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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] [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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Chen Q, Chen H, Kong H, Chen R, Gao S, Wang Y, Zhou P, Huang W, Cheng H, Li L, Feng J. Enzyme-free sensitive SERS biosensor for the detection of thalassemia-associated microRNA-210 using a cascade dual-signal amplification strategy. Anal Chim Acta 2024; 1292:342255. [PMID: 38309848 DOI: 10.1016/j.aca.2024.342255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/28/2023] [Accepted: 01/15/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND β-thalassemia is a blood disorder caused by autosomal mutations. Gene modulation therapy to activate the γ-globin gene to induce fetal hemoglobin (HbF) synthesis has become a new option for the treatment of β-thalassemia. MicroRNA-210 (miR-210) contributes to studying the mechanism regulating γ-globin gene expression and is a potential biomarker for rapid β-thalassemia screening. Traditional miRNA detection methods perform well but necessitate complex and time-consuming miRNA sample processing. Therefore, the development of a sensitive, accurate, and simple miRNA level monitoring method is essential. RESULTS We have developed a non-enzymatic surface-enhanced Raman scattering (SERS) biosensor utilizing a signal cascade amplification of catalytic hairpin assembly reaction (CHA) and proximity hybridization-induced hybridization chain reaction (HCR). Au@Ag NPs were used as the SERS substrate, and methylene blue (MB)- modified DNA hairpins were used as the SERS tags. The SERS assay involved two stages: implementing the CHA-HCR cascade signal amplification strategy and conducting SERS measurements on the resulting product. The HCR was started by the products of target-triggered CHA, which formed lengthy nicked double-stranded DNA (dsDNA) on the Au@Ag NPs surface to which numerous SERS tags were attached, leading to a significant increase in the SERS signal intensity. High specificity and sensitivity for miR-210 detection was achieved by monitoring MB SERS intensity changes. The suggested SERS biosensor has a low detection limit of 5.13 fM and is capable of detecting miR-210 at concentration between 10 fM and 1.0 nM. SIGNIFICANCE The biosensor can detect miR-210 levels in the erythrocytes of β-thalassemia patients, enabling rapid screening for β-thalassemia and suggesting a novel approach for investigating the regulation mechanism of miR-210 on γ-globin gene expression. In the meantime, this innovative technique has the potential to detect additional miRNAs and to become an important tool for the early diagnosis of diseases and for biomedical research.
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Affiliation(s)
- Qiying Chen
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Huagan Chen
- Department of Clinical Laboratory, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, PR China
| | - Hongxing Kong
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China
| | - Ruijue Chen
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Si Gao
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Ying Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Pei Zhou
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Wenyi Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China
| | - Hao Cheng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China
| | - Lijun Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China.
| | - Jun Feng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China.
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3
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Wu P, Fang N, Tao Y, Wang Y, Jia W, Zhang H, Cai C, Zhu JJ. Enhancing the Reliability of SERS Detection in Ampicillin Using Oriented Tetrahedral Framework Nucleic Acid Probes and a Long-Range SERS Substrate. Anal Chem 2023; 95:14271-14278. [PMID: 37695688 DOI: 10.1021/acs.analchem.3c02356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Indirect surface-enhanced Raman scattering (SERS)-based methods are highly efficient in detecting and quantitatively analyzing trace antibiotics in complex samples. However, the poor reproducibility of indirect SERS assays caused by the diffusion and orientation changes of the probing molecules on SERS substrates still presents a significant challenge. To address this issue, this study reports the construction of a novel SERS sensing platform using tetrahedral framework nucleic acid (tFNA) as SERS probes in conjunction with a long-range SERS (LR-SERS) substrate. The tFNA was modified with sulfhydryl groups at three vertices and appended with a probing DNA at the remaining vertex, anchored on the substrate surface with a well-ordered orientation and stable coverage density, resulting in highly reproducible SERS signals. Owing to the weak SERS signal of tFNA inherited from its size being larger than the effective range of the enhancing electric field (E-field) of conventional SERS substrates, we utilized an LR-SERS substrate to enhance the signal of tFNA probes by capitalizing on its extended E-field. Correspondingly, the LR-SERS substrate demonstrated a 54-fold increase in the intensity of tFNA probes compared to the conventional substrate. Using this novel platform, we achieved a highly reliable detection of the antibiotic ampicillin with a wide linear range (10 fM to 1 nM), low detection limit (3.1 fM), small relative standard deviation (3.12%), and yielded quantitative recoveries of 97-102% for ampicillin in water, milk, and human serum samples. These findings, therefore, effectively demonstrate the achievement of highly reliable SERS detection of antibiotics using framework nucleic acids and an LR-SERS substrate.
