples was successfully detected. The results shown significant differences in methylation levels of the vimentin gene between healthy volunteers and colorectal cancer patients. These results lead us to believe that the proposed method has great application potential for DNA methylation analysis as a complement to bisulfite conversion-based methods.
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Affiliation(s)
- Yunlong Liu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Xiaoming Wang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, 210009, PR China
| | - Yujiao Li
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China
| | - Haiping Wu
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China.
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Gupta N, Kumar D, Das A, Sood S, Malhotra BD. Conductive Ink-Coated Paper-Based Supersandwich DNA Biosensor for Ultrasensitive Detection of Neisseria gonorrhoeae. BIOSENSORS 2023; 13:bios13040486. [PMID: 37185561 PMCID: PMC10136323 DOI: 10.3390/bios13040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Herein, we report results of the studies relating to the development of an impedimetric, magnetic bead-assisted supersandwich DNA hybridization assay for ultrasensitive detection of Neisseria gonorrhoeae, the causative agent of a sexually transmitted infection (STI), gonorrhea. First, a conductive ink was formulated by homogenously dispersing carboxylated multiwalled carbon nanotubes (cMWCNTs) in a stable emulsion of terpineol and an aqueous suspension of carboxymethyl cellulose (CMC). The ink, labeled C5, was coated onto paper substrates to fabricate C5@paper conductive electrodes. Thereafter, a magnetic bead (MB)-assisted supersandwich DNA hybridization assay was optimized against the porA pseudogene of N. gonorrhoeae. For this purpose, a pair of specific 5' aminated capture probes (SCP) and supersandwich detector probes (SDP) was designed, which allowed the enrichment of target gonorrheal DNA sequence from a milieu of substances. The SD probe was designed such that instead of 1:1 binding, it allowed the binding of more than one T strand, leading to a 'ladder-like' DNA supersandwich structure. The MB-assisted supersandwich assay was integrated into the C5@paper electrodes for electrochemical analysis. The C5@paper electrodes were found to be highly conductive by a four-probe conductivity method (maximum conductivity of 10.1 S·cm-1). Further, the biosensing assay displayed a wide linear range of 100 aM-100 nM (109 orders of magnitude) with an excellent sensitivity of 22.6 kΩ·(log[concentration])-1. The clinical applicability of the biosensing assay was assessed by detecting genomic DNA extracted from N. gonorrhoeae in the presence of DNA from different non-gonorrheal bacterial species. In conclusion, this study demonstrates a highly sensitive, cost-effective, and label-free paper-based device for STI diagnostics. The ink formulation prepared for the study was found to be highly thixotropic, which indicates that the paper electrodes can be screen-printed in a reproducible and scalable manner.
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Affiliation(s)
- Niharika Gupta
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India
| | - D Kumar
- Department of Applied Chemistry, Delhi Technological University, Delhi 110042, India
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110016, India
| | - Bansi D Malhotra
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India
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10
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Kumar RR, Kumar A, Chuang CH, Shaikh MO. Recent Advances and Emerging Trends in Cancer Biomarker Detection Technologies. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Rajkumar Rakesh Kumar
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Amit Kumar
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Cheng-Hsin Chuang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Muhammad Omar Shaikh
- Sustainability Science and Management, Tunghai University, Taichung 407224, Taiwan
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Ultrasensitive photoelectrochemical biosensor for DNA 5-methylcytosine analysis based on co-sensitization strategy combined with bridged DNA nanoprobe. Talanta 2023; 254:124140. [PMID: 36463802 DOI: 10.1016/j.talanta.2022.124140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Altered DNA methylation in the form of 5-methylcytosine (5-mC) patterns is correlated with disease diagnosis, prognosis, and treatment response. Therefore, accurate analysis of 5-mC is of great significance for the diagnosis of diseases. Here, an efficient enhanced photoelectrochemical (PEC) biosensor was designed for the quantitative analysis of DNA 5-mC based on a cascaded energy level aligned co-sensitization strategy coupling with the bridged DNA nanoprobe (BDN). Firstly, Au nanoparticle/graphite phase carbon nitride/titanium dioxide (AuNPs/g-C3N4@TiO2) nanocomposite was synthesized through in situ growth of AuNPs on g-C3N4@TiO2 surface as a matrix to provide a stable background signal. Next, BDN with a high mass transfer rate synthesized from a pair of DNA tetrahedral as nanomechanical handles was used as a capture probe to bind to the target sequence. The polydopamine nanosphere was applied to load with CdTe QDs (PDANS-CdTe QDs) as a photocurrent label of 5-mC antibodies. When the 5-mC existed, a large number of PDANS-Ab-CdTe QDs were introduced to the electrode surface, the formed CdTe QDs/AuNPs/g-C3N4@TiO2 co-sensitive structure could effectively enhance the electron transfer capability and photocurrent response rate due to the effective cascade energy level arrangement, leading to a significantly enhanced photocurrent signal. The proposed PEC biosensor manifested a wide range from 10-17 M to 10-7 M and a detection limit of 2.2 aM. Meanwhile, the excellent performance indicated the practicability of the designed strategy, thus being capable of the clinical diagnosis of 5-mC.
