1
|
He S, Chen L, Chen Z, Zhang G, Huang Y, Zheng H, Yang Q, Mo Z, Lin X, Wen J. The sensing of circRNA with tetrahedral DNA nanostructure modified microfluidic chip. Anal Chim Acta 2024; 1319:342951. [PMID: 39122270 DOI: 10.1016/j.aca.2024.342951] [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: 05/12/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Circular ribonucleic acids (circRNAs) are a type of covalently closed noncoding RNA with disease-relevant expressions, making them promising biomarkers for diagnosis and prognosis. Accurate quantification of circRNA in biological samples is a necessity for their clinical application. So far, methods developed for detecting circRNAs include northern blotting, reverse transcription quantitative polymerase chain reaction (RT-qPCR), microarray analysis, and RNA sequencing. These methods generally suffer from disadvantages such as large sample consumption, cumbersome process, low selectivity, leading to inaccurate quantification of circRNA. It was thought that the above drawbacks could be eliminated by the construction of a microfluidic sensor. RESULTS Herein, for the first time, a microfluidic sensor was constructed for circRNA analysis by using tetrahedral DNA nanostructure (TDN) as the skeleton for recognition probes and target-initiated hybridization chain reaction (HCR) as the signal amplification strategy. In the presence of circRNA, the recognition probe targets the circRNA-specific backsplice junction (BSJ). The captured circRNA then triggers the HCR by reacting with two hairpin species whose ends were labeled with 6-FAM, producing long DNA strands with abundant fluorescent labels. By using circ_0061276 as a model circRNA, this method has proven to be able to detect circRNA of attomolar concentration. It also eliminated the interference of linear RNA counterpart, showing high selectivity towards circRNA. The detection process can be implemented isothermally and does not require expensive complicated instruments. Moreover, this biosensor exhibited good performance in analyzing circRNA targets in total RNA extracted from cancer cells. SIGNIFICANCE This represents the first microfluidic system for detection of circRNA. The biosensor showed merits such as ease of use, low-cost, small sample consumption, high sensitivity and specificity, and good reliability in complex biological matrix, providing a facile tool for circRNA analysis and related disease diagnosis in point-of care application scenes.
Collapse
Affiliation(s)
- Shiliang He
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China.
| | - Lei Chen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| | - Zhuolang Chen
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Guihao Zhang
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Yongjin Huang
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Huaxiao Zheng
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Qing Yang
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Zhuoxi Mo
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Xinyi Lin
- College of Pharmacy, Shenzhen Technology University, Shenzhen, 518118, China
| | - Jiancheng Wen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| |
Collapse
|
2
|
Liu B, Shi C, Wang F, Xu F, Chao J, Zhu J, Yang D, Ouyang X. A non-enzymatic, isothermal amplification sensor for quantifying the relative abundance of Akkermansia muciniphila. Chem Commun (Camb) 2024; 60:9089-9092. [PMID: 39108142 DOI: 10.1039/d4cc03087g] [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: 08/21/2024]
Abstract
Herein, we have developed a non-enzymatic, isothermal amplification assay (NIA sensor) based on a catalytic hairpin assembly (CHA) reaction for quantifying the relative abundance of Akkermansia muciniphila. Through detection of the MUC-1437 gene (limit of detection: 8.3 fM) in a dynamic range from 10 fM to 1 nM, the NIA sensor shows high sensitivity and selectivity in preclinical models of mice fed a normal or high-fat diet (HFD), and treated with antibiotics (ATB). The NIA sensor, which operates without the use of any enzymes, leading to simplicity and cost-effectiveness, has great potential for biosensing research and clinical diagnostic applications.
Collapse
Affiliation(s)
- Bing Liu
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
- Key Laboratory for Organic Electronics and Information Displays and Jiangsu, Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, China
| | - Chen Shi
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Fan Wang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Fangling Xu
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays and Jiangsu, Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, China
| | - Jiapeng Zhu
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Dongliang Yang
- Key Laboratory for Organic Electronics and Information Displays and Jiangsu, Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, China
| | - Xiangyuan Ouyang
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, China.
| |
Collapse
|
3
|
Dong Z, Su R, Fu Y, Wang Y, Chang L. Recent Progress in DNA Biosensors for Detecting Biomarkers in Living Cells. ACS Biomater Sci Eng 2024. [PMID: 39143919 DOI: 10.1021/acsbiomaterials.4c01339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Analysis of biomarkers in living cells is crucial for deciphering the dynamics of cells as well as for precise diagnosis of diseases. DNA biosensors employ DNA sequences as probes to offer insights into living cells, and drive progress in disease diagnosis and drug development. In this review, we present recent advances in DNA biosensors for detecting biomarkers in living cells. The basic structural components of DNA biosensors and the signal output method are presented. The strategies of DNA biosensors crossing the cell membrane are also described, including coincubation, nanocarriers, and nanoelectroporation techniques. Based on biomarker categorization, we detail recent applications of DNA biosensors for detecting small molecules, RNAs, proteins, and integrated targets in living cells. Furthermore, the future development directions of DNA biosensors are summarized to encourage further research in this growing field.
Collapse
Affiliation(s)
- Zaizai Dong
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Rongtai Su
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yao Fu
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Yupei Wang
- Gansu Provincial Maternity and Child-Care Hospital (Gansu Provincial Central Hospital), Lanzhou 730050, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| |
Collapse
|
4
|
Wang H, Zou H, Wang F. Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications. Chembiochem 2024; 25:e202400266. [PMID: 38801028 DOI: 10.1002/cbic.202400266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on-demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA-based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.
Collapse
Affiliation(s)
- Hong Wang
- Biological Products Laboratory, Chongqing Institute for Food and Drug Control, Chongqing, 430072, P. R. China
| | - Hanyan Zou
- Biological Products Laboratory, Chongqing Institute for Food and Drug Control, Chongqing, 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| |
Collapse
|
5
|
Mou J, Zhang H, Zhang L, Zhang B, Liu J, Zheng S, Kou Q, Wang H, Su X, Guo S, Ke Y, Zhang Y. Simulation-Guided Rational Design of DNA Walker-Based Theranostic Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400963. [PMID: 38686696 DOI: 10.1002/smll.202400963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/11/2024] [Indexed: 05/02/2024]
Abstract
Biomolecule-functionalized nanoparticles represent a type of promising biomaterials in biomedical applications owing to their excellent biocompatibility and versatility. DNA-based reactions on nanoparticles have enabled emerging applications including intelligent biosensors, drug delivery, and biomimetic devices. Among the reactions, strand hybridization is the critical step to control the sensitivity and specificity of biosensing, and the efficiency of drug delivery. However, a comprehensive understanding of DNA hybridization on nanoparticles is still lacking, which may differ from the process in homogeneous solutions. To address this limitation, coarse-grained model-based molecular dynamic simulation is harnessed to disclose the critical factors involved in intermolecular hybridization. Based on simulation guidance, DNA walker-based smart theranostic platform (DWTP) based on "on-particle" hybridization is developed, showing excellent consistency with simulation. DWTP is successfully applied for highly sensitive miRNA 21 detection and tumor-specific miRNA 21 imaging, driven by tumor-endogenous APE 1 enzyme. It enables the precise release of antisense oligonucleotide triggered by tumor-endogenous dual-switch miRNA 21 and APE 1, facilitating effective gene silencing therapy with high biosafety. The simulation of "on-particle" DNA hybridization has improved the corresponding biosensing performance and the release efficiency of therapeutic agents, representing a conceptually new approach for DNA-based device design.
Collapse
Affiliation(s)
- Jingyan Mou
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Haoping Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Linghao Zhang
- State Key Laboratory of Organic-Inorganic Composites College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Beibei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Jiajia Liu
- State Key Laboratory of Organic-Inorganic Composites College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Shasha Zheng
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Qiaoni Kou
- State Key Laboratory of Organic-Inorganic Composites College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Hong Wang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Xin Su
- State Key Laboratory of Organic-Inorganic Composites College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Shaojun Guo
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| |
Collapse
|
6
|
Li M, Li J, Zheng H, Liu M, Zhou H, Zhang L, Zhang H, Shen Q. Dark-field imaging and fluorescence dual-mode detection of microRNA-21 in living cells by core-satellite plasmonic nanoprobes. Talanta 2024; 273:125936. [PMID: 38503126 DOI: 10.1016/j.talanta.2024.125936] [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: 11/15/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
The in situ precise quantification and simultaneous imaging of low abundance microRNAs (miRNAs) within living cells is critical for cancer diagnosis, yet it remains a significant challenge. Leveraging the excellent sensitivity and spatiotemporal resolution of dark-field microscopy (DFM) and fluorescence imaging, we have successfully devised a novel detection approach using dual-signal reporter probes (DSRPs). These probes allow for highly sensitive detection of miRNA-21 in living cells via toehold-mediated strand displacement cascades. The DSRPs were constructed by Au nanoparticles and Ag nanoclusters core-satellite nanostructures. After the recognition of miRNA-21, the strand displacement cascades were triggered, inducing the disassembly of the Au/Ag core-satellite nanostructure with apparent scattering intensity decrease and peak wavelength shifts. Additionally, the fluorescence of Ag clusters could be recovered and further enhanced when in close proximity to specific guanine-rich strands. The dual-signal response capability enables the accurate detection of miRNA-21 from 1 fM to 1 nM, with a limit of detection reached 0.75 fM. DFM and fluorescent imaging of living cells efficiently confirms the applicable detection of miRNA-21 in complex detection media. The biosensor based on DSRPs represents a promising nanoplatform for visual monitoring and imaging of biomolecules in living cells, even at the single particle level.
