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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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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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Methylation-sensitive transcription-enhanced single-molecule biosensing of DNA methylation in cancer cells and tissues. Anal Chim Acta 2023; 1251:340996. [PMID: 36925287 DOI: 10.1016/j.aca.2023.340996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
As a major epigenetic modification, DNA methylation participates in diverse cellular functions and emerges as a promising biomarker for disease diagnosis and monitoring. Herein, we developed a methylation-sensitive transcription-enhanced single-molecule biosensor to detect DNA methylation in human cells and tissues. In this biosensor, a rationally designed transcription machine is split into two parts including a promoter sequence (probe-P) for initiating transcription and a template sequence (probe-T) for RNA synthesis. The presence of specific DNA methylation leads to the formation of full-length transcription machine through sequence-specific ligation of probe-P and probe-T, initiating the synthesis of abundant ssRNA transcripts. The resultant ssRNAs can activate CRISPR/Cas12a to catalyze cyclic cleavage of fluorophore- and quencher-dual labeled signal probes, resulting in the recovery of the fluorophore signal that can be quantified by single-molecule detection. Taking advantages of the high-fidelity ligation of split transcription machine and the high efficiency of transcription- and CRISPR/Cas12a cleavage-mediated dual signal amplification, this single-molecule biosensor achieves a low detection limit of 337 aM and high selectivity. Moreover, it can distinguish 0.01% methylation level, and even accurately detect genomic DNA methylation in single cell and clinical samples, providing a powerful tool for epigenetic researches and clinical diagnostics.
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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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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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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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7
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Yao Y, Xue M, Mao W, Li Y, Zhu A, Chen T, Shen W, Liu C, Chen L, Tang S. Ni/Fe layered double hydroxide nanosheet/G-quadruplex as a new complex DNAzyme with highly enhanced peroxidase-mimic activity. Analyst 2021; 146:6470-6473. [PMID: 34609387 DOI: 10.1039/d1an01405f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel and low-cost DNAzyme, Ni/Fe layered double hydroxide (LDH) nanosheet/G-quadruplex (without hemin) with enhanced peroxidase-mimic activity was designed. The catalytic mechanism was investigated. The detection of Cu(II) in actual serum samples could be realized sensitively via this efficient DNAzyme-based method.
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Affiliation(s)
- Yao Yao
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Mingliang Xue
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Wei Mao
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Yana Li
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Anni Zhu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Tianyu Chen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Lizhuang Chen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China.
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8
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Gong PX, Xu F, Cheng L, Gong X, Zhang J, Gu WJ, Han W. Iron-catalyzed domino decarboxylation-oxidation of α,β-unsaturated carboxylic acids enabled aldehyde C-H methylation. Chem Commun (Camb) 2021; 57:5905-5908. [PMID: 34008616 DOI: 10.1039/d1cc01536b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A practical and general iron-catalyzed domino decarboxylation-oxidation of α,β-unsaturated carboxylic acids enabling aldehyde C-H methylation for the synthesis of methyl ketones has been developed. This mild, operationally simple method uses ambient air as the sole oxidant and tolerates sensitive functional groups for the late-stage functionalization of complex natural-product-derived and polyfunctionalized molecules.
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Affiliation(s)
- Pei-Xue Gong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Fangning Xu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Lu Cheng
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Xu Gong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Jie Zhang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Wei-Jin Gu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Wei Han
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China. and Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biofunctional Materials, Key Laboratory of Applied Photochemistry, Nanjing 210023, China
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Jiang H, Ji P, Xu Y, Liu X, Kong D. Self-paired dumbbell DNA -assisted simple preparation of stable circular DNAzyme and its application in Pb 2+ sensor. Anal Chim Acta 2021; 1175:338733. [PMID: 34330440 DOI: 10.1016/j.aca.2021.338733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 01/20/2023]
Abstract
During its development in recent decades, DNAzyme has become a promising candidate for application in biosensor field. However, it still suffers from the problem of thermodynamic and biological instability such as nuclease digestion, which limits its applications in complex samples. Here we have presented a simple and common strategy to resolve this problem by engineering the linear DNAzyme into a circular shape DNAzyme based on the integration of substrate and enzyme parts into one single-stranded sequence. This circular DNAzyme system is indeed endowed with excellent stability due to the stable intramolecular double-stranded formation and extraordinary resistance to nuclease digestion due to the closed structure. We demonstrated that this circular DNAzyme system gained excellent stability and could active under conditions across a broader range of temperature, salt concentrations, and pH. Depending on this circular DNAzyme, combing with Terminal deoxynucleotidyl transferase (TdT)-generated G-quadruplexes, a label free colorimetric sensing platform for Pb2+ quantitation was developed, and a detection limit of 0.085 nM was achieved. Then the enzyme digestion cycle amplification was introduced to further improve the sensitivity of the sensing system, an ultralow detection limit of 0.0015 nM for this fluorescence method was achieved. Based on the two sensing platforms, ultrasensitive analysis of Pb2+ in environmental water and food samples was successfully realized. It is anticipated that this stable circular DNAzyme design will be helpful for trace detection in complex samples.
