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Liu Y, Fan Z, Xiang XW, Tao X, Xia X, Shi Q, Lu Y, Lu J, Gu H, Liu YJ, Liu B. Engineering of Multivalent Membrane-Anchored DNA Frameworks for Precise Profiling of Variable Membrane Permeability During Reversible Electroporation. SMALL METHODS 2024; 8:e2301198. [PMID: 38152955 DOI: 10.1002/smtd.202301198] [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: 09/05/2023] [Revised: 12/08/2023] [Indexed: 12/29/2023]
Abstract
Electroporation techniques have emerged as attractive tools for intracellular delivery, rendering promising prospects towards clinical therapies. Transient disruption of membrane permeability is the critical process for efficient electroporation-based cargo delivery. However, smart nanotools for precise characterization of transient membrane changes induced by strong electric pulses are extremely limited. Herein, multivalent membrane-anchored fluorescent nanoprobes (MMFNPs) that take advantages of flexible functionalization and spatial arrangement of DNA frameworks are developed for in situ evaluation of electric field-induced membrane permeability during reversible electroporation . Single-molecule fluorescence imaging techniques are adopted to precisely verify the excellent analytical performance of the engineered MMFNPs. Benefited from tight membrane anchoring and sensitive adenosine triphosphate (ATP) profiling, varying degrees of membrane disturbances are visually exhibited under different intensities of the microsecond pulse electric field (µsPEF). Significantly, the dynamic process of membrane repair during reversible electroporation is well demonstrated via ATP fluctuations monitored by the designed MMFNPs. Furthermore, molecular dynamics (MD) simulations are performed for accurate verification of electroporation-driven dynamic cargo entry via membrane nanopores. This work provides an avenue for effectively capturing transient fluctuations of membrane permeability under external stimuli, offering valuable guidance for developing efficient and safe electroporation-driven delivery strategies for clinical diagnosis and therapeutics.
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Affiliation(s)
- Yixin Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zihui Fan
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiao-Wei Xiang
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Xiaonan Tao
- School of Information Science and Technology, Fudan University, Shanghai, 200032, China
| | - Xinwei Xia
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Qian Shi
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yanwei Lu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiayin Lu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Hongzhou Gu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan-Jun Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
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2
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Song L, Zuo X, Li M. Concept and Development of Algebraic Topological Framework Nucleic Acids. Chempluschem 2024; 89:e202300760. [PMID: 38529703 DOI: 10.1002/cplu.202300760] [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: 12/19/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Nucleic acids are considered as promising materials for developing exquisite nanostructures from one to three dimensions. The advances of DNA nanotechnology facilitate ingenious design of DNA nanostructures with diverse shapes and sizes. Especially, the algebraic topological framework nucleic acids (ATFNAs) are functional DNA nanostructures that engineer guest molecules (e. g., nucleic acids, proteins, small molecules, and nanoparticles) stoichiometrically and spatially. The intrinsic precise properties and tailorable functionalities of ATFNAs hold great promise for biological applications, such as cell recognition and immunotherapy. This Perspective highlights the concept and development of precisely assembled ATFNAs, and outlines the new frontiers and opportunities for exploiting the structural advantages of ATFNAs for biological applications.
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Affiliation(s)
- Lu Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
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3
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Mao D, Tang X, Zhang R, Chen T, Liu C, Gou H, Sun P, Mao Y, Deng J, Li W, Sun F, Zhu X. DNA-Programmed Four-Bit Quaternary Fluorescence Encoding (FLUCO) Enables 51-Colored Bioimaging Analysis. J Am Chem Soc 2024. [PMID: 38859621 DOI: 10.1021/jacs.4c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Color encoding plays a crucial role in painting, digital photography, and spectral analysis. Achieving accurate, target-responsive color encoding at the molecular level has the potential to revolutionize scientific research and technological innovation, but significant challenges persist. Here, we propose a multibit DNA self-assembly system based on computer-aided design (CAD) technology, enabling accurate, target-responsive, amplified color encoding at the molecular level, termed fluorescence encoding (FLUCO). As a model, we establish a quaternary FLUCO system using four-bit DNA self-assembly, which can accurately encode 51 colors, presenting immense potential in applications such as spatial proteomic imaging and multitarget analysis. Notably, FLUCO enables the simultaneous imaging of multiple targets exceeding the limitations of channels using conventional imaging equipment, and marks the integration of computer science for molecular encoding and decoding. Overall, our work paves the way for target-responsive, controllable molecular encoding, facilitating spatial omics analysis, exfoliated cell analysis, and high-throughput liquid biopsy.
