1
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Wang H, Zou H, Wang F. Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications. Chembiochem 2024:e202400266. [PMID: 38801028 DOI: 10.1002/cbic.202400266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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
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2
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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.
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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
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3
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Li H, Wang Y, Wan Y, Li M, Xu J, Wang Q, Wu D. Stimuli-responsive incremental DNA machine auto-catalyzed CRISPR-Cas12a feedback amplification permits ultrasensitive molecular diagnosis of esophageal cancer-related microRNA. Talanta 2024; 271:125675. [PMID: 38245957 DOI: 10.1016/j.talanta.2024.125675] [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: 11/28/2023] [Revised: 01/07/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Development of new diagnostic methods is essential for disease diagnosis and treatment. In this work, we present a stimuli-responsive incremental DNA machine auto-catalyzed CRISPR-Cas12a (SRI-DNA machine/CRISPR-Cas12a) feedback amplification for ultrasensitive molecular detection of miRNA-21, which is an important biomarker related closely to the initiation and development of cancers, such as esophageal cancer. Strategically, the powerful SRI-DNA machine and efficient trans-cleavage activity of the CRISPR-Cas12a system are ingeniously integrated via a rationally designed probe termed as stem-elongated functional hairpin probe (SEF-HP). The SRI-DNA machine begins with the target miRNA, the trigger of the reaction, binding complementarily to the SEF-HP, followed by autonomously performed mechanical strand replication, cleavage, and displacement circuit at multiple sites. This conversion process led to the amplified generation of numerous DNA activators that are complementary with CRISPR RNA (CrRNA). Once formed the DNA activator/CrRNA heteroduplex, the trans-cleavage activity of the CRISPR-Cas12a was activated to nonspecific cleavage of single-stranded areas of a reporter probe for fluorescence emission. Under optimal conditions, the target miRNA can be detected with a wide linear range and an excellent specificity. As a proof-of-concept, this SRI-DNA machine/CRISPR-Cas12a feedback amplification system is adaptable and scalable to higher-order artificial amplification circuits for biomarkers detection, highlighting its promising potential in early diagnosis and disease treatment.
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Affiliation(s)
- Hongxia Li
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Yi Wang
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Yu Wan
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Meimei Li
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Jianguo Xu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, PR China; Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological, Hefei University of Technology, Hefei, 230009, PR China.
| | - Qi Wang
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, PR China.
| | - Donglei Wu
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China.
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4
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Ye Z, Ma M, Chen Y, Liu R, Zhang Y, Ma P, Song D. Dual-microRNA-Controlled Electrochemiluminescence Biosensor for Breast Cancer Diagnosis and Supplemental Identification of Breast Cancer Metastasis. Anal Chem 2024; 96:3636-3644. [PMID: 38357821 DOI: 10.1021/acs.analchem.3c05766] [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: 02/16/2024]
Abstract
Breast cancer remains the most frequently diagnosed cancer globally, and the metastasis of this malignancy is the primary cause of mortality in breast cancer patients. Hence, prompt diagnosis and timely detection of metastatic breast cancer are critical for effective therapeutic intervention. Both progression and metastasis of this malignancy are closely associated with aberrant expression of specific microRNAs (miRNAs) and enzymes. To facilitate breast cancer diagnosis and concomitant identification of metastatic breast cancer, we have engineered an innovative electrochemiluminescence (ECL)-based sensing platform integrated with enzyme-free DNA amplification circuits for dual functionality. Specifically, microRNA-21 (miR-21) is employed as a biomarker for breast cancer, and miR-21 induces the quenching of the ECL signal from luminophores via a strategically designed catalytic three-hairpin assembly (CTHA) circuit. Subsequently, miR-105 levels are measured via toehold-mediated strand displacement reactions (TSDR). Here, miR-105 restores the initially quenched ECL signal, enabling the assessment of the metastatic propensity. Our experimental data demonstrate that the devised ECL biosensor offers broad linear detection ranges and low detection limits for both miR-21 and miR-105. Importantly, our novel platform was also successfully validated by using cellular and serum samples. This biosensor not only discriminates breast cancer cell lines MCF-7 and MDA-MB-231 from nonbreast cancer cells like HepG2, TPC-1, and HeLa, but it also distinguishes between malignant MCF-7 and metastatic MDA-MB-231 cells. Consequently, our novel approach holds significant promise for clinical applications and precise cancer screening.
