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Ban Y, Zhou F, Wang H, Zhang F, Xia M, Wan Y, Yang S, Liu R, Wang X, Wang G. Dual-Stimuli Regulation of DNAzyme Cleavage Reaction by Coordination-Driven Nanoprobes for Cancer Cell Imaging. ACS APPLIED MATERIALS & INTERFACES 2024; 16:30766-30775. [PMID: 38833714 DOI: 10.1021/acsami.4c04033] [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: 06/06/2024]
Abstract
Endowing current artificial chemical reactions (ACRs) with high specificity and intricate activation capabilities is crucial for expanding their applications in accurate bioimaging within living cells. However, most of the reported ACR-based evaluations relied on either single biomarker stimuli or dual activators without obvious biological relevance, still limiting their accuracy and fidelity. Herein, taking the metal-ion-dependent DNAzyme cleavage reaction as a model ACR, two regulators, glutathione (GSH) and telomerase (TE) activated DNAzyme cleavage reactions, were exploited for precise discrimination of cancerous cells from normal cells. DNA probe was self-assembled into the ZIF-90 nanoparticle framework to construct coordination-driven nanoprobes. This approach enhances the stability and specificity of tumor imaging by utilizing biomarkers associated with rapid tumor proliferation and those commonly overexpressed in tumors. In conclusion, the research not only paves the way for new perspectives in cell biology and pathology studies but also lays a solid foundation for the advancement of biomedical imaging and disease diagnostic technologies.
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Affiliation(s)
- Yinbo Ban
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Fu Zhou
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Hao Wang
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Fuqiang Zhang
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Mengmeng Xia
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Yifei Wan
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Suwan Yang
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Rong Liu
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, P. R. China
| | - Guangfeng Wang
- College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, and Anhui Province Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000, China
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2
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Zhang F, Yang N, Zhou F, Qiao R, Wan Y, Liu R, Yang S, Gu M, Xu H, Dong X, Wang G. Orthogonally Sequential Activation of Self-Powered DNAzymes Cascade for Reliable Monitoring of mRNA in Living Cells. Adv Healthc Mater 2024; 13:e2303074. [PMID: 38197479 DOI: 10.1002/adhm.202303074] [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: 09/13/2023] [Revised: 12/06/2023] [Indexed: 01/11/2024]
Abstract
Ratiometric imaging of tumor-related mRNA is significant, yet spatiotemporally resolved regulation on the ratiometric signals to avoid non-specific activation in the living cells remains challenging. Herein, orthogonally sequential activation of concatenated DNAzyme circuits is, first, developed for Spatio Temporally regulated Amplified and Ratiometric (STAR) imaging of TK1 mRNA inside living cells with enhanced reliability and accuracy. By virtue of the synthesized CuO/MnO2 nanosheets, orthogonally regulated self-powered DNAzyme circuits are operated precisely in living cells, sequentially activating two-layered DNAzyme cleavage reactions to achieve the two ratiometric signal readouts successively for reliable monitoring of low-abundance mRNA in living cells. It is found that the ratiometric signals can only be derived from mRNA over-expressed tumor cells, also irrespective of probes' delivery concentration. The presented approach could provide new insight into orthogonally regulated ratiometric systems for reliable imaging of specific biomarkers in living cells, benefiting disease precision diagnostics.