Collapse
Affiliation(s)
- Meixing Li
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China.
| | - Jiaxin Li
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Haitao Zheng
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Mengwei Liu
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Huiyu Zhou
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Lei Zhang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Hui Zhang
- 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, China
| | - Qingming Shen
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing, 210023, China.
| |
Collapse
|
7
|
Liu X, Shi Q, Qi P, Wang Z, Zhang T, Zhang S, Wu J, Guo Z, Chen J, Zhang Q. Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis. Asian J Pharm Sci 2024; 19:100910. [PMID: 38948397 PMCID: PMC11214190 DOI: 10.1016/j.ajps.2024.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 07/02/2024] Open
Abstract
The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.
Collapse
Affiliation(s)
- Xuyao Liu
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Qi Shi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Peng Qi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Ziming Wang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Tongyue Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Sijia Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jiayan Wu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhaopei Guo
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jie Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Qiang Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| |
Collapse
|
8
|
Gu Y, Bai R, Qiu X, Wang X, Lu S, Li CM, Guo C. In Vivo Imaging MicroRNA with Bright Fluorescent RNA Aptamer Through Target-Mediated Entropy-Driven Toehold Exchange. Anal Chem 2024; 96:7609-7617. [PMID: 38687631 DOI: 10.1021/acs.analchem.4c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
MicroRNAs (miRNAs) play vital roles in biological activities, but their in vivo imaging is still challenging due to the low abundance and the lack of efficient fluorescent tools. RNA aptamers with high affinity and low background emerge for bioimaging yet suffering from low brightness. We introduce a rational design based on target-mediated entropy-driven toehold exchange (EDTE) to induce the release of RNA aptamer and subsequently light up corresponding fluorophore, which achieves selective imaging of miRNAs with good stability in both living cells and tumor-bearing mouse. Through tailoring recognition unit of the EDTE probes, highly sensitive imaging of different miRNAs including miRNA-125b and miRNA-21 is achieved, confirming its universal bioimaging applications. In comparison with the reported "one-to-one" model, the EDTE strategy shows a remarkable 4.6-time improvement in signal/noise ratio for intracellular imaging of the same miRNA. Particularly, it realizes sensitive imaging of miRNA in vivo, providing a promising tool in investigating functions and interactions of disease-associated miRNAs.
Collapse
Affiliation(s)
- Yu Gu
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Rui Bai
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Xingchen Qiu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Xuefu Road, Suzhou 215009, P. R. China
| | - Xiaobao Wang
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Shasha Lu
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Chang-Ming Li
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Chunxian Guo
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| |
Collapse
|
9
|
Qian D, Zhang J, Sun G, Zhang Y, Xu Q, Li J, Li H. Programmable Entropy-Driven Circuit-Cascaded Self-Feedback DNAzyme Network for Ultra-Sensitive Fluorescence and Photoelectrochemical Dual-Mode Biosensing. Anal Chem 2024; 96:7274-7280. [PMID: 38655584 DOI: 10.1021/acs.analchem.4c01168] [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: 04/26/2024]
Abstract
Inspired by natural DNA networks, programmable artificial DNA networks have become an attractive tool for developing high-performance biosensors. However, there is still a lot of room for expansion in terms of sensitivity, atom economy, and result self-validation for current microRNA sensors. In this protocol, miRNA-122 as a target model, an ultrasensitive fluorescence (FL) and photoelectrochemical (PEC) dual-mode biosensing platform is developed using a programmable entropy-driven circuit (EDC) cascaded self-feedback DNAzyme network. The well-designed EDC realizes full utilization of the DNA strands and improves the atomic economy of the signal amplification system. The unique and rational design of the double-CdSe quantum-dot-released EDC substrate and the cascaded self-feedback DNAzyme amplification network significantly avoids high background signals and enhances sensitivity and specificity. Also, the enzyme-free, programmable EDC cascaded DNAzyme network effectively avoids the risk of signal leakage and enhances the accuracy of the sensor. Moreover, the introduction of superparamagnetic Fe3O4@SiO2-cDNA accelerates the rapid extraction of E2-CdSe QDs and E3-CdSe QDs, which greatly improves the timeliness of sensor signal reading. In addition to the strengths of linear range (6 orders of magnitude) and stability, the biosensor design with dual signal reading makes the test results self-confirming.
Collapse
Affiliation(s)
- Defu Qian
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Jingling Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Guoshuai Sun
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Yuye Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Qin Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, P. R. China
| | - Jing Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Hongbo Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| |
Collapse
|
10
|
Pang H, Zhao Q. Antibody-Bridged DNAzyme Walker for Sensitive Detection of Small Molecules. Anal Chem 2024; 96:6366-6372. [PMID: 38598690 DOI: 10.1021/acs.analchem.4c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Sensitive detection of small molecules with biological and environmental interests is important for many applications, such as food safety, disease diagnosis, and environmental monitoring. Herein, we propose a highly selective antibody-bridged DNAzyme walker to sensitively detect small molecules. The antibody-bridged DNAzyme walker consists of a track, small-molecule-labeled DNAzyme walking strand, and antibody against small molecules. The track is built by co-modifying fluorophore-labeled substrates and small-molecule-labeled DNA linkers onto a gold nanoparticle (AuNP). In the absence of the target molecule, the antibody binds small molecule labels at the DNAzyme walking strand and the DNA linker, driving the DNAzyme walking strand on the surface of the AuNP. The attached DNAzyme walking strand moves along the track and cleaves substrates to generate high fluorescence signals to achieve signal amplification. As target molecules exist, they competitively bind with antibody to displace the small-molecule-labeled linker and DNAzyme walking strand, rendering the DNAzyme walker inactive in substrate cleavage and causing weak fluorescence. By using this antibody-bridged DNAzyme walker, we achieved sensitive detection of two biologically important small molecules, digoxin and folic acid. This work provides a new paradigm by combining the signal amplification strategy of a DNA walker and immunorecognition for sensitive and selective detection of small molecules.
Collapse
Affiliation(s)
- Han Pang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| |
Collapse
|
11
|
Kim H, Noh H. Signal Amplification by Spatial Concentration for Immunoassay on Cellulose Media. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307556. [PMID: 38012537 DOI: 10.1002/smll.202307556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Immunoassay is one of the most common bioanalytical techniques from lab-based to point-of-care settings. Over time, various approaches have been developed to amplify signals for greater sensitivity. However, the need for effective, versatile, and simple signal amplification methods persists yet. This paper presents a novel signal amplification method for immunoassay that utilizes spatial concentration of a cellulose-based plate possessing sensor transducers, specifically gold nanoparticles. By modifying the dimensions of the plate, the density of nanoparticles increased, resulting in intensified color signals. The coating material, polydopamine, which is utilized to protect the gold nanoparticles. Chemical changes in nanocomposites are characterized using scanning electron microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and scanning electron microscopy. The application of this method to colorimetric quantification demonstrated great consistency across various concentrations of nanoparticles, with better reliability at lower concentration ranges. A model immunoassay is designed to evaluate the analytical performance. As a result, this method successfully corrected a false-negative result with a lowered Kd of 0.509 pmol per zone. This method shows strong signal enhancement capability that can correct false-negative signals in the immunoassays, with potential benefits including versatility, simplicity, low cost, and the ability to operate multiple plates simultaneously.
