1
|
Yuan W, Xiao K, Liu X, Lai Y, Luo F, Xiao W, Wu J, Pan P, Li Y, Xiao H. A programmable DNA nanodevice for colorimetric detection of DNA methyltransferase activity using functionalized hemin/G-quadruplex DNAzyme. Anal Chim Acta 2023; 1273:341559. [PMID: 37423656 DOI: 10.1016/j.aca.2023.341559] [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: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
Abstract
The measurement of DNA methyltransferase (MTase) activity and screening of DNA MTase inhibitors holds significant importance for the diagnosis and therapy of methylation-related illness. Herein, we developed a colorimetric biosensor (PER-FHGD nanodevice) to detect DNA MTase activity by integrating the primer exchange reaction (PER) amplification and functionalized hemin/G-quadruplex DNAzyme (FHGD). By replacing the native hemin cofactor into the functionalized cofactor mimics, FHGD has exhibited significantly improved catalytic efficiency, thereby enhancing the detection performance of the FHGD-based system. The proposed PER-FHGD system is capable of detecting Dam MTase with excellent sensitivity, exhibiting a limit of detection (LOD) as low as 0.3 U/mL. Additionally, this assay demonstrates remarkable selectivity and ability for Dam MTase inhibitors screening. Furthermore, using this assay, we successfully detect the Dam MTase activity both in serum and in E. coli cell extracts. Importantly, this system has the potential to serve as a universal strategy for FHGD-based diagnosis in point-of-care (POC) tests, by simply altering the recognition sequence of the substrate for other analytes.
Collapse
Affiliation(s)
- Wenxu Yuan
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Kaiting Xiao
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Xingxing Liu
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Yanming Lai
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Fazeng Luo
- Foshan Institute of Medical Microbiology, Foshan, Guangdong, 528315, PR China
| | - Wei Xiao
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, 510317, PR China
| | - Jinjun Wu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Pan Pan
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China.
| | - Yongkui Li
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China.
| | - Heng Xiao
- Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, Institute of Medical Microbiology, The First Affiliated Hospital of Jinan University, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, PR China.
| |
Collapse
|
2
|
Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
|
3
|
Dong Y, Wan L, Lv S, Zhu D, Su S, Chao J, Wang L. Construction of a Molybdenum Disulfide-Based Colorimetric Sensor for Label-Free Infectious Disease Analysis Coupled with a Catalyzed Hairpin Assembly Reaction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1791-1796. [PMID: 35084864 DOI: 10.1021/acs.langmuir.1c02891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The simple and accurate determination of pathogenic infectious diseases is very beneficial to public health prevention and control. For this purpose, we designed a colorimetric sensor for label-free avian influenza A (H7N9) virus gene sequence detection based on gold@platinum core-shell bimetallic-nanoparticle-decorated molybdenum disulfide (MoS2-Au@Pt) nanocomposites. MoS2-Au@Pt nanocomposites were used as nanoenzymes to catalyze 3,3',5,5'-tetramethylbenzidine (TMB) by hydrogen peroxide (H2O2) because of their intrinsic peroxidase-mimicking activity. Coupled with different affinities of MoS2-Au@Pt nanocomposites toward single-stranded (ss) and double-stranded (ds) DNA and the target-triggered catalyzed hairpin assembly (CHA) reaction, the proposed sensor can qualitatively and quantitatively determine H7N9 by the naked eye. Experimental results showed that this sensor can detect H7N9 in buffer and real samples because of its high sensitivity, selectivity, and repeatability.
Collapse
Affiliation(s)
- Yan Dong
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Ling Wan
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Suo Lv
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| |
Collapse
|
4
|
Huang Y, Zhang W, Zhao S, Xie Z, Chen S, Yi G. Ultra-sensitive detection of DNA N6-adenine methyltransferase based on a 3D tetrahedral fluorescence scaffold assisted by symmetrical double-ring dumbbells. Anal Chim Acta 2021; 1184:339018. [PMID: 34625260 DOI: 10.1016/j.aca.2021.339018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/13/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic modification that plays a vital role in X chromosome inactivation, genome imprinting, and gene expression. DNA methyltransferase establishes and maintains a stable methylation state in genomic DNA. Efficient and specific DNA methyltransferase testing is essential for the early diagnosis and treatment of cancer. In this study, we designed an ultra-sensitive fluorescent biosensor, based on a 3D tetrahedral fluorescent scaffold assisted by symmetrical double-ring dumbbells, for the detection of DNA-[N 6-adenine]-methyltransferase (Dam MTase). Double-stranded DNA was methylated by Dam MTase and then digested by DpnI to form two identical dumbbell rings. The 3D tetrahedral fluorescent scaffold was synthesized from four oligonucleotide chains containing hairpins. When the sheared dumbbells reacted with the 3D tetrahedral fluorescent scaffold, the hairpins opened and a fluorescence signal could be detected. The strategy was successful over a wide detection range, from 0.002 to 100 U mL-1 Dam MTase, and the lowest detection limit was 0.00036 U mL-1. Control experiments with M.SssI methyltransferase and HpaII methylation restriction endonuclease confirmed the specificity of the method. Experiments with spiked human serum and the 5-fluorouracil inhibitor proved the suitability of the method for early cancer diagnosis.