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Affiliation(s)
- Fuqiang Zhang
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Nan Yang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Fu Zhou
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Ruonan Qiao
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Yifei Wan
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Rong Liu
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Suwan Yang
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Mingzheng Gu
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Huae Xu
- Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, 210009, China
| | - Xiaochen Dong
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, China
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Guangfeng Wang
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
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3
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Chen Y, Song Y, Wang X, Tang H, Li C. Genetically engineered virus-like particle-armoured and multibranched DNA scaffold-corbelled ultra-sensitive hierarchical hybridization chain reaction for targeting-enhanced imaging in living biosystems under spatiotemporal light powering. Biosens Bioelectron 2024; 247:115943. [PMID: 38141440 DOI: 10.1016/j.bios.2023.115943] [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: 09/28/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Although nucleic acids-based fluorescent biosensors, exemplified by the hybridization chain reaction (HCR), have exhibited promise as an imaging tool for detecting disease-related biomolecular makers in living biosystems, they still face certain challenges. These include the need for improved sensitivity, poor bio-targeting capability, the absence of signal enrichment interface and the uncontrollable biosensing initiation. Herein, we present a range of effective solutions. First, a stacking design resembling building blocks is used to construct a special hierarchical HCR (termed H-HCR), for which a hierarchical bridge is employed to graft multiunit HCR products. Furthermore, the H-HCR components are encapsulated into a virus-like particle (VLP) endowed with a naturally peptide-mediated targeting unit through genetic engineering of plasmids, after which the biosensor can specifically identify cancer cytomembranes. By further creating a multibranched DNA scaffold to enrich the H-HCR produced detection signals, the biosensor's analyte recognition module is inserted with a photocleavage-linker, allowing that the biosensing process can be spatiotemporally initiated via a light-powered behavior. Following these innovations, this genetically engineered VLP-armoured and multibranched DNA-scaffold-corbelled H-HCR demonstrates an ultra-sensitive and specific biosensing performance to a cancer-associated microRNA marker (miRNA-155). Beyond the worthy in vitro analysis, our method is also effective in performing imaging assays for such low-abundance analyte in living cells and even bodies, thus providing a roust platform for disease diagnosis.
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Affiliation(s)
- Yaling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Yongyao Song
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Xiaomei Wang
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
| | - Hongwu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chengyu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
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Zhou X, Geng H, Shi P, Wang H, Zhang G, Cui Z, Lv S, Bi S. NIR-driven photoelectrochemical-fluorescent dual-mode biosensor based on bipedal DNA walker for ultrasensitive detection of microRNA. Biosens Bioelectron 2024; 247:115916. [PMID: 38104392 DOI: 10.1016/j.bios.2023.115916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Optical biosensors have become powerful tools for bioanalysis, but most of them are limited by optic damage, autofluorescence, as well as poor penetration ability of ultraviolet (UV) and visible (Vis) light. Herein, a near-infrared light (NIR)-driven photoelectrochemical (PEC)-fluorescence (FL) dual-mode biosensor has been proposed for ultrasensitive detection of microRNA (miRNA) based on bipedal DNA walker with cascade amplification. Fueled by toehold-mediated strand displacement (TMSD), the bipedal DNA walker triggered by target miRNA-21 is formed through catalytic hairpin assembly (CHA), which can efficiently move along DNA tracks on CdS nanoparticles (CdS NPs)-modified fluorine doped tin oxide (FTO) electrode, resulting in the introduction of upconversion nanoparticles (UCNPs) on electrode surface. Under 980 nm laser irradiation, the UCNPs serve as the energy donor to emit UV/Vis light and excite CdS NPs to generate photocurrent for PEC detection, while the upconversion luminescence (UCL) at 803 nm is monitored for FL detection. This PEC-FL dual-mode biosensor has achieved the ultrasensitive and accurate analysis of miRNA-21 in human serum and different gynecological cancer cells. Overall, the proposed dual-mode biosensor can not only couple the inherent features of each single-mode biosensor but also provide mutual authentication of testing results, which opens up a new avenue for early diagnosis of miRNA-related diseases in clinic.
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Affiliation(s)
- Xuemin Zhou
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; Department of Ultrasonic Medicine, Binzhou Medical University Hospital, Binzhou, 256603, PR China
| | - Hongyan Geng
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China
| | - Pengfei Shi
- College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China; Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, PR China
| | - Huijie Wang
- College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China
| | - Guofang Zhang
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China.
| | - Shuzhen Lv
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China.
| | - Sai Bi
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China.