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Affiliation(s)
- Zhuoxin Ye
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Mo Ma
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
- School of Pharmacy, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yuxuan Chen
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Ruiyan Liu
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yan Zhang
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Pinyi Ma
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Daqian Song
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
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5
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Li T, Meng F, Fang Y, Luo Y, He Y, Dong Z, Tian B. Multienzymatic disintegration of DNA-scaffolded magnetic nanoparticle assembly for malarial mitochondrial DNA detection. Biosens Bioelectron 2024; 246:115910. [PMID: 38086308 DOI: 10.1016/j.bios.2023.115910] [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: 10/23/2023] [Revised: 11/20/2023] [Accepted: 12/02/2023] [Indexed: 12/30/2023]
Abstract
Early diagnosis of malaria can prevent the spread of disease and save lives, which, however, remains challenging in remote and less developed regions. Here we report a portable and low-cost optomagnetic biosensor for rapid amplification and detection of malarial mitochondrial DNA. Bioresponsive magnetic nanoparticle assemblies are constructed by using nucleic acid scaffolds containing endonucleolytic DNAzymes and their substrates, which can be activated by the presence of target DNA and self-disintegrated to release magnetic nanoparticles for optomagnetic quantification. Specifically, target molecules can induce padlock probe ligation and subsequent one-pot homogeneous cascade reactions consisting of nicking-enhanced rolling circle amplification, DNAzyme-assisted nucleic acid recycling, and strand-displacement-driven disintegration of the magnetic assembly. With an optimized magnetic actuation process for reaction acceleration, a detection limit of 1 fM can be achieved by the proposed biosensor with a total assay time of ca. 90 min and a dynamic detection range spanning 3 orders of magnitude. The robustness of the system was validated by testing target molecules spiked in 5% serum samples. Clinical sample validation was conducted by testing malaria-positive clinical blood specimens, obtaining quantitative results concordant with qPCR measurements.
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Affiliation(s)
- Tingting Li
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China
| | - Fanming Meng
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
| | - Yuan Fang
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; College of Biology, Hunan University, Changsha, 410082, China
| | - Yifei Luo
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China
| | - Yilong He
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China
| | - Zhuxin Dong
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; Furong Laboratory, Changsha, 410008, China
| | - Bo Tian
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; Furong Laboratory, Changsha, 410008, China.
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6
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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.
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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
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7
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Zhang YW, Li S, Wang SM, Li XQ, Cui MR, Kang B, Chen HY, Xu JJ. An intelligent DNA nanomachine for amplified MicroRNA imaging and MicroRNA-Guided efficient gene silencing. Talanta 2023; 265:124820. [PMID: 37331040 DOI: 10.1016/j.talanta.2023.124820] [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: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
The DNA nanomachines as excellent synthetic biological tools have been widely used for the sensitive detection of intracellular microRNA (miRNA) and DNAzyme-involved gene silencing. However, intelligent DNA nanomachines which have the ability to sense intracellular specific biomolecules and respond to external information in complex environments still remain challenging. Herein, we develop a miRNA-responsive DNAzyme cascaded catalytic (MDCC) nanomachine to perform multilayer cascade reactions, enabling the amplified intracellular miRNA imaging and miRNA-guided efficient gene silencing. The intelligent MDCC nanomachine is designed based on multiple DNAzyme subunit-encoded catalyzed hairpin assembly (CHA) reactants sustained by the pH-responsive Zeolitic imidazolate framework-8 (ZIF-8) nanoparticles. After cellular uptake, the MDCC nanomachine degrades in acidic endosome and releases three hairpin DNA reactants and Zn2+, and the latter can act as an effective cofactor for DNAzyme. In the presence of miRNA-21, a catalytic hairpin assembly (CHA) reaction is triggered, which produces a large number of Y-shaped fluorescent DNA constructs containing three DNAzyme modules for gene silencing. The construction of Y-shaped DNA modified with multisite fluorescence and the circular reaction realizes ultrasensitive miRNA-21 imaging of cancer cells. Moreover, miRNA-guided gene silencing inhibits the cancer cell proliferation through the DNAzyme-specific recognition and cleavage of target EGR-1 (Early Growth Response-1) mRNA, which is one key tumor-involved mRNA. The strategy may provide a promising platform for highly sensitive determination of biomolecules and accurate gene therapy of cancer cells.