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Affiliation(s)
- Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Ningning Fang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Yutong Tao
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Yuan Wang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Wenyu Jia
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
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4
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Luo X, Yue W, Zhang S, Liu H, Chen Z, Qiao L, Wu C, Li P, He Y. SARS-CoV-2 proteins monitored by long-range surface plasmon field-enhanced Raman scattering with hybrid bowtie nanoaperture arrays and nanocavities. LAB ON A CHIP 2023; 23:388-399. [PMID: 36621932 DOI: 10.1039/d2lc01006b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The identification of biomacromolecules by using surface-enhanced Raman scattering (SERS) remains a challenge because of the near-field effect of traditional substrates. Long-range surface plasmon resonance (LRSPR) is a special type of surface optical phenomenon that provides higher electromagnetic field enhancement and longer penetration depth than conventional surface plasmon resonance. To break the limit of SERS detection distance and obtain a SERS substrate with increased enhancement ability, a bowtie nanoaperture array was sandwiched between two symmetric dielectric environments. Then, an Au mirror was inserted to form a metal-insulator-metal configuration. Finite-difference time-domain simulations revealed that numerous hybrid modes can be provided by this novel configuration (denoted as long-range SERS [LR-SERS] substrate). In particular, the LRSPR mode can be excited and reach the maximum value through the regulation of the polarizations of the incident light and the geometrical parameters of the LR-SERS substrate. The optimized LR-SERS substrate was then applied to detect SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. This substrate displayed ultralow detection limits of ∼9.2 and ∼11.3 pg mL-1 for the S and N proteins, respectively. Moreover, with the help of principal component analysis and receiver operating characteristic methods, our fabricated sensors exhibited excellent selectivity and hold great potential for the diagnosis of SARS-CoV-2 proteins in real samples.
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Affiliation(s)
- Xiaojun Luo
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Weiling Yue
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Shutong Zhang
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Haopeng Liu
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Zhinan Chen
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Ling Qiao
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Caijun Wu
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Panjie Li
- School of Chemistry and Chemical Engineering, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Yi He
- School of Science, Xihua University, Chengdu 610039, P. R. China.
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5
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A sensing strategy combining T7 promoter-contained DNA probe with CRISPR/Cas13a for detection of bacteria and human methyltransferase. Anal Chim Acta 2022; 1227:340266. [DOI: 10.1016/j.aca.2022.340266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]
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6
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Simple Detection of DNA Methyltransferase with an Integrated Padlock Probe. BIOSENSORS 2022; 12:bios12080569. [PMID: 35892466 PMCID: PMC9332213 DOI: 10.3390/bios12080569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022]
Abstract
DNA methyltransferases (MTases) can be regarded as biomarkers, as demonstrated by many studies on genetic diseases. Many researchers have developed biosensors to detect the activity of DNA MTases, and nucleic acid amplification, which need other probe assistance, is often used to improve the sensitivity of DNA MTases. However, there is no integrated probe that incorporates substrates and template and primer for detecting DNA MTases activity. Herein, we first designed a padlock probe (PP) to detect DNA MTases, which combines target detection with rolling circle amplification (RCA) without purification or other probe assistance. As the substrate of MTase, the PP was methylated and defended against HpaII, lambda exonuclease, and ExoI cleavage, as well as digestion, by adding MTase and the undestroyed PP started RCA. Thus, the fluorescent signal was capable of being rapidly detected after adding SYBRTM Gold to the RCA products. This method has a detection limit of approximately 0.0404 U/mL, and the linear range was 0.5–110 U/mL for M.SssI. Moreover, complex biological environment assays present prospects for possible application in intricacy environments. In addition, the designed detection system can also screen drugs or inhibitors for MTases.