Collapse
Affiliation(s)
- Hyeokjung Kim
- Department of Optometry, Seoul National University of Science and Technology, Seoul, 01811, South Korea
| | - Hyeran Noh
- Department of Optometry, Seoul National University of Science and Technology, Seoul, 01811, South Korea
| |
Collapse
|
12
|
Qin H, Chen Z, Zuo F, Cao R, Wang F, Wu H, Wang S, Xie Y, Ding S, Min X, Duan X. "DSN-mismatched CRISPR″sensor for highly selective and sensitive detection of under-expressed miR-let-7a. Anal Chim Acta 2024; 1295:342273. [PMID: 38355234 DOI: 10.1016/j.aca.2024.342273] [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: 11/16/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
Several microRNAs (miRNAs) are expressed at lower levels in specific tumors, e.g., miR-let-7a in non-small cell lung cancer (NSCLC). This makes it challenging to analyze their lower abundance versus specifically elevated miRNAs. Here, we describe a novel fluorescent biosensor for the highly selective and sensitive detection of miR-let-7a constructed by combining miRNA screening assisted by a duplex-specific nuclease (DSN) with CRISPR-Cas12a system signal amplification. We meticulously designed a mismatch in the first three to four bases at the 5'-end of the capture DNA to improve the signal-to-noise ratio of the CRISPR-Cas12a system. Within this "DSN-mismatched CRISPR" fluorescence strategy, miR-let-7a was accurately screened by DSN-assisted cleavage, and the mismatched capture DNA unbound to target miRNA could trigger the CRISPR-Cas12a system to produce a mass of trans-cleave fluorescence signals. This "turn-off" approach was suitable for detecting decreased levels of miRNAs. This approach can not only discriminate the single-base mismatched let-7 family but also reach a limit of detection at 64.17 fM as well as be quantified from 100 fM to 500 pM. The miR-let-7a levels were then measured in clinical serum samples from healthy volunteers and patients with NSCLC. This study holds promise for the development of a universal under-expressed miRNA assay for early diagnosis and treatment of cancers.
Collapse
Affiliation(s)
- Huijun Qin
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China; Department of Clinical Laboratory, Dazhou Central Hospital, Dazhou, 635000, PR China
| | - Zhuoying Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Fujiang Zuo
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Rufei Cao
- College of Basic Medicine, Zunyi Medical University, Zunyi, 563000, PR China
| | - Fangyuan Wang
- College of Basic Medicine, Zunyi Medical University, Zunyi, 563000, PR China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Shuji Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Yuanjiang Xie
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China.
| | - Xiaolei Duan
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, PR China; College of Basic Medicine, Zunyi Medical University, Zunyi, 563000, PR China.
| |
Collapse
|
13
|
Li D, Huang Q, Wang K. Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics. Mikrochim Acta 2024; 191:173. [PMID: 38436735 DOI: 10.1007/s00604-024-06208-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 03/05/2024]
Abstract
MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100 pM and achieves a detection limit of 5 fM (3σ criterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.
Collapse
Affiliation(s)
- Dengke Li
- Department of Rehabilitation Medicine, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, 223300, China.
| | - Qiuyan Huang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Kun Wang
- Department of Physics, New York University, New York, NY, 10003, USA
| |
Collapse
|
14
|
Ishikawa T, Sugawara K, Zhang J, Funatsu T, Okabe K. Direct observation of cytoskeleton-dependent trafficking of miRNA visualized by the introduction of pre-miRNA. iScience 2024; 27:108811. [PMID: 38303695 PMCID: PMC10831896 DOI: 10.1016/j.isci.2024.108811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNA (miRNA) plays physiologically and pathologically important roles in post-transcriptional regulation. Although miRNA has been suggested to dynamically interact with cellular organelles, the dynamicity of intracellular miRNA behavior has remained unclear. Here, by introducing fluorescently labeled pre-miRNA into living cells, we improved the miRNA visualization method using exogenous miRNA precursors. Through the combination of our miRNA visualization method and single-molecule sensitive fluorescence microscopy, we quantitatively analyzed the process of miRNA maturation. Furthermore, single-particle tracking of fluorescent miRNA in cells revealed the directed movements of miRNA on cytoskeletal components (i.e., microtubules and actin filaments). Our results also suggest that cytoskeleton-dependent miRNA trafficking is associated with the interaction of miRNAs with the nucleus and the endoplasmic reticulum/Golgi apparatus. Our method should facilitate the elucidation of the mechanism and physiological significance of the subcellular localization and organelle interaction of miRNA.
Collapse
Affiliation(s)
- Toshinari Ishikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Sugawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junwei Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, PRESTO, 4-8-1 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
15
|
Chen J, Hu F, Lin S, Song Z, Duan Z, Zhang L, Jiang M. Hybridization chain reaction assisted terahertz metamaterial biosensor for highly sensitive detection of microRNAs. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123646. [PMID: 37980831 DOI: 10.1016/j.saa.2023.123646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/22/2023] [Accepted: 11/11/2023] [Indexed: 11/21/2023]
Abstract
MicroRNA (miRNA) is closely related to the occurrence and development of cancer. Accurate determination of the miRNA concentration is of great significance for early cancer diagnosis. However, due to the short sequence and low concentration of miRNA, it is still a challenge to achieve low-concentration detection. In this work, we proposed a method for the highly sensitive detection of miRNA-21 using a terahertz (THz) metamaterial sensor combined with a Hybridization chain reaction (HCR). First, a capture hairpin probe was combined with gold nanoparticles (AuNPs), which were then modified to the surface of the sensor for specific binding of miRNA-21. Then the signal amplification technique of HCR is used to amplify the trace amount of miRNA, and the super-long dendritic DNA macromolecules are formed on the surface of the sensor. This changes the dielectric environment of the sensor surface, and the resonance frequency of the sensor is shifted. The method has good specificity and sensitivity, and the concentration of miRNA-21 in the range of 100 aM to 10 nM shows excellent linear relationship with frequency shift. Most importantly, it paves the way for low-cost, easy-to-operate and marker-free miRNA detection.
Collapse
Affiliation(s)
- Jie Chen
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| | - Fangrong Hu
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China.
| | - Shangjun Lin
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| | - Zihang Song
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| | - Zhitao Duan
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| | - Longhui Zhang
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China.
| | - Mingzhu Jiang
- College of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| |
Collapse
|
16
|
Guo H, Chen J, Feng Y, Dai Z. A Simple and Robust Exponential Amplification Reaction (EXPAR)-Based Hairpin Template (exp-Hairpin) for Highly Specific, Sensitive, and Universal MicroRNA Detection. Anal Chem 2024; 96:2643-2650. [PMID: 38295438 DOI: 10.1021/acs.analchem.3c05323] [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: 02/02/2024]
Abstract
Specific and sensitive detection of microRNAs continues to encounter significant challenges, especially in the development of rapid and efficient isothermal amplification strategies for point-of-care settings. The exponential amplification reaction (EXPAR) has garnered significant attention owing to its simplicity and rapid amplification of signals within a short period. However, a substantial loss of amplification efficiency, difficulty in distinguishing closely related homologous sequences, and adapting the designed templates to other targets seriously hamper the practical application of the EXPAR. In this work, a hairpin template tailored for the EXPAR system (exp-Hairpin) was constructed by adding identical trigger sequences and enzyme cleavage sites on two arms of the hairpin, achieving theoretically more than 2n amplification efficiency and minimal background amplification of EXPAR. Modulating the stability of the exp-Hairpin template by increasing the stem length, the specificity of detecting target miRNA in highly homologous sequences could be significantly improved. Using miRNA let-7a as a target model, the exp-Hairpin with 8 bp stem length for EXPAR amplification curves could effectively distinguish target let-7a and nontarget let-7b/7c/7f/7g/7i homologous sequences. This strategy enabled the sensitive and accurate analysis of let-7a in diluted human serum with satisfactory recoveries. By simply replacing the loop recognition sequence of exp-Hairpin, the specific detection of miR-200b was also achieved, demonstrating the universality of this strategy. The exp-Hairpin EXPAR accelerates simple and rapid molecular diagnostic applications for short nucleic acids.
Collapse
Affiliation(s)
- Haijing Guo
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Yaqiang Feng
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou 510006, PR China
| |
Collapse
|
17
|
Liu B, Zhao D, Chen J, Shi M, Yuan K, Sun H, Meng HM, Li Z. DNA Logical Device Combining an Entropy-Driven Catalytic Amplification Strategy for the Simultaneous Detection of Exosomal Multiplex miRNAs In Situ. Anal Chem 2024; 96:1733-1741. [PMID: 38227423 DOI: 10.1021/acs.analchem.3c04883] [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: 01/17/2024]
Abstract
Exosomal miRNAs are considered promising biomarkers for cancer diagnosis, but their accuracy is severely compromised by the low content of miRNAs and the large amount of exosomal miRNAs released from normal cells. Here, we presented a dual-specific miRNA's logical recognition triggered by an entropy-driven catalysis (EDC)-enhanced system in exosomes for accurate detection of liver cancer-cell-derived exosomal miR-21 and miR-122. Taking advantage of the accurate analytical performance of the logic device, the excellent membrane penetration of gold nanoparticles, and the outstanding amplification ability of the EDC reaction, this method exhibits high sensitivity and selectivity for the detection of tumor-derived exosomal miRNAs in situ. Moreover, due to its excellent performance, this logic device can effectively distinguish liver cancer patients from healthy donors by determining the amount of cancer-cell-derived exosomal miRNAs. Overall, this strategy has great potential for analyzing various types of exosomes and provides a viable tool to improve the accuracy of cancer diagnosis.