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Affiliation(s)
- Dongsheng Mao
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
| | - Runchi Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Hongquan Gou
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Pei Sun
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Jie Deng
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Wenxing Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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4
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Li C, Chen J, Man T, Chen B, Li J, Li Q, Yang X, Wan Y, Fan C, Shen J. DNA Framework-Engineered Assembly of Cyanine Dyes for Structural Identification of Nucleic Acids. JACS AU 2024; 4:1125-1133. [PMID: 38559725 PMCID: PMC10976577 DOI: 10.1021/jacsau.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Abstract
DNA nanostructures serve as precise templates for organizing organic dyes, enabling the creation of programmable artificial photonic systems with efficient light-harvesting and energy transfer capabilities. However, regulating the organization of organic dyes on DNA frameworks remains a great challenge. In this study, we investigated the factors influencing the self-assembly behavior of cyanine dye K21 on DNA frameworks. We observed that K21 exhibited diverse assembly modes, including monomers, H-aggregates, J-aggregates, and excimers, when combined with DNA frameworks. By manipulating conditions such as the ion concentration, dye concentration, and structure of DNA frameworks, we successfully achieved precise control over the assembly modes of K21. Leveraging K21's microenvironment-sensitive fluorescence properties on DNA nanostructures, we successfully discriminated between the chirality and topology structures of physiologically relevant G-quadruplexes. This study provides valuable insights into the factors influencing the dynamic assembly behavior of organic dyes on DNA framework nanostructures, offering new perspectives for constructing functional supramolecular aggregates and identifying DNA secondary structures.
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Affiliation(s)
- Cong Li
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jielin Chen
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Tiantian Man
- School
of Mechanical Engineering, Nanjing University
of Science and Technology, Nanjing 210094, China
| | - Bin Chen
- School
of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jiang Li
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Qian Li
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Xiurong Yang
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Ying Wan
- School
of Mechanical Engineering, Nanjing University
of Science and Technology, Nanjing 210094, China
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
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5
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Zhao X, Xu Y, Chen Z, Tang C, Mi X. Encoding fluorescence intensity with tetrahedron DNA nanostructure based FRET effect for bio-detection. Biosens Bioelectron 2024; 248:115994. [PMID: 38181517 DOI: 10.1016/j.bios.2023.115994] [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: 07/26/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
Biocoding technology constructed by readable tags with distinct signatures is a brand-new bioanalysis method to realize multiplexed identification and bio-information decoding. In this study, a novel fluorescence intensity coding technology termed Tetra-FICT was reported based on tetrahedron DNA nanostructure (TDN) carrier and Főrster Resonance Energy Transfer (FRET) effect. By modulating numbers and distances of Cy3 and Cy5 at four vertexes of TDN, different fluorescence intensities of twenty-six samples were produced at ∼565.0 nm (FICy3) and ∼665.0 nm (FICy5) by detecting fluorescence spectra. By developing an error correction mechanism, eleven codes were established based on divided intensity ranges of the final FICy3 together with FICy5 (Final-FICy3&FICy5). These resulting codes were used to construct barcode probes, with three miRNA biomarkers (miRNA-210, miRNA-199a and miRNA-21) as cases for multiplexed bio-assay. The high specificity and sensitivity were also demonstrated for the detection of miRNA-210. Overall, the proposed Tetra-FICT enriched the toolbox of fluorescence coding, which could be applied to multiplexing biomarkers detection.
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Affiliation(s)
- Xiaoshuang Zhao
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; School of Physics and Optoelectronic Engineering, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Yi Xu
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Ziting Chen
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Chengren Tang
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Xianqiang Mi
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China; School of Physics and Optoelectronic Engineering, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; University of Chinese Academy of Science, Beijing, 100049, China.
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6
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Xie Y, Tong Z, Xia T, Worch JC, Rho JY, Dove AP, O'Reilly RK. 2D Hierarchical Microbarcodes with Expanded Storage Capacity for Optical Multiplex and Information Encryption. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308154. [PMID: 38014933 DOI: 10.1002/adma.202308154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/16/2023] [Indexed: 11/29/2023]
Abstract
The design of nanosegregated fluorescent tags/barcodes by geometrical patterning with precise dimensions and hierarchies could integrate multilevel optical information within one carrier and enhance microsized barcoding techniques for ultrahigh-density optical data storage and encryption. However, precise control of the spatial distribution in micro/nanosized matrices intrinsically limits the accessible barcoding applications in terms of material design and construction. Here, crystallization forces are leveraged to enable a rapid, programmable molecular packing and rapid epitaxial growth of fluorescent units in 2D via crystallization-driven self-assembly. The fluorescence encoding density, scalability, information storage capacity, and decoding techniques of the robust 2D polymeric barcoding platform are explored systematically. These results provide both a theoretical and an experimental foundation for expanding the fluorescence storage capacity, which is a longstanding challenge in state-of-the-art microbarcoding techniques and establish a generalized and adaptable coding platform for high-throughput analysis and optical multiplexing.