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Affiliation(s)
- Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Shan Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Shu-Min Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Mei-Rong Cui
- 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 and Telecommunications, Nanjing, 210023, PR China.
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
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8
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Wang S, Shang J, Zhao B, Wang H, Yang C, Liu X, Wang F. Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications. Chempluschem 2023; 88:e202300432. [PMID: 37706615 DOI: 10.1002/cplu.202300432] [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: 08/06/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023]
Abstract
The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.
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Affiliation(s)
- Siyuan Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Jinhua Shang
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Bingyue Zhao
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Huimin Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Changying Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Xiaoqing Liu
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Fuan Wang
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
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Li XQ, Jia YL, Zhang YW, Chen HY, Xu JJ. Intracellular activated logic nanomachines based on framework nucleic acids for low background detection of microRNAs in living cells. Chem Sci 2023; 14:7699-7708. [PMID: 37484658 PMCID: PMC10356544 DOI: 10.1039/d3sc01162c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/18/2023] [Indexed: 07/25/2023] Open
Abstract
DNA molecular machines based on DNA logic circuits show unparalleled potential in precision medicine. However, delivering DNA nanomachines into real biological systems and ensuring that they perform functions specifically, quickly and logically remain a challenge. Here, we developed an efficient DNA molecular machine integrating transfer-sensor-computation-output functions to achieve high fidelity detection of intracellular biomolecules. The introduction of pH nanoswitches enabled the nanomachines to be activated after entering the cell, and the spatial-confinement effect of the DNA triangular prism (TP) enables the molecular machine to process complex information at the nanoscale, with higher sensitivity and shorter response time than diffuse-dominated logic circuits. Such cascaded activation molecular machines follow the logic of AND to achieve specific capture and detection of biomolecules in living cells through a multi-hierarchical response, providing a new insight into the construction of efficient DNA molecular machines.
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Affiliation(s)
- Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yi-Lei Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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Luo H, Wang Z, Mo Q, Yang J, Yang F, Tang Y, Liu J, Li X. Framework Nucleic Acid-Based Multifunctional Tumor Theranostic Nanosystem for miRNA Fluorescence Imaging and Chemo/Gene Therapy. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37421332 DOI: 10.1021/acsami.3c01611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
Intelligent stimulus-responsive theranostic systems capable of specifically sensing low-abundance tumor-related biomarkers and efficiently killing tumors remain a pressing endeavor. Here, we report a multifunctional framework nucleic acid (FNA) nanosystem for simultaneous imaging of microRNA-21 (miR-21) and combined chemo/gene therapy. To achieve this, two FNA nanoarchitectures labeled with Cy5/BHQ2 signal tags were designed, each of which contained an AS1411 aptamer, two pairs of DNA/RNA hybrids, a pH-sensitive DNA catcher, and doxorubicin (DOX) intercalating between cytosine and guanine in the tetrahedral DNA nanostructure (TDN). In the acidic tumor microenvironment, the DNA catchers spontaneously triggered to form an i-motif and create an FNA dimer (dFNA) while releasing DOX molecules to exert a cytotoxic effect. In addition, the overexpressed miR-21 in tumor cells dismantled the DNA/RNA hybrids to produce vascular endothelial growth factor-associated siRNA via a toehold-mediated strand displacement reaction, thus enabling a potent RNA interfering. Also importantly, the liberated miR-21 could initiate cascade-reaction amplification to efficiently activate the Cy5 signal reporters, thereby realizing on-site fluorescence imaging of miR-21 in living cells. The exquisitely designed FNA-based nanosystem showed favorable biocompatibility and stability as well as acid-driven DOX release characteristics. Owing to the aptamer-guided targeting delivery, specific uptake of the FNA-based theranostic nanosystem by HepG2 cells was verified with confocal laser scanning microscopy and flow cytometry analyses, which therefore resulted in apoptosis of HepG2 cells while doing minimal damage to normal H9c2 and HL-7702 cells. Strikingly, both in vitro and in vivo experiments demonstrated the achievements of the FNA-enabled miR-21 imaging and synergistically enhanced chemo/gene therapy. This work thus represents a noteworthy advance on the FNA-based theranostic strategy that can effectively avoid the undesirable premature leakage of anticarcinogen and off-target of siRNA, and achieve on-demand reagents release for tumor diagnostics and treatment.