Collapse
Affiliation(s)
- Bojun Liu
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Di Zhao
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Juan Chen
- Zhengzhou Key Laboratory of Criminal Science and Technology, Department of Criminal Science and Technology, Zhengzhou Police College, Zhengzhou 450053, China
| | - Mingqing Shi
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Kun Yuan
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Hongzhi Sun
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Min Meng
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Zhaohui Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou 450001, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| |
Collapse
|
18
|
Zhou Y, Tang L, Lyu J, Shiyi L, Liu Q, Pang R, Li W, Guo X, Zhong X, He H. A dual signal amplification system with specific signal identification for rapid and sensitive detection of miRNA. Talanta 2024; 266:125097. [PMID: 37611369 DOI: 10.1016/j.talanta.2023.125097] [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: 05/16/2023] [Revised: 08/06/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
False positive which is mostly caused by the nonspecific amplification has severely hindered the development of nucleic acid detection and it is hard to avoid. Therefore, specific signals recognition and output in nucleic acid amplification are crucial to reliability of clinical diagnosis. Herein, we proposed a one-step and rapid miRNA detection strategy with specific signal identification, dual amplification and output. And this strategy was named as high-temperature hybridization chain reaction coupled with strand displacement amplification (HSA). In HSA, we well designed a target signal recognition, replication, and output probe (RRO probe). If the target miRNA exists, RRO probe can initiate a strand displacement amplification and output a target-related special single-stranded DNA (trigger). And the trigger can be identified by a high-temperature hybridization chain reaction and initiate a secondary signal amplification. As a result, the quantitative determination of HSA for miRNA-21 was in the range of 100 fM to 100 pM in 30 min, and with a detection limit of 82 fM. Moreover, with high sensitivity and rapidity, HSA has been successfully used to detect miRNA-21 in real samples.
Collapse
Affiliation(s)
- Yan Zhou
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China
| | - Jiazhen Lyu
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lixi Shiyi
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qinhao Liu
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Ruonan Pang
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Wenxin Li
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xiaolan Guo
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xiaowu Zhong
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Hongfei He
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China.
| |
Collapse
|
19
|
Nie L, Zeng X, Li H, Wang S, Yu R. Enzyme-assisted amplification of target cycle triggers the unlocking of locked hairpin probes for let-7a detection. Talanta 2024; 266:125023. [PMID: 37549569 DOI: 10.1016/j.talanta.2023.125023] [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: 06/09/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
The detection of miRNA in cells is difficult owing to its substantially low cellular content. Therefore, developing a highly sensitive sensor to detect cellular miRNA remains a significant challenge. Herein, we report an enzyme-assisted biosensor with target cycle amplification that can trigger the unlocking of locked hairpin probes for sensitive and robust let-7a gene detection. In the research, three kinds of hairpin probes were skillfully designed. The hairpin probe comprises a complementary sequence of a target, primer, and recognition site of Nt. BbvCI restriction endonucleases. In addition, the alternating synergistic impact of polymerase and the nicking enzyme generates considerable triggers to unlock the locked hairpin probe LH1, consequently triggering a subsequent circulating strand displacement reaction to form a stable H1-H2 double strand to ensure sufficient distance between a fluorophore on H1 and a quenching group on bolt DNA (bDNA), and resulting in the recovery of fluorescence. Furthermore, this process does not require complicated operation procedures and instruments, and the target gene let-7a can be sensitively detected. Specifically, the detection limit of the biosensor is as low as 160 fM, and its linear range is 0.5 pM-250 nM. Moreover, this biosensor can be employed to detect let-7a in human serum with good selectivity.
Collapse
Affiliation(s)
- Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Xiaogang Zeng
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Hongbo Li
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| |
Collapse
|
20
|
Gong X, Zhang J, Zhang P, Jiang Y, Hu L, Jiang Z, Wang F, Wang Y. Engineering of a Self-Regulatory Bidirectional DNA Assembly Circuit for Amplified MicroRNA Imaging. Anal Chem 2023; 95:18731-18738. [PMID: 38096424 DOI: 10.1021/acs.analchem.3c02822] [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: 12/27/2023]
Abstract
The engineering of catalytic hybridization DNA circuits represents versatile ways to orchestrate a complex flux of molecular information at the nanoscale, with potential applications in DNA-encoded biosensing, drug discovery, and therapeutics. However, the diffusive escape of intermediates and unintentional binding interactions remain an unsolved challenge. Herein, we developed a compact, yet efficient, self-regulatory assembly circuit (SAC) for achieving robust microRNA (miRNA) imaging in live cells through DNA-templated guaranteed catalytic hybridization. By integrating the toehold strand with a preblocked palindromic fragment in the stem domain, the proposed miniature SAC system allows the reactant-to-template-controlled proximal hybridization, thus facilitating the bidirectional-sustained assembly and the localization-intensified signal amplification without undesired crosstalk. With condensed components and low reactant complexity, the SAC amplifier realized high-contrast intracellular miRNA imaging. We anticipate that this simple and template-controlled design can enrich the clinical diagnosis and prognosis toolbox.
Collapse
Affiliation(s)
- Xue Gong
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Jiajia Zhang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Pu Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yuqian Jiang
- Research Institute of Shenzhen, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Lianzhe Hu
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Zhongwei Jiang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Fuan Wang
- Research Institute of Shenzhen, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yi Wang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| |
Collapse
|
21
|
Cheng X, Li X, Kang Y, Zhang D, Yu Q, Chen J, Li X, Du L, Yang T, Gong Y, Yi M, Zhang S, Zhu S, Ding S, Cheng W. Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction. Nucleic Acids Res 2023; 51:e111. [PMID: 37941139 PMCID: PMC10711451 DOI: 10.1093/nar/gkad953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency and time-consuming operation hinder its clinical application. Here, we first proposed a new strand displacement reaction (SDR) model (Cas12a thrusting SDR, CtSDR), in which Cas12a could overcome the inherent reaction limitation and dramatically enhance efficiency through energy replenishment and by-product consumption. The target-initiated CtSDR amplification was established for RNA analysis, with order of magnitude lower limit of detection (LOD) than the Cas13a system. The CtSDR-based RNA in situ imaging strategy was developed to monitor intra-cellular microRNA expression change and delineate the landscape of oncogenic RNA in 66 clinic tissue samples, possessing a clear advantage over classic in situ hybridization (ISH) in terms of operation time (1 h versus 14 h) while showing comparable sensitivity and specificity. This work presents a promising approach to developing advanced molecular diagnostic tools.
Collapse
Affiliation(s)
- Xiaoxue Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
- Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiaosong Li
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yuexi Kang
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Decai Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510000, PR China
| | - Qiubo Yu
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Li Du
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yao Gong
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ming Yi
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Songzhi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shasha Zhu
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
- Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| |
Collapse
|
22
|
Wang H, Yang B, Tang H, Ding S, Liu G. Hairpin DNA-based electrochemical amplification strategy for miRNA sensing by using single gold nanoelectrodes. Analyst 2023; 148:5636-5641. [PMID: 37846736 DOI: 10.1039/d3an01551c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
A new sensor has been developed to detect miRNA-15 using nanoelectrodes and a hairpin DNA-based electrochemical amplification technique. By utilizing a complex DNA cylinder connected with hairpin DNA1, the sensor is able to absorb more methylene blue (MB) than simple double-stranded DNA. Another hairpin DNA2 is modified on an Au nanoelectrode surface and, when miRNA-15 is introduced, it triggers a chain reaction. This reaction unlocks two hairpins alternatively to polymerize into a complex structure that attaches more MB. The miRNA-15 is then replaced by DNA1 due to strand displacement reactions and continues to react with the next DNA2 to achieve circular amplification. The electrochemical signal from MB oxidation has a linear relationship with the miRNA-15 concentrations, making it possible to detect miRNA-15. Moreover, this method can be readily adapted for the detection of various other miRNA species. The newly devised nanosensor holds promising applications for the in vivo detection of miRNA-15 within biological systems, which is achieved by leveraging the advantageous characteristics of nanoelectrodes, including their low resistance-capacitance time constant, rapid mass transfer kinetics, and small diameter.