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12
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Koowattanasuchat S, Ngernpimai S, Matulakul P, Thonghlueng J, Phanchai W, Chompoosor A, Panitanarak U, Wanna Y, Intharah T, Chootawiriyasakul K, Anata P, Chaimnee P, Thanan R, Sakonsinsiri C, Puangmali T. Rapid detection of cancer DNA in human blood using cysteamine-capped AuNPs and a machine learning-enabled smartphone. RSC Adv 2023; 13:1301-1311. [PMID: 36686949 PMCID: PMC9814906 DOI: 10.1039/d2ra05725e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation occurs when a methyl group is added to a cytosine (C) residue's fifth carbon atom, forming 5-methylcytosine (5-mC). Cancer genomes have a distinct methylation landscape (Methylscape), which could be used as a universal cancer biomarker. This study developed a simple, low-cost, and straightforward Methylscape sensing platform using cysteamine-decorated gold nanoparticles (Cyst/AuNPs), in which the sensing principle is based on methylation-dependent DNA solvation. Normal and cancer DNAs have distinct methylation profiles; thus, they can be distinguished by observing the dispersion of Cyst/AuNPs adsorbed on these DNA aggregates in MgCl2 solution. After optimising the MgCl2, Cyst/AuNPs, DNA concentration, and incubation time, the optimised conditions were used for leukemia screening, by comparing the relative absorbance (ΔA 650/525). Following the DNA extraction from actual blood samples, this sensor demonstrated effective leukemia screening in 15 minutes with high sensitivity, achieving 95.3% accuracy based on the measurement by an optical spectrophotometer. To further develop for practical realisation, a smartphone assisted by machine learning was used to screen cancer patients, achieving 90.0% accuracy in leukemia screening. This sensing platform can be applied not only for leukemia screening but also for other cancers associated with epigenetic modification.
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Affiliation(s)
| | - Sawinee Ngernpimai
- Department of Physics, Faculty of Science, Khon Kaen UniversityKhon Kaen 40002Thailand
| | - Piyaporn Matulakul
- Department of Physics, Faculty of Science, Khon Kaen UniversityKhon Kaen 40002Thailand
| | - Janpen Thonghlueng
- Department of Physics, Faculty of Science, Khon Kaen UniversityKhon Kaen 40002Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen UniversityKhon Kaen 40002Thailand
| | - Apiwat Chompoosor
- Department of Chemistry, Faculty of Science, Ramkhamhaeng UniversityBangkok10240Thailand
| | - Uthumporn Panitanarak
- Department of Biostatistics, Faculty of Public Health, Mahidol UniversityBangkok10400Thailand
| | - Yupaporn Wanna
- Department of Statistics, Faculty of Science, Khon Kaen UniversityKhon Kaen40002Thailand
| | - Thanapong Intharah
- Department of Statistics, Faculty of Science, Khon Kaen UniversityKhon Kaen40002Thailand
| | | | - Pimjai Anata
- Molecular Diagnosis Unit, Central Laboratory, Srinagarind Hospital, Khon Kaen UniversityKhon Kaen40002Thailand
| | - Prajuab Chaimnee
- Molecular Diagnosis Unit, Central Laboratory, Srinagarind Hospital, Khon Kaen UniversityKhon Kaen40002Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen UniversityKhon Kaen40002Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen UniversityKhon Kaen40002Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen UniversityKhon Kaen 40002Thailand
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13
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Glucometer-based electrochemical biosensor for determination of microRNA (let-7a) using magnetic-assisted extraction and supersandwich signal amplification. Mikrochim Acta 2022; 189:444. [DOI: 10.1007/s00604-022-05544-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
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14
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Maduraiveeran G. Nanomaterials-based portable electrochemical sensing and biosensing systems for clinical and biomedical applications. J Anal Sci Technol 2022. [DOI: 10.1186/s40543-022-00344-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMiniaturized electrochemical sensing systems are employed in day-to-day uses in the several area from public health to scientific applications. A variety of electrochemical sensor and biosensor systems may not be effectively employed in real-world diagnostic laboratories and biomedical industries due to their limitation of portability, cost, analytical period, and need of skilled trainer for operating devices. The design of smart and portable sensors with high sensitivity, good selectivity, rapid measurement, and reusable platforms is the driving strength for sensing glucose, lactate, hydrogen peroxide, nitric oxide, mRNA, etc. The enhancement of sensing abilities of such sensor devices through the incorporation of both novel sensitive nanomaterials and design of sensor strategies are evidenced. Miniaturization, cost and energy efficient, online and quantitative detection and multiple sensing ability are the beneficial of the nanostructured-material-based electrochemical sensor and biosensor systems. Owing to the discriminating catalytic action, solidity and biocompatibility for designing sensing system, nanoscale materials empowered electrochemical detection systems are accomplished of being entrenched into/combined with portable or miniaturized devices for specific applications. In this review, the advance development of portable and smart sensing/biosensing systems derived from nanoscale materials for clinical and biomedical applications is described.
