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Huang Y, Zhao Z, Yi G, Zhang M. Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays. J Mater Chem B 2024; 12:4063-4079. [PMID: 38572575 DOI: 10.1039/d3tb02947f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.
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Affiliation(s)
- Yuqi Huang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
| | - Zixin Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Gang Yi
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Mingjun Zhang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
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2
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Wang T, Tan HS, Wang AJ, Li SS, Feng JJ. Fluorescent metal nanoclusters: From luminescence mechanism to applications in enzyme activity assays. Biosens Bioelectron 2024; 257:116323. [PMID: 38669842 DOI: 10.1016/j.bios.2024.116323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/09/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
Metal nanoclusters (MNCs) have outstanding fluorescence property and biocompatibility, which show widespread applications in biological analysis. Particularly, evaluation of enzyme activity with the fluorescent MNCs has been developed rapidly within the past several years. In this review, we first introduced the fluorescent mechanism of mono- and bi-metallic nanoclusters, respectively, whose interesting luminescence properties are mainly resulted from electron transfer between the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels. Meanwhile, the charge migration within the structure occurs through ligand-metal charge transfer (LMCT) or ligand-metal-metal charge transfer (LMMCT). On such foundation, diverse enzyme activities were rigorously evaluated, including three transferases and nine hydrolases, in turn harvesting rapid research progresses within past 5 years. Finally, we summarized the design strategies for evaluating enzyme activity with the MNCs, presented the major issues and challenges remained in the relevant research, coupled by showing some improvement measures. This review will attract researchers dedicated to the studies of the MNCs and provide some constructive insights for their further applications in enzyme analysis.
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Affiliation(s)
- Tong Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Hong-Sheng Tan
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Ai-Jun Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Shan-Shan Li
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao, 266071, China.
| | - Jiu-Ju Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China.
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3
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Du Z, Zhu L, Wang P, Lan X, Lin S, Xu W. Coordination-Driven One-Step Rapid Self-Assembly Synthesis of Dual-Functional Ag@Pt Nanozyme. Small 2023; 19:e2301048. [PMID: 37078838 DOI: 10.1002/smll.202301048] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/16/2023] [Indexed: 05/03/2023]
Abstract
Realizing high-precise and adjustable regulation of engineering nanozyme is important in nanotechnology. Here, Ag@Pt nanozymes with excellent peroxidase-like and antibacterial effects are designed and synthesized by nucleic acid and metal ions coordination-driven one-step rapid self-assembly. The adjustable NA-Ag@Pt nanozyme is synthesized within 4 min using single-stranded nucleic acid as templates, and peroxidase-like enhancing FNA-Ag@Pt nanozyme is received by regulating functional nucleic acids (FNA) based on NA-Ag@Pt nanozyme. Both Ag@Pt nanozymes that are developed not only has simple and general synthesis approaches, but also can produce artificial precise adjustment and possess dual-functional. Moreover, when lead ion-specific aptamers as FNA are introduced to NA-Ag@Pt nanozyme, the Pb2+ aptasensor is successfully constructed by increasing electron conversion efficiency and improving the specificity of nanozyme. In addition, both nanozyme has good antibacterial properties, with ~100% and ~85% antibacterial efficiency against Escherichia coli and Staphylococcus aureus, respectively. This work provides a synthesis method of novelty dual-functional Ag@Pt nanozymes and successful application in metal ions detection and antibacterial agents.
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Affiliation(s)
- Zaihui Du
- Food Laboratory of Zhongyuan, and Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, and Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Pengfei Wang
- Food Laboratory of Zhongyuan, and Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, and Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Shenghao Lin
- Food Laboratory of Zhongyuan, and Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, and Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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4
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Mousavizadegan M, Hosseini M, Sheikholeslami MN, Hamidipanah Y, Reza Ganjali M. Smartphone image analysis-based fluorescence detection of tetracycline using machine learning. Food Chem 2023; 403:134364. [DOI: 10.1016/j.foodchem.2022.134364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022]
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5
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Wang C, Guo Z, Tian R, Zhang K, Wang H, Li F, Shi H, Wang Z. Ratiometric Electrochemical Biosensing of Methyltransferase Activity. Catalysts 2022; 12:1362. [DOI: 10.3390/catal12111362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).