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7
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Luo X, Qiao L, Xia Z, Yu J, Wang X, Huang J, Shu C, Wu C, He Y. Shape- and Size-Dependent Refractive Index Sensing and SERS Performance of Gold Nanoplates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6454-6463. [PMID: 35549353 DOI: 10.1021/acs.langmuir.2c00663] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plasmonic sensors are promising for ultrasensitive chemical and biological analysis. Gold nanoplates (Au NPLs) show unique geometrical structures with high ratios of surface to bulk atoms, which display fascinating plasmonic properties but require optimization. This study presented a systematic investigation of the influence of different parameters (shape, aspect ratio, and resonance mode) on localized surface plasmon resonance properties, refractive index (RI, n) sensitivities, and surface-enhanced Raman scattering (SERS) enhancement ability of different types of Au NPLs through finite-difference time-domain (FDTD) simulations. As a proof of concept, triangular, circular, and hexagonal Au NPLs with varying aspect ratios were fabricated via a three-step seed-mediated growth method by the experiment. Both FDTD-simulated and measured experimental results confirm that the RI sensitivities increase with the aspect ratio. Furthermore, choosing a lower order resonance mode of Au NPLs benefits higher RI sensitivities. The SERS enhancement abilities of Au NPLs also predicted to be highly dependent on the shape and aspect ratio. The triangular Au NPLs showed the highest SERS enhancement ability, while it drastically decreased for circular Au NPLs after the rounding process. The SERS enhancement ability gradually became more intense as the hexagonal Au NPLs overgrown on circular Au NPLs with increasing volumes of HAuCl4 solution. The results are expected to help develop effective biosensors.
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Affiliation(s)
- Xiaojun Luo
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Ling Qiao
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P.R. China
| | - Zhichao Xia
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Jiaming Yu
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Xiaozhou Wang
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Juhong Huang
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Chang Shu
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Caijun Wu
- School of Science, Xihua University, Chengdu 610039, P. R. China
| | - Yi He
- School of Science, Xihua University, Chengdu 610039, P. R. China
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8
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Hossain MK, Drmosh QAQ, Arifuzzaman M. Silver Nanoparticles, Nanoneedles and Nanorings: Impact of Electromagnetic Near-Field on Surface-Enhanced Raman Scattering. Phys Chem Chem Phys 2022; 24:8787-8799. [DOI: 10.1039/d1cp05681f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimension of plasmonic nanostructures does matter in localizing electromagnetic (EM) field and enhanced surface-enhanced Raman scattering (SERS)-activity. Zero-dimensional (0D) -, one-dimensional (1D) - and two-dimensional (2D) - plasmonic nanostructures are...
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9
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From lab to field: Surface-enhanced Raman scattering-based sensing strategies for on-site analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116488] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Zhou R, Zeng Z, Sun R, Liu W, Zhu Q, Zhang X, Chen C. Traditional and new applications of the HCR in biosensing and biomedicine. Analyst 2021; 146:7087-7103. [PMID: 34775502 DOI: 10.1039/d1an01371h] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hybridization chain reaction is a very popular isothermal nucleic acid amplification technology. A single-stranded DNA initiator triggers an alternate hybridization event between two hairpins forming a double helix polymer. Due to isothermal, enzyme-free and high amplification efficiency characteristics, the HCR is often used as a signal amplification technology for various biosensing and biomedicine fields. However, as an enzyme-free self-assembly reaction, it has some inevitable shortcomings of relatively slow kinetics, low cell internalization efficiency, weak biostability of DNA probes and uncontrollable reaction in these applications. More and more researchers use this reaction system to synthesize new materials. New materials can avoid these problems skillfully by virtue of their inherent biological characteristics, molecular recognition ability, sequence programmability and biocompatibility. Here, we summarized the traditional application of the HCR in biosensing and biomedicine in recent years, and also introduced its new application in the synthesis of new materials for biosensing and biomedicine. Finally, we summarized the development and challenges of the HCR in biosensing and biomedicine in recent years. We hope to give readers some enlightenment and help.