Collapse
Affiliation(s)
- Yuqi Huang
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wenxiu Zhang
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shuhui Zhao
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zuowei Xie
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyi Chen
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Gang Yi
- Key Laboratory of Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| |
Collapse
|
5
|
Wang H, Wu T, Li M, Tao Y. Recent advances in nanomaterials for colorimetric cancer detection. J Mater Chem B 2020; 9:921-938. [PMID: 33367450 DOI: 10.1039/d0tb02163f] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The early diagnosis of cancer can significantly improve patient survival rates. Colorimetric methods for real-time naked-eye detection have aroused growing interest owing to their low cost, simplicity, and practicability. With the rapid development of nanotechnology, compared with conventional diagnostic methods, nanomaterials with unique physical and chemical properties were applied to improve selectivity and sensitivity in colorimetric detection of cancer biomarkers, such as MUC1 aptamer conjugated PtAuNPs to specifically recognize MUC1 proteins on the cancer cell surfaces, etching of silver nanoprisms to detect prostate-specific antigen, and aggregation or dispersion of AuNPs to sense prostate cancer antigen gene 3 or glutathione, by which the limit of detection (LOD) could approach values down to a few cancer cells per mL, several fg per mL proteins, several ng of nucleic acids, or even tens of nM of organic molecules. Herein, we review the recent progress achieved in developing colorimetric nanosensors for cancer diagnosis, particularly providing an overview of the sensing principles, target biomarkers, advanced nanomaterials employed in the fabrication of sensing platforms, and strategies for improving signal sensitivity and specificity. Finally, we sum up the nanomaterial-based colorimetric cancer detection as well as existing challenges that should be resolved to extend their clinical application.
Collapse
Affiliation(s)
- Haixia Wang
- Laboratory of Biomaterials and Translational Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | | | | | | |
Collapse
|
6
|
Araiza-Olivera D, Gutierrez-Aguilar M, Espinosa-García AM, García-García JA, Tapia-Orozco N, Sánchez-Pérez C, Palacios-Reyes C, Escárcega D, Villalón-López DN, García-Arrazola R. From bench to bedside: Biosensing strategies to evaluate endocrine disrupting compounds based on epigenetic events and their potential use in medicine. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103450. [PMID: 32622887 DOI: 10.1016/j.etap.2020.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The relationship between endocrine system disorders and health risks due to chemical environmental compounds has become a growing concern in recent years. Involuntary exposure to endocrine disruptors (EDCs) is associated with the worldwide increase of diseases such as cancer, obesity, diabetes, and neurocortical disorders. EDCs are compounds that target the nuclear hormonereceptors (NHR) leading to epigenetic changes. Consequently, the use of biosensing strategies based on epigenetic events have a great potential to provide outstanding information about the exposition of EDCs and their evaluation in human health. This review addresses the novel trends in biosensing EDCs evaluation based on DNA methylation assays associated with different human diseases.
Collapse
Affiliation(s)
- D Araiza-Olivera
- Department of Chemistry and Biomolecules, Institute of Chemistry, UNAM, Mexico.
| | | | - A M Espinosa-García
- Unidad de Medicina Genómica, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - J A García-García
- Department of Education, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - N Tapia-Orozco
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Sánchez-Pérez
- Institute of Applied Sciences and Technology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Palacios-Reyes
- Laboratory of Genetics and Molecular Diagnostics, Juarez Hospital of Mexico, Mexico City, Mexico.
| | - D Escárcega
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Ciudad de México, calle del Puente 222, Ejidos de Huipulco, Tlalpan 14380, Mexico City, Mexico.
| | - Demelza N Villalón-López
- Instituto Politénico Nacional-Escuela Nacional de Ciencias Biológicas, Departamento de Química Orgánica, Prolongación de Carpio y Plande Ayala, colonia Casco de Santo Tomás. Del, Miguel Hidalgo, 11350, Mexico.
| | - R García-Arrazola
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| |
Collapse
|
7
|
Chen L, Zhang Y, Xia Q, Luo F, Guo L, Qiu B, Lin Z. Fluorescence biosensor for DNA methyltransferase activity and related inhibitor detection based on methylation-sensitive cleavage primer triggered hyperbranched rolling circle amplification. Anal Chim Acta 2020; 1122:1-8. [PMID: 32503739 DOI: 10.1016/j.aca.2020.04.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/20/2020] [Accepted: 04/25/2020] [Indexed: 11/29/2022]
Abstract
Highly sensitive and selective detection of DNA adenine methylation methyltransferase (Dam MTase) activity is essential for clinical diagnosis and treatment as Dam MTase can catalyze DNA methylation and has a profound effect on gene regulation. In this study, a fluorescence biosensor has been developed for label-free detection of Dam MTase activity via methylation-sensitive cleavage primers triggered hyperbranched rolling circle amplification (HRCA). A hairpin DNA probe (HP) with a Dam MTase specific recognition sequence on the stem acting as a substrate has been designed. This substrate probe can be methylated by the target in the system and subsequently cleaved by DpnI, which results in the release of the primer release probe (RP) and hence in turn triggers the subsequent HRCA reaction. As the HRCA products contain many double-strand DNA (dsDNA) with different lengths, and the SYBR Green I can be embedded in the dsDNA to produce a strong fluorescence signal. However, in the absence of the target, the presence of the probe HP in the form of a hairpin cannot induce the HRCA reaction, and only weak fluorescence intensity can be detected. Under the optimized conditions, the fluorescence of the system has a linear relationship with the logarithm of the concentration of Dam MTase in the range of 2.5-70 U/mL with a detection limit of 1.8 U/mL. The Dam MTase can be well distinguished from other MTase analogs. The developed sensor was applied to detect target in serum and E. coli cell lysate, and the standard recovery rates were in the range of 96%-105%. The results showed that this method has great potential for assessing Dam MTase activity in complex biological samples. In addition, the method has been applied to detect the related inhibitors with high efficiency.