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Alaei A, Hosseini M, Nemati F, Karimi-Maleh H. The synthesis of Pt doped WO 3 nanosheets and application on colorimetric detection of cysteine by naked eye using response surface methodology for optimization. Environ Res 2022; 212:113246. [PMID: 35398080 DOI: 10.1016/j.envres.2022.113246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
We present a simple, sensitive, and specific colorimetric using the peroxidase properties method based on Pt doped WO3 nanosheets to detect the cysteine. Pt@WO3NSs were synthesized by hydrothermal method and characterized by Fourier transform infrared (FTIR), Transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), and X-ray diffraction patterns (XRD) methods. The response surface methodology (RSM) method based on the central composite design (CCD) was used to optimize test parameters such as pH, nanosheet concentration, and temperature. When cysteine is present in the environment due to its competition with 3,3', 5,5'-Tetramethylbenzidine (TMB) in the use of hydrogen peroxide, the blue discoloration is reduced compared to the absence of cysteine and leads to its detection. We have favorably created a peculiar approach for sensing cysteine based on the colorimetric method in solution and paper with linear range 0.01-15 μM, 0.005-14 μM and R2 = 0.9887 and R2 = 0.9871 respectively. The detection limit for solution-based is 1.2 nM and for paper-based is 1 nM.
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Affiliation(s)
- Aida Alaei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran; Medical Biomaterials Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Fatemeh Nemati
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Hassan Karimi-Maleh
- School of Resources and Environment, University of Electronic Science and Technology of China, P.O. Box 611731, Xiyuan Ave, Chengdu, PR China; Department of Chemical Engineering, Quchan University of Technology, Quchan, Iran; Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, 2028, Johannesburg, South Africa.
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7
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Alaei A, Hosseini M, Shokri E, Ganjali MR. Peroxidase Effect of Ce 2 (WO 4 ) 3 Nanoparticles to Detection of Glucose as a Colorimetric Sensor. ChemistrySelect 2022; 7. [DOI: 10.1002/slct.202104389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Zhang L, Zhao X, Hu X, Zhang Y, Liu R, Peng H, Chen Y, Zhang H, Luo Y. Probing low abundant DNA methylation by CRISPR-Cas12a-assisted cascade exponential amplification. Analyst 2022; 147:2655-2661. [PMID: 35579071 DOI: 10.1039/d2an00170e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aberrant DNA methylation plays a pivotal role in tumor development and metastasis, and is regarded as a valuable non-invasive cancer biomarker. However, the sensitive and accurate quantification of DNA methylation from clinical samples remains a challenge. Herein, we propose an easy-to-operate Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system Assisted Methylation (CAM) approach for the sensitive detection of DNA methylation through the integration of rolling circle amplification and CRISPR-Cas12a-assisted cascade amplification. Briefly, bisulfite was employed to prepare the clinical samples so that the methylated DNA sequences trigger the subsequent triple signal amplifications, whilst the normal counterparts do not. The triple signal amplification procedure consists of methylated DNA sequence-based rolling circle amplification for a preliminary signal enhancement, a nicking enzyme-initiated target cleavage for a secondary amplification, and CRISPR-Cas12a enzyme-mediated trans-cleavage for a tertiary signal enhancement. This proposed approach reveals high sensitivity, which can even distinguish as low as 0.01% methylation levels from mixtures, paving the way towards the acceleration of methylation-based cancer diagnostics and management.
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Affiliation(s)
- Liangliang Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China. .,Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, College of Bioengineering, Chongqing University, Chongqing 400044, P.R. China
| | - Xianxian Zhao
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China.
| | - Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China. .,Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, College of Bioengineering, Chongqing University, Chongqing 400044, P.R. China
| | - Yi Zhang
- Zhejiang Provincial People's Hospital, Hangzhou, 310014, PR. China
| | - Ruining Liu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China.
| | - Hai Peng
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China.
| | - Youhao Chen
- Department of Orthopaedics, Three Gorges Hospital, Chongqing University, Chongqing, 404100, PR. China
| | - Hong Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China. .,Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, P.R. China.
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400030, P.R. China. .,Department of Clinical Laboratory, Fuling Hospital, Chongqing University, Chongqing 408099, P.R. China.