Graphical Abstract
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15
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Yang Y, Qing Y, Hao X, Fang C, Ouyang P, Li H, Wang Z, Liao Y, Fang H, Du J. APTES-Modified Remote Self-Assembled DNA-Based Electrochemical Biosensor for Human Papillomavirus DNA Detection. BIOSENSORS 2022; 12:bios12070449. [PMID: 35884252 PMCID: PMC9312881 DOI: 10.3390/bios12070449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022]
Abstract
High-risk human papillomavirus (HPV) infection is an important cause of cervical cancer formation; therefore, being able to detect high-risk HPV (e.g., HPV-16) is important for the early treatment and prevention of cervical cancer. In this study, a combination of a 3-aminopropyltriethoxysilane (APTES) modified gold electrode and a super sandwich structure was creatively developed, resulting in the development of a biosensor that is both sensitive and stable for the detection of HPV-16. The electrochemical biosensor possesses a lower detection limit compared with previous studies with an LOD of 5.475 × 10−16 mol/L and it possesses a wide linear range from 1.0 × 10−13 mol/L to 1.0 × 10−6 mol/L (R2 = 0.9923) for the target DNA. The experimental data show that the sensor has good stability, and there is no significant decrease in the current response value after 7 days in the low-temperature environment. In addition, the sensor proved to be a powerful clinical tool for disease diagnosis because it showed good interference resistance in complex human serum samples.
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16
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Chen D, Wu Y, Tilley RD, Gooding JJ. Rapid and ultrasensitive electrochemical detection of DNA methylation for ovarian cancer diagnosis. Biosens Bioelectron 2022; 206:114126. [PMID: 35240438 DOI: 10.1016/j.bios.2022.114126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/04/2023]
Abstract
Alterations in DNA methylation, a stable epigenetic marker, are important components in the development of cancer. It is vital to develop diagnostic systems with the ability to rapidly quantify DNA methylation with high sensitivity and selectivity. However, the analysis of DNA methylation must address two main challenges: (i) ultralow abundance and (ii) differentiating methylated cytosine from normal cytosine on target DNA sequence in the presence of an overwhelming background of circulating cell-free DNA. Here we report the development of an ultrasensitive and highly-selective electrochemical biosensor for the rapid detection of DNA methylation in blood. The sensing of DNA methylation involves the hybridization on a network of probe DNA modified gold-coated magnetic nanoparticles (DNA-Au@MNPs) complementary to target DNA, and subsequently enzymatic cleavage to differentiate methylated DNA strands from corresponding unmethylated DNA strands. The biosensor presents a dynamic range from 2 aM to 20 nM for 110 nucleotide DNA sequences containing a single-site methylation with the lowest detected concentration of 2 aM. This DNA-Au@MNPs based sensor provides a promising method to achieve 35 min response time and minimally invasive diagnosis of ovarian cancer.
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Affiliation(s)
- Dongfei Chen
- School of Chemistry, Australian Centre for NanoMedicine, and Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine, and Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales, 2052, Australia.
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, and Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales, 2052, Australia.
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17
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Khoshfetrat SM, Seyed Dorraji P, Shayan M, Khatami F, Omidfar K. Smartphone-Based Electrochemiluminescence for Visual Simultaneous Detection of RASSF1A and SLC5A8 Tumor Suppressor Gene Methylation in Thyroid Cancer Patient Plasma. Anal Chem 2022; 94:8005-8013. [PMID: 35616262 DOI: 10.1021/acs.analchem.2c01132] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Visual one-step simultaneous detection of low-abundance methylation is a crucial challenge in early cancer diagnosis in a simple manner. Through the design of a closed split bipolar electrochemistry system (BE), detection of promoter methylation of tumor suppressor genes in papillary thyroid cancer, RASSF1A and SLC5A8, was achieved using electrochemiluminescence. For this purpose, electrochemiluminescence of luminol loaded into the Fe3O4@UiO-66 and gold nanorod-functionalized graphite-like carbon nitride nanosheet (AuNRs@C3N4 NS), separately, on the anodic and cathodic pole bipolar electrodes (BPEs) in two different chambers of a bipolar cell were recorded on a smartphone camera. To provide the same electric potential (ΔEelec) through the BPEs to conduct simultaneous light emission, as well as to achieve higher sensitivity, anodic and cathodic poles BPEs were separately connected to ruthenium nanoparticles electrodeposited on nitrogen-doped graphene-coated Cu foam (fCu/N-GN/RuNPs) to provide a hydrogen evolution reaction (HER) and polycatechol-modified reduced graphene oxide/pencil graphite electrode (PC-rGO/PGE) to provide electrooxidation of hydrazine. Moreover, taking advantages of the strong cathodic ECL activity due to the roles of AuNRs, as well as the high density of capture probes on the UiO-66 and Fe3O4 roles in improving the signal-to-background ratio (S/B) in complicated plasma media, a sensitive visual ECL immunosensor was developed to detect two different genes as model target analytes in patient plasma samples. The ability of discrimination of methylation levels as low as 0.01% and above 90% clinical sensitivity in thyroid cancer patient plasma implies that the present strategy is able to diagnose cancer early, as well as monitor responses of patients to therapeutic agents.