Collapse
Affiliation(s)
- Liping Chen
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Ying Zhang
- Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350005, China
| | - Qian Xia
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Fang Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Longhua Guo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China.
| |
Collapse
|
8
|
Dadmehr M, Karimi MA, Korouzhdehi B. A signal-on fluorescence based biosensing platform for highly sensitive detection of DNA methyltransferase enzyme activity and inhibition. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117731. [PMID: 31753656 DOI: 10.1016/j.saa.2019.117731] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
DNA methylation mediated by DNA methyltransferase (MTase) enzyme is internal cell mechanism which regulate the expression or suppression of crucial genes involve in cancer early diagnosis. Herein, highly sensitive fluorescence biosensing platform was developed for monitoring of DNA Dam MTase enzyme activity and inhibition based on fluorescence signal on mechanism. The specific Au NP functionalized oligonucleotide probe with overhang end as a template for the synthesis of fluorescent silver nanoclusters (Ag NCs) was designed to provide the FRET occurrence. Following, methylation and cleavage processes by Dam MTAse and DpnI enzymes respectively at specific probe recognition site could resulted to release of AgNCs synthesizer DNA fragment and returned the platform to fluorescence signal-on state through interrupting in FRET. Subsequently, amplified fluorescence emission signals of Ag NCs showed increasing linear relationship with amount of Dam MTase enzyme at the range of 0.1-20 U/mL and the detection limit was estimated at 0.05 U/mL. Superior selectivity of experiment was illustrated among other tested MTase and restriction enzymes due to the specific recognition of MTase toward its substrate. Furthermore, the inhibition effect of applied Dam MTase drug inhibitors screened and evaluated with satisfactory results which would be helpful for discovery of antimicrobial drugs. The real sample assay also showed the applicability of proposed method in human serum condition. This novel strategy presented an efficient and cost effective platform for sensitive monitoring of DNA MTase activity and inhibition which illustrated its great potential for further application in medical diagnosis and drug discovery.
Collapse
Affiliation(s)
- Mehdi Dadmehr
- Department of Biology, Payame Noor University, Tehran, Iran.
| | | | | |
Collapse
|
9
|
Abrosimova LA, Kisil OV, Romanova EA, Oretskaya TS, Kubareva EA. Nicking Endonucleases as Unique Tools for Biotechnology and Gene Engineering. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019050017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
Li Y, Wang L, Ding C, Luo X. Highly selective ratiometric electrogenerated chemiluminescence assay of DNA methyltransferase activity via polyaniline and anti-fouling peptide modified electrode. Biosens Bioelectron 2019; 142:111553. [DOI: 10.1016/j.bios.2019.111553] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
|
11
|
Wang LJ, Luo ML, Yang XY, Li XF, Wu Y, Zhang CY. Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells. Am J Cancer Res 2019; 9:4450-4460. [PMID: 31285772 PMCID: PMC6599653 DOI: 10.7150/thno.35393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/17/2019] [Indexed: 11/24/2022] Open
Abstract
DNA alkylation and oxidation are two most common forms of cytotoxic damage with the characteristics of mutagenic and carcinogenic. Human alkyladenine DNA glycosylase (hAAG) is the only glycosylase known to repair a wide variety of alkylative and oxidative DNA lesions. However, few approaches are capable of real-time monitoring hAAG activity. Methods: Herein, we develop a facile fluorescent strategy for homogeneous and sensitive sensing of hAAG activity based on the controllable autocatalytic cleavage-mediated fluorescence recovery. The presence of hAAG enables the cleavage of hairpin probe 1 (HP1) at the damaged 2′-deoxyinosine site by AP endonuclease 1 (APE1), forming a DNA duplex. The trigger 1 built in the resultant DNA duplex may hybridize with hairpin probe 2 (HP2) to induce the T7 exonuclease (T7 exo)-catalyzed recycling cleavage of HP2 (Cycle I) to release trigger 2. The trigger 2 can further hybridize with the signal probe (a fluorophore (FAM) and a quencher (BHQ1) modified at its 5′ and 3′ ends) to induce the subsequent recycling cleavage of signal probes (Cycle II) to liberate FAM molecules. Through two-recycling autocatalytic cleavage processes, large amounts of fluorophore molecules (i.e., FAM) are liberated from the FAM-BHQ1 fluorescence resonance energy transfer (FRET) pair, leading to the amplified fluorescence recovery. Results: Taking advantage of the high accuracy of in vivo DNA repair mechanism, the high specificity of T7 exo-catalyzed mononucleotides hydrolysis, and the high efficiency of autocatalytic recycling amplification, this strategy exhibits high sensitivity with a detection limit of 4.9 × 10-6 U/μL and a large dynamic range of 4 orders of magnitude from 1 × 10-5 to 0.1 U/μL, and it can further accurately evaluate the enzyme kinetic parameters, screen the potential inhibitors, and even quantify the hAAG activity from 1 cancer cell. Conclusion: The proposed strategy can provide a facile and universal platform for the monitoring of DNA damage-related repair enzymes, holding great potential for DNA repair-related biochemical research, clinical diagnosis, drug discovery, and cancer therapy.
Collapse
|
12
|
Chen Y, Meng XZ, Gu HW, Yi HC, Sun WY. A dual-response biosensor for electrochemical and glucometer detection of DNA methyltransferase activity based on functionalized metal-organic framework amplification. Biosens Bioelectron 2019; 134:117-122. [DOI: 10.1016/j.bios.2019.03.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/16/2019] [Accepted: 03/26/2019] [Indexed: 11/16/2022]
|
13
|
Zhao H, Ma C, Yan Y, Chen M. A sensitive cyclic signal amplification fluorescence strategy for determination of methyltransferase activity based on graphene oxide and RNase H. J Mater Chem B 2019. [DOI: 10.1039/c9tb00743a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A sensitive fluorometric method for DNA methyltransferase activity detection based on graphene oxide and RNase H-assisted signal amplification.