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9
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Jiang C, Bai Z, Yuan F, Ruan Z, Wang W. A colorimetric sensor based on Glutathione-AgNPs as peroxidase mimetics for the sensitive detection of Thiamine (Vitamin B1). Spectrochim Acta A Mol Biomol Spectrosc 2022; 265:120348. [PMID: 34507032 DOI: 10.1016/j.saa.2021.120348] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/31/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
A label-free sensing strategy based on the enzyme-mimicking property of Glutathione-Ag nanoparticles (GSH-AgNPs) was demonstrated for colorimetric detection of vitamin B1 (VB1). Firstly, obvious blue color accompanied with an absorption peak at 652 nm was observed due to the high peroxidase-like activity of GSH-AgNPs towards 3,3',5,5'-tetramethylbenzidine (TMB). Then, in the presence of VB1, the mimetic activity of GSH-AgNPs could be strongly restrained, evidenced as a promiment colorimetric change to colorless, which can be used to achieve the visualization detection VB1. Linear relationship between absorbance response and VB1 concentration from 0 to 0.2 µM were obtained. The detection limit was calculated as low as 40 nM. The inhibition reasons were thoroughly discussed. Considering the advantages of rapid response, easy procedure and high selectivity, the proposed method possesses potential application in environment and biological analysis for VB1 detection.
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Affiliation(s)
- Cuifeng Jiang
- School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Ziyan Bai
- School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Fan Yuan
- School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Zhifan Ruan
- School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu 224051, China
| | - Wei Wang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu 224051, China.
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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11
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Bagheri Pebdeni A, Mousavizadegan M, Hosseini M. Sensitive detection of S. Aureus using aptamer- and vancomycin -copper nanoclusters as dual recognition strategy. Food Chem 2021; 361:130137. [PMID: 34051601 DOI: 10.1016/j.foodchem.2021.130137] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023]
Abstract
The proposed aptamer- and antibiotic-based dual detection sensor, combines copper nanoclusters (CuNCs) as an effective approach for the recognition and quantification of Staphylococcus aureus (S. aureus) as a pathogenic bacteria. A facile method for CuNCs based on vancomycin as the template using a fluorescence platform was proposed for the recognition of the S. aureus whole cells via antibiotic and aptamer. Using dual receptor functionalized CuNCs linked to vancomycin and a specific aptamer and during aggregation induce emission process enhanced fluorescence signal linearly with S. aureus concentrations between 102-108 CFU/mL, and the detection limit was 80 CFU/mL after 45 min as the optimum incubation time. Non-target bacteria generated negative results, proving the high specificity of the presented sensor. This strategy showed recoveries ranging 86%-98% in milk as real sample and can be used for the development of universal detection platforms for efficient and specific S. aureus detection with great potential applications for monitoring pathogenic bacteria.
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Affiliation(s)
- Azam Bagheri Pebdeni
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Maryam Mousavizadegan
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran; Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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Zhu S, Liu L, Sun J, Shi F, Zhao XE. A ratiometric fluorescence assay for bleomycin based on dual-emissive chameleon DNA-templated silver nanoclusters. Spectrochim Acta A Mol Biomol Spectrosc 2021; 252:119521. [PMID: 33581576 DOI: 10.1016/j.saa.2021.119521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/26/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
The authors design dual-emissive DNA-templated silver nanoclusters (DNA-AgNCs) for ratiometric fluorescence sensing bleomycin (BLM) for the first time. A hairpin probe containing two different C-rich DNA templates at two terminals is used to synthesize chameleon DNA-AgNCs, which possess two emission peaks when they are in close proximity. A strong emission is founded at 622 nm (λex = 570 nm) while a weak one is located at 572 nm (λex = 504 nm). Meanwhile, the loop of this probe contains the scission site (5'-GC-3') of BLM. The loop can be cleaved into two parts by BLM-Fe(II) complex, inducing the two DNA-AgNCs away from each other. The fluorescence intensity at 572 nm and 622 nm increases and decreases, respectively. Such chameleon DNA-AgNCs exhibit an obvious fluorescence discoloration from orange to yellow. Therefore, a sensitive ratiometric fluorescent strategy for BLM detection has been proposed with the detection limit of 67 pM. Finally, this ratiometric method is used to detect BLM in serum samples.
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Affiliation(s)
- Shuyun Zhu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Lingyuan Liu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Jing Sun
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Fengjin Shi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China.
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Abstract
Since the discovery of the enzyme-like activities of nanomaterials, the study of nanozymes has become one of the most popular research frontiers of diverse areas including biosensors. DNA also plays a very important role in the construction of biosensors. Thus, the idea of combined applications of nanozymes with DNA (DNA-nanozyme) is very attractive for the development of nanozyme-based biosensors, which has attracted considerable interest of researchers. To date, many sensors based on DNA-functionalized or templated nanozymes have been reported for the detection of various targets and highly accelerated the development of nanozyme-based sensors. In this review, we summarize the main applications and advances of DNA-nanozyme-based sensors. Additionally, perspectives and challenges are also discussed at the end of the review.