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Affiliation(s)
- Yujie Xie
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Zaizai Tong
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- College of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tianlai Xia
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Joshua C Worch
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Julia Y Rho
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andrew P Dove
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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7
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Sandberg E, Demirbay B, Kulkarni A, Liu H, Piguet J, Widengren J. Fluorescence Bar-Coding and Flowmetry Based on Dark State Transitions in Fluorescence Emitters. J Phys Chem B 2024; 128:125-136. [PMID: 38127267 PMCID: PMC10788918 DOI: 10.1021/acs.jpcb.3c06905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Reversible dark state transitions in fluorophores represent a limiting factor in fluorescence-based ultrasensitive spectroscopy, are a necessary basis for fluorescence-based super-resolution imaging, but may also offer additional, largely orthogonal fluorescence-based readout parameters. In this work, we analyzed the blinking kinetics of Cyanine5 (Cy5) as a bar-coding feature distinguishing Cy5 from rhodamine fluorophores having largely overlapping emission spectra. First, fluorescence correlation spectroscopy (FCS) solution measurements on mixtures of free fluorophores and fluorophore-labeled small unilamellar vesicles (SUVs) showed that Cy5 could be readily distinguished from the rhodamines by its reversible, largely excitation-driven trans-cis isomerization. This was next confirmed by transient state (TRAST) spectroscopy measurements, determining the fluorophore dark state kinetics in a more robust manner, from how the time-averaged fluorescence intensity varies upon modulation of the applied excitation light. TRAST was then combined with wide-field imaging of live cells, whereby Cy5 and rhodamine fluorophores could be distinguished on a whole cell level as well as in spatially resolved, multiplexed images of the cells. Finally, we established a microfluidic TRAST concept and showed how different mixtures of free Cy5 and rhodamine fluorophores and corresponding fluorophore-labeled SUVs could be distinguished on-the-fly when passing through a microfluidic channel. In contrast to FCS, TRAST does not rely on single-molecule detection conditions or a high time resolution and is thus broadly applicable to different biological samples. Therefore, we expect that the bar-coding concept presented in this work can offer an additional useful strategy for fluorescence-based multiplexing that can be implemented on a broad range of both stationary and moving samples.
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Affiliation(s)
- Elin Sandberg
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Baris Demirbay
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Abhilash Kulkarni
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Haichun Liu
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Joachim Piguet
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Jerker Widengren
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
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8
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Tang D, Shi J, Wu Y, Luo H, Yan J, Huang KJ, Tan X. Flexible Self-Powered Sensing System Based on Novel DNA Circuit Strategy and Graphdiyne for Thalassemia Gene by Rapid Naked-Eye Tracking and Open-Circuit Voltage. Anal Chem 2023; 95:16374-16382. [PMID: 37871958 DOI: 10.1021/acs.analchem.3c03841] [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: 10/25/2023]
Abstract
Based on the controllable instantaneous self-assembly ability of long-chain branched DNA nanostructures and the synergistic effect between nucleic acid amplification without enzymes, a highly sensitive and highly specific self-powered biosensing platform is developed. Two-dimensional graphdiyne is prepared, modified on flexible carbon cloth, and then functionalized with gold nanoparticles. When DNA mi-tubes are applied on it, target thalassemia gene CD122 triggers a dual-catalytic hairpin assembly reaction. The generated nanoscale DNA is precisely captured by the DNA mi-tube, exposing binding sites and activating the hybridization chain reaction to form long-chain branched DNA. Double-stranded DNA, along with dendritic DNA carrying a large number of guanine bases, precisely captures the signal molecule methylene blue (MB), generating a significant electrochemical signal. The redox reaction of MB also causes a proportional change in the system's color, achieving a colorimetric detection functionality. An efficient dual-mode self-powered sensing platform, therefore, is established for detecting the thalassemia gene CD122. The linear response range of target concentration to open-circuit voltage and RGB Blue value is 0.0001-10,000 pM. The detection limit under electrochemical mode is 36.3 aM (S/N = 3), and under colorimetric mode, it is as low as 12.1 aM (S/N = 3). The new method exhibits high sensitivity, excellent selectivity, and high accuracy, providing a universal strategy for designing novel biosensing platforms that can be extended to the detection of other biomolecules.
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Affiliation(s)
- Danyao Tang
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Jinyue Shi
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Yeyu Wu
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Hu Luo
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Jun Yan
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Ke-Jing Huang
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Xuecai Tan
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
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9
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Huang W, Cheng Y, Zhai J, Qin Y, Zhang W, Xie X. Expanded single-color barcoding in microspheres with fluorescence anisotropy for multiplexed biochemical detection. Analyst 2023; 148:4406-4413. [PMID: 37552039 DOI: 10.1039/d3an00938f] [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: 08/09/2023]
Abstract
Single-color barcoding strategies could break the limits of spectral crosstalk in conventional intensity-based fluorescence barcodes. Fluorescence anisotropy (FA), a self-referencing quantity able to differentiate spectrally similar fluorophores, is highly attractive in designing fluorescent barcodes within a limited emission window. In this study, FA-based encoding of polystyrene (PS) microspheres was realized for the first time. The FA signals of fluorophores were stabilized inside PS microspheres owing to hampered rotational motion. Fluorescent labels were incorporated with similar emission but different structures, symmetries, and lifetimes. On the one hand, Förster Resonance Energy Transfer (FRET) including homo-FRET and hetero-FRET resulted in a decrease of steady-state FA with increasing dye loading, converting conventional intensity-based codes into FA-based codes. On the other hand, mixing dyes with different intrinsic FA values generated different FA values at the same fluorescence intensity level. Single color 5-plex FA-encoded microspheres were demonstrated and decoded on a homemade microscopic FA imaging platform in real time. The FA-encoded microspheres were successfully applied to detect the oligonucleotide of the foodborne bacterium, Bacillus cereus, without spectral crosstalk between the encoding and reporting dyes. Overall, FA-based encoding with an expanded coding capacity in the FA dimension holds great potential in multiplexed high-throughput chemical and biological analyses.