Collapse
Affiliation(s)
- Han Zhao
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Changbei Ma
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Ying Yan
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Mingjian Chen
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| |
Collapse
|
14
|
Mittal S, Thakur S, Mantha AK, Kaur H. Bio-analytical applications of nicking endonucleases assisted signal-amplification strategies for detection of cancer biomarkers -DNA methyl transferase and microRNA. Biosens Bioelectron 2019; 124-125:233-243. [DOI: 10.1016/j.bios.2018.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022]
|
15
|
Bhattacharjee R, Moriam S, Umer M, Nguyen NT, Shiddiky MJA. DNA methylation detection: recent developments in bisulfite free electrochemical and optical approaches. Analyst 2018; 143:4802-4818. [PMID: 30226502 DOI: 10.1039/c8an01348a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is one of the significant epigenetic modifications involved in mammalian development as well as in the initiation and progression of various diseases like cancer. Over the past few decades, an enormous amount of research has been carried out for the quantification of DNA methylation in the mammalian genome. Earlier, most of these methodologies used bisulfite treatment. However, the low conversion, false reading, longer assay time and complex chemical reaction are the common limitations of this method that hinder their application in routine clinical screening. Thus, as an alternative to bisulfite conversion-based DNA methylation detection, numerous bisulfite-free methods have been proposed. In this regard, electrochemical biosensors have gained much attention in recent years for being highly sensitive yet cost-effective, portable, and simple to operate. On the other hand, biosensors with optical readouts enable direct real time detection of biological molecules and are easily adaptable to multiplexing. Incorporation of electrochemical and optical readouts into bisulfite free DNA methylation analysis is paving the way for the translation of this important biomarker into standard patient care. In this review, we provide a critical overview of recent advances in the development of electrochemical and optical readout based bisulfite free DNA methylation assays.
Collapse
Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
| | | | | | | | | |
Collapse
|
16
|
Zhang H, Wang LJ, Wang L, Chen H, Chen X, Zhang CY. Development of a cascade isothermal amplification approach for the sensitive detection of DNA methyltransferase. J Mater Chem B 2018; 7:157-162. [PMID: 32254960 DOI: 10.1039/c8tb02096e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methyltransferase (MTase) is an important epigenetic modification enzyme responsible for DNA methylation, and the dysregulation of DNA MTase activity is associated with various diseases in humans. Herein, we take advantage of the DNA lesion repair mechanism in vivo to develop a new fluorescence approach for the specific and sensitive detection of DNA methyltransferase (DNA MTase) on the basis of the DNA lesion repair-directed cascade isothermal amplification. Due to the high amplification efficiency of the uracil repair-mediated exponential isothermal amplification reaction (EXPAR), the efficient cleavage of endonuclease IV (Endo IV)-induced cyclic catalysis, and the low background signal caused by single uracil repair-mediated inhibition of nonspecific amplification, this approach exhibits high sensitivity with a detection limit of 0.014 U mL-1 for pure Dam MTase and 0.61 × 10-6 mg mL-1 for Dam MTase in E. coli cells and it can be further applied for the screening of DNA MTase inhibitors. More importantly, this approach can be applied to detect other DNA MTases by designing appropriate substrates, showing great potential in biomedical research and clinical diagnosis.
Collapse
Affiliation(s)
- Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | | | | | | | | | | |
Collapse
|
17
|
Niu L, Wang X, Mao G, Li Z, Ji X, He Z. Sensitive fluorescent detection of methyltransferase based on thermosensitive poly(N-isopropylacrylamide). Talanta 2018; 189:579-584. [PMID: 30086963 DOI: 10.1016/j.talanta.2018.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022]
Abstract
DNA methyltransferase (MTase) has a crucial role in many biological processes, its abnormal expression level has been regarded as a predictive cancer biomarker. Herein, a sensitive fluorescence method based on thermosensitive poly (N-isopr-opylacrylamide) was developed to assay of M.SssI activity. When the M.SssI was introduced, dsDNA was methylated at palindromic sequence 5'-CmCGG-3' and became resistant to cleavage by the endonuclease HpaII. Therefore, a biotin modified ssDNA and a FAM modified ssDNA were designed including the recognized sites for both methyltransferase M.SssI and endonuclease HpaII. By SA-biotin intereaction, the DNA was conjugated to thermosensitive poly (N-isopropylacrylamide) modified by SA, the methylated substrate fluorescence was increased with the concentration of M.SssI increasing. The proposed method has a low detection limit of 0.18 U/mL. This simple method can be a useful tool to apply in diagnosis and biomedical research, which was successfully investigated in the serum sample.
Collapse
Affiliation(s)
- Longqing Niu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinxin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Guobin Mao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zheng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
18
|
Amplification strategy for sensitive detection of methyltransferase activity based on surface plasma resonance techniques. Anal Chim Acta 2018. [DOI: 10.1016/j.aca.2018.02.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
19
|
Kermani HA, Hosseini M, Miti A, Dadmehr M, Zuccheri G, Hosseinkhani S, Ganjali MR. A colorimetric assay of DNA methyltransferase activity based on peroxidase mimicking of DNA template Ag/Pt bimetallic nanoclusters. Anal Bioanal Chem 2018; 410:4943-4952. [DOI: 10.1007/s00216-018-1143-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 01/31/2023]
|
20
|
Wang K, Feng M, He MQ, Zhai FH, Dai Y, He RH, Yu YL. DNA-fueled target recycling-induced two-leg DNA walker for amplified electrochemical detection of nucleic acid. Talanta 2018; 188:685-690. [PMID: 30029432 DOI: 10.1016/j.talanta.2018.06.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
Taking advantage of the homogeneous and heterogeneous electrochemical biosensors, a simple, sensitive, and selective electrochemical biosensor is constructed by combining entropy-driven amplification (EDA) with DNA walker. This electrochemical biosensor realizes the biorecognition and EDA operation in homogeneous solution, which is beneficial to improve the recognition and amplification efficiency. A two-leg DNA walker generated by EDA can walk on the surface of gold electrode for cleaving the immobilized substrate DNA and releasing the electroactive labels, giving rise to a significant decrease of the electrochemical signal. The immobilization of the electroactive labels ensures the reproducibility and reliability of the biosensor. The present cascade amplification assay can be applied to detect target DNA with a detection limit of 0.29 fM, and base mutations can be easily distinguished. Moreover, the proposed electrochemical biosensor shows a satisfactory performance for the detection of target DNA in human serum. Thus, the novel electrochemical biosensor holds promising potential for a future application in disease diagnosis.