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Affiliation(s)
- Seyyed Mehdi Khoshfetrat
- Department of Chemistry, Faculty of Basic Science, Ayatollah Boroujerdi University, Boroujerd 6869199-69737, Iran.,Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, P.O. Box 1411713137, Islamic Republic of Iran
| | - Parisa Seyed Dorraji
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Tehran 199389373, Iran
| | - Mohsen Shayan
- Department of Chemistry, Dalhousie University, 6274 Coburg Road B3H 4R2 Halifax, Canada
| | - Fatemeh Khatami
- Urology Research Center, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, P.O. Box 1411713137, Islamic Republic of Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, P.O. Box 1411713137, Iran
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18
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A novel methyl-dependent DNA endonuclease GlaI coupling with double cascaded strand displacement amplification and CRISPR/Cas12a for ultra-sensitive detection of DNA methylation. Anal Chim Acta 2022; 1212:339914. [DOI: 10.1016/j.aca.2022.339914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/26/2022]
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19
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Li H, Li Q, Zhao S, Wang X, Li F. Aptamer-Target Recognition-Promoted Ratiometric Electrochemical Strategy for Evaluating the Microcystin-LR Residue in Fish without Interferences. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:680-686. [PMID: 35012307 DOI: 10.1021/acs.jafc.1c06476] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Given the significance of food safety, it is highly urgent to develop a sensitive yet reliable sensor for the practical analysis of algal toxins. As most of the developed sensors are disturbed by interfering substances and the target toxin is detected in a single-signal manner based on the immunoassay technology. Herein, we developed an aptamer-based dual-signal ratiometric electrochemical sensor for the sensitive and accurate analysis of microcystin-LR (MC-LR), using it as a proof-of-concept analyte. Methylene blue-tagged ssDNA (MB-ssDNA) was immobilized at the gold electrode surface accompanied with the absence of ferrocene-tagged ssDNA (Fc-ssDNA), resulting in a high differential pulse voltammetry (DPV) current of MB and a low DPV current of Fc. The recognition of MB-ssDNA by MC-LR stimulated the formation of MC-LR@MB-ssDNA, which induced the removal of MB-ssDNA from the electrode and the exposure of SH-ssDNA, enabling Fc-ssDNA to be captured at the electrode surface via nucleic acid hybridization. In comparison with MC-LR deficiency, the DPV signal of MB dropped along with an improved DPV signal of Fc, contributing to the ratiometric detection of MC-LR, with the limit of detection down to 0.0015 nM. Furthermore, this ratiometric electrochemical sensor was successfully explored to assess the bioaccumulated amount of MC-LR in the liver and meat of fish. The aptamer-based ratiometric strategy to develop an electrochemical MC-LR assay will offer a promising avenue to develop high-performance sensors, and the sensor will find more useful application in MC-LR-related aquatic product safety studies.
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Affiliation(s)
- Haiyin Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Qian Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Suixin Zhao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Xuemei Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
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20
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Yang K, Feng X, Yu G, Han W, Liu F, Xie Y, Zhang H, Yu Y, Zou G. Single polymeric microfiber waveguide platform for sensitive detection and discrimination of DNA methylation. Analyst 2022; 147:1892-1898. [DOI: 10.1039/d1an02243a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel sensitive detection platform for p16 and p16 methylation based on a single polymeric fluorescent microfiber waveguide with sandwich-structured hybridization designs.
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Affiliation(s)
- Kexin Yang
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Xiaohui Feng
- Division of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gaoyuan Yu
- Undergraduate major in clinical medicine, grade 2017, class 1, Medical College of Hubei University of Science and Technology, Xianning, Hubei 437100, P. R. China
| | - Wenjie Han
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Funing Liu
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Yifan Xie
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Hongli Zhang
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Yue Yu
- Division of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gang Zou
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
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21
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Cheng W, Ma J, Tao Q, Adeel K, Xiang L, Liu D, Zhang Z, Li J. Demethylation of m1A assisted degradation of the signal probe for rapid electrochemical detection of ALKBH3 activity with practical applications. Talanta 2021; 240:123151. [PMID: 34942472 DOI: 10.1016/j.talanta.2021.123151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022]
Abstract
ALKBH3 is an important marker for early diagnosis and histopathological grading of prostate cancer. However, the lack of a rapid and sensitive method to quantify the enzyme's activity in the current time necessitates the development of a new quantitative assay. Herein, we first tried to quantitative assay for ALKBH3 activity using an electrochemical method based on the degradation of the signal probe due to alkyl group of the m1A removal by ALKBH3. A strong electrochemical signal can be obtained when the ferrocene (Fc) labeled dsDNAs with 1-methyladenine are immobilized on the electrode. In the presence of ALKBH3, the 3' blunt of DNA can be formed because of the removal of alkyl group of the Fc-DNA probe, which can be recognized and degraded by Exonuclease III (Exo III). As a result, the electrochemical signal produced by Fc greatly decreases, and the activity of ALKBH3 can be easily detected via changes in electrochemical signal. Quantitative analysis of ALKBH3 activity showed a wide detection range (0.1 and 20 ng/mL) and low detection limit (0.04 ng/mL). Furthermore, the method can be applied to detect 1-methyladenine through ALKBH3 in cell lysates and tissue samples, providing a new method for clinical detection of prostate cancer.