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5
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He JW, Sun X, Tang HW, Liu D, Li CY. Photoresponsive CHA-Integrated Self-Propelling 3D DNA Walking Amplifier within the Concentration Localization Effect of DNA Molecular Framework Enables Highly Efficient Fluorescence Bioimaging. Anal Chem 2024; 96:2142-2151. [PMID: 38258616 DOI: 10.1021/acs.analchem.3c04920] [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: 01/24/2024]
Abstract
While three-dimensional (3D) DNA walking amplifiers hold considerable promise in the construction of advanced DNA-based fluorescent biosensors for bioimaging, they encounter certain difficulties such as inadequate sensitivity, premature activation, the need for exogenous propelling forces, and low reaction rates. In this contribution, a variety of profitable solutions have been explored. First, a catalytic hairpin assembly (CHA)-achieved nonenzymatic isothermal nucleic acid amplification is integrated to enhance sensitivity. Subsequently, one DNA component is simply functionalized with a photocleavage-bond to conduct a photoresponsive manner, whereby the target recognition occurs only when the biosensor is exposed to an external ultraviolet light source, overcoming premature activation during biodelivery. Furthermore, a special self-propelling walking mechanism is implemented by reducing biothiols to MnO2 nanosheets, thereby propelling forces that are self-supplied to a Mn2+-reliant DNAzyme. By carrying the biosensing system with a DNA molecular framework to induce a unique concentration localization effect, the nucleic acid contact reaction rate is notably elevated by 6 times. Following these, an ultrasensitive in vitro detection performance with a limit of detection down to 2.89 fM is verified for a cancer-correlated microRNA biomarker (miRNA-21). Of particular importance, our multiple concepts combined 3D DNA walking amplifier that enables highly efficient fluorescence bioimaging in live cells and even bodies, exhibiting a favorable application prospect in disease analysis.
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Affiliation(s)
- 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
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Hong-Wu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Da Liu
- 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
| | - 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
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Hu X, Qiu D, Jiang Q, Xu Q, Li J. Cu 2+-doped zeolitic imidazolate frameworks and gold nanoparticle (AuNPs@ZIF-8/Cu) nanocomposites enable label-free and highly sensitive electrochemical detection of oral cancer-related biomarkers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:615-623. [PMID: 38197313 DOI: 10.1039/d3ay01918g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
It is of great significance to accurately and sensitively detect oral cancer-related biomarkers (ORAOV 1) for the early diagnosis of oral cancer. Present here is a novel electrochemical biosensor based on Cu2+-doped zeolitic imidazolate frameworks and gold nanoparticle (AuNPs@ZIF-8/Cu) nanocomposites and a one-step strand displacement reaction for label-free, simple and sensitive detection of ORAOV 1 in saliva. It is worth noting that AuNPs@ZIF-8/Cu nanocomposites show large electrochemically effective surface area, good electrical conductivity and electrocatalytic activity due to the synergistic effect of metal nanoparticles (MNPs) and ZIF-8. Consequently, the newly developed electrochemical sensor displays a wide linear range of 0.1-104 pM and a low limit of detection (LOD) of 63 fM. Meanwhile, the electrochemical biosensor can distinguish single base mismatch. The relative standard deviation (RSD) of intra-assays and inter-assays is 1.46% and 1.76%, respectively, and the peak current values decline by 9.20% with a RSD value of 1.35% after being stored at 4 °C for 7 days, suggesting that the newly designed electrochemical sensor exhibits good selectivity, reproducibility and stability to detect ORAOV 1. More importantly, this novel electrochemical sensor is found to be applicable for detecting ORAOV 1 in human saliva samples with a satisfactory result. The RSD values range from 1.15% to 1.77%, and the recoveries range from 95.46% to 112.98%.
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Affiliation(s)
- Xueting Hu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Dengxue Qiu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Qi Jiang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Qin Xu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
| | - Jing Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, P. R. China.