Collapse
Affiliation(s)
- Kun Wang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Min Feng
- The first Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Meng-Qi He
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Fu-Heng Zhai
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yu Dai
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Rong-Huan He
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
| | - Yong-Liang Yu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
| |
Collapse
|
21
|
Huang Y, Xu W, Liu G, Tian L. A pure DNA hydrogel with stable catalytic ability produced by one-step rolling circle amplification. Chem Commun (Camb) 2018; 53:3038-3041. [PMID: 28239729 DOI: 10.1039/c7cc00636e] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A rolling-circle-amplification method was developed to produce DNA hydrogels with horseradish-peroxidase-like catalytic capability. The catalytic hydrogel exhibits highly improved stability at elevated temperatures or during a long-term storage. Integrated with glucose oxidase, the complex hydrogel can be applied to the sensitive and reliable detection of glucose.
Collapse
Affiliation(s)
- Yishun Huang
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Wanlin Xu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| |
Collapse
|
22
|
Commercial glucometer as signal transducer for simple evaluation of DNA methyltransferase activity and inhibitors screening. Anal Chim Acta 2018; 1001:18-23. [DOI: 10.1016/j.aca.2017.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
|
23
|
Zhou X, Zhao M, Duan X, Guo B, Cheng W, Ding S, Ju H. Collapse of DNA Tetrahedron Nanostructure for "Off-On" Fluorescence Detection of DNA Methyltransferase Activity. ACS APPLIED MATERIALS & INTERFACES 2017; 9:40087-40093. [PMID: 29111659 DOI: 10.1021/acsami.7b13551] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites. These sites can be recognized and cut by the restriction endonuclease DpnI to bring about the collapse of the DNA tetrahedron, which leads to the separation of the dual-labeled reporters from the quenchers, and thus the recovery of fluorescence signal to produce an "ON" state. The proposed DNA tetrahedron-based sensing method can detect Dam methyltransferase in the range of 0.1-90 U mL-1 with a detection limit of 0.045 U mL-1 and shows good specificity and reproducibility for detection of Dam methyltransferase in a real sample. It has been successfully applied for screening various methylation inhibitors. Thus, this work possesses a promising prospect for detection of DNA methyltransfrase in the field of clinical diagnostics.
Collapse
Affiliation(s)
- Xiaoyan Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
- Department of Clinical Laboratory, The Affiliated Hospital of Medical College, Qingdao University , Qingdao 266101, China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Xiaolei Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| |
Collapse
|
24
|
A label-free electrochemical biosensor for methyltransferase activity detection and inhibitor screening based on graphene quantum dot and enzyme-catalyzed reaction. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.06.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
25
|
Gao F, Fan T, Ou S, Wu J, Zhang X, Luo J, Li N, Yao Y, Mou Y, Liao X, Geng D. Highly efficient electrochemical sensing platform for sensitive detection DNA methylation, and methyltransferase activity based on Ag NPs decorated carbon nanocubes. Biosens Bioelectron 2017; 99:201-208. [PMID: 28759870 DOI: 10.1016/j.bios.2017.07.063] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022]
Abstract
In this paper, we reported a sensitive and selective electrochemical method for quantify DNA methylation, analyzing DNA MTase activity and screening of MTase inhibitor based on silver nanoparticles (Ag NPs) decorated carbon nanocubes (CNCs) as signal tag. The Ag NPs/CNCs was prepared by in situ growth of nanosilver on carboxylated CNCs and used as a tracing tag to label antibody. The sensor was prepared by immobilizing the double DNA helix structure on the surface of gold electrode. When DNA MTase was introduced, the probe was methylated. Successively, anti-5-methylcytosine antibody labeled Ag NPs/CNCs was specifically conjugated on the CpG methylation site. The electrochemical stripping signal of the Ag NPs was used to monitor the activity of MTase. The electrochemical signal has a linear relationship with M.SssI activities ranging from 0.05 to 120U/mL with a detection limit of 0.03U/mL. In addition, we also demonstrated the method could be used for rapid evaluation and screening of the inhibitors of MTase. The newly designed strategy avoid the requirement of deoxygenation for electrochemical assay, and thus provide a promising potential in clinical application.
Collapse
Affiliation(s)
- Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China; Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Taotao Fan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Shanshan Ou
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Jing Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Xing Zhang
- The Graduate School, Xuzhou Medical University, 221004 Xuzhou, China
| | - Jianjun Luo
- The Graduate School, Xuzhou Medical University, 221004 Xuzhou, China
| | - Na Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Yao Yao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Yingfeng Mou
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Xianjiu Liao
- School of Pharmacy, Youjiang Medical University for Nationalities, 533000 Baise, China.
| | - Deqin Geng
- The Graduate School, Xuzhou Medical University, 221004 Xuzhou, China; Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China.