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Affiliation(s)
- Wenyu Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yu Cheng
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Jingying Zhai
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuemin Qin
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Weian Zhang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xiaojiang Xie
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
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10
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Yao T, Chen J, Kong L, Liu Y, Yuan R, Chai Y. Efficient Three-Dimensional DNA Nanomachine Guided by a Robust Tetrahedral DNA Nanoarray Structure for the Rapid and Ultrasensitive Electrochemical Detection of Matrix Metalloproteinase 2. Anal Chem 2023; 95:13211-13219. [PMID: 37607331 DOI: 10.1021/acs.analchem.3c02212] [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: 08/24/2023]
Abstract
Herein, a giant-sized DNA nanoarray was subtly assembled by two kinds of independent tetrahedral DNA structures as the DNA track for a multi-armed three-dimensional (3D) DNA nanomachine to perform signal transduction and amplification efficiently, which was developed as an electrochemical biosensor for the rapid and ultrasensitive detection of matrix metalloproteinase 2 (MMP-2). Impressively, in contrast to conventional DNA walkers with inefficiency, which walked on random DNA tracks composed of a two-dimensional (2D) probe or a one-dimensional (1D) single-stranded (ss)DNA probe, the multi-armed 3D DNA nanomachine from exonuclease III (Exo III) enzyme-assisted target recycling amplification would be endowed with faster reaction speed and better walking efficiency because of the excellent rigidity and orderliness of the tetrahedral DNA nanoarray structure. Once the hairpin H3-label with the signal substance ferrocene (Fc) was added to the modified electrode surface, the multi-armed 3D DNA nanomachine would be driven to move along the well-designed nanoarray tracks by toehold-mediated DNA strand displacement, resulting in most of the ferrocene (Fc) binding to the electrode surface and a remarkable increase in electrochemical signals within 60 min. As a proof of concept, the prepared biosensor attained a low detection limit of 11.4 fg/mL for the sensitive detection of the target MMP-2 and was applied in Hela and MCF-7 cancer cell lysates. As a result, this strategy provided a high-performance sensing platform for protein detection in tumor diagnosis.
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Affiliation(s)
- Tong Yao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jie Chen
- Department of Endocrinology, 9th People's Hospital of Chongqing, Chongqing 400700, P. R. China
| | - Lingqi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ying Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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11
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Magnetic quantum dots barcodes using Fe 3O 4/TiO 2 with weak spectral absorption in the visible region for high-sensitivity multiplex detection of tumor markers. Biosens Bioelectron 2023; 227:115153. [PMID: 36805273 DOI: 10.1016/j.bios.2023.115153] [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: 01/03/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
Magnetic quantum dot (QD) barcode holds great potential for automatic suspension array and rapid point-of-care detection since it enables simultaneous target encoding, enrichment and separation. However, a serious obstacle to enhancing the encoding capacity of magnetic QD microbeads (MBs) is the fluorescence quenching of magnetic nanoparticles (MNPs) to quantum dots (QDs) in the visible wavelength range due to the broad and strong optical absorption spectrum of MNPs. Here, we report Fe3O4/TiO2 core/shell MNPs and CdSe/ZnS QDs for the construction of dual-function magnetic QD barcodes. Fe3O4/TiO2 MNPs can significantly inhibit fluorescence quenching because the weak absorption of visible light by the TiO2. The two-dimension barcode library of 30 magnetic QD barcodes was constructed based on Fe3O4/TiO2 MNPs and CdSe/ZnS QDs. Moreover, the magnetic QD barcodes showed high sensitivity for the multiplex detection of four tumor markers, cancer antigen 125 (CA125), cancer antigen 199 (CA199), alpha-fetoprotein (AFP), and neuron specific enolase (NSE) with detection limits of 0.89 KU/L, 0.72 KU/L, 0.05 ng/mL, and 0.15 ng/mL, respectively. This bifunctional magnetic QD barcodes are promising for automatic high-sensitivity multiplex bioassay.