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7
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Huang X, Li Z, Shi Y, Zhang Y, Shen T, Chen M, Huang Z, Tong Y, Liu SY, Guo J, Zou X, Dai Z. A DNAzyme dual-feedback autocatalytic exponential amplification biocircuit for microRNA imaging in living cells. Biosens Bioelectron 2023; 241:115669. [PMID: 37688849 DOI: 10.1016/j.bios.2023.115669] [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: 07/15/2023] [Revised: 08/21/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023]
Abstract
Autocatalytic biocircuit are powerful tools for analysing intracellular biomarkers, but these tools are constrained by limitations in amplification capacity and intracellular delivery efficiency. In this work, we developed a DNAzyme-based dual-feedback autocatalytic exponential amplification biocircuit sustained by a honeycomb MnO2 nanosponge (EDA2@hMNS) for live-cell imaging of intracellular low-abundance microRNAs (miRNA). The EDA2 biocircuit comprises a blocked DNAzyme (b-DNAzyme), a Fuel strand and a Substrate strand. In the EDA2 biocircuit, target miRNAs are recycled and feedback for rounds of DNAzymatic amplification, and the DNAzymatic reactions continuously generate target miRNA analogues for dual-feedback to achieve multiple parallel cascade DNAzymatic reactions that improve amplification capacity substantially. In addition, the hMNS ensures high loading and delivery efficiency of biocircuit probes into living cells and also provides sufficient Mn2+ DNAzyme cofactor from in situ decomposition by intracellular glutathione (GSH). The EDA2@hMNS realized a detection limit of 17 pM, which is 288-fold lower than the b-DNAzyme lacking the DNAzymatic amplification. These results demonstrate the great promise for this critical tool in analysing low-abundance biomarkers and cancer diagnostics.
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Affiliation(s)
- Xing Huang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zihao Li
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yakun Shi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Taorong Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Meng Chen
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zhan Huang
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanli Tong
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Si-Yang Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jianhe Guo
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China.
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8
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Lu Y, Yu Y, Wang Y, Zhou W, Cheng Z, Yu L, Zheng S, Gao R. A micro-nano interface integrated SERS-based microfluidic sensor for miRNA detection using DNAzyme walker amplification. Anal Chim Acta 2023; 1283:341957. [PMID: 37977782 DOI: 10.1016/j.aca.2023.341957] [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: 09/06/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Precise and specific miRNA detection plays a vital role in exploring development mechanisms of cancer disease, thereby it can significantly improve relevant prevention and treatment strategies. RESULTS In this work, a surface-enhanced Raman spectroscopy (SERS)-based microfluidic chip has been devised with a microcone array SERS substrate (MCASS) for the miR-141 detection. This substrate excels in unique SERS activity and large surface area for DNA oligonucleotide modification. As the presence of miR-141, the DNAzyme walker induced cleavage reaction took place on the finely designed and prepared dual DNA conjugated SERS nanoprobes. The SERS nanoprobes can anchor on MCASS by the DNA hybridization that achieved an impressive detection limit in the femtomolar level. SIGNIFICANCE With this integrated SERS-based microfluidic chip, we provided a miRNA detection strategy using DNAzyme walker amplification technology. It is believed that this strategy could be a powerful tool for miRNA detection and related cancer screening test.
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Affiliation(s)
- Yang Lu
- College of Control Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Yiyue Yu
- College of Control Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Yeru Wang
- College of Control Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wenbo Zhou
- College of Control Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Ziyi Cheng
- Hainan Cancer Medical Center of The First Affiliated Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Women and Children Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Liandong Yu
- College of Control Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Shaojiang Zheng
- Hainan Cancer Medical Center of The First Affiliated Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Women and Children Medical Center, Hainan Medical University, Haikou, 571199, China.
| | - Rongke Gao
- College of Control Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
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9
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Wei R, Wang K, Liu X, Shi M, Pan W, Li N, Tang B. Stimuli-responsive probes for amplification-based imaging of miRNAs in living cells. Biosens Bioelectron 2023; 239:115584. [PMID: 37619479 DOI: 10.1016/j.bios.2023.115584] [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: 07/02/2023] [Revised: 07/29/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
MicroRNAs (miRNAs) have emerged as important biomarkers in biomedicine and bioimaging due to their roles in various physiological and pathological processes. Real-time and in situ monitoring of dynamic fluctuation of miRNAs in living cells is crucial for understanding these processes. However, current miRNA imaging probes still have some limitations, including the lack of effective amplification methods for low abundance miRNAs bioanalysis and uncontrollable activation, leading to background signals and potential false-positive results. Therefore, researchers have been integrating activatable devices with miRNA amplification techniques to design stimuli-responsive nanoprobes for "on-demand" and precise imaging of miRNAs in living cells. In this review, we summarize recent advances of stimuli-responsive probes for the amplification-based imaging of miRNAs in living cells and discuss the future challenges and opportunities in this field, aiming to provide valuable insights for accurate disease diagnosis and monitoring.