Collapse
Affiliation(s)
- Hao Wang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Binbin Yang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Haoran Tang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Sufang Ding
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Gen Liu
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| |
Collapse
|
23
|
Ang YS, Yung LYL. Design strategies for countering the effect of fluorophore-quencher labelling on DNA hairpin thermodynamics. Chem Commun (Camb) 2023; 59:13167-13170. [PMID: 37849331 DOI: 10.1039/d3cc02427j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
We report the impact of fluorophore-quencher labelling on the thermodynamics of hairpin opening by testing five fluorophores and two quenchers labelled at the end and/or internal positions. Two counter strategies were introduced, i.e. label the hairpin probe at an internal position or append an external hairpin stem on the trigger strand to promote coaxial stacking hybridization. The observations remained valid for complex hairpin opening operations such as hybridization chain reaction.
Collapse
Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.
| |
Collapse
|
24
|
Zhang X, Li H, Zhao W, Xu J, Wang S, Yu R. Development of a separation platform comprising magnetic beads combined with the CRISPR/Cas12a system enabling ultrasensitive and rapid detection of miRNA-21. Mikrochim Acta 2023; 190:458. [PMID: 37917353 DOI: 10.1007/s00604-023-06038-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
Abstract
A separation platform has been developed mediated by a combination of magnetic beads and the CRISPR/Cas12a system to achieve ultrasensitive and rapid detection of miRNA-21 at a low level. In this system, with the assistance of an auxiliary probe, the target miRNA-21 can be specifically combined with three-stranded probes to initiate the SDR reaction. Abundant aptamer A3 was added to the solution that can activate the CRISPR/Cas12a system and initiate the trans-cleavage reaction to recover the fluorescence signal. Using magnetic beads to mediate the separation considerably greatly improves the signal conversion efficiency and detection sensitivity. At the 492 nm excitation wavelength, and 502-650 nm scan range, through analyzing the fluorescence peak intensity at 520 nm, the biosensor's determination range and limit of detection is 8 fM-250 nM and 2.42 fM, respectively, and the RSD is 19.03-37.80. Compared with other biosensors, the biosensor developed exhibited superior performance and the signal recovered excellently in 1% human serum and the LOD is 12.12 fM. This method provides a novel highly sensitive scheme for detecting miRNA .
Collapse
Affiliation(s)
- Xinyi Zhang
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, People's Republic of China
| | - Hongbo Li
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, People's Republic of China.
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, People's Republic of China.
| | - Weihua Zhao
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, People's Republic of China
| | - Jun Xu
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, People's Republic of China
| | - Suqin Wang
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, People's Republic of China
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, People's Republic of China
| |
Collapse
|
25
|
Liu WJ, Wang LJ, Zhang CY. Progress in quantum dot-based biosensors for microRNA assay: A review. Anal Chim Acta 2023; 1278:341615. [PMID: 37709484 DOI: 10.1016/j.aca.2023.341615] [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: 05/04/2023] [Revised: 06/15/2023] [Accepted: 07/11/2023] [Indexed: 09/16/2023]
Abstract
MicroRNAs (miRNAs) are responsible for post-transcriptional gene regulation, and may function as valuable biomarkers for diseases diagnosis. Accurate and sensitive analysis of miRNAs is in great demand. Quantum dots (QDs) are semiconductor nanomaterials with superior optoelectronic features, such as high quantum yield and brightness, broad absorption and narrow emission, long fluorescence lifetime, and good photostability. Herein, we give a comprehensive review about QD-based biosensors for miRNA assay. Different QD-based biosensors for miRNA assay are classified by the signal types including fluorescent, electrochemical, electrochemiluminescent, and photoelectrochemical outputs. We highlight the features, principles, and performances of the emerging miRNA biosensors, and emphasize the challenges and perspectives in this field.
Collapse
Affiliation(s)
- Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Li-Juan Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| |
Collapse
|
26
|
Su J, Wang M, Lin P, Huang Z, Li G, Chen X, Yan H, Zhou L. Trigger-activated autonomous DNA machine for amplified liver cancer biomarker microRNA21 imaging. ANAL SCI 2023; 39:1661-1667. [PMID: 37552462 DOI: 10.1007/s44211-023-00397-3] [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: 07/06/2022] [Accepted: 09/03/2022] [Indexed: 08/09/2023]
Abstract
MicroRNA-21 (miRNA-21) is a kind of RNA that exists in biological fluids such as blood, urine and saliva. It has over expression in liver cancer and has different expression in different stages of cancer. However, due to the characteristics of small base number, short length, low abundance and easy degradation of miRNA-21, the detection of miRNA-21 is a challenging subject. Visualization, sensitive, specific and stable detection of tumor suppressor or oncogene microRNAs (miRNAs) remains challenging and is highly significant for clinical diagnostics. To solve this problem, we have developed a target-triggered hybridization assembly DNA machine for intracellular miRNA imaging based on strand displacement amplification (SDA) and branched hybridization chain reaction (B-HCR). In this approach, the target miRNA could hybridize with the template probe to trigger the SDA, resulting in the formation of nicked fragments (NFs) that hybridized with hairpin probe1 (HP1). The opened HP1 could hybridize with hairpin probe2 (HP2), leading to the self-assembly of hyperbranched DNA nanostructures through B-HCR. As expected, the newly developed method exhibits a detection limit down to 11.3 pM miRNA-21 and achieves high selectivity toward miRNA-21 against other interfering miRNAs. Due to its superior sensitivity and selectivity, our method can be further used to detect miRNA-21 in human serum samples. By taking advantage of intelligent design, the proposed method was also used for image miRNA-21 expression levels in different cell lines. This method shows a broad application in clinical diagnosis.
Collapse
Affiliation(s)
- Jiqin Su
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Maolin Wang
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Peiyi Lin
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Zhishu Huang
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Guibin Li
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Xiangru Chen
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Huidi Yan
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China.
| | - Lixin Zhou
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China.
| |
Collapse
|
27
|
Chen X, Huang C, Nie F, Hu M. Enzyme-free and sensitive method for single-stranded nucleic acid detection based on CHA and HCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4243-4251. [PMID: 37592315 DOI: 10.1039/d3ay00975k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Simple, rapid, and highly sensitive methods for single-stranded nucleic acid detection are of great significance in clinical testing. Meanwhile, common methods are inseparable from the participation of enzymes, which greatly increases their complexity. Herein, an enzyme-free and sensitive method combining HCR and CHA is established to detect single-stranded nucleic acid. A target induces the auxiliary hairpin strands to open their secondary structure, exposing partial sequences that can trigger catalytic hairpin assembly (CHA) and hybridization chain reactions (HCR), respectively. To avoid additional signaling substances, 2-aminopurines (which fluoresces differently in double-stranded DNA and G-quadruplex) are modified in the substrate chains of CHA and HCR. Compared with methods that adopt CHA or HCR alone, the sensitivity of this method is increased by nearly 10 times. Moreover, this method can effectively improve the specific recognition of the target. To "turn on" the method, two regions that can pair with H5 and H6 are required. Taking foot-and-mouth disease virus (FMDV) as the object, this method can specifically detect FMDV to 2.78 × 101 TCID50. Although the sensitivity is not as good as RT-qPCR, it owns the advantages of simplicity and speed. We think this method can be used for the primary screening of FMDV, and has application potential in some grassroots.
Collapse
Affiliation(s)
- Xiaolong Chen
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing 400037, China.
| | - Chaowang Huang
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing 400037, China.
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Chongqing Customs Technology Center, Chongqing, 400020, P. R. China
| | - Mingdong Hu
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing 400037, China.
- Department of Health Management, Xinqiao Hospital, Army Military Medical University, Chongqing 400037, China
| |
Collapse
|
28
|
Nie L, Zeng X, Hongbo L, Wang S, Lu Z, Yu R. Entropy-driven DNA circuit with two-stage strand displacement for elegant and robust detection of miRNA let-7a. Anal Chim Acta 2023; 1269:341392. [PMID: 37290851 DOI: 10.1016/j.aca.2023.341392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) research in cancer diagnosis is expanding, on account of miRNAs were demonstrated to be key indicator of gene expression and hopeful candidates for biomarkers. In this study, a stable miRNA-let-7a fluorescent biosensor was successfully designed based on an exonuclease Ⅲ-assisted two-stage strand displacement reaction (SDR). First, an entropy-driven SDR containing a three-chain structure of the substrate is used in our designed biosensor, leading to reduce the reversibility of the target recycling process in each step. The target acts on the first stage to start the entropy-driven SDR, which generates the trigger used to stimulate the exonuclease Ⅲ-assisted SDR in the second stage. At the same time, we design a SDR one-step amplification strategy as a comparison. Expectly, this developed two-stage strand displacement system has a low detection limit of 25.0 pM as well as a broad detection range of 4 orders of magnitude, making it more sensitive than the SDR one-step sensor, whose detection limit is 0.8 nM. In addition, this sensor has high specificity across members of the miRNA family. Therefore, we can take advantage of this biosensor to promote miRNA research in cancer diagnosis sensing systems.