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Affiliation(s)
- Wenting Cheng
- Department of Clinical Laboratory, Nanjing Gaochun People's Hospital, Nanjing, 211300, PR China
| | - Jiehua Ma
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, PR China
| | - Qinfang Tao
- Department of Clinical Laboratory, Nanjing Gaochun People's Hospital, Nanjing, 211300, PR China
| | - Khan Adeel
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210000, PR China
| | - Liangliang Xiang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Duxian Liu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Zhaoli Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China.
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22
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Zhou J, Li Z, Hu J, Wang C, Liu R, Lv Y. HOGG1-assisted DNA methylation analysis via a sensitive lanthanide labelling strategy. Talanta 2021; 239:123136. [PMID: 34920255 DOI: 10.1016/j.talanta.2021.123136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 01/09/2023]
Abstract
The assessment of DNA methylation level is an important indicator for the diagnosis and treatment of some diseases. DNA methylation assays are usually based on nucleic acid amplification strategies, which are time-consuming and complicated in operation procedures. Herein, we proposed a sensitive lanthanide-labelled ICP-MS method for DNA methylation analysis that exploited the feature of Human 8-oxoGuanine DNA Glycosylase (hOGG1), which specifically recognizes 8-oxo-G/5mC base pairs to effectively distinguish methylated DNA. A low limit of detection of 84 pM was achieved, and a 0.1% methylation level can be discriminated in the mixture, without any amplification procedure. Compared with commonly used nucleic acid amplification strategies, this proposed method is time-saving and low probability of false positive. Moreover, this work has been successfully validated in human serum samples, the recovery rates is between 96.7% and 105%, and the relative standard deviation (RSD) is in the range of 3.0%-3.5%, indicating that this method has the potential to be applied in clinical and biological samples quantitative analysis.
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Affiliation(s)
- Jing Zhou
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Ziyan Li
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Jianyu Hu
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Chaoqun Wang
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Rui Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 WangJiang Road, Chengdu, 610064, PR China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China; Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 WangJiang Road, Chengdu, 610064, PR China.
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23
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Detection of average methylation level of specific genes by binary-probe hybridization. Talanta 2021; 234:122630. [PMID: 34364439 DOI: 10.1016/j.talanta.2021.122630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/24/2021] [Accepted: 06/17/2021] [Indexed: 01/13/2023]
Abstract
We developed a simple and highly-selective method for 5-methylcytosine detection of specific gene sequence based on binary-probe DNA hybridization. The sequence complementary to the target was designed into two probes, and each fragment of binary probes bound to a relatively short sequence of the target, which made it sensitive to the base mismatches introduced by bisulfite treatment. The advantages of a low detection limit of methylation abundance of 0.1% for the fully methylated target and high sensitivity of 10 pM have been proved by the successful design of binary-probe hybridization. The successful design of the binary probes makes it possible to quantify the average methylation levels of five CpG sites. Thirty-two DNA strands containing 5, 4, 3, 2, 1 and 0 CpG sites were successfully analyzed with the same pair of binary probes. The higher the average methylation level of the target was, the higher the degree of the hybridization reaction. Based on the simple construction of the binary-probe hybridization, the developed biosensor exhibited signals proportional to the average methylation level of the vimentin gene and could evaluate the average methylation level of artificial mixtures. Furthermore, the method has been used to detect vimentin methylation in a genomic context with good specificity, which indicated its potential in the pre-diagnosis of methylation related disease.