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12
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Xie TJ, Xie JL, Luo YJ, Mao K, Huang CZ, Li YF, Zhen SJ. CRISPR-Cas12a Coupled with DNA Nanosheet-Amplified Fluorescence Anisotropy for Sensitive Detection of Biomolecules. Anal Chem 2023; 95:7237-7243. [PMID: 37120835 DOI: 10.1021/acs.analchem.3c00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
DNA nanosheets (DNSs) have been utilized effectively as a fluorescence anisotropy (FA) amplifier for biosensing. But, their sensitivity needs to be further improved. Herein, CRISPR-Cas12a with strong trans-cleavage activity was utilized to enhance the FA amplification ability of DNSs for the sensitive detection of miRNA-155 (miR-155) as a proof-of-principle target. In this method, the hybrid of the recognition probe of miR-155 (T1) and a blocker sequence (T2) was immobilized on the surface of magnetic beads (MBs). In the presence of miR-155, T2 was released by a strand displacement reaction, which activated the trans-cleavage activity of CRISPR-Cas12a. The single-stranded DNA (ssDNA) probe modified with a carboxytetramethylrhodamine (TAMRA) fluorophore was cleaved in large quantities and could not bind to the handle chain on DNSs, inducing a low FA value. In contrast, in the absence of miR-155, T2 could not be released and the trans-cleavage activity of CRISPR-Cas12a could not be activated. The TAMRA-modified ssDNA probe remained intact and was complementary to the handle chain on the DNSs, and a high FA value was obtained. Thus, miR-155 was detected through the obviously decreased FA value with a low limit of detection (LOD) of 40 pM. Impressively, the sensitivity of this method was greatly improved about 322 times by CRISPR-Cas12a, confirming the amazing signal amplification ability of CRISPR-Cas12a. At the same time, the SARS-CoV-2 nucleocapsid protein was detected by the strategy successfully, indicating that this method was general. Moreover, this method has been applied in the analysis of miR-155 in human serum and the lysates of cells, which provides a new avenue for the sensitive determination of biomarkers in biochemical research and disease diagnosis.
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Affiliation(s)
- Tian Jin Xie
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Jia Li Xie
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Yu Jie Luo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Kai Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, 400715 Chongqing, P. R. China
| | - Yuan Fang Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Shu Jun Zhen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
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13
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Zhang XL, Li SS, Liu YJ, Liu WW, Kong LQ, Chai YQ, Luo XL, Yuan R. High-Efficiency 3D DNA Walker Immobilized by a DNA Tetrahedral Nanostructure for Fast and Ultrasensitive Electrochemical Detection of MiRNA. Anal Chem 2023; 95:4077-4085. [PMID: 36787389 DOI: 10.1021/acs.analchem.2c04847] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Herein, by directly limiting the reaction space, an ingenious three-dimensional (3D) DNA walker (IDW) with high walking efficiency is developed for rapid and sensitive detection of miRNA. Compared with the traditional DNA walker, the IDW immobilized by the DNA tetrahedral nanostructure (DTN) brings stronger kinetic and thermodynamic favorability resulting from its improved local concentration and space confinement effect, accompanied by a quite faster reaction speed and much better walking efficiency. Once traces of target miRNA-21 react with the prelocked IDW, the IDW could be largely activated and walk on the interface of the electrode to trigger the cleavage of H2 with the assistance of Mg2+, resulting in the release of amounts of methylene blue (MB) labeled on H2 from the electrode surface and the obvious decrease of the electrode signal. Impressively, the IDW reveals a conversion efficiency as high as 9.33 × 108 in 30 min with a much fast reaction speed, which is at least five times beyond that of typical DNA walkers. Therefore, the IDW could address the inherent challenges of the traditional DNA walker easily: slow walking speed and low efficiency. Notably, the IDW as a DNA nanomachine was utilized to construct a sensitive sensing platform for rapid miRNA-21 detection with a limit of detection (LOD) of 19.8 aM and realize the highly sensitive assay of biomarker miRNA-21 in the total RNA lysates of cancer cell. The strategy thus helps in the design of a versatile nucleic acid conversion and signal amplification approach for practical applications in the areas of biosensing assay, DNA nanotechnology, and clinical diagnosis.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Sha-Sha Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yi-Jia Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wei-Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xi-Liang Luo
- Key Laboratory of Sensor Analysis of Tumor Markers, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266061, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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14
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Zhao Y, Guo L, Cao S, Xie M, Peng H, Li J, Luo S, Ma L, Wang L. DNA framework carriers with asymmetric hydrophobic drug patterns for enhanced cellular cytotoxicity. Chem Commun (Camb) 2023; 59:306-309. [PMID: 36507912 DOI: 10.1039/d2cc05763h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We devise a class of amphiphilic drug complexes by programming hydrophobic drug patterns (HDPs) on DNA frameworks. We investigate the effect of HDPs on cellular uptake efficiency and drug potency. We achieve enhanced cytotoxicity against tumor cells by using an asymmetric HDP.