Collapse
Affiliation(s)
- Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Xiaogang Zeng
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Li Hongbo
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Zhanghui Lu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| |
Collapse
|
29
|
Chen YL, Sun X, He JW, Xin MK, Liu D, Li CY. Light-Driven and Metal-Organic Framework Synergetic Loaded DNA Tetrahedral Amplifier for Exonuclease III-Powered All-in-One Biosensing and Chemotherapy in Live Biosystems. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37410886 DOI: 10.1021/acsami.3c06626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
As a result of inaccurate biosensing and difficult synergetic loading, it is challenging to further impel DNA amplifiers to perform therapeutic application. Herein, we introduce some innovative solutions. First, a smart light-driven biosensing concept based on embedding nucleic acid modules with a simple photocleavage-linker is proposed. In this system, the target identification component is exposed on irradiation with ultraviolet light, thus avoiding an always-on biosensing response during biological delivery. Further, in addition to providing controlled spatiotemporal behavior and precise biosensing information, a metal-organic framework is used for the synergetic loading of doxorubicin in the internal pores, whereafter a rigid DNA tetrahedron-sustained exonuclease III-powered biosensing system is attached to prevent drug leakage and enhance resistance to enzymatic degradation. By selecting a next-generation breast cancer correlative noncoding microRNA biomarker (miRNA-21) as a model low-abundance analyte, a highly sensitive in vitro detection ability even allowing to distinguish single-base mismatching is demonstrated. Moreover, the all-in-one DNA amplifier shows excellent bioimaging competence and good chemotherapy efficacy in live biosystems. These findings will drive research into the use of DNA amplifiers in diagnosis and therapy integrated fields.
Collapse
Affiliation(s)
- Ya-Ling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Jing-Wei He
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Meng-Kun Xin
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| |
Collapse
|
30
|
Chen W, Zhang H, Zhang Y, Hui M, Chen H, Ren C, Di D, Zhang H. Construction of dual exponential amplification accompanied by multi-terminal signal output method for convenient detection of tumor biomarker FEN1 activity. Anal Chim Acta 2023; 1263:341275. [PMID: 37225333 DOI: 10.1016/j.aca.2023.341275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/23/2023] [Indexed: 05/26/2023]
Abstract
As an important 5'-nuclease in DNA replication and damage repair, Flap endonuclease 1 (FEN1) has been considered as a potential tumor biomarker due to its overexpression in different human cancer cells. Here, we developed a convenient fluorescent method based on dual enzymatic repairing exponential amplification accompanied by multi-terminal signal output to realize the rapid and sensitive detection of FEN1. In the presence of FEN1, the double-branched substrate could be cleaved to produce 5' flap single strand DNA (ssDNA) which subsequently was used as a primer to initiate the dual exponential amplification (EXPAR) to generate abundant ssDNAs (X' and Y'), then the ssDNAs can respectively hybridize with the 3' and 5' ends of the signal probe to form partially complementary double strands (dsDNAs). Subsequently, the signal probe on the dsDNAs could be digested under the assistance of Bst. polymerase and T7 exonuclease, as well as releasing the fluorescence signals. The method displayed high sensitivity with the detection limit of 9.7 × 10-3 U mL-1 (1.94 × 10-4 U) and also exhibited good selectivity towards FEN1 under the challenge from complicated samples including extracts of normal and cancer cells. Furthermore, it was successfully applied to screen FEN1 inhibitors, holding great promise in the screening of potential drugs targeting FEN1. This sensitive, selective and convenient method could be used for FEN1 assay without the complicated nanomaterial synthesis/modification, showing great potential in FEN1- related prediction and diagnosis.
Collapse
Affiliation(s)
- Wei Chen
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Huige Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China; Key Laboratory of Special Function Materials and Structure Design (MOE), Lanzhou University, Lanzhou, 730000, China.
| | - Yanning Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Meiyi Hui
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Hongli Chen
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Cuiling Ren
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Duolong Di
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Haixia Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
31
|
Meng F, Yu W, Niu M, Tian X, Miao Y, Li X, Zhou Y, Ma L, Zhang X, Qian K, Yu Y, Wang J, Huang L. Ratiometric electrochemical OR gate assay for NSCLC-derived exosomes. J Nanobiotechnology 2023; 21:104. [PMID: 36964516 PMCID: PMC10037838 DOI: 10.1186/s12951-023-01833-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/26/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological type of LC and ranks as the leading cause of cancer deaths. Circulating exosomes have emerged as a valuable biomarker for the diagnosis of NSCLC, while the performance of current electrochemical assays for exosome detection is constrained by unsatisfactory sensitivity and specificity. Here we integrated a ratiometric biosensor with an OR logic gate to form an assay for surface protein profiling of exosomes from clinical serum samples. By using the specific aptamers for recognition of clinically validated biomarkers (EpCAM and CEA), the assay enabled ultrasensitive detection of trace levels of NSCLC-derived exosomes in complex serum samples (15.1 particles μL-1 within a linear range of 102-108 particles μL-1). The assay outperformed the analysis of six serum biomarkers for the accurate diagnosis, staging, and prognosis of NSCLC, displaying a diagnostic sensitivity of 93.3% even at an early stage (Stage I). The assay provides an advanced tool for exosome quantification and facilitates exosome-based liquid biopsies for cancer management in clinics.
Collapse
Affiliation(s)
- Fanyu Meng
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Wenjun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Minjia Niu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xvelian Li
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yan Zhou
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongchun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| |
Collapse
|
32
|
Yang X, Yuan L, Xu Y, He B. Target-catalyzed self-assembled spherical G-quadruplex/hemin DNAzymes for highly sensitive colorimetric detection of microRNA in serum. Anal Chim Acta 2023; 1247:340879. [PMID: 36781247 DOI: 10.1016/j.aca.2023.340879] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
The accurate and visual detection of circulating microRNA (miRNA) has attracted increasing interest due to its pivotal role in clinical disease diagnosis. Taking advantages of nucleic acid isothermal amplification and enzyme-catalyzed chromogenic reaction, here, a colorimetric sensing strategy was proposed for sensitive miRNA analysis. When the target miRNA was present, local catalytic hairpin assembly (CHA) would be triggered and proceed continuously to form dozens of double-stranded oligonucleotides with G-rich sticky ends on the gold nanoparticle, which could self-assemble into a spherical G-quadruplex (GQ)/hemin DNAzyme by binding with hemin and potassium ions. As a horseradish peroxidase-mimic, GQ/hemin DNAzyme could catalyze the redox reaction and color change of the substrates. Taking miRNA-21 as an example, the developed method exhibited satisfactory specificity as well as high sensitivity with a detection limit of 90.3 fM. Furthermore, the sensing platform has been successfully employed to detect miRNA-21 in spiked serum, providing a promising tool for early diagnosis of cancers.
Collapse
Affiliation(s)
- Xuejiao Yang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China.
| | - Liquan Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Yue Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| |
Collapse
|
33
|
Kuang J, Wang L, Yin Y, Shen W, Liu C, Lee HK, Tang S. Spatial Confinement of Single-Drop System to Enhance Aggregation-Induced Emission for Detection of MicroRNAs. Anal Chem 2023; 95:5346-5353. [PMID: 36931686 DOI: 10.1021/acs.analchem.2c05462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Due to high incidence, poor prognosis, and easy transformation into pancreatic cancer (PC) with high mortality, early diagnosis and prevention of acute pancreatitis (AP) have become significant research focuses. In this work, we proposed a magnetic single-drop microextraction (SDME) system with spatial confinement to enhance the aggregation-induced emission (AIE) effect for simultaneous fluorescence detection of miRNA-155 (associated with AP) and miRNA-196a (associated with PC). The target miRNAs were selectively recognized by the hairpin probe and triggered the DNA amplification reaction; then, the DNA strands with two independent probes of G-quadruplex/TAIN and Cy5 were constructed on the surfaces of the magnetic beads. The SDME process, in which a drop containing the fluorescence probes was formed at the tip of the magnetic microextraction rod rapidly within 10 s, was performed by magnetic extraction. In this way, G-quadruplex/TAIN was enriched owing to the spatial confinement of the single-drop system, and the fluorescence signal given off (by G-quadruplex/TAIN) was highly enhanced (AIE effect). This was detected directly by fluorescence spectrophotometry. The approach achieved low limits of detection of 2.1 aM for miRNA-196a and 8.1 aM for miRNA-155 and wide linear ranges from 10 aM to 10 nM for miRNA-196a and from 25 aM to 10 nM for miRNA-155. This novel method was applied to the fluorescence detection of miRNAs in human serum samples. High relative recoveries from 95.6% to 104.8% were obtained.