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24
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Hadian-Ghazvini S, Dashtestani F, Hakimian F, Ghourchian H. An electrochemical genosensor for differentiation of fully methylated from fully unmethylated states of BMP3 gene. Bioelectrochemistry 2021; 142:107924. [PMID: 34474202 DOI: 10.1016/j.bioelechem.2021.107924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
The methylation state of a part of the BMP3 gene was detected by our genosensor. This epigenetic biomarker is involved in the biomarker panel of the sDNA test, which is an FDA approved test for colorectal cancer screening. In the present genosensor, polyethyleneimine-stabilized silver nanoparticles (PEI-AgNPs) were used as a non-specific nanolabel for signal generation/amplification and lowering the limit of detection. After immobilization of capture probes and mercaptoethanol molecules on the gold electrode, a thermally treated mixture of the BMP3 targets and reporter probes was introduced to the electrode. Because of the specificity of the reporter probes for fully methylated targets, complete sandwich-like complexes are formed only with them. Therefore, such full-length double-stranded hybrids compared to fully unmethylated targets have more negative charges and can more attract positively charged PEI-AgNPs. For discrimination between methylated and unmethylated targets, electroimpedance spectroscopy and cyclic voltammetry were used for electrode modification monitoring and signal measurement. The sharp and narrow anodic peaks of cyclic voltammograms, which resulted from silver oxidation, were utilized for calibration plot analysis. The genosensor showed a linear response for the target concentration range from 1fM to 100 nM, while the detection limit for methylated and unmethylated target discrimination was 1 fM.
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Affiliation(s)
- Samaneh Hadian-Ghazvini
- Laboratory of Bioanalysis, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Fariba Dashtestani
- Laboratory of Bioanalysis, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Fatemeh Hakimian
- Laboratory of Bioanalysis, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Hedayatolah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran.
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Cui K, Zhou C, Zhang B, Zhang L, Liu Y, Hao S, Tang X, Huang Y, Yu J. Enhanced Catalytic Activity Induced by the Nanostructuring Effect in Pd Decoration onto Doped Ceria Enabling an Origami Paper Analytical Device for High Performance of Amyloid-β Bioassay. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33937-33947. [PMID: 34279896 DOI: 10.1021/acsami.1c09760] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work, we fabricated a novel origami paper-based analytical device (oPAD) assisted by the nanostructuring effect of in situ Pd decoration of Cu/Co-doped CeO2 (CuCo-CeO2-Pd) nanospheres, functionalized with their strongly enhanced electrocatalytic properties to realize an electrochemical and visual signal readout system in oPAD, for highly sensitive detection of amyloid-β (Aβ). The CuCo-CeO2-Pd nanospheres were introduced as an enhanced "signal transducer layer" on account of the electron transfer acceleration caused by catalyzing glucose to produce H2O2 for differential pulse voltammetry signal readout and further 3,3'5,5'-tetramethylbenzidine (TMB) oxidation for colorimetric analysis. Meanwhile, for achieving superior performance of the proposed oPAD, in situ growth of urchin-like gold nanoparticles (Au NPs) onto cellulose fibers was adopted to improve "the recognition layer" in favor of immobilizing antibodies for targeting Aβ through specific antigen-antibody interactions. Combined with the delicate design of oPAD, exhibiting actuation of the conversion procedure between hydrophobicity and hydrophilicity on paper tabs in the assay process, the oPAD successfully enabled sensitive diagnosis of Aβ in a linear range from 1.0 pM to 100 nM with a limit of detection of 0.05 pM (S/N = 3) for electrochemical detection, providing a reliable strategy for quantifying the Aβ protein in clinical applications.
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Affiliation(s)
- Kang Cui
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, Shandong, P. R. China
| | - Chenxi Zhou
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, Shandong, P. R. China
| | - Bowei Zhang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials, University of Jinan, Jinan 250022, Shandong, P. R. China
| | - Yue Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, Shandong, P. R. China
| | - Shiji Hao
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Xiaohong Tang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yizhong Huang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, Shandong, P. R. China
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26
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Wang L, Zhang L, Yu Y, Lin B, Wang Y, Guo M, Cao Y. DNA cyclic assembling control in an electrochemical strategy with MoS 2@AuNPs for determination of kanamycin. Mikrochim Acta 2021; 188:264. [PMID: 34287718 DOI: 10.1007/s00604-021-04916-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Abstract
A sensitive electrochemical strategy was established for kanamycin determination. A specific aptamer was modified on the electrode as the probe, followed by a cyclic hybridization chain reaction (HCR) with methylene blue, causing an increasing signal response. In the presence of kanamycin, it can initiatively convolve the aptamer and prevent further DNA assembling, resulting in a signal distinction sensitive to the target amount. However, the signal reproducibility is low. To improve the precision, the HCR procedure was investigated. The results demonstrated that the optimal amount of assembled DNA is 12-fold to that of aptamer. This amount was then controlled in further assays. Admittedly, controlled DNA assembling commonly indicates a limited signal amplification. To further enhance the sensitivity, a nanocomposite based on MoS2 and AuNPs was modified on the electrode. The results of the assay proved that the signal distinction sensitive to target amount increased by 50%. A linearity range is obtained from 0.01 nM to 1.0 μM of kanamycin, and the LOD is 8.4 pM. Subsequently, this strategy was employed to detect kanamycin in chicken liver and milk sample; the recovery results suggest that it possess a satisfactory application prospect in analysis of agricultural products.