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Affiliation(s)
- Haikun Luo
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Zhao Wang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
- School of Medicine, Xiamen University, Xiang-an South Road, Xiamen 361102, China
| | - Qian Mo
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Jianying Yang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Fan Yang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Yujin Tang
- Department of Orthopedics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Jia Liu
- Department of Orthopedics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Xinchun Li
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, China
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11
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Yao S, Zou R, Chen F, Gong H, Cai C. Engineering of catalytic hairpin-rigidified Y-shaped DNA-functionalized nanomachine to rapidly detect mRNA. Mikrochim Acta 2023; 190:210. [PMID: 37169940 DOI: 10.1007/s00604-023-05708-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/19/2023] [Indexed: 05/13/2023]
Abstract
The catalytic hairpin-rigidified Y-shaped DNA through layer-by-layer assembly has been fixed on the surface of copper sulfide nanoparticles for the detection of survivin mRNA. The distance between the CHA probes fixed on the Y-shaped DNA is significantly shortened. The results show that the fluorescence of this nanomachine reached the maximum value in 50 min (excitation wavelength at 488 nm and emission wavelength 526 nm), and its reaction rate is more than 5-fold faster than that of the free-CHA control system. In addition, the nanomachine showed high sensitivity (LOD of 3.5 pM) and high specificity for the survivin mRNA detection. Given its fast response time and excellent detection performance, we envision that the catalytic hairpin-rigidified Y-shaped DNA-functionalized nanomachine will offer potential applications in disease diagnostics and clinical applications.
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Affiliation(s)
- Shufen Yao
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Rong Zou
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Feng Chen
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
| | - Hang Gong
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Changqun Cai
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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12
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Li H, Zhang Z, Gan L, Fan D, Sun X, Qian Z, Liu X, Huang Y. Signal Amplification-Based Biosensors and Application in RNA Tumor Markers. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094237. [PMID: 37177441 PMCID: PMC10180857 DOI: 10.3390/s23094237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Tumor markers are important substances for assessing cancer development. In recent years, RNA tumor markers have attracted significant attention, and studies have shown that their abnormal expression of post-transcriptional regulatory genes is associated with tumor progression. Therefore, RNA tumor markers are considered as potential targets in clinical diagnosis and prognosis. Many studies show that biosensors have good application prospects in the field of medical diagnosis. The application of biosensors in RNA tumor markers is developing rapidly. These sensors have the advantages of high sensitivity, excellent selectivity, and convenience. However, the detection abundance of RNA tumor markers is low. In order to improve the detection sensitivity, researchers have developed a variety of signal amplification strategies to enhance the detection signal. In this review, after a brief introduction of the sensing principles and designs of different biosensing platforms, we will summarize the latest research progress of electrochemical, photoelectrochemical, and fluorescent biosensors based on signal amplification strategies for detecting RNA tumor markers. This review provides a high sensitivity and good selectivity sensing platform for early-stage cancer research. It provides a new idea for the development of accurate, sensitive, and convenient biological analysis in the future, which can be used for the early diagnosis and monitoring of cancer and contribute to the reduction in the mortality rate.
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Affiliation(s)
- Haiping Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
| | - Zhikun Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Lu Gan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Dianfa Fan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Xinjun Sun
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Zhangbo Qian
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Yong Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
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13
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Wang S, Li H, Dong K, Shu W, Zhang J, Zhang J, Zhao R, Wei S, Feng D, Xiao X, Zhang W. A universal and specific RNA biosensor via DNA circuit-mediated PAM-independent CRISPR/Cas12a and PolyA-rolling circle amplification. Biosens Bioelectron 2023; 226:115139. [PMID: 36774734 DOI: 10.1016/j.bios.2023.115139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Point of care testing (POCT) has important clinical significance for the diagnosis and prognosis evaluation of diseases. At present, the biosensor based on CRISPR/Cas12a has become a powerful diagnostic tool due to its high sensitivity. However, CRISPR/Cas12a requires PAM sequence to recognize target double strand and only can recognize specific sequence, so it is not universal. The current RNA detection techniques either lack consideration for specificity and universality, are expensive and difficult, or both. Therefore, it is crucial to create a CRISPR/Cas12a-based RNA detection system that is easy to use, cheap, specific, and universal in order to further its use in molecular diagnostics. Here, we established a DNA circuit-mediated PAM-independent CRISPR/Cas12a coupled PolyA-rolling circle amplification for RNA detection biosensor, namely DCPRBiosensor. The DCPRBiosensor not only functions as a simple, inexpensive, and highly sensitive RNA detection sensor, but it also boasts innovative specificity and universality features. More importantly, DCPRBiosensor removes the PAM restriction of CRISPR/Cas12a. The DCPRBiosensor's detection limit reached 100 aM and it had a linear relationship between 100 aM and 10 pM. We detected four piRNAs to verify the universality and stability of DCPRBiosensor. Then, we verified that DCPRBiosensor has good discrimination ability for single-base mismatch. Finally, we successfully detected piRNA in DLD-1 and HCT-116 cells and urine mixed samples within 4.5 h. In conclusion, we believe that DCPRBiosensor will have a substantial impact on both the development of CRISPR/as12a's applications and the investigation of the clinical value of piRNA.