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Affiliation(s)
- Ruyue Wei
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Kaixian Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Xiaohan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Mingwan Shi
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China.
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China; Laoshan Laboratory, Qingdao, 266237, PR China.
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10
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Jin Y, Huang Z, Xu B, Chen J. Localization of multiple DNAzymes as a branchedzyme-powered nanodevice for the immunoassay of tumor biomarkers. Anal Chim Acta 2023; 1274:341580. [PMID: 37455088 DOI: 10.1016/j.aca.2023.341580] [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: 04/19/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Traditional immunoassay methods often face challenges due to the labeling procedure of protein enzymes, the use of multiple antibodies, and severe conditions. To address these limitations, we propose the concept of incorporating branchedzyme-powered nanodevices into immunoassays. In this strategy, multiple DNAzymes are localized onto gold nanoparticles (AuNPs) along with substrates. The localization format facilitates intramolecular reactions between DNAzymes and substrates, leading to accelerated kinetics of the nanodevice. Upon the formation of an immunocomplex with an antibody on a 96-well plate, the branchedzyme-powered nanodevice catalytically releases multiple fluorescent signals under ambient temperature, eliminating the need for secondary antibodies. The branched DNAzymes exhibit catalytic properties similar to those of protein enzymes, thus simplifying the assay procedure and achieving isothermal detection. Furthermore, the detection process can be controlled by the addition or deletion of cofactors. Additionally, the affinity ligand can be easily modified to construct nanodevices specific to different targets without requiring extensive redesign. This strategy has demonstrated successful quantification of tumor biomarkers such as alpha-fetoprotein (AFP) and prostate-specific antigen (PSA) at subpicomolar concentrations, showcasing its suitability for clinical applications. Consequently, the branchedzyme-powered nanodevice represents a valuable addition to the immunoassay toolbox, opening new possibilities for clinical diagnostics.
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Affiliation(s)
- Yanwen Jin
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan Universtity, Chengdu, Sichuan, 610064, China
| | - Zhuochun Huang
- Department of Laboratory Medicine, West China Hospital, Sichuan Universtity, Chengdu, Sichuan, 610064, China
| | - Bingyan Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan Universtity, Chengdu, Sichuan, 610064, China
| | - Junbo Chen
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan, 610064, China.
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11
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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12
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25300-25312. [PMID: 37204867 PMCID: PMC10331730 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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13
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Zhou N, Cai R. Quantitative Determination of Staphylococcus aureus Using Aptamer-Based Recognition and DNA Amplification Machinery. Methods Mol Biol 2023; 2681:1-18. [PMID: 37405639 DOI: 10.1007/978-1-0716-3279-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Staphylococcus aureus (S. aureus) is a common foodborne pathogen that threatens human health and safety. It is significant to develop sensitive detection methods for the monitoring of S. aureus contamination in food and environment. Herein, a novel machinery based on aptamer recognition, DNA walker, and rolling circle amplification (RCA) was designed, which can form unique DNA nanoflower and subsequently detect low-level S. aureus contamination in samples. To this end, two rationally designed DNA duplexes were modified on the surface of the electrode to identify S. aureus through the high affinity between aptamers and S. aureus. Combined with the repeated movement of DNA walker machinery on the electrode surface and RCA technology, a unique DNA nanoflower structure was formed. This can effectively transform the biological information of aptamer recognition of S. aureus into a significantly amplified electrochemical signal. Through reasonable design and optimization of the parameters of each part, the linear response range of the S. aureus biosensor is from 60 to 6 × 107 CFU/mL and the detection limit is as low as 9 CFU/mL.
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Affiliation(s)
- Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Rongfeng Cai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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14
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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]
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15
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Ratiometric Electrochemical Biosensing of Methyltransferase Activity. Catalysts 2022. [DOI: 10.3390/catal12111362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).