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Affiliation(s)
- Renzhong Yu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Rui Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zhaoyin Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Qinshu Zhu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China. and Nanjing Normal University Centre for Analysis and Testing, Nanjing, 210023, P.R. China
| | - Zhihui Dai
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China. and Nanjing Normal University Centre for Analysis and Testing, Nanjing, 210023, P.R. China
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14
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Tarokh A, Pebdeni AB, Othman HO, Salehnia F, Hosseini M. Sensitive colorimetric aptasensor based on g-C3N4@Cu2O composites for detection of Salmonella typhimurium in food and water. Mikrochim Acta 2021; 188. [DOI: 10.1007/s00604-021-04745-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/03/2021] [Indexed: 12/28/2022]
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15
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Bagheri pebdeni A, Hosseini M. Fast and selective whole cell detection of Staphylococcus aureus bacteria in food samples by paper based colorimetric nanobiosensor using peroxidase-like catalytic activity of DNA-Au/Pt bimetallic nanoclusters. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105475] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Mesgari F, Beigi SM, Fakhri N, Hosseini M, Aghazadeh M, Ganjali MR. Paper-based chemiluminescence and colorimetric detection of cytochrome c by cobalt hydroxide decorated mesoporous carbon. Microchem J 2020; 157:104991. [DOI: 10.1016/j.microc.2020.104991] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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18
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Cao X, Xia Z, Yan W, He S, Xu X, Wei Z, Ye Y, Zheng H. Colorimetric biosensing of nopaline synthase terminator using Fe 3O 4@Au and hemin-functionalized reduced graphene oxide. Anal Biochem 2020; 602:113798. [PMID: 32505706 DOI: 10.1016/j.ab.2020.113798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022]
Abstract
In this paper, we present a simple and label-free colorimetric biosensor for detection of the nopaline synthase (NOS) terminator in genetically modified (GM) plants. The "signal on" colorimetric biosensor was developed using a nanocomposite consisted of gold nanoparticles doped magnetic Fe3O4 nanoparticles (Fe3O4@Au NP), capture probe DNA (cDNA), and hemin-functionalized reduced graphene oxide nanosheets (H-GN). The nanocomposite was successfully prepared by means of Au-S bonds and the strong π interactions between cDNA and H-GN. The sensing approach is based on the excellent peroxidase-mimicking activity of H-GN and its different electrostatic interactions with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). In presence of the target NOS, the cDNA in the nanocomposite will hybridize with its complementary sequence, and form dsDNA structure. Due to the weak π interactions between dsDNA and H-GN, a portion of H-GN will be released from the surface of Fe3O4@Au NPs and transferred into solution. After magnetic separation was performed, the supernatant was incubated with 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H2O2. The released H-GN can catalyze the oxidation reaction of TMB and turn the colorless solution blue. This "signal-on" colorimetric biosensor shows a broad linear range of 0.5-100 nM for the target NOS, with a 0.19 nM detection limit. The application of the biosensor for determination of NOS segments in samples of GM and non-GM tomatoes shows that it can discriminate between GM and non-GM plants. The reliability of the method for samples of NOS-spiked GM tomato suggests satisfactory recoveries in the range of 93.6%-94.2%.
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Affiliation(s)
- Xiaodong Cao
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Zihao Xia
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Wuwen Yan
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shudong He
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xuan Xu
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhaojun Wei
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yongkang Ye
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Haisong Zheng
- Technology Center of Hefei Customs, Hefei, 230032, China
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19
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Dadmehr M, Karimi MA, Korouzhdehi B. A signal-on fluorescence based biosensing platform for highly sensitive detection of DNA methyltransferase enzyme activity and inhibition. Spectrochim Acta A Mol Biomol Spectrosc 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Mehdi Dadmehr
- Department of Biology, Payame Noor University, Tehran, Iran.