Collapse
Affiliation(s)
- Jingyu Kuang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Lina Wang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Yuqi Yin
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Hian Kee Lee
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| |
Collapse
|
34
|
Zhang Q, Zhang X, Zou X, Ma F, Zhang CY. CRISPR/Cas-Based MicroRNA Biosensors. Chemistry 2023; 29:e202203412. [PMID: 36477884 DOI: 10.1002/chem.202203412] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
As important post-transcriptional regulators, microRNAs (miRNAs) play irreplaceable roles in diverse cellular functions. Dysregulated miRNA expression is implicated in various diseases including cancers, and thus miRNAs have become the valuable biomarkers for disease monitoring. Recently, clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) system has shown great promise for the development of next-generation biosensors because of its precise localization capability, good fidelity, and high cleavage activity. Herein, we review recent advance in development of CRISPR/Cas-based biosensors for miRNA detection. We summarize the principles, features, and performance of these miRNA biosensors, and further highlight the remaining challenges and future directions.
Collapse
Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, 528458, P.R. China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University Institution, Nanjing, 211189, P.R. China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| |
Collapse
|
35
|
Hu Y, Jia Y, Yang Y, Liu Y. Controllable DNA nanodevices regulated by logic gates for multi-stimulus recognition. RSC Adv 2023; 13:9003-9009. [PMID: 36950078 PMCID: PMC10025943 DOI: 10.1039/d3ra00295k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
DNA biosensors have attracted considerable attention due to their great potential in environmental monitoring and medical diagnosis. Despite the great achievements, the single function and uncontrollability of the sensors restrict their further application. Therefore, it is necessary to construct controllable nanodevices with both sensing and responding capabilities to external stimuli. Herein, we develop a strategy to engineer structure-switching biosensors which can respond to external stimuli while preserving the sensing capability. The engineered nanodevice consists of an actuation module and a sensing module. Initially, the sensing module is disabled by a blocker strand which acts as an allosteric switch. Once the stimuli-responsive actuation module displaces the blocker DNA, the sensing module is activated. Based on the strategy, the engineered nanodevice could recognize both the target and external stimuli. As a demonstration of this strategy, a controllable Hg2+ sensor was designed, in which a 'YES', 'AND', and 'OR' logic gate is employed as the actuation module respectively to facilitate recognition of oligonucleotide inputs. The modular nature of the proposed strategy makes it easily generalizable to other structure-switching sensors. As a demonstration of this, we successfully apply it to the ATP sensor. The proposed strategy has potential in the fields of programmable biosensing, disease diagnosis, DNA computing, and intelligent nanodevices.
Collapse
Affiliation(s)
- Yingxin Hu
- School of Information Science and Technology, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| | - Yufeng Jia
- School of Management, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| | - Yuefei Yang
- School of Information Science and Technology, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| | - Yanjun Liu
- School of Information Science and Technology, Shijiazhuang Tiedao University Shijiazhuang 050043 P. R. China
| |
Collapse
|
36
|
He H, Zhou Y, Chen B, Zhang Y, Zhong X, Xu L, Guo B, Yin C, Zhou X, Li Q, Huang Z, Luo G, Guo X. Nucleic acid amplification with specific signal filtration and magnification for ultrasensitive colorimetric detection. Talanta 2023; 253:123978. [PMID: 36209643 DOI: 10.1016/j.talanta.2022.123978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.
Collapse
Affiliation(s)
- Hongfei He
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China; School of Pharmacy & School of Preclinical Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Chen
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Yi Zhang
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lei Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Chong Yin
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xi Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qingrong Li
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China.
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
| |
Collapse
|
37
|
Park G, Park H, Park SC, Jang M, Yoon J, Ahn JH, Lee T. Recent Developments in DNA-Nanotechnology-Powered Biosensors for Zika/Dengue Virus Molecular Diagnostics. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:361. [PMID: 36678114 PMCID: PMC9864780 DOI: 10.3390/nano13020361] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Zika virus (ZIKV) and dengue virus (DENV) are highly contagious and lethal mosquito-borne viruses. Global warming is steadily increasing the probability of ZIKV and DENV infection, and accurate diagnosis is required to control viral infections worldwide. Recently, research on biosensors for the accurate diagnosis of ZIKV and DENV has been actively conducted. Moreover, biosensor research using DNA nanotechnology is also increasing, and has many advantages compared to the existing diagnostic methods, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). As a bioreceptor, DNA can easily introduce a functional group at the 5' or 3' end, and can also be used as a folded structure, such as a DNA aptamer and DNAzyme. Instead of using ZIKV and DENV antibodies, a bioreceptor that specifically binds to viral proteins or nucleic acids has been fabricated and introduced using DNA nanotechnology. Technologies for detecting ZIKV and DENV can be broadly divided into electrochemical, electrical, and optical. In this review, advances in DNA-nanotechnology-based ZIKV and DENV detection biosensors are discussed.
Collapse
Affiliation(s)
- Goeun Park
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Hanbin Park
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Sang-Chan Park
- Department of Electronics Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Moonbong Jang
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Jinho Yoon
- Department of Biomedical-Chemical Engineering, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
| | - Jae-Hyuk Ahn
- Department of Electronics Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
- TL Bioindustry, 20 Kwangwoon-ro, Nowon-gu, Seoul 01897, Republic of Korea
| |
Collapse
|
38
|
Feng W, Zhang H, Le XC. Signal Amplification by the trans-Cleavage Activity of CRISPR-Cas Systems: Kinetics and Performance. Anal Chem 2023; 95:206-217. [PMID: 36625124 PMCID: PMC9835055 DOI: 10.1021/acs.analchem.2c04555] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
39
|
He S, Zhou Y, Xie Y, Zhang K, He Q, Yin G, Zou H, Hu Q, Zhang S, He H, Wang D. Isothermal amplification based on specific signal extraction and output for fluorescence and colorimetric detection of nucleic acids. Talanta 2023; 252:123823. [DOI: 10.1016/j.talanta.2022.123823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/23/2022] [Accepted: 08/04/2022] [Indexed: 10/15/2022]
|
40
|
Liu J, Xie G, Lv S, Xiong Q, Xu H. Recent applications of rolling circle amplification in biosensors and DNA nanotechnology. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
41
|
Shi G, Yan C, Chen J. Ultrasensitive Aptasensor for Microcystin-LR Detection in Food Samples Based on Target-Activated Assembly of Y-Shaped Hairpin Probes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16446-16452. [PMID: 36524375 DOI: 10.1021/acs.jafc.2c07661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
As a kind of algal toxin, microcystin-LR (MC-LR) causes a tremendous treat to food safety and the detection of trace levels of MC-LR is highly desirable. Herein, we developed an ultrasensitive aptasensor for MC-LR detection based on target-activated assembly of Y-shaped hairpins. The aptamer-target recognition initiates the assembly step between two Y-shaped hairpin probes through toehold-mediated DNA replacement. One of the hairpins was modified with FAM and BHQ. Through cyclic assembly reactions, a high fluorescence signal can be observed in the product. The detection limit is 0.2 pM for MC-LR detection. In addition, the biosensor is robust and has been successfully explored to assess the MC-LR concentrations in real fish and water samples with satisfactory recovery rates and good accuracy. The signal amplification can be gained through the cyclic Y-shaped hairpin assembly, which offers a simple, ultrasensitive, and reliable method for MC-LR monitoring in food samples.