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Affiliation(s)
- Sidan Wang
- Queen Mary School, Nanchang University, Nanchang, 330006, China
| | - Haojia Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jiarui Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Dilu Feng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
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14
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Chen L, Fang Y, Zhou X, Zhang M, Yao R, Tian B. Magnetic DNA Nanomachine for On-Particle Cascade Amplification-Based Ferromagnetic Resonance Detection of Plant MicroRNA. Anal Chem 2023; 95:5411-5418. [PMID: 36917201 DOI: 10.1021/acs.analchem.3c00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plant microRNAs play critical roles in post-transcriptional gene regulation of many processes, thus motivating the development of accurate and user-friendly microRNA detection methods for better understanding of, e.g., plant growth, development, and abiotic/biotic stress responses. By integrating the capture probe, fuel strand, primer, and template onto the surface of a magnetic nanoparticle (MNP), we demonstrated a magnetic DNA nanomachine that could conduct an on-particle cascade amplification reaction in response to the presence of target microRNA. The cascade amplification consists of an exonuclease III-assisted target recycling step and a rolling circle amplification step, leading to changes in the MNP arrangement that can be quantified by ferromagnetic resonance spectroscopy. After a careful investigation of the exonuclease III side reaction, the biosensor offers a detection limit of 15 fM with a total assay time of ca. 70 min. Moreover, our magnetic DNA nanomachine is capable of discriminating the target microRNA from its family members. Our biosensor has also been tested on total endogenous microRNAs extracted from Arabidopsis thaliana leaves, with a performance comparable to qRT-PCR.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Yuan Fang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China.,Department of Biomedical Engineering, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Xuemei Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Bo Tian
- Department of Biomedical Engineering, School of Basic Medical Science, Central South University, Changsha 410013, China
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15
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Cui M, Zhang D, Wang Q, Chao J. An intelligent, autocatalytic, DNAzyme biocircuit for amplified imaging of intracellular microRNAs. NANOSCALE 2023; 15:578-587. [PMID: 36533380 DOI: 10.1039/d2nr05165f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNAzymes hold great promise as transducing agents for the analysis of intracellular biomarkers. However, their low intracellular delivery efficiency and limited signal amplification capability (including an additional supply of cofactors) hinder their application in low-abundance biomarker analysis. Herein, a general strategy to design an intelligent, autocatalytic, DNAzyme biocircuit is developed for amplified microRNA imaging in living cells. The DNAzyme biocircuit is constructed based on a nanodevice composed of catalytic hairpin assembly (CHA) and DNAzyme biocatalytic functional units, sustained by Au nanoparticles (AuNPs) and MnO2 nanosheets (CD/AM nanodevices). Once the CD/AM nanodevices are endocytosed by cells, the MnO2 nanosheets are reduced by intracellular glutathione (GSH), which not only releases the different units of the DNAzyme circuit, but also generates the cofactor Mn2+ for DNAzyme autocatalysis. The intracellular analytes could trigger the coordinated cross-activation of CHA and autocatalytic DNAzymes on AuNPs, enabling reliable and accurate detection of miRNAs in living cells. This intelligent autocatalytic multilayer DNAzyme biocircuit can effectively avoid signal leakage and obtain high amplification gain, expanding the application of programmable complex DNA nanocircuits in biosensing, nanomaterial assembly, and biomedicine.
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Affiliation(s)
- Meirong Cui
- 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 and Telecommunications, Nanjing 210023, P. R. China.
| | - Dan 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 and Telecommunications, Nanjing 210023, P. R. China.
| | - Qingfu 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 and Telecommunications, Nanjing 210023, P. R. China.
| | - Jie Chao
- 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 and Telecommunications, Nanjing 210023, P. R. China.