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Affiliation(s)
- Lina Wang
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.,Department of Environmental Engineering, Guangdong Polytechnic of Environmental Protection Engineering, Foshan, 528216, People's Republic of China
| | - Li Zhang
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.
| | - Ying Yu
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.
| | - Bixia Lin
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Yumin Wang
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Manli Guo
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Yujuan Cao
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China
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27
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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28
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Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA Methylation in Solid Tumors: Functions and Methods of Detection. Int J Mol Sci 2021; 22:ijms22084247. [PMID: 33921911 PMCID: PMC8073724 DOI: 10.3390/ijms22084247] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.
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29
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Wang Y, Zheng J, Duan C, Jiao J, Gong Y, Shi H, Xiang Y. Detection of locus-specific N6-methyladenosine modification based on Ag +-assisted ligation and supersandwich signal amplification. Analyst 2021; 146:1355-1360. [PMID: 33393556 DOI: 10.1039/d0an02214d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Emerging evidence reveals that the epitranscriptomic mark N6-methyladenosine (m6A) plays vital roles in organisms, including gene regulation and disease progression. However, developing sensitive methods to detect m6A modification, especially the identification of m6A marks at the single-site level, remains a challenge. Therefore, based on target-specific triggered signal amplification, we developed a highly sensitive electrochemical method to detect site-specific m6A modifications in DNA. In this work, the m6A site in DNA can restrict the ligation assisted by Ag+, and this restriction effect can activate the subsequent strand displacement reaction and hybridization chain reaction (HCR), thus achieving signal amplification from the m6A site, and finally realizing high sensitivity analysis of m6A methylation. Benefiting from the high specificity of base pairs and the extremely weak binding affinity between Ag+ and m6A, the proposed method was used for not only detecting the target DNA with a putative m6A site, but also identifying m6A marks at the single-site level in DNA. In addition, this study does not rely on antibodies and radiolabeling, so it has the advantage of cost-effectiveness. Therefore, we believe that the proposed strategy may provide a new perspective for methylation research, which can be used to test more clinical samples in further research.
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Affiliation(s)
- Yanxia Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Ji Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Jin Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Youjing Gong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
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30
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Zhou Y, Yin H, Zhao WW, Ai S. Electrochemical, electrochemiluminescent and photoelectrochemical bioanalysis of epigenetic modifiers: A comprehensive review. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213519] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Ouyang J, Zhan X, Guo S, Cai S, Lei J, Zeng S, Yu L. Progress and trends on the analysis of nucleic acid and its modification. J Pharm Biomed Anal 2020; 191:113589. [DOI: 10.1016/j.jpba.2020.113589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/18/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022]
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32
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Mi X, Li H, Tan R, Tu Y. Dual-Modular Aptasensor for Detection of Cardiac Troponin I Based on Mesoporous Silica Films by Electrochemiluminescence/Electrochemical Impedance Spectroscopy. Anal Chem 2020; 92:14640-14647. [PMID: 33090771 DOI: 10.1021/acs.analchem.0c03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A simple, dual-modular aptasensor for accurate determination of cardiac troponin I (cTnI), a sensitive biomarker of acute myocardial infarction, is reported. It has the parallel output of electrochemiluminescence (ECL) and electrochemical impedance spectroscopy (EIS) based on target-gated transportation of signal probes (luminol/H2O2 or Fe(CN)63-/4-). The sensing capacity is originated from the amino-functionalized mouth margin of the nanochannels in a vertically oriented mesoporous silica film, which was in situ-grown on indium tin oxide-coated glass. With the linkage of glutaraldehyde to couple the aptamer as a trapper, it brings in the high specific target-gated response toward cTnI as decreased ECL or increased EIS. The concentration of cTnI is measurable by the ECL response within a wide linear range from 0.05 pg mL-1 to 10 ng mL-1, as well as the EIS response for a linear range between 0.05 pg mL-1 and 1 ng mL-1. Significantly, the self-verification of these two data from ECL and EIS validated each other with a satisfactory linear correlation (R2 = 0.999), thereby realizing the more reliable and accurate quantification to avoid false results. The designed strategy is an effective method for detection of cTnI, which is of great potential to apply in clinical detection.
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Affiliation(s)
- Xiaona Mi
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou 215123, P. R. China
| | - Hui Li
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P. R. China
| | - Rong Tan
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou 215123, P. R. China
| | - Yifeng Tu
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou 215123, P. R. China
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33
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Zhang Q, Wu Y, Xu Q, Ma F, Zhang CY. Recent advances in biosensors for in vitro detection and in vivo imaging of DNA methylation. Biosens Bioelectron 2020; 171:112712. [PMID: 33045657 DOI: 10.1016/j.bios.2020.112712] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/25/2020] [Accepted: 10/07/2020] [Indexed: 02/08/2023]
Abstract
DNA methylation is the predominant epigenetic modification that participates in many fundamental cellular processes through posttranscriptional regulation of gene expression. Aberrant DNA methylation is closely associated with a variety of human diseases including cancers. Therefore, accurate and sensitive detection of DNA methylation may greatly facilitate the epigenetic biological researches and disease diagnosis. In recent years, a series of novel biosensors have been developed for highly sensitive detection of DNA methylation, but an overview of recent advances in biosensors for in vitro detection and especially live-cell imaging of DNA methylation is absent. In this review, we summarize the emerging biosensors for in vitro and in vivo DNA methylation assays in the past five years (2015-2020). Based on the signal types, the biosensors for in vitro DNA methylation assay are classified into five categories including fluorescent, electrochemical, colorimetric, surface enhanced Raman spectroscopy, mass spectrometry, and surface plasmon resonance biosensors, while the biosensors for in vivo DNA methylation assay mainly rely on fluorescent imaging. We review the strategies, features and applications of these biosensors, and provide a new insight into the challenges and future directions in this area.