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20
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Fakhri N, Abarghoei S, Dadmehr M, Hosseini M, Sabahi H, Ganjali MR. Paper based colorimetric detection of miRNA-21 using Ag/Pt nanoclusters. Spectrochim Acta A Mol Biomol Spectrosc 2020; 227:117529. [PMID: 31703998 DOI: 10.1016/j.saa.2019.117529] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/26/2019] [Accepted: 09/12/2019] [Indexed: 05/27/2023]
Abstract
Abnormal expression of MicroRNA-21 (miRNA-21) is considered to be a reliable biomarker for the early diagnosis of cancer. In this work, a novel paper based biosensor was fabricated to detect sub-micro molar concentrations of miRNA-21 based on peroxidase mimetic activity of DNA-templated Ag/Pt nanoclusters (DNA-Ag/Pt NCs), which could catalyze the reaction of hydrogen peroxide and 3,3',5,5' tetramethylbenzidine (TMB), to produce a blue color. The Mechanism of reaction was based on the inhibition effect of miRNA-21 on peroxidase-like activity of nanosensor which resulted to quantitative determination of miRNA-21 concentration. It was found that miRNA-21 could be linearly detected in the range from 1-700 pM (A652 = 0.16x-0.96, R2 = 0.99; x = -log [miRNA-21]) with a detection limit of 0.6 pM. Moreover, a paper assay was carried out on a Y-shaped paper-based microfluidic device in order to use the distinctive features of micro-channels such as short response time, very low reagent volume, low fabrication cost, etc. After performing paper based assay, a good linear range was observed between 10-1000 pM (y = 0.06x+147.48, R2 = 0.99; x = [miRNA-21]) with detection limit of 4.1 pM. The practical application of proposed method for detection of miRNA-21 in real sample was assayed in the human urine sample and indicated the colorimetric method had acceptable accuracy.
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Affiliation(s)
- Neda Fakhri
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Shima Abarghoei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mehdi Dadmehr
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Hossein Sabahi
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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21
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Dehghani Z, Hosseini M, Mohammadnejad J, Ganjali MR. New Colorimetric DNA Sensor for Detection of
Campylobacter jejuni
in Milk Sample Based on Peroxidase‐Like Activity of Gold/Platinium Nanocluster. ChemistrySelect 2019. [DOI: 10.1002/slct.201901815] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zahra Dehghani
- Department of Life Science EngineeringFaculty of New Sciences & TechnologiesUniversity of Tehran Tehran Iran
| | - Morteza Hosseini
- Department of Life Science EngineeringFaculty of New Sciences & TechnologiesUniversity of Tehran Tehran Iran
- Department of Pharmaceutical Biomaterials and Medicinal Biomaterials Research CenterFaculty of PharmacyTehran University of Medical Sciences Tehran Iran E-Mail address
| | - Javad Mohammadnejad
- Department of Life Science EngineeringFaculty of New Sciences & TechnologiesUniversity of Tehran Tehran Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in ElectrochemistrySchool of ChemistryCollege of ScienceUniversity of Tehran Tehran Iran
- Biosensor Research CenterEndocrinology and Metabolism Molecular-Cellular Sciences InstituteTehran University of Medical Sciences Tehran Iran
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22
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Su Z, Wang X, Luo M, Li L, Tu Y, Yan J. Fluorometric determination of nitrite through its catalytic effect on the oxidation of iodide and subsequent etching of gold nanoclusters by free iodine. Mikrochim Acta 2019; 186:619. [PMID: 31410575 DOI: 10.1007/s00604-019-3729-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
A method for sensitive detection of nitrite is presented. It is found that the red fluorescence of gold nanoclusters (with excitation/emission maxima at 365/635 nm) is quenched by traces of iodine via etching. Free iodide is formed by oxidation of iodide by bromate anion under the catalytic effect of nitrite. This catalytic process provides a sensitive means for nitrite detection. Under the optimal conditions, fluorescence linearly dropos in the 10 nM to 0.8 μM nitrite concentration range. The limit of detection is 1.1 nM. This is a few orders of magnitude lower than the maximum concentration allowed by authorities. Graphical abstract Schematic representation of a method for detection of nitrite via a redox reaction. Iodine was produced in the reaction and subsequently quenched the fluorescence from gold nanoclusters by etching their metallic cores, and a sensitive assay for nitrite down to 1.1 nM was developed.