| |
Collapse
|
26
|
Chen S, Ma H, Li W, Nie Z, Yao S. An entropy-driven signal amplifying strategy for real-time monitoring of DNA methylation process and high-throughput screening of methyltransferase inhibitors. Anal Chim Acta 2017; 970:57-63. [DOI: 10.1016/j.aca.2017.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/31/2022]
|
27
|
Huang J, Li XY, Du YC, Zhang LN, Liu KK, Zhu LN, Kong DM. Sensitive fluorescent detection of DNA methyltransferase using nicking endonuclease-mediated multiple primers-like rolling circle amplification. Biosens Bioelectron 2016; 91:417-423. [PMID: 28063390 DOI: 10.1016/j.bios.2016.12.061] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/29/2016] [Indexed: 11/19/2022]
Abstract
Sensitive and reliable detection of DNA methyltransferase (MTase) is of great significance for both early tumor diagnosis and therapy. In this study, a simple, label-free and sensitive DNA MTase-sensing method was developed on the basis of a nicking endonuclease-mediated multiple primers-like rolling circle amplification (RCA) strategy. In this method, a dumbbell RCA template was prepared by blunt-end ligation of two molecules of hairpin DNA. In addition to the primer-binding sequence, the dumbbell template contained another three important parts: 5'-CCGG-3' sequences in double-stranded stems, nicking endonuclease recognition sites and C-rich sequences in single-stranded loops. The introduction of 5'-CCGG-3' sequences allows the dumbbell template to be destroyed by the restriction endonuclease, HpaII, but is not destroyed in the presence of the target MTase-M.SssI MTase. The introduction of nicking endonuclease recognition sites makes the M.SssI MTase-protected dumbbell template-mediated RCA proceed in a multiple primers-like exponential mode, thus providing the RCA with high amplification efficiency. The introduction of C-rich sequences may promote the folding of amplification products into a G-quadruplex structure, which is specifically recognized by the commercially available fluorescent probe thioflavin T. Improved RCA amplification efficiency and specific fluorescent recognition of RCA products provide the M.SssI MTase-sensing platform with high sensitivity. When a dumbbell template containing four nicking endonuclease sites is used, highly specific M.SssI MTase activity detection can be achieved in the range of 0.008-50U/mL with a detection limit as low as 0.0011U/mL. Simple experimental operation and mix-and-detection fluorescent sensing mode ensures that M.SssI MTase quantitation works well in a real-time RCA mode, thus further simplifying the sensing performance and making high throughput detection possible. The proposed MTase-sensing strategy was also demonstrated to be applicable for screening and evaluating the inhibitory activity of MTase inhibitors.
Collapse
Affiliation(s)
- Juan Huang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China
| | - Li-Na Zhang
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Ke-Ke Liu
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Li-Na Zhu
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China.
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China.
| |
Collapse
|
28
|
Li X, Meng M, Zheng L, Xu Z, Song P, Yin Y, Eremin SA, Xi R. Chemiluminescence Immunoassay for S-Adenosylhomocysteine Detection and Its Application in DNA Methyltransferase Activity Evaluation and Inhibitors Screening. Anal Chem 2016; 88:8556-61. [DOI: 10.1021/acs.analchem.6b01579] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiaogang Li
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Meng Meng
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Lei Zheng
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Zhihuan Xu
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Pei Song
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Yongmei Yin
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Sergei A. Eremin
- Faculty
of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Rimo Xi
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| |
Collapse
|
29
|
Zhang L, Liu Y, Li Y, Zhao Y, Wei W, Liu S. Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy. Anal Chim Acta 2016; 933:75-81. [DOI: 10.1016/j.aca.2016.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022]
|
30
|
DNA methyltransferase detection based on digestion triggering the combination of poly adenine DNA with gold nanoparticles. Biosens Bioelectron 2016; 80:74-78. [DOI: 10.1016/j.bios.2015.12.100] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/27/2015] [Accepted: 12/28/2015] [Indexed: 01/29/2023]
|
31
|
Liu P, Zhang K, Zhang R, Yin H, Zhou Y, Ai S. A colorimetric assay of DNA methyltransferase activity based on the keypad lock of duplex DNA modified meso-SiO2@Fe3O4. Anal Chim Acta 2016; 920:80-5. [DOI: 10.1016/j.aca.2016.03.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/08/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
|
32
|
Ma C, Liu H, Li W, Chen H, Jin S, Wang J, Wang J. Label-free monitoring of DNA methyltransferase activity based on terminal deoxynucleotidyl transferase using a thioflavin T probe. Mol Cell Probes 2016; 30:118-21. [DOI: 10.1016/j.mcp.2016.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/09/2016] [Accepted: 02/02/2016] [Indexed: 01/17/2023]
|
33
|
Jin S, Liu H, Xia K, Ma C, He H, Wang K. Real-time monitoring of DNA methyltransferase activity using a hemimethylated smart probe. Mol Cell Probes 2016; 30:185-7. [PMID: 27039360 DOI: 10.1016/j.mcp.2016.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 01/20/2023]
Abstract
A real-time assay for DNA methyltransferase (MTase) activity has been developed. A hemimethylated smart probe is used as the substrate for DNA MTase. Cleavage of the methylated product leads to separation of fluorophore from quencher, giving a proportional increase in fluorescence. The method permits real-time monitoring of DNA methylation process and makes it easy to characterize the activity of DNA MTase. It also has the potential to screen suitable inhibitor drugs for DNA MTase.