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Affiliation(s)
- Qian 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
| | - Yanxia Wu
- Department of Pathology and Pathological Diagnosis & Research Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Fei Ma
- 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.
| | - 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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34
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Wang ZY, Li P, Cui L, Xu Q, Zhang CY. Construction of a Universal and Label-Free Chemiluminescent Sensor for Accurate Quantification of Both Bacteria and Human Methyltransferases. Anal Chem 2020; 92:13573-13580. [DOI: 10.1021/acs.analchem.0c03303] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zi-yue 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
| | - Peng 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
| | - Lin Cui
- 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
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, P. R. 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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35
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Liu Z, Lei S, Zou L, Li G, Ye B. Grafting homogenous electrochemical biosensing strategy based on reverse proximity ligation and Exo III assisted target circulation for multiplexed communicable disease DNA assay. Biosens Bioelectron 2020; 167:112487. [PMID: 32810705 DOI: 10.1016/j.bios.2020.112487] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Rapid and effective diagnosis of communicable disease is one of the critical issues of the modern society, especially for detecting different targets at the same time. In this work, a grafting homogenous electrochemical biosensing strategy is proposed by integrating of reverse proximity ligation and exonuclease III (Exo III) assisted target circulation to analyze hepatitis B (HBV) and human immunodeficiency (HIV). Specially, a two-wing nanodevice (TWD) with two detection paths is elaborately designed based on analogous proximity ligation assay. The reverse proximity ligation process provides a new way of signal conversion and amplification, what accomplished by demolishing the TWD in the presence of targets. Meanwhile, a vast number of signal probes are released via Exo III assisted target circulation. Then the signal probes are grafted on the universal sensing interface, which is decorated with graftable tetrahedron DNA (GTD). These lead to a highly amplified electrochemical signal. Compared with the conventional strategies, the grafting homogenous electrochemical biosensing strategy not only achieves convenient sensitive detection of multiple communicable diseases DNA simultaneously, but also performs well in the detection of sole target. This strategy effectively decreases the background, homogenizes the distribution of probes, and avoids the complex and time-consuming modification process of the working electrode, which holds great potential application in early diagnosis for communicable disease in the future.
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Affiliation(s)
- Zi Liu
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Sheng Lei
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Baoxian Ye
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China.
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36
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Feng Q, Wang M, Han X, Chen Q, Dou B, Wang P. Construction of an Electrochemical Biosensing Platform Based on Hierarchical Mesoporous NiO@N-Doped C Microspheres Coupled with Catalytic Hairpin Assembly. ACS APPLIED BIO MATERIALS 2020; 3:1276-1282. [DOI: 10.1021/acsabm.9b01145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Mengying Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xiguang Han
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Qian Chen
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
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37
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Feng Q, Qin L, Wang M, Wang P. Signal-on electrochemical detection of DNA methylation based on the target-induced conformational change of a DNA probe and exonuclease III-assisted target recycling. Biosens Bioelectron 2019; 149:111847. [PMID: 31733487 DOI: 10.1016/j.bios.2019.111847] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/29/2019] [Accepted: 11/02/2019] [Indexed: 11/16/2022]
Abstract
A promising electrochemical system was explored for DNA methylation detection according to the construction of a signal-on biosensor. Based on the ingenious design of probe DNA and auxiliary DNA, methylated target DNA triggered the exonuclease III (Exo III) digestion of auxiliary DNA from 3'-terminus, resulting in the conformational change of probe DNA with an electroactive methylene blue (MB) tag at 5'-terminus. Consequently, the MB tag in the probe DNA was close to the electrode surface for electron transfer, generating an increased current signal. Because of the target recycling of methylated DNA, significant signal amplification was obtained. Moreover, bisulfite conversion conferred an efficient approach for the universal analysis of any CpG sites without the restriction of specific DNA sequence. As a result, the target DNA with different methylation statuses were clearly recognized, and the fully methylated DNA was quantified in a wide range from 10 fM to 100 pM, with a detection limit of 4 fM. The present work realized the assay of methylated target DNA in serum samples with satisfactory results, illustrating the application performance of the system in complex sample matrix.
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Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Li Qin
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mengying Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China.
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