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Affiliation(s)
- Hongxin Jiang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Pingping Ji
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Yaping Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Xiaowei Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Deming Kong
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China
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Zhang Y, Hu J, Zou X, Ma F, Qiu JG, Zhang CY. Integration of single-molecule detection with endonuclease IV-assisted signal amplification for sensitive DNA methylation assay. Chem Commun (Camb) 2021; 57:2073-2076. [PMID: 33507186 DOI: 10.1039/d0cc08306b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We demonstrate the development of a new fluorescent biosensor for sensitive DNA methylation assay by integrating single-molecule detection with endo IV-assisted signal amplification. This biosensor possesses the characteristics of good selectivity and high sensitivity with a detection limit of 7.3 × 10-17 M. It can distinguish as low as 0.01% methylation level, and can analyze genomic DNA methylation even in a single cancer cell.
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Affiliation(s)
- Yan Zhang
- 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, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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11
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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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12
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Li ZM, Pi T, Yan XL, Tang XM, Deng RH, Zheng XJ. Label-free and enzyme-free one-step rapid colorimetric detection of DNA methylation based on unmodified gold nanoparticles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118375. [PMID: 32438293 DOI: 10.1016/j.saa.2020.118375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation has been identified as one of the important causes of tumorigenesis, so it is important to develop some advanced methods for detecting and quantifying DNA methylation. In this study, a label-free and enzyme-free one-step rapid colorimetric detection of DNA methylation based on unmodified Au nanoparticles(Au NPs)has been proposed. This method can quickly, efficiently, economically and easily colorimetric detect methylated DNA only by the color change of unmodified Au NPs solution without the covalent modification of Au NPs in advance or complicated instruments for implementation with practical limitations or expensive biological enzymes or traditional organic dyes during the reaction. The strategy employed the difference in electrostatic attraction of single-stranded DNA and double-stranded DNA against salt-induced aggregation of Au NPs. The method has a DNA methylated detection limit of 8.47 nM and it is distinctly visible to detect methylated DNA with the naked eye as low as 20 nM. Furthermore, the strategy has an ability to detect methylated DNA in the presence of abundant unmethylated DNA with the detection limit of 0.13% and as low as 1% methylated DNA can be distinguished in heterogeneous samples with the naked eye. Also, the stratagem provides a convenient and rapid platform for methylated DNA detection of human serum samples in one step, which displays a huge potential for clinical diagnosis and treatment of oncological diseases.
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Affiliation(s)
- Zhi-Mei Li
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Ting Pi
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Xi-Luan Yan
- College of resources, environment and chemical engineering, Nanchang university, Nanchang 330031, PR China
| | - Xiao-Meng Tang
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Rui-Hong Deng
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Xiang-Juan Zheng
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China.
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Zhai M, Zhao Z, Yang M, Liang Y, Liang H, Xie Y, Han J. The effect of GNAQ methylation on GnRH secretion in sheep hypothalamic neurons. J Cell Biochem 2019; 120:19396-19405. [PMID: 31452255 DOI: 10.1002/jcb.29021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 12/24/2022]
Abstract
Kazakh sheep are seasonal estrous animals, and gonadotropin-releasing hormone (GnRH) is the key to fertility regulation. The nutritional level has a certain regulatory effect on estrous, and vitamin B folate plays a role in DNA methylation, directly participating in the process. The goal of this study was to determine whether folate is involved in GnAQ methylation and its effect on GnRH secretion. The hypothalamic neurons of Kazakh fetal sheep were treated with folate at concentrations of 0 mg/mL, 4 mg/mL, 40 mg/mL, and 80 mg/mL. GnAQ promoter methylation, DNMT1, GnAQ expression, and GnRH secretion following treatment with different concentrations of folate were analyzed. One CpG site was methylated in the GNAQ promoter with 40 mg/mL folic acid, and no CpG methylation was found in the other groups. GnAQ expression was related to folate concentration and showed a trend of increasing first and then decreasing. The GnRH expression level in the 40 mg/mL folate group was significantly higher than in the other three groups ( P < .05). These results demonstrate that the appropriate folate concentration promoted GANQ promoter methylation, which in turn affected GnRH secretion.
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Affiliation(s)
- Manjun Zhai
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Min Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yanping Liang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Huihui Liang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yifan Xie
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jilong Han
- College of Animal Science and Technology, Shihezi University, Shihezi, China
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Cao T, Wang Y, Zhao LL, Wang Y, Tao Y, Heyman JA, Weitz DA, Zhou YL, Zhang XX. A simple mix-and-read bacteria detection system based on a DNAzyme and a molecular beacon. Chem Commun (Camb) 2019; 55:7358-7361. [DOI: 10.1039/c9cc03746b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A simple improved mix-and-read method for the detection of bacteria is developed based on a DNAzyme and a molecular beacon.
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Affiliation(s)
- Ting Cao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Yongcheng Wang
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
- Wyss Institute for Biologically Inspired Engineering
| | - Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Ye Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Ye Tao
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
| | - John A. Heyman
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
- Wyss Institute for Biologically Inspired Engineering
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
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