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16
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Liu Q, Hou L, Zhang Y, Liu M, Jin Y, Li B. Improving efficiency of entropy-driven DNA amplification biosensing through producing two label-free signal strands in one cycle. Anal Chim Acta 2022; 1232:340484. [DOI: 10.1016/j.aca.2022.340484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/01/2022]
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17
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Wang Y, Chen Y, Wan Y, Hong C, Shang J, Li F, Liu X, Wang F. An Autocatalytic DNA Circuit Based on Hybridization Chain Assembly for Intracellular Imaging of Polynucleotide Kinase. ACS APPLIED MATERIALS & INTERFACES 2022; 14:31727-31736. [PMID: 35786848 DOI: 10.1021/acsami.2c08523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polynucleotide kinase (PNK) plays an essential role in various cellular events by regulating phosphorylation processes, and abnormal homeostasis of PNK could cause many human diseases. Herein, we proposed an autocatalytic hybridization system (AHS) through the elaborate integration of hybridization chain assembly (HCA) and catalytic DNA assembly (CDA) that enables a highly efficient positive feedback amplification. The PNK-targeting AHS biosensor is composed of three modules: a recognition module, an HCA amplification module, and a CDA autocatalytic module. In the presence of PNK, the recognition module could transform the PNK input into an exposed nucleic acid initiator (I). Then the initiator strand I could trigger the autonomous HCA process in the amplification module, and the resulted HCA products could reassemble the split CDA trigger strand T, subsequently inducing the CDA process in the autocatalytic module to form abundant DNA duplex products. Consequently, the embedded initiator strand I was liberated from the CDA duplex product to autonomously trigger the new rounds of HCA circuit. The rational integration and cooperative cross-activation between the HCA and CDA module could prominently accelerate the reaction and realize the exponential amplification efficiency by initiator regeneration. As a result, the self-sustainable AHS amplifier could implement the sensitive detection of PNK in vitro and in biological samples and further fulfill accurate monitoring of the intracellular PNK activity and the effective screening of PNK inhibitors. This work paves a way for exploiting highly efficient artificial DNA circuits to analyze low-abundance biomarkers, holding great potential in biochemical research and clinical diagnosis.
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Affiliation(s)
- Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yeqing Wan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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18
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Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
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Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
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19
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Xing C, Chen S, Lin Q, Lin Y, Wang M, Wang J, Lu C. An aptamer-tethered DNA origami amplifier for sensitive and accurate imaging of intracellular microRNA. NANOSCALE 2022; 14:1327-1332. [PMID: 35014654 DOI: 10.1039/d1nr06399e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate detection and imaging of low-abundance microRNA (miRNA) in living cells are essential for the diagnosis and prognosis of diseases. Designing nanoprobes with resistance to enzyme degradation, effective cell-binding, and efficient signal amplification is crucial for in vivo imaging. In this study, we present an aptamer-tethered DNA origami amplifier (ADOA) that functions inside living cells to detect miRNA with high sensitivity and stability. In the design, cancer cell-targeting aptamers were tethered onto the border of the DNA origami to improve the discrimination between cancer cells and normal cells. Two substrate modules for the intramolecular entropy-driven reaction (EDR) circuit were alternately arranged on the DNA origami plane. The target miRNA will initiate the sequential hybridization of the two substrate modules on the DNA origami, generating amplified fluorescence signals. The proposed ADOA achieved an accelerated cascade reaction due to the "confinement effect" and significantly enhanced the sensitivity compared with a traditional EDR. Meanwhile, with the rigid structure of the DNA origami, the ADOA possessed excellent signalling stability in living cells. Therefore, the ADOA could expand the application of DNA origami in miRNA sensing and has potential value in early-stage clinical diagnosis.
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Affiliation(s)
- Chao Xing
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, P. R. China.
| | - Shan Chen
- College of Geography and Ocean, Minjiang University, Fuzhou 350108, P. R. China
| | - Qitian Lin
- College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China.
| | - Yuhong Lin
- College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China.
| | - Min Wang
- College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China.
| | - Jun Wang
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, P. R. China.
| | - Chunhua Lu
- College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China.