Collapse
Affiliation(s)
- Shunxin Jin
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Haisheng Liu
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China; State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China.
| | - Hailun He
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China
| |
Collapse
|
34
|
Cui W, Wang L, Jiang W. A dual amplification fluorescent strategy for sensitive detection of DNA methyltransferase activity based on strand displacement amplification and DNAzyme amplification. Biosens Bioelectron 2016; 77:650-5. [DOI: 10.1016/j.bios.2015.10.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
|
35
|
Chen F, Zhang D, Zhang Q, Zuo X, Fan C, Zhao Y. Zero-Background Helicase-Dependent Amplification and Its Application to Reliable Assay of Telomerase Activity in Cancer Cell by Eliminating Primer-Dimer Artifacts. Chembiochem 2016; 17:1171-6. [PMID: 26690725 DOI: 10.1002/cbic.201500605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Indexed: 11/09/2022]
Abstract
Primer-dimer artifacts resulting from unintended template-independent primer-primer interactions often hinder the specific amplification of nucleic acids. We demonstrate, for the first time, zero-background helicase-dependent amplification (HDA), with low concentrations of both ATP and dNTPs. This strategy achieved the reliable evaluation of telomerase activity in cancer cells by eliminating primer-dimer artifacts, which have plagued many previous methods with reduced specificity. We found that the performance of the telomerase assay by zero-background HDA was negatively affected by highly concentrated cellular proteins. This inhibitory effect is attributed to the binding of DNA templates to proteins, thus making them unavailable for polymerases. However, gold nanoparticles were demonstrated to highly attenuate such inhibition by abundant proteins, and to enhance the assay sensitivity and reliability when the reaction was performed with concentrated cell extracts.
Collapse
Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi, 710049, P. R. China
| | - Dexin Zhang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xiwu Road, Xi'an, Shaanxi, 710049, P. R. China
| | - Qing Zhang
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi, 710049, P. R. China
| | - Xiaolei Zuo
- Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Yuquan Road, Shanghai, 201800, P. R. China
| | - Chunhai Fan
- Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Yuquan Road, Shanghai, 201800, P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi, 710049, P. R. China.
| |
Collapse
|
36
|
Poh WJ, Wee CPP, Gao Z. DNA Methyltransferase Activity Assays: Advances and Challenges. Am J Cancer Res 2016; 6:369-91. [PMID: 26909112 PMCID: PMC4737724 DOI: 10.7150/thno.13438] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/12/2015] [Indexed: 12/28/2022] Open
Abstract
DNA methyltransferases (MTases), a family of enzymes that catalyse the methylation of DNA, have a profound effect on gene regulation. A large body of evidence has indicated that DNA MTase is potentially a predictive biomarker closely associated with genetic disorders and genetic diseases like cancer. Given the attention bestowed onto DNA MTases in molecular biology and medicine, highly sensitive detection of DNA MTase activity is essential in determining gene regulation, epigenetic modification, clinical diagnosis and therapeutics. Conventional techniques such as isotope labelling are effective, but they often require laborious sample preparation, isotope labelling, sophisticated equipment and large amounts of DNA, rendering them unsuitable for uses at point-of-care. Simple, portable, highly sensitive and low-cost assays are urgently needed for DNA MTase activity screening. In most recent technological advances, many alternative DNA MTase activity assays such as fluorescent, electrochemical, colorimetric and chemiluminescent assays have been proposed. In addition, many of them are coupled with nanomaterials and/or enzymes to significantly enhance their sensitivity. Herein we review the progress in the development of DNA MTase activity assays with an emphasis on assay mechanism and performance with some discussion on challenges and perspectives. It is hoped that this article will provide a broad coverage of DNA MTase activity assays and their latest developments and open new perspectives toward the development of DNA MTase activity assays with much improved performance for uses in molecular biology and clinical practice.
Collapse
|
37
|
Zhao H, Yin H, Yang Y. Label-free electrochemical detection of DNA methyltransferase activity via a DNA tetrahedron-structured probe. RSC Adv 2016. [DOI: 10.1039/c6ra01845a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Label-free electrochemical detection of DNA methyltransferase activityviaDNA tetrahedron-structured probe.
Collapse
Affiliation(s)
- Hongyu Zhao
- The Second Hospital of Nanjing
- Affiliated to Medical School of Southeast University
- Nanjing
- China
| | - Hai Yin
- Chinese People's Liberation Army 454 Hospital
- Nanjing
- China
| | - Yongfeng Yang
- The Second Hospital of Nanjing
- Affiliated to Medical School of Southeast University
- Nanjing
- China
| |
Collapse
|
38
|
Zhao H, Wang L, Jiang W. Target-protected dumbbell molecular probe mediated cascade rolling circle amplification strategy for the sensitive assay of DNA methyltransferase activity. Chem Commun (Camb) 2016; 52:2517-20. [DOI: 10.1039/c5cc09147k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel fluorescence detection system is developed for DNA methyltransferase activity assay based on target-protected dumbbell molecular probe mediated cascade rolling circle amplification strategy.
Collapse
Affiliation(s)
- Haiyan Zhao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Lei Wang
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
- P. R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| |
Collapse
|
39
|
Liu Z, Lei C, Deng H, Lu G, Huang Y, Yao S. Sensitive and versatile fluorescent enzymatic assay of nucleases and DNA methyltransferase based on a supercharged fluorescent protein. RSC Adv 2016. [DOI: 10.1039/c6ra02711c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ScGFP-based platform takes advantage of the DNA length-dependent binding affinity between ScGFP and DNA for multiple DNA enzyme detection including nucleases and DNA MTase.