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16
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Cheng S, Shi Y, Su C, Li Y, Zhang X. MnO 2 nanosheet-mediated generalist probe: Cancer-targeted dual-microRNAs detection and enhanced CDT/PDT synergistic therapy. Biosens Bioelectron 2022; 214:114550. [PMID: 35834977 DOI: 10.1016/j.bios.2022.114550] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 11/02/2022]
Abstract
While integrated nanoplatform for diagnosis and therapy has received much recent interest, its widespread application has been hampered by the complicated preparation process, high-cost and low-efficacy. Herein, we designed a MnO2 nanosheet-mediated generalist probe (MNSGP), for intracellular dual-microRNAs (miRNAs) imaging and enhanced synergistic therapy of chemodynamic therapy (CDT) and photodynamic therapy (PDT). Because MNSGP can specifically target nucleolin receptor overexpressed on the cancer cell surface, it can be internalized via a receptor-mediated endocytosis pathway. After entering the cells, MnO2 NS was degraded to Mn2+ by the excessive glutathione (GSH), releasing the DNA probes for cyclic amplification detection of miR-155 and miR-21 based on toehold-mediated strand displacement amplification (TSDA). Meanwhile, the produced O2 by MnO2 NS catalysis can promote the photosensitizer TMPyP4 to produce singlet oxygen (1O2) for PDT. The degraded Mn2+, as Fenton reagent, can convert endogenous H2O2 to cytotoxic hydroxyl radical (·OH) for CDT. In addition, the depletion of GSH impairs the antioxidant defense system (ADS), enhancing the CDT/PDT synergistic effect. The prepared generalist probe was fully characterized. Accuracy of dual-miRNAs detection and the high curative effect of enhanced CDT/PDT synergistic therapy were attested via in vitro and in vivo experiments. Unarguably, MNSGP broadens new horizons in the design of nucleic acid nanoplatform, cancer-targeted detection and theranostic application.
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Affiliation(s)
- Simin Cheng
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Ying Shi
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Cong Su
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Ying Li
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Xiaoru Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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17
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Zhang J, Yu J, Jin J, Zhou X, Liang H, Zhou F, Jiang W. Bridge DNA guided assembly of nanoparticles to program chemical reaction networks. NANOSCALE 2022; 14:12162-12173. [PMID: 35968811 DOI: 10.1039/d2nr03948f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bridge DNA is an essential structure for programming chemical reaction networks. In this work, a bridge DNA guided assembly of nanoparticles has been constructed to program one-step and multi-step reactions via toehold-mediated strand displacement reaction for higher structural complexity and dynamic regulation behaviors. The structures of the bridge DNA linker and the length of the toeholds have an essential effect on successful construction of a molecular machine and achievement of multi-step reactions. A six-base toehold is enough to achieve the toehold-mediated strand displacement reaction in bridge DNA. When the difference between toehold length-2 and toehold length-1 is equal to or larger than one, the multi-step reaction can be triggered and performed by the driving of bridge DNA. For application, both simultaneous detection of two target DNA strands as well as the construction of logic gates can be achieved by changing the four single-stranded tails on the bridge DNA. In principle, this approach of the bridge DNA guiding the assembly of AuNPs can implement any behavior that can be expressed mathematically.
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Affiliation(s)
- Jianing Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jiayu Yu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jing Jin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
| | - Xiang Zhou
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Haojun Liang
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Feng Zhou
- Personalized Prescribing Inc., Toronto, ON M3C 3E5, Canada
| | - Wei Jiang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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18
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Zhu X, Xu N, Zhang L, Wang D, Zhang P. Novel design of multifunctional nanozymes based on tumor microenvironment for diagnosis and therapy. Eur J Med Chem 2022; 238:114456. [DOI: 10.1016/j.ejmech.2022.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/26/2022]
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19
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pH-activated DNA nanomachine for miRNA-21 imaging to accurately identify cancer cell. Mikrochim Acta 2022; 189:266. [PMID: 35776208 DOI: 10.1007/s00604-022-05340-3] [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: 01/21/2022] [Accepted: 05/14/2022] [Indexed: 10/17/2022]
Abstract
MicroRNA (miRNA) imaging has been employed to distinguish cancer cells from normal cells by exploiting the overexpression of miRNA in cancer. Inspired by the acidic extracellular tumor microenvironment, we designed a pH-activated DNA nanomachine to enable the specific detection of cancer cells using miRNA imaging. The DNA nanomachine was engineered by assembling two hairpins (Y1 and Y2) onto the surface of a ZIF-8 metal-organic framework (MOF), which decomposed under acidic conditions to release the adsorbed DNA hairpin molecules in situ. The released hairpins were captured by the target miRNA-21 and underwent catalytic hairpin assembly amplification between Y1 and Y2. The detection limit for miRNA assays using the DNA nanomachine was determined to be 27 pM, which is low enough for sensitive detection in living cells. Living cell imaging of miRNA-21 further corroborated the application of the DNA nanomachine in the identification of cancer cell.