Collapse
Affiliation(s)
- Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
42
|
Glucometer-based electrochemical biosensor for determination of microRNA (let-7a) using magnetic-assisted extraction and supersandwich signal amplification. Mikrochim Acta 2022; 189:444. [DOI: 10.1007/s00604-022-05544-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
|
43
|
DNA walker for signal amplification in living cells. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
44
|
Li M, Cheng J, Zheng H, Shi J, Shen Q. Label-free homogeneous electrochemical sensing strategy for microRNA detection. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
45
|
Li L, Fang X, Le J, Zheng Y, Tan X, Jiang Z, Li H, Xu J, Xu H. Highly sensitive detection and intracellular imaging of MicroRNAs based on target-triggered cascade catalytic hairpin assembly. Talanta 2022; 250:123753. [DOI: 10.1016/j.talanta.2022.123753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022]
|
46
|
Chen Z, Wang WT, Wang W, Huang J, Liao JY, Zeng S, Qian L. Sensitive Imaging of Cellular RNA via Cascaded Proximity-Induced Fluorogenic Reactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:44054-44064. [PMID: 36153979 DOI: 10.1021/acsami.2c10355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Owing to its important biological functions, RNA has become a promising molecular biomarker of various diseases. With a dynamic change in its expression level and a relatively low amount within the complicated biological matrix, signal amplification detection based on DNA probes has been put forward, which is helpful for early diagnosis and prognostic prediction. However, conventional methods are confined to cell lysates or dead cells and are not only time-consuming in sample preparation but also inaccessible to the spatial-temporal information of target RNAs. To achieve live-cell imaging of specific RNAs, both the detection sensitivity and intracellular delivery issues should be addressed. Herein, a new cascaded fluorogenic system based on the combination of hybridization chain reactions (HCRs) and proximity-induced bioorthogonal chemistry is developed, in which a bioorthogonal reaction pair (a tetrazine-quenched dye and its complementary dienophile) is brought into spatial proximity upon target RNA triggering the HCR to turn on and amplify the fluorescence in one step, sensitively indicating the cellular distribution of RNA with minimal false positive results caused by unspecific degradation. Facilitated by a biodegradable carrier based on black phosphorus with high loading capacity and excellent biocompatibility, the resulting imaging platform allows wash-free tracking of target RNAs inside living cells.
Collapse
Affiliation(s)
- Zhiyan Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wen-Tao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wenchao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinsong Huang
- Department of Liver Disease, Hangzhou Xixi Hospital, Hangzhou 310023, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
47
|
Zhang Q, Zhao R, Li CC, Zhang Y, Tang C, Luo X, Ma F, Zhang CY. Construction of an Entropy-Driven Dumbbell-Type DNAzyme Assembly Circuit for Lighting Up Uracil-DNA Glycosylase in Living Cells. Anal Chem 2022; 94:13978-13986. [PMID: 36179339 DOI: 10.1021/acs.analchem.2c03223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sensitive monitoring of intracellular uracil-DNA glycosylase (UDG) in living cells is essential to understanding the DNA repair pathways and discovery of anticancer drugs. Herein, we demonstrate the construction of an entropy-driven dumbbell-type DNAzyme assembly circuit for lighting up UDG in living cells via the integration of entropy-driven DNA catalysis (EDC) with the DNAzyme biocatalyst. Target UDG excises the damaged uracil base, causing the breakage of detection probe and the release of trigger. The released trigger can initiate the downstream EDC reaction to form two catalytically active DNAzyme units. The resultant dual Mg2+-DNAzyme units serve as the signal transducers to cyclically cleave the fluorophore/quenched-modified reporters, generating an enhanced fluorescence signal. In contrast to the single-layered EDC method with a linear amplification, the proposed doublet EDC-DNAzyme strategy exhibits high signal gain and achieves a detection limit of 8.71 × 10-6 U/mL. Notably, this assay can be performed in one-step manner at room temperature without the requirement of strict temperature control and complicated reaction procedures, and it can further screen the UDG inhibitors, measure kinetic parameters, and discriminate cancer cells from normal cells. Moreover, this strategy can monitor intracellular UDG activity with improved signal gain, and it may be exploited for sensing and imaging of other types of DNA modifying enzymes with the integration of the corresponding detection substrate, providing a facile and robust approach for biological research studies and clinical diagnosis.
Collapse
Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Ran Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chen-Chen Li
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chunying Tang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| |
Collapse
|
48
|
Zhang J, Miao X, Song C, Chen N, Xiong J, Gan H, Ni J, Zhu Y, Cheng K, Wang L. Non-enzymatic signal amplification-powered point-of-care SERS sensor for rapid and ultra-sensitive assay of SARS-CoV-2 RNA. Biosens Bioelectron 2022; 212:114379. [PMID: 35635970 PMCID: PMC9110061 DOI: 10.1016/j.bios.2022.114379] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/12/2022] [Accepted: 05/13/2022] [Indexed: 01/25/2023]
Abstract
The development of rapid and ultra-sensitive detection technology of SARS-CoV-2 RNA for shortening the diagnostic window and achieving early detection of virus infections is a huge challenge to the efficient prevention and control of COVID-19. Herein, a novel ultra-sensitive surface-enhanced Raman spectroscopy (SERS) sensor powered by non-enzymatic signal amplification is proposed for rapid and reliable assay of SARS-CoV-2 RNA based on SERS-active silver nanorods (AgNRs) sensing chips and a specially designed smart unlocking-mediated target recycling signal amplification strategy. The SERS sensing was carried out by a one-pot hybridization of the lock probes (LPs), hairpin DNAs and SERS tags with SARS-CoV-2 RNA samples on an arrayed SERS sensing chip to achieve the recognition of SARS-CoV-2 RNA, the execution of nuclease-free unlocking-mediated target recycling signal amplification, and the combination of SERS tags to generate SERS signal. The SERS sensor for SARS-CoV-2 RNA can be achieved within 50 min with an ultra-high sensitivity low to 51.38 copies/mL, and has good selectivity in discriminating SARS-CoV-2 RNA against other respiratory viruses in representative clinical samples, which is well adapted for rapid, ultra-sensitive, multi-channel and point-of-care testing of viral nucleic acids, and is expected to achieve detection of SARS-CoV-2 infection in earlier detection windows for efficient COVID-19 prevention and control.
Collapse
Affiliation(s)
- Jingjing Zhang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Xiaping Miao
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, 10 Luoxuan 3rd Road, Guangzhou International Biotech Island, Guangdong, 510005, Guangdong, China; Guangzhou Laboratory, No.9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China
| | - Chunyuan Song
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China.
| | - Na Chen
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, 10 Luoxuan 3rd Road, Guangzhou International Biotech Island, Guangdong, 510005, Guangdong, China
| | - Jingrong Xiong
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Hongyu Gan
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Jie Ni
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Yunfeng Zhu
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China
| | - Kaiting Cheng
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, 10 Luoxuan 3rd Road, Guangzhou International Biotech Island, Guangdong, 510005, Guangdong, China; Guangzhou Laboratory, No.9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
| | - Lianhui Wang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, China.
| |
Collapse
|
49
|
Su J, Du J, Ge R, Sun C, Qiao Y, Wei W, Pang X, Zhang Y, Lu H, Dong H. Metal–Organic Framework-Loaded Engineering DNAzyme for the Self-Powered Amplified Detection of MicroRNA. Anal Chem 2022; 94:13108-13116. [DOI: 10.1021/acs.analchem.2c02547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Rujiao Ge
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yuchun Qiao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Xuejiao Pang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yufan Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Huiting Lu
- Department of Chemistry, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P. R. China
| |
Collapse
|
50
|
Deng W, Xu JY, Peng H, Huang CZ, Le XC, Zhang H. DNAzyme motor systems and logic gates facilitated by toehold exchange translators. Biosens Bioelectron 2022; 217:114704. [PMID: 36113301 DOI: 10.1016/j.bios.2022.114704] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
DNAzyme motor systems using gold nanoparticles (AuNPs) as scaffolds are useful for biosensing and in situ amplification because these systems are free of protein enzymes, isothermal, homogeneous, and sensitive. However, detecting different targets using the available DNAzyme motor techniques requires redesigns of the DNAzyme motor. We report here a toehold-exchange translator and the translator-mediated DNAzyme motor systems, which enable sensitive responses to various nucleic acid targets using the same DNAzyme motor without requiring redesign. The translator is able to efficiently convert different nucleic acid targets into a specific output DNA that further activates the pre-silenced DNAzyme motor and consequently initiates the autonomous walking of the DNAzyme motor. Simply adjusting the target-binding region of the translator enables the same DNAzyme motor system to respond to various nucleic acid targets. The translator-mediated DNAzyme motor system is able to detect as low as 2.5 pM microRNA-10b and microRNA-21 under room temperature without the need of separation or washing. We further demonstrate the versatility of the translator and the DNAzyme motor by successful construction and operation of four logic gates, including OR, AND, NOR, and NAND logic gates. These logic gates use two microRNA targets as inputs and generate amplified fluorescence signals from the operation of the same DNAzyme motor. Incorporation of the toehold-exchange translator into the DNAzyme motor technology improves the biosensing applications of DNA motors to diverse nucleic acid targets.
Collapse
Affiliation(s)
- Wenchan Deng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada; College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Jing Yang Xu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hanyong Peng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Cheng Zhi Huang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
| |
Collapse
|