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23
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Öğüt E, Kip Ç, Gökçal B, Tuncel A. Aggregation-resistant nanozyme containing accessible magnetite nanoparticles immobilized in monodisperse-porous silica microspheres for colorimetric assay of human genomic DNA. J Colloid Interface Sci 2019; 550:90-8. [DOI: 10.1016/j.jcis.2019.04.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
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24
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Abstract
The use of graphene quantum dots can be extended for bio-sensing and metal ion detection. Synergistic combination of graphene quantum dots (GQDs) with DNA leads to high performance Ag-ion detection system. The thoroughly characterized GQDs were found to have spherical morphology, with dimensions in the range of 5-10 nm. The atomic force microscopy studies proved that the synthesized GQDs were mostly comprised of two to four graphene layers. To make the system biocompatible, GQDs/NGQDs were combined with DNA. Two properties of DNA were exploited, capacity to provide nitrogen to GQDs; and to synergistically contribute to Ag+ detection. In addition to Ag+, the strong green photoluminescence (PL) of GQDs showed significant quenching, owing to the appearance of associated Förster resonance energy transfer processes. This led to high sensing efficiencies.
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Affiliation(s)
- Debabrata Mandal
- School of Nanoscience and Technology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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25
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Dehghani Z, Mohammadnejad J, Hosseini M. A new colorimetric assay for amylase based on starch-supported Cu/Au nanocluster peroxidase-like activity. Anal Bioanal Chem 2019; 411:3621-9. [DOI: 10.1007/s00216-019-01844-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/25/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
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26
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Soltaninejad H, Sadeghan AA, Hosseinkhani S, Asadollahi MA, Hosseini M, Ganjali MR. Application of intercalating molecules in detection of methylated DNA in the presence of silver ions. Methods Appl Fluoresc 2019; 7:035005. [DOI: 10.1088/2050-6120/ab025b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Karimi MA, Dadmehr M, Hosseini M, Korouzhdehi B, Oroojalian F. Sensitive detection of methylated DNA and methyltransferase activity based on the lighting up of FAM-labeled DNA quenched fluorescence by gold nanoparticles. RSC Adv 2019; 9:12063-12069. [PMID: 35516994 PMCID: PMC9063544 DOI: 10.1039/c9ra01564g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 12/27/2022] Open
Abstract
DNA methylation of cytosine bases, which is catalyzed by methyltransferase enzymes, involve biochemical processes that contribute to gene expression and gene regulation in cells. Detection of abnormal patterns of both methylated DNA and methyltransferase enzyme activity at early stages could be considered as promising targets for early cancer diagnosis. In the present study, a novel and facile method is introduced for the sensitive detection of the M.SssI methyltransferase (M.SssI MTase) enzyme and methylated DNA based on the fluorescence recovery of FAM-labeled DNA coupled with gold nanoparticles (AuNPs). Thiol-modified probes were functionalized with AuNPs, which brought the FAM fluorophore into the close proximity of the AuNPs. This led to the overlap between the FAM fluorescence emission and AuNPs absorption spectra, introducing a FRET occurrence and causing fluorescence quenching. The hybridization of the probe and its complementary target provided specific CpG sites for M.SssI MTase enzyme activity. The methylation process gradually converted the quenched FAM fluorophore into an emissive fluorophore upon the addition of the MTase enzyme, and the observed fluorescence recovery proved the efficiency of the assay for the detection of MTase enzyme. The fluorescence intensity showed an increasing trend with M.SssI MTase enzyme activity in the range of 1–8 U mL−1 with a detection limit of 0.14 U mL−1. The addition of methylated ssDNA targets to a ssDNA FAM-labeled probe resulted in a DNA duplex formation, leading to a strong fluorescence signal emission due to the recovery of the fluorophore signal. Conversely, the unmethylated ssDNA target caused no changes in the fluorescence signal. In the presence of methylated DNA targets, the biosensor could specifically recognize it and accordingly trigger the methylated targets through a fluorescence enhancement in the range of 5–100 pM by monitoring the increase in the fluorescence intensity with a detection limit of 2.2 pM. The obtained results showed that the assay could realize the detection of M.SssI MTase and methylated DNA effectively in diluted human serum samples. Human serum conditions showed no significant interference with the assay performance, indicating that the present method has great potential for further application in real samples. A novel method for detection of DNA methylation based on fluorescence recovery of FAM labeled DNA/Au NPs was introduced.![]()
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Affiliation(s)
| | - Mehdi Dadmehr
- Department of Biology
- Payame Noor University
- Tehran
- Iran
| | - Morteza Hosseini
- Department of Life Science Engineering
- Faculty of New Sciences & Technologies
- University of Tehran
- Tehran
- Iran
| | | | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies
- School of Medicine
- North Khorasan University of Medical Sciences
- Bojnurd
- Iran
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