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Affiliation(s)
- Rong Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Ruowei Sun
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang 410300, Hunan, China
| | - Wenfang Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Xun Zhang
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang 410300, Hunan, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
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11
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Chai H, Cheng W, Jin D, Miao P. Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing. ACS APPLIED MATERIALS & INTERFACES 2021; 13:38931-38946. [PMID: 34374513 DOI: 10.1021/acsami.1c09000] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.
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Affiliation(s)
- Hua Chai
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Wenbo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Dayong Jin
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia
- UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
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12
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Ge S, Ran M, Mao Y, Sun Y, Zhou X, Li L, Cao X. A novel DNA biosensor for the ultrasensitive detection of DNA methyltransferase activity based on a high-density "hot spot" SERS substrate and rolling circle amplification strategy. Analyst 2021; 146:5326-5336. [PMID: 34319337 DOI: 10.1039/d1an01034d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Herein, we proposed a novel biosensor based on a high-density "hot spot" Au@SiO2 array substrate and rolling circle amplification (RCA) strategy for the ultrasensitive detection of CpG methyltransferase (M.SssI) activity. In the presence of M.SssI, the RCA process can be triggered, causing the augmentation of the single-stranded DNA (ssDNA) at the tail of the double-stranded DNA (dsDNA), and the ssDNA can be hybridized with numerous DNA probes labeled with Raman reporters in the next steps. Afterwards, the resultant ssDNA can be modified to the Au@SiO2 array substrate with the SERS enhancement factor of 7.49 × 106. The substrate was synthesized by using a monolayer SiO2 array to pick up the Au nanoparticle (AuNP) array and finite-difference time-domain (FDTD) simulation showed its excellent SERS effect. Particularly, the developed biosensor displayed a significant sensitivity with a broad detection range covering from 0.005 to 50 U mL-1, and the limits of detection (LODs) in PBS buffer and human serum were 2.37 × 10-4 U mL-1 and 2.51 × 10-4 U mL-1, respectively. Finally, in order to verify the feasibility of its clinical application, the serum samples of healthy subjects and breast cancer, prostate cancer, gastric cancer and cervical cancer patients were analyzed, and the reliability of the results was also confirmed by western blot (WB) experiments. Taking advantage of these merits, the proposed biosensor can be a very promising alternative tool for the detection of M.SssI activity, which is of vital importance in the early detection and prevention of tumors.
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Affiliation(s)
- Shengjie Ge
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China.
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13
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Luo X, Zhu J, Jia W, Fang N, Wu P, Cai C, Zhu JJ. Boosting Long-Range Surface-Enhanced Raman Scattering on Plasmonic Nanohole Arrays for Ultrasensitive Detection of MiRNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:18301-18313. [PMID: 33821612 DOI: 10.1021/acsami.1c01834] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A fundamental challenge, particularly, in surface-enhanced Raman scattering (SERS) analysis is the detection of analytes that are distant from the sensing surface. To tackle this challenge, we herein report a long-range SERS (LR-SERS) substrate supporting an extension of electric field afforded by long-range surface plasmon resonance (LRSPR) excited in symmetrical dielectric environments. The LR-SERS substrate has a sandwich configuration with a triangle-shaped gold nanohole array embedded between two dielectrics with similar refractive indices (i.e., MgF2 and water). The finite-difference time-domain simulation was applied to guide the design of the LR-SERS substrate, which was engineered to have a wavelength-matched LRSPR with 785 nm excitation. The simulations predict that the LR-SERS substrate exhibits great SERS enhancement at distances of more than 10 nm beyond its top surface, and the enhancement factor (EF) has been improved by three orders of magnitude on LR-SERS substrates compared to that on conventional substrates. The experimental results show good agreement with the simulations, an EF of 4.1 × 105 remains available at 22 nm above the LR-SERS substrate surface. The LR-SERS substrate was further applied as a sensing platform to detect microRNA (miRNA) let-7a coupled with a hybridization chain reaction (HCR) strategy. The developed sensor displays a wide linear range from 10 aM to 1 nM and an ultralow detection limit of 8.5 aM, making it the most sensitive among the current detection strategies for miRNAs based on the SERS-HCR combination to the best of our knowledge.
