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Quazi MZ, Choi JH, Kim M, Park N. DNA and Nanomaterials: A Functional Combination for DNA Sensing. ACS APPLIED BIO MATERIALS 2024; 7:778-786. [PMID: 38270150 DOI: 10.1021/acsabm.3c01190] [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] [Indexed: 01/26/2024]
Abstract
Recent decades have experienced tough situations due to the lack of reliable diagnostic facilities. The most recent cases occurred during the pandemic, where researchers observed the lack of diagnostic facilities with precision. Microorganisms and viral disease's ability to escape diagnosis has been a global challenge. DNA always has been a unique moiety with a strong and precise base-paired structure. DNA in human and foreign particles makes identification possible through base pairing. Since then, researchers have focused heavily on designing diagnostic assays targeting DNA in particular. Moreover, DNA nanotechnology has contributed vastly to designing composite nanomaterials by combining DNA/nucleic acids with functional nanomaterials and inorganic nanoparticles exploiting their physicochemical properties. These nanomaterials often exhibit unique or enhanced properties due to the synergistic activity of the many components. The capabilities of DNA and additional nanomaterials have shown the combination of robust and advanced tailoring of biosensors. Preceding findings state that the conventional strategies have exhibited certain limitations such as a low range of target detection, less biodegradability, subordinate half-life, and high susceptibility to microenvironments; however, a DNA-nanomaterial-based biosensor has overcome these limitations meaningfully. Additionally, the unique properties of nucleic acids have been studied extensively due to their high signal conduction abilities. Here, we review recent studies on DNA-nanomaterial-based biosensors, their mechanism of action, and improved/updated strategies in vivo and in situ. Furthermore, this review highlights the recent methodologies on DNA utilization to exploit the interfacial properties of nanomaterials in DNA sensing. Lastly, the review concludes with the limitations/challenges and future directions.
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Affiliation(s)
- Mohzibudin Z Quazi
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Jang Hyeon Choi
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Minchul Kim
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
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2
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Liu B, Duan H, Liu Z, Liu Y, Chu H. DNA-functionalized metal or metal-containing nanoparticles for biological applications. Dalton Trans 2024; 53:839-850. [PMID: 38108230 DOI: 10.1039/d3dt03614f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The conjugation of DNA molecules with metal or metal-containing nanoparticles (M/MC NPs) has resulted in a number of new hybrid materials, enabling a diverse range of novel biological applications in nanomaterial assembly, biosensor development, and drug/gene delivery. In such materials, the molecular recognition, gene therapeutic, and structure-directing functions of DNA molecules are coupled with M/MC NPs. In turn, the M/MC NPs have optical, catalytic, pore structure, or photodynamic/photothermal properties, which are beneficial for sensing, theranostic, and drug loading applications. This review focuses on the different DNA functionalization protocols available for M/MC NPs, including gold NPs, upconversion NPs, metal-organic frameworks, metal oxide NPs and quantum dots. The biological applications of DNA-functionalized M/MC NPs in the treatment or diagnosis of cancers are discussed in detail.
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Affiliation(s)
- Bei Liu
- College of Science, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Huijuan Duan
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
| | - Zechao Liu
- College of Science, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Yuechen Liu
- College of Science, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Hongqian Chu
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
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Yang R, Hu J, Zhang L, Liu X, Huang Y, Zhang L, Fan Q. Recent advances in optical biosensing and imaging of telomerase activity and relevant signal amplification strategies. Analyst 2024; 149:290-303. [PMID: 38099470 DOI: 10.1039/d3an01900d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Telomerase as a new valuable biomarker for early diagnosis and prognosis evaluation of cancer has attracted much interest in the field of biosensors, cell imaging, and drug screening. In this review, we mainly focus on different optical techniques and various signal amplification strategies for telomerase activity determination. Fluorometric, colorimetry, chemiluminescence, surface-enhanced Raman scattering (SERS), and dual-mode techniques for telomerase sensing and imaging are summarized. Signal amplification strategies include two categories: one is nucleic acid-based amplification, such as rolling circle amplification (RCA), the hybridization chain reaction (HCR), and catalytic hairpin assembly (CHA); the other is nanomaterial-assisted amplification, including metal nanoclusters, quantum dots, transition metal compounds, graphene oxide, and DNA nanomaterials. Challenges and prospects are also discussed to provide new insights for future development of multifunctional strategies and techniques for in situ and in vivo analysis of biomarkers for accurate cancer diagnosis.
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Affiliation(s)
- Ruining Yang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Junbo Hu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Longsheng Zhang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Xingfen Liu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yanqin Huang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lei Zhang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Quli Fan
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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Pradhan S, Swanson CJ, Leff C, Tengganu I, Bergeman MH, Wisna GBM, Hogue IB, Hariadi RF. Viral Attachment Blocking Chimera Composed of DNA Origami and Nanobody Inhibits Pseudorabies Virus Infection In Vitro. ACS NANO 2023; 17:23317-23330. [PMID: 37982733 PMCID: PMC10787579 DOI: 10.1021/acsnano.3c01408] [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] [Indexed: 11/21/2023]
Abstract
Antivirals are indispensable tools that can be targeted at viral domains directly or at cellular domains indirectly to obstruct viral infections and reduce pathogenicity. Despite their transformative use in healthcare, antivirals have been clinically approved to treat only 10 of the more than 200 known pathogenic human viruses. Additionally, many virus functions are intimately coupled with host cellular processes, which presents challenges in antiviral development due to the limited number of clear targets per virus, necessitating extensive insight into these molecular processes. Compounding this challenge, many viral pathogens have evolved to evade effective antivirals. We hypothesize that a viral attachment blocking chimera (VirABloC) composed of a viral binder and a bulky scaffold that sterically blocks interactions between a viral particle and a host cell may be suitable for the development of antivirals that are agnostic to the extravirion epitope that is being bound. We test this hypothesis by modifying a nanobody that specifically recognizes a nonessential epitope presented on the extravirion surface of pseudorabies virus strain 486 with a 3-dimensional wireframe DNA origami structure ∼100 nm in diameter. The nanobody switches from having no inhibitory properties to 4.2 ± 0.9 nM IC50 when conjugated with the DNA origami scaffold. Mechanistic studies support that inhibition is mediated by the noncovalent attachment of the DNA origami scaffold to the virus particle, which obstructs the attachment of the viruses onto host cells. These results support the potential of VirABloC as a generalizable approach to developing antivirals.
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Affiliation(s)
- Swechchha Pradhan
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
| | - Carter J Swanson
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
| | - Chloe Leff
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Isadonna Tengganu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
| | - Melissa H Bergeman
- School of Life Science, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, Arizona 85281, United States
| | - Gde B M Wisna
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85281, United States
| | - Ian B Hogue
- School of Life Science, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, Arizona 85281, United States
| | - Rizal F Hariadi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85281, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85281, United States
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Leitão MIPS, Orsini G, Murtinheira F, Gomes CSB, Herrera F, Petronilho A. Synthesis, Base Pairing Properties, and Biological Activity Studies of Platinum(II) Complexes Based on Uracil Nucleosides. Inorg Chem 2023; 62:16412-16425. [PMID: 37768109 DOI: 10.1021/acs.inorgchem.3c02071] [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: 09/29/2023]
Abstract
The synthesis and base pairing properties of platinum complexes based on uridine and deoxyuridine nucleosides and preliminary studies of their antiproliferative activity are described. Platinum(II) uridine and deoxyuridine complexes were synthesized by