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20
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Li CY, Liu JX, Yuheng L, Gao JL, Chen YL, He JW, Xin MK, Liu D, Zheng B, Sun X. Upconversion Luminescence-Initiated and GSH-Responsive Self-Driven DNA Motor for Automatic Operation in Living Cells and In Vivo. Anal Chem 2022; 94:5450-5459. [PMID: 35324151 DOI: 10.1021/acs.analchem.2c00830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In light of the worthy design flexibility and the good signal amplification capacity, the recently developed DNA motor (especially the DNA walker)-based fluorescent biosensors can offer an admirable choice for realizing bioimaging. However, this attractive biosensing strategy not only has the disadvantage of uncontrollable initiation but also usually demands the supplement of exogenous driving forces. To handle the above obstacles, some rewarding solutions are proposed here. First, on the surface of an 808 nm near-infrared light-excited low-heat upconversion nanoparticle, a special ultraviolet upconversion luminescence-initiated three-dimensional (3D) walking behavior is performed by embedding a photocleavage linker into the sensing elements, and such light-controlled target recognition can perfectly overcome the pre-triggering of the biosensor during the biological delivery to significantly boost the sensing precision. After that, a peculiar self-driven walking pattern is constructed by employing MnO2 nanosheets as an additional nanovector to physically absorb the sensing frame, for which the reduction of the widespread glutathione in the biological medium can bring about sufficient self-supplied Mn2+ to guarantee the walking efficiency. By selecting an underlying next-generation broad-spectrum cancer biomarker (survivin messenger RNA) as the model target, we obtain that the newly formed autonomous 3D DNA motor shows a commendable sensitivity (where the limit of detection is down to 0.51 pM) and even an outstanding specificity for distinguishing single-base mismatching. Beyond this sound assay performance, our sensing approach is capable of working as a powerful imaging platform for accurately operating in various living specimens such as cells and bodies, showing a favorable diagnostic ability for cancer care.
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Affiliation(s)
- Cheng-Yu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Jun-Xian Liu
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Liu Yuheng
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Jia-Ling Gao
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Ya-Ling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Jing-Wei He
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Meng-Kun Xin
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, People's Republic of China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Bei Zheng
- Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou 310024, People's Republic of China
| | - Xiaoming Sun
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, People's Republic of China
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21
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Metal-organic framework nanoreactor-based electrochemical biosensor coupled with three-dimensional DNA walker for label-free detection of microRNA. Biosens Bioelectron 2022; 207:114188. [PMID: 35339822 DOI: 10.1016/j.bios.2022.114188] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs), serving as the regulators for gene expression and cellular function, have emerged as the important biomarkers for diagnosis of cancers. In this study, a label-free electrochemical biosensing platform equipped with metal-organic frameworks (MOFs)-based nanoreactors has been developed by coupling three-dimensional (3D) DNA walker for amplification detection of miRNA. The MOF-based nanoreactors are constructed via the encapsulation of GOx in zeolitic imidazolate framework-8 (ZIF-8) driven by the rapid GOx-triggered nucleation of ZIF-8 with high catalytic activity, which also contributes to preserve the biological activity of GOx even in harsh environments. The gold nanoparticles (AuNPs) are further loaded on the surface of ZIF-8 by electrostatic adsorption, which can be used to not only anchor the orbit of 3D DNA walker by Au-S covalent bond but also promote the electron transfer on electrode interface. In the presence of target miRNA-21, the 3D DNA walker is initiated, resulting in the recycling of targets and the immobilization of numerous fuel DNAs with G-quadruplex/hemin complex on the nanoreactors spontaneously. As a result, a cascade catalysis reaction is triggered in the confined space of ZIF-8 nanoreactors, where the H2O2 as an intermediate is generated with the oxidization of glucose catalyzed by GOx and subsequently decomposed by G-quadruplex/hemin HRP-mimicking DNAzyme for the further oxidation of ABTS to obtain a differential pulse voltammetry (DPV) signal. Under the optimal conditions, the proposed electrochemical biosensor exhibits an excellent performance for amplification detection of miRNA-21 in the dynamic working range from 0.1 nM to 10 μM with a detection limit of 29 pM, which opens a new way for clinical analysis of miRNAs and early diagnosis of cancers.