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20
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Asa TA, Ravi Kumara GS, Seo YJ. Highly sensitive, selective, and rapid detection of miRNA-21 using an RCA/G-quadruplex/QnDESA probing system. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:97-100. [PMID: 34918721 DOI: 10.1039/d1ay01696b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this study we developed a very simple and rapid miRNA 21 detection system using a novel quinolinium diethylamino salicylaldehyde (QnDESA) probe for sensing the 22AG hybrid G-quadruplex with a single-step rolling circle amplification (RCA) reaction. We synthesized a circular DNA padlock template containing a sequence complementary to the 22AG hybrid G-quadruplex, used SplintR ligase to ensure perfect hybridization with miRNA 21, applied this circular DNA and phi-29 DNA polymerase for tandem amplification of the 22AG hybrid G-quadruplex sequence, and then probed the product using QnDESA. This combination of RCA-G-quadruplex and QnDESA allowed the rapid (1 h) and simple one-pot detection of miRNA 21 based on a change in fluorescence. In addition, this system displayed high sensitivity (limit of detection: 1.37 fM) and selectivity. This probing system should also be useful for identifying a diverse range of DNA- and RNA-based biomarkers.
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Affiliation(s)
- Tasnima Alam Asa
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, Republic of Korea.
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, Republic of Korea.
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21
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Gong X, He S, Li R, Chen Y, Tan K, Wan Y, Liu X, Wang F. Monitoring and modulating a catalytic hybridization circuit for self-adaptive bioorthogonal DNA assembly. Chem Sci 2022; 13:10428-10436. [PMID: 36277649 PMCID: PMC9473505 DOI: 10.1039/d2sc03757b] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
A localized catalytic circuit, facilitating the self-assembly of DNA nanosponges, is developed for robust and accurate monitoring of miRNA targets in live cells and mice.
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Affiliation(s)
- Xue Gong
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Kaiyue Tan
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Yeqing Wan
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072 Wuhan, P. R. China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430072, China
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22
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Jiang Q, Yue S, Yu K, Tian T, Zhang J, Chu H, Cui Z, Bi S. Endogenous microRNA triggered enzyme-free DNA logic self-assembly for amplified bioimaging and enhanced gene therapy via in situ generation of siRNAs. J Nanobiotechnology 2021; 19:288. [PMID: 34565382 PMCID: PMC8474761 DOI: 10.1186/s12951-021-01040-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Small interfering RNA (siRNA) has emerged as a kind of promising therapeutic agents for cancer therapy. However, the off-target effect and degradation are the main challenges for siRNAs delivery. Herein, an enzyme-free DNA amplification strategy initiated by a specific endogenous microRNA has been developed for in situ generation of siRNAs with enhanced gene therapy effect on cervical carcinoma. METHODS This strategy contains three DNA hairpins (H1, H2/PS and H3) which can be triggered by microRNA-21 (miR-21) for self-assembly of DNA nanowheels (DNWs). Notably, this system is consistent with the operation of a DNA logic circuitry containing cascaded "AND" gates with feedback mechanism. Accordingly, a versatile biosensing and bioimaging platform is fabricated for sensitive and specific analysis of miR-21 in HeLa cells via fluorescence resonance energy transfer (FRET). Meanwhile, since the vascular endothelial growth factor (VEGF) antisense and sense sequences are encoded in hairpin reactants, the performance of this DNA circuit leads to in situ assembly of VEGF siRNAs in DNWs, which can be specifically recognized and cleaved by Dicer for gene therapy of cervical carcinoma. RESULTS The proposed isothermal amplification approach exhibits high sensitivity for miR-21 with a detection limit of 0.25 pM and indicates excellent specificity to discriminate target miR-21 from the single-base mismatched sequence. Furthermore, this strategy achieves accurate and sensitive imaging analysis of the expression and distribution of miR-21 in different living cells. To note, compared to naked siRNAs alone, in situ siRNA generation shows a significantly enhanced gene silencing and anti-tumor effect due to the high reaction efficiency of DNA circuit and improved delivery stability of siRNAs. CONCLUSIONS The endogenous miRNA-activated DNA circuit provides an exciting opportunity to construct a general nanoplatform for precise cancer diagnosis and efficient gene therapy, which has an important significance in clinical translation.
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Affiliation(s)
- Qinghua Jiang
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People's Republic of China
| | - Shuzhen Yue
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Kaixin Yu
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Tian Tian
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People's Republic of China
| | - Jian Zhang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Huijun Chu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People's Republic of China
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People's Republic of China.
| | - Sai Bi
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People's Republic of China.
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China.
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