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Affiliation(s)
- Yan Zhao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Linjie Guo
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Shuting Cao
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Mo Xie
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, China
| | - Hongzhen Peng
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Lan Ma
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
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15
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Cao X, Chen F, Xue J, Zhao Y, Bai M, Zhao Y. Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging. Nucleic Acids Res 2022; 51:e13. [PMID: 36478047 PMCID: PMC9943671 DOI: 10.1093/nar/gkac1138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Spatial visualization of single-cell transcripts is limited by signal specificity and multiplexing. Here, we report hierarchical DNA branch assembly-encoded fluorescent nanoladders, which achieve denoised and highly multiplexed signal amplification for single-molecule transcript imaging. This method first offers independent RNA-primed rolling circle amplification without nonspecific amplification based on circular DNAzyme. It then executes programmable DNA branch assembly on these amplicons to encode virtual signals for visualizing numbers of targets by FISH. In theory, more virtual signals can be encoded via the increase of detection spectral channels and repeats of the same sequences on barcode. Our method almost eliminates nonspecific amplification in fixed cells (reducing nonspecific spots of single cells from 16 to nearly zero), and achieves simultaneous quantitation of nine transcripts by using only two detection spectral channels. We demonstrate accurate RNA profiling in different cancer cells, and reveal diverse localization patterns for spatial regulation of transcripts.
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Affiliation(s)
- Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P.R. China
| | - Feng Chen
- Correspondence may also be addressed to Feng Chen.
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P.R. China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P.R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P.R. China
| | - Yongxi Zhao
- To whom correspondence should be addressed. Tel: +86 29 82668908; Fax: +86 29 82668908;
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16
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Wang W, Gao Y, Chen Y, Wang W, Li Q, Huang Z, Zhang J, Xiang Q, Wu Z. Outward Movement of Targeting Ligands from a Built-In Reserve Pool in Nuclease-Resistant 3D Hierarchical DNA Nanocluster for in Vivo High-Precision Cancer Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203698. [PMID: 36253152 PMCID: PMC9685459 DOI: 10.1002/advs.202203698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Nanostructures made entirely of DNAs display great potential as chemotherapeutic drug carriers but so far cannot achieve sufficient clinic therapy outcomes due to off-target toxicity. In this contribution, an aptamer-embedded hierarchical DNA nanocluster (Apt-eNC) is constructed as an intelligent carrier for cancer-targeted drug delivery. Specifically, Apt-eNC is designed to have a built-in reserve pool in the interior cavity from which aptamers may move outward to function as needed. When surface aptamers are degraded, ones in reserve pool can move outward to offer the compensation, thereby magically preserving tumor-targeting performance in vivo. Even if withstanding extensive aptamer depletion, Apt-eNC displays a 115-fold enhanced cell targeting compared with traditional counterparts and at least 60-fold improved tumor accumulation. Moreover, one Apt-eNC accommodates 5670 chemotherapeutic agents. As such, when systemically administrated into HeLa tumor-bearing BALB/c nude mouse model, drug-loaded Apt-eNC significantly inhibits tumor growth without systemic toxicity, holding great promise for high precision therapy.
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Affiliation(s)
- Weijun Wang
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Yansha Gao
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Wenqing Wang
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Qian Li
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Zhiyi Huang
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Jingjing Zhang
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
| | - Qi Xiang
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medicine GeneticsSchool of Laboratory Medicine and Life SciencesInstitute of Functional Nucleic Acids and Personalized Cancer TheranosticsWenzhou Medical UniversityWenzhou325035China
| | - Zai‐Sheng Wu
- Cancer Metastasis Alert and Prevention CenterFujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and ChemotherapyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou350108China
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17
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Zhang XL, Li SS, Liu WW, Kong LQ, Chai YQ, Yuan R. Programmable mismatch-fueled high-efficiency DNA signal amplifier. Chem Sci 2022; 13:11926-11935. [PMID: 36320909 PMCID: PMC9580486 DOI: 10.1039/d2sc04814k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/23/2022] [Indexed: 08/11/2023] Open
Abstract
Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Sha-Sha Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Wei-Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
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18
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Kong L, Han Z, Zhao M, Zhang X, Zhuo Y, Chai Y, Li Z, Yuan R. Versatile Electrochemical Biosensor Based on the Target-Controlled Capture and Release of DNA Nanotubes for the Ultrasensitive Detection of Multiplexed Biomarkers. Anal Chem 2022; 94:11416-11424. [PMID: 35930307 DOI: 10.1021/acs.analchem.2c02541] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, an ultrasensitive and versatile electrochemical biosensor was developed through the target-controlled capture and release of signal probe-loaded DNA nanotube for the ultrasensitive detection of two different types of cancer-related biomarkers, microRNA-21 (miRNA-21) and glutathione (GSH). In this system, target 1 (miRNA-21) first triggered duplex-specific nuclease (DSN)-assisted recycle amplification to generate numerous disulfide-linked DNA strands (DL), which could effectively capture DNA nanotube to immobilize methylene blue (MB) to produce remarkable electrochemical signals and achieve the ultrasensitive detection of miRNA-21 with a detection limit down to 32.6 aM. Furthermore, in the presence of target 2 (GSH), the electrochemical signal was significantly reduced by a thiol-disulfide bond exchange reaction on DL to release MB-immobilized DNA nanotubes away from the sensing interface, which enabled the sensitive analysis of GSH with a detection limit of 0.379 nM. Impressively, this strategy could achieve ultrasensitive detection of different types of biomarkers to prominently lessen false-positive responses from the current sensing methods toward a single biomarker or the same type of biomarker and remarkably heighten the accuracy and precision of early cancer diagnosis. Meanwhile, the proposed electrochemical biosensor made it possible to realize the regenerative analysis of targets over four times without extra fuel, which could conspicuously improve the analytical efficiency compared with that of traditional biosensing assays. As a result, this study might open up novel insights to design a versatile and multifunctional sensing platform and encourage deeper exploration for detecting different types of biomarkers in the fields of early disease diagnosis and biochemical research.