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22
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Poly-adenine-mediated spherical nucleic acid probes for live cell fluorescence imaging of tumor-related microRNAs. Mol Biol Rep 2022; 49:3705-3712. [DOI: 10.1007/s11033-022-07210-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/27/2022] [Indexed: 11/24/2022]
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23
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Chen M, Duan R, Xu S, Duan Z, Yuan Q, Xia F, Huang F. Photoactivated DNA Walker Based on DNA Nanoflares for Signal-Amplified MicroRNA Imaging in Single Living Cells. Anal Chem 2021; 93:16264-16272. [PMID: 34797071 DOI: 10.1021/acs.analchem.1c04505] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Specific and sensitive detection and imaging of cancer-related miRNA in living cells are desirable for cancer diagnosis and treatment. Because of the spatiotemporal variability of miRNA expression level during different cell cycles, signal amplification strategies that can be activated by external stimuli are required to image miRNAs on demand at desired times and selected locations. Herein, we develop a signal amplification strategy termed as the photoactivated DNA walker based on DNA nanoflares, which enables photocontrollable signal amplification imaging of cancer-related miRNA in single living cells. The developed method is achieved via combining photoactivated nucleic acid displacement reaction with the traditional exonuclease III (EXO III)-assisted DNA walker based on DNA nanoflares. This method is capable of on-demand activation of the DNA walker for dictated signal amplification imaging of cancer-related miRNA in single living cells. The developed method was demonstrated as a proof of concept to achieve photoactivated signal amplification imaging of miRNA-21 in single living HeLa cells via selective two-photon irradiation (λ = 740 nm) of single living HeLa cells by using confocal microscopy equipped with a femtosecond laser.
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Affiliation(s)
- Mengxi Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Ruilin Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shijun Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhijuan Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Feng C, Zhang C, Guo J, Li G, Ye B, Zou L. Novel preparation method of bipedal DNA walker based on hybridization chain reaction for ultrasensitive DNA biosensing. Anal Chim Acta 2021; 1176:338781. [PMID: 34399897 DOI: 10.1016/j.aca.2021.338781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 11/27/2022]
Abstract
In this work, a novel strategy for preparation of bipedal DNA walker (BDW) based on hybridization chain reaction (HCR) with the assistance of Exonuclease III (Exo III) was proposed. Based on this strategy, an electrochemical biosensor was constructed to achieve sensitive detection of CYFRA 21-1 DNA. Firstly, target recognition and circulation were achieved through a one-step catalytic hairpin assembly (CHA) reaction. For further amplification, hybridization chain reaction (HCR) was employed to form duplex-stranded DNA (dsDNA) nanostructure in homogeneous solution. In particular, the elongated single strand of the hairpin DNA for HCR was designed as the Mg2+ DNAzyme sequence. With the assistance of Exo III, dsDNA nanostructure can be digested and transformed into large amounts of BDW. These BDW can cleave the signal probe driven by Mg2+, which was modified on the electrode surface and thus achieved "signal-off" detection of target. This BDW preparation method based on HCR with the digestion of Exo III converted one target input into large amount of BDW. Coupled with the walking cleavage of BDW, a series of cascade amplification endowed high sensitivity with this biosensor and realized ultrasensitive detection of target DNA with the detection limit as low as 3.01 aM.
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Affiliation(s)
- Changrui Feng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Chi Zhang
- Department of Orthopedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jiaxin Guo
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Baoxian Ye
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China.
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