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Wang H, Zou H, Wang F. Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications. Chembiochem 2024; 25:e202400266. [PMID: 38801028 DOI: 10.1002/cbic.202400266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on-demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA-based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.
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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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Zhang Q, Yu S, Shang J, He S, Liu X, Wang F. Spatiotemporally Programmed Disassembly of Multifunctional Integrated DNAzyme Nanoplatfrom for Amplified Intracellular MicroRNA Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305672. [PMID: 37670211 DOI: 10.1002/smll.202305672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/12/2023] [Indexed: 09/07/2023]
Abstract
The sensing performance of DNAzymes in live cells is tremendously hampered by the inefficient and inhomogeneous delivery of DNAzyme probes and their incontrollable off-site activation, originating from their susceptibility to nuclease digestion. This requires the development of a more compact and robust DNAzyme-delivering system with site-specific DNAzyme activation property. Herein, a highly compact and robust Zn@DDz nanoplatform is constructed by integrating the unimolecular microRNA-responsive DNA-cleaving DNAzyme (DDz) probe with the requisite DNAzyme Zn2+ -ion cofactors, and the amplified intracellular imaging of microRNA via the spatiotemporally programmed disassembly of Zn@DDz nanoparticles is achieved. The multifunctional Zn@DDz nanoplatform is simply composed of a structurally blocked self-hydrolysis DDz probe and the inorganic Zn2+ -ion bridge, with high loading capacity, and can effectively deliver the initially catalytic inert DDz probe and Zn2+ into living cells with enhanced stabilities. Upon their entry into the acidic microenvironment of living cells, the self-sufficient Zn@DDz nanoparticle is disassembled to release DDz probe and simultaneously supply Zn2+ -ion cofactors. Then, endogenous microRNA-21 catalyzes the reconfiguration and activation of DDz for generating the amplified readout signal with multiply guaranteed imaging performance. Thus, this work paves an effective way for promoting DNAzyme-based biosensing systems in living cells, and shows great promise in clinical diagnosis.
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Affiliation(s)
- Qingqing Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen, 518057, P. R. China
| | - Shanshan Yu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen, 518057, P. R. China
| | - Jinhua Shang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen, 518057, P. R. China
| | - Shizhen He
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen, 518057, P. R. China
| | - Xiaoqing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen, 518057, P. R. China
| | - Fuan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen, 518057, P. R. China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430072, China
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Zeng Y, Peng R, Hu Y, Luo P, Yang R, Li J, Zheng J. Endogenous Enzyme-Activatable Spherical Nucleic Acids for Spatiotemporally Controlled Signal Amplification Molecular Imaging and Combinational Tumor Therapy. Anal Chem 2023; 95:14710-14719. [PMID: 37728636 DOI: 10.1021/acs.analchem.3c02831] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Due to the adjustable hybridization activity, antinuclease digestion stability, and superior endocytosis, spherical nucleic acids (SNAs) have been actively developed as probes for molecular imaging and the development of noninvasive diagnosis and image-guided surgery. However, since highly expressed biomarkers in tumors are not negligible in normal tissues, an inevitable background signal and the inability to precisely release probes at the chosen region remain a challenge for SNAs. Herein, we proposed a rationally designed, endogenous enzyme-activatable functional SNA (Ep-SNA) for spatiotemporally controlled signal amplification molecular imaging and combinational tumor therapy. The self-assembled amphiphilic polymer micelles (SM-ASO), which were obtained by a simple and rapid copper-free strain-promoted azide-alkyne cycloaddition click reaction between dibenzocyclooctyne-modified antisense oligonucleotide and azide-containing aliphatic polymer polylactic acid, were introduced as the core elements of Ep-SNA. This Ep-SNA was then constructed by connecting two apurinic/apyrimidinic (AP) site-containing trailing DNA hairpins, which could occur via a hybridization chain reaction in the presence of low-abundance survivin mRNA to SM-ASO through complementary base pairing. Notably, the AP site-containing trailing DNA hairpins also empowered the SNA with the feasibility of drug delivery. Once this constructed intelligent Ep-SNA nanoprobe was specifically cleaved by the highly expressed cytoplasmic human apurinic/apyrimidinic endonuclease 1 in tumor cells, three key elements (trailing DNA hairpins, antisense oligonucleotide, and doxorubicin) could be released to enable subsequent high-sensitivity survivin mRNA imaging and combinational cancer therapy (gene silencing and chemotherapy). This strategy shows great application prospects of SNAs as a precise platform for the integration of disease diagnosis and treatment and can contribute to basic biomedical research.
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Affiliation(s)
- Youhui Zeng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Ruiying Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yingcai Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Pan Luo
- Yueyang Central Hospital, Yueyang 414020, China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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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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Wen Y, Liu WY, Wang JH, Yu YL, Chen S. Simultaneous Imaging of Multiple miRNAs in Mitochondria Controlled by Fluorescently Encoded Upconversion Optical Switches for Drug Resistance Studies. Anal Chem 2023; 95:12152-12160. [PMID: 37535000 DOI: 10.1021/acs.analchem.3c02403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Mitochondrial miRNAs (mitomiRs) are essential regulators of biological processes by influencing mitochondrial gene expression and function. To comprehensively understand related pathological processes and treatments, simultaneous imaging of multiple mitomiRs is crucial. In this study, we present a technique that enables simultaneous monitoring of multiple mitomiRs in living cells using a near-infrared (NIR) photoactivated controlled detection probe (PD-mFleU) with a fluorescence-encoded error correction module and a nonsupervised machine learning data-processing algorithm. This method allows controlled sensing imaging of mitomiRs with a DNA reporter probe that can be activated by NIR light after targeted mitochondrial localization. Multilayer upconversion nanoparticles (UCNPs) are used for encoding probes and error correction. Additionally, the density-based spatial clustering of applications with the noise (DBSCAN) algorithm is used to process and analyze the image. Using this technique, we achieved rapid in situ imaging of the abnormal expression of three mitomiRs (miR-149, miR-590, and miR-671) related to mt-ND1 in drug-resistant cells. Furthermore, upregulating the three mitomiRs simultaneously efficiently reverted drug-resistant cells to sensitive cells. Our study provides an analytical strategy for multiplex imaging of mitomiRs in living cells with potential clinical applications.
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Affiliation(s)
- Yun Wen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Wen-Ye Liu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Shuai Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
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