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Affiliation(s)
- Lingqi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Zeshuai Han
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Mingzhou Zhao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xiaolong Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Zhaohui Li
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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19
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Song L, Zhuge Y, Zuo X, Li M, Wang F. DNA Walkers for Biosensing Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200327. [PMID: 35460209 PMCID: PMC9366574 DOI: 10.1002/advs.202200327] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Indexed: 05/07/2023]
Abstract
The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer-associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection- of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker-based biosensors are discussed.
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Affiliation(s)
- Lu Song
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Ying Zhuge
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
| | - Xiaolei Zuo
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Min Li
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Fang Wang
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
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20
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Abstract
Lipid-DNA conjugates have emerged as highly useful tools to modify the cell membranes. These conjugates generally consist of a lipid anchor for membrane modification and a functional DNA nanostructure for membrane analysis or regulation. There are several unique properties of these lipid-DNA conjugates, especially including their programmability, fast and efficient membrane insertion, and precise sequence-specific assembly. These unique properties have enabled a broad range of biophysical applications on live cell membranes. In this review, we will mainly focus on recent tremendous progress, especially during the past three years, in regulating the biophysical features of these lipid-DNA conjugates and their key applications in studying cell membrane biophysics. Some insights into the current challenges and future directions of this interdisciplinary field have also been provided.
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21
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Guo L, Zhang Y, Wang Y, Xie M, Dai J, Qu Z, Zhou M, Cao S, Shi J, Wang L, Zuo X, Fan C, Li J. Directing Multivalent Aptamer-Receptor Binding on the Cell Surface with Programmable Atom-Like Nanoparticles. Angew Chem Int Ed Engl 2022; 61:e202117168. [PMID: 35226386 DOI: 10.1002/anie.202117168] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Indexed: 11/08/2022]
Abstract
Multivalent interactions of biomolecules play pivotal roles in physiological and pathological settings. Whereas the directionality of the interactions is crucial, the state-of-the-art synthetic multivalent ligand-receptor systems generally lack programmable approaches for orthogonal directionality. Here, we report the design of programmable atom-like nanoparticles (aptPANs) to direct multivalent aptamer-receptor binding on the cell interface. The positions of the aptamer motifs can be prescribed on tetrahedral DNA frameworks to realize atom-like orthogonal valence and direction, enabling the construction of multivalent molecules with fixed aptamer copy numbers but different directionality. These directional-yet-flexible aptPAN molecules exhibit the adaptability to the receptor distribution on cell surfaces. We demonstrate the high-affinity tumor cell binding with a linear aptPAN oligomer (≈13-fold improved compared to free aptamers), which leads to ≈50 % suppression of cell growth.