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Affiliation(s)
- Xiaojun Luo
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Jingtian Zhu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Wenyu Jia
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Ningning Fang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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Luo X, Zhao X, Wallace GQ, Brunet MH, Wilkinson KJ, Wu P, Cai C, Bazuin CG, Masson JF. Multiplexed SERS Detection of Microcystins with Aptamer-Driven Core-Satellite Assemblies. ACS APPLIED MATERIALS & INTERFACES 2021; 13:6545-6556. [PMID: 33522805 DOI: 10.1021/acsami.0c21493] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe surface-enhanced Raman spectroscopy (SERS) aptasensors that can indirectly detect MC-LR and MC-RR, individually or simultaneously, in natural water and in algal culture. The sensor is constructed from nanoparticles composed of successive layers of Au core-SERS label-silver shell-gold shell (Au@label@Ag@Au NPs), functionalized on the outer Au surface by MC-LR and/or MC-RR aptamers. These NPs are immobilized on asymmetric Au nanoflowers (AuNFs) dispersed on planar silicon substrates through DNA hybridization of the aptamers and capture DNA sequences with which the AuNFs are functionalized, thereby forming core-satellite nanostructures on the substrates. This construction led to greater electromagnetic (EM) field enhancement of the Raman label-modified region, as supported by finite-difference time-domain (FDTD) simulations of the core-satellite assembly. In the presence of MC-LR and/or MC-RR, the aptamer-functionalized NPs dissociate from the AuNFs because of the stronger affinity of the aptamers with the MCs, which decreases the SERS signal, thus allowing indirect detection of the MCs. The improved SERS sensitivity significantly decreased the limit of detection (LOD) for separate MC-LR detection (0.8 pM) and for multiplex detection (1.5 pM for MC-LR and 1.3 pM for MC-RR), compared with other recently reported SERS-based methods for MC-LR detection. The aptasensors show excellent selectivity to MC-LR/MC-RR and excellent recoveries (96-105%). The use of these SERS aptasensors to monitor MC-LR production over 1 week in a culture medium of M. aeruginosa cells demonstrates the applicability of the sensors in a realistic environment.
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Affiliation(s)
- Xiaojun Luo
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
- Centre québécois des matériaux fonctionnels (CQMF), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Regroupement québécois des matériaux de pointe (RQMP), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
| | - Xingjuan Zhao
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Centre québécois des matériaux fonctionnels (CQMF), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Regroupement québécois des matériaux de pointe (RQMP), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
| | - Gregory Q Wallace
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Centre québécois des matériaux fonctionnels (CQMF), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Regroupement québécois des matériaux de pointe (RQMP), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
| | - Marie-Hélène Brunet
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Regroupement québécois des matériaux de pointe (RQMP), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
| | - Kevin J Wilkinson
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Regroupement québécois des matériaux de pointe (RQMP), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - C Geraldine Bazuin
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Centre québécois des matériaux fonctionnels (CQMF), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
| | - Jean-Francois Masson
- Département de chimie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Centre québécois des matériaux fonctionnels (CQMF), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
- Regroupement québécois des matériaux de pointe (RQMP), Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7
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