Collapse
Affiliation(s)
- Zhuoliang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Honghua Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Guoyan Lu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| |
Collapse
|
40
|
Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
Collapse
Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
| |
Collapse
|
41
|
Label-free electrochemical detection of methyltransferase activity and inhibitor screening based on endonuclease HpaII and the deposition of polyaniline. Biosens Bioelectron 2015; 73:188-194. [DOI: 10.1016/j.bios.2015.05.066] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 11/22/2022]
|
42
|
Li W, Liu X, Hou T, Li H, Li F. Ultrasensitive homogeneous electrochemical strategy for DNA methyltransferase activity assay based on autonomous exonuclease III-assisted isothermal cycling signal amplification. Biosens Bioelectron 2015; 70:304-9. [DOI: 10.1016/j.bios.2015.03.060] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 12/13/2022]
|
43
|
Chen J, Zhou G, Liu Y, Ye T, Xiang X, Ji X, He Z. Assembly-line manipulation of droplets in microfluidic platform for fluorescence encoding and simultaneous multiplexed DNA detection. Talanta 2015; 134:271-277. [DOI: 10.1016/j.talanta.2014.11.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/23/2022]
|
44
|
Hu Y, Zhang L, Zhang Y, Wang B, Wang Y, Fan Q, Huang W, Wang L. Plasmonic nanobiosensor based on hairpin DNA for detection of trace oligonucleotides biomarker in cancers. ACS APPLIED MATERIALS & INTERFACES 2015; 7:2459-66. [PMID: 25546579 DOI: 10.1021/am507218g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs), a class of small, endogenous, noncoding RNA molecules, can serve as biomarkers for potential applications in cancer diagnosis, prognosis, and prediction due to its abnormal expression. As a result, a novel label-free biosensor with nanometer scale was prepared and employed in the detection of trace oligonucleotides based on the localized surface plasmon resonance (LSPR). The dielectric constant on the surface of DNA modified gold nanoparticle would change when probe single-strand DNA hybridized with target oligonucleotides, which resulted in the notable red shift of scattering peak position. The biosensor with excellent selectivity can be used in a real-time monitoring hybridization process. Notably, this method provided label-free detection of DNA and miRNA at single nanoparticle level with limit of detection up to 3 nM. Due to the advantages of LSPR scattering spectra, single nanoparticle biosensor can be designed for trace cancer-relevant miRNAs detection in the future.
Collapse
Affiliation(s)
- Yanling Hu
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials, National Jiangsu Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Zhao HF, Liang RP, Wang JW, Qiu JD. One-pot synthesis of GO/AgNPs/luminol composites with electrochemiluminescence activity for sensitive detection of DNA methyltransferase activity. Biosens Bioelectron 2015; 63:458-464. [DOI: 10.1016/j.bios.2014.07.079] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/27/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
|
46
|
Ma Y, Chen L, Zhang L, Liao S, Zhao J. A sensitive strategy for the fluorescence detection of DNA methyltransferase activity based on the graphene oxide platform and T7 exonuclease-assisted cyclic signal amplification. Analyst 2015; 140:4076-82. [DOI: 10.1039/c5an00417a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A sensitive fluorescence detection method for DNA methyltransferase is developed based on graphene oxide and T7 exonuclease-assisted signal amplification.
Collapse
Affiliation(s)
- Yefei Ma
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry
- Guangxi Normal University
- Guilin
- China
| | - Lini Chen
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry
- Guangxi Normal University
- Guilin
- China
| | - Liangliang Zhang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry
- Guangxi Normal University
- Guilin
- China
| | - Suqi Liao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry
- Guangxi Normal University
- Guilin
- China
| | - Jingjin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry
- Guangxi Normal University
- Guilin
- China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Conservation of Education Ministry
| |
Collapse
|
47
|
Liu Y, Wei M, Zhang L, Wei W, Zhang Y, Liu S. Evaluation of DNA methyltransferase activity and inhibition via chiroplasmonic assemblies of gold nanoparticles. Chem Commun (Camb) 2015; 51:14350-3. [DOI: 10.1039/c5cc05375g] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MTase activity is detected based on the chiroplasmonic assemblies of gold nanoparticles and endonuclease HpaII.
Collapse
Affiliation(s)
- Yuanjian Liu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| | - Min Wei
- College of Food Science and Technology
- Henan University of Technology
- Zhengzhou
- China
| | - Linqun Zhang
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| | - Wei Wei
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| | - Yuanjian Zhang
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| | - Songqin Liu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| |
Collapse
|
48
|
Zeng S, Huang H, Huang Y, Liu X, Qin J, Zhao S, Chen ZF, Liang H. Label-free and amplified colorimetric assay of ribonuclease H activity and inhibition based on a novel enzyme-responsive DNAzyme cascade. RSC Adv 2015. [DOI: 10.1039/c5ra05712d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A simple, label-free and amplified colorimetric assay strategy based on a novel enzyme-responsive DNAzyme cascade is developed for assay of ribonuclease H activity and inhibition. This assay exhibits high sensitivity and selectivity.
Collapse
Affiliation(s)
- Shulan Zeng
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
| | - Huakui Huang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Yong Huang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Xiaoqian Liu
- College of Chemistry and Pharmacy
- Guangxi Normal University
- Guilin
- China
| | - Jian Qin
- College of Chemistry and Pharmacy
- Guangxi Normal University
- Guilin
- China
| | - Shulin Zhao
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Zhen-Feng Chen
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
| | - Hong Liang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| |
Collapse
|
49
|
Wei W, Gao C, Xiong Y, Zhang Y, Liu S, Pu Y. A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII. Talanta 2015; 131:342-7. [DOI: 10.1016/j.talanta.2014.07.094] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 07/25/2014] [Accepted: 07/30/2014] [Indexed: 01/07/2023]
|
50
|
Zhang Y, Xu WJ, Zeng YP, Zhang CY. Sensitive detection of DNA methyltransferase activity by transcription-mediated duplex-specific nuclease-assisted cyclic signal amplification. Chem Commun (Camb) 2015; 51:13968-71. [DOI: 10.1039/c5cc05922d] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We develop transcription-mediated duplex-specific nuclease-assisted cyclic signal amplification for sensitive detection of DNA methyltransferase activity.
Collapse
Affiliation(s)
- Yan Zhang
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| | - Wen-jing Xu
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| | - Ya-ping Zeng
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| |
Collapse
|