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Affiliation(s)
- Linjie Guo
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yueyue Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yue Wang
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mo Xie
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jiangbing Dai
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Mo Zhou
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Shuting Cao
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jiye Shi
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Jiang Li
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
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22
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Guo L, Zhang Y, Wang Y, Xie M, Dai J, Qu Z, Zhou M, Cao S, Shi J, Wang L, Zuo X, Fan C, Li J. Directing Multivalent Aptamer‐Receptor Binding on the Cell Surface with Programmable Atom‐Like Nanoparticles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Linjie Guo
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- The Interdisciplinary Research Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Yueyue Zhang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yue Wang
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Mo Xie
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiangbing Dai
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University 200240 Shanghai China
| | - Mo Zhou
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Shuting Cao
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiye Shi
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Lihua Wang
- The Interdisciplinary Research Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University Shanghai 200241 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University 200240 Shanghai China
| | - Jiang Li
- Division of Physical Biology Department CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- The Interdisciplinary Research Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University 200240 Shanghai China
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23
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Zhang X, Zhang M, Zhou M, Zhang T, Gao Y, Li S, Lin Y, Cai X. Tetrahedral-Framework Nucleic Acids Carry Small Interfering RNA to Downregulate Toll-Like Receptor 2 Gene Expression for the Treatment of Sepsis. ACS APPLIED MATERIALS & INTERFACES 2022; 14:6442-6452. [PMID: 35080860 DOI: 10.1021/acsami.1c23708] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sepsis is caused by the invasion of pathogenic microorganisms, which can lead to excessive expression of toll-like receptors (TLRs) in cells and uncontrollable amplification of the inflammatory response. TLR2, as an essential part of the TLR family, has a significant feature in the identification of innate immune responses. Therefore, blocking the expression and activation of TLR2 can inhibit the synthesis and release of inflammatory factors and avoid the occurrence of excessive inflammatory reactions. Small interfering RNA (siRNA) can selectively target the silencing or downregulation of pathogenic genes and has the advantages of high specificity, a strong effect, and fewer adverse reactions. However, the application of siRNA is limited by its high molecular weight, poor biostability, and difficulty in passive uptake into cells. Tetrahedral-framework nucleic acid (tFNA) is a new kind of three-dimensional nucleic acid nanomaterial, which has the advantages of good biocompatibility, stable structure, and editability. In this study, we used tFNA as carriers to deliver siRNA-targeting downregulation of TLR2 expression for anti-inflammatory therapy. We show that siRNA can specifically reduce lipopolysaccharide (LPS)-induced TLR2 elevation and reduce release of inflammatory factors in LPS-induced experimental sepsis, which provides a new idea for the prevention and treatment of sepsis.
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Affiliation(s)
- Xiaolin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Mei Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Mi Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yang Gao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
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24
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Guo C, Zhai J, Wang Y, Du X, Wang Z, Xie X. Photoswitch-Based Fluorescence Encoding of Microspheres in a Limited Spectral Window for Multiplexed Detection. Anal Chem 2022; 94:1531-1536. [PMID: 35025214 DOI: 10.1021/acs.analchem.1c04856] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence barcoding with multicolor fluorophores is limited by spectral crowding. Herein, we propose a fluorescence encoding method in a single-color channel with photoswitches. The photochromic naphthopyran was used to mediate the fluorescence of polystyrene microspheres through resonance energy transfer. The initial fluorescence intensity (F0) and the fluorescence after UV light activation (F/F0) were combined to generate hundreds of 2-dimensional barcodes. The coding capacity was further expanded with the different chemical kinetics of the photoswitches. The photoswitch-based fluorescence barcodes were applied to simultaneously and selectively detect the DNA sequences of COVID-19 (with related mutations) as a proof-of-concept for real applications. The compatibility with the state-of-the-art fluorescence microscopes and simple encoding and decoding make the method very attractive for multiplexed and high-throughput analyses.
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Affiliation(s)
- Chao Guo
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jingying Zhai
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yifu Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xinfeng Du
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zige Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaojiang Xie
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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25
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Feng DQ, Liu G. Target-Activating and Toehold Displacement Ag NCs/GO Biosensor-Mediating Signal Shift and Enhancement for Simultaneous Multiple Detection. Anal Chem 2021; 93:16025-16034. [PMID: 34817158 DOI: 10.1021/acs.analchem.1c03570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we demonstrate that a new multicolor silver nanoclusters/graphene oxide (Ag NCs/GO) hybrid material, upon target response, undergoes a configuration transformation, based on entropy-driven enzyme-free toehold-mediated strand displacement reaction, achieving emission shift and enhancement. To realize the aim above, two different synthesis routes (route I and II) of synthesizing fluorescent Ag NCs for constructing toehold displacement Ag NCs/GO biosensor is designed and performed. Influenza A virus subtype genes (H1N1 and H5N1) as a model can efficiently initiate the operation of entropy-driven displacement reaction, resulting in activatable fluorescence. Red-emitting and green-emitting Ag NCs tethering the complementary sequence of H1N1 (pDNA1) and H5N1 (pDNA2) are indirectly immobilized on GO surface through binding with capture DNA (cDNA1 and cDNA2), respectively, forming multicolor pDNA-Ag NCs/GO nanohybrid materials. However, they do not exhibit nearly fluorescence signals attributed to energy transfer from donor Ag NCs to acceptor GO. Upon adding targets H1N1 and H5N1 (tDNA1 and tDNA2), pDNA1-Ag NCs and pDNA2-Ag NCs detach from GO, based on toehold-mediated strand displacement reaction, which interferes the energy transfer and leads to significant fluorescence enhancement. More interestingly, the activatable process is accompanied by remarkable hypsochromic shift (19 nm) or bathochromic shift (21 nm) emission with quite high fluorescence recovery rates (823.35% and 693.62%). Therefore, based on these phenomena, a novel multiple approach has been developed with the assistance of toehold displacement and Ag NCs/GO nanohybrid materials. As for the remarkable emission recovery and multichannel signal, the proposed approach displays the promising application prospect in accurate diagnosis and treatment.
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Affiliation(s)
- Da-Qian Feng
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Guoliang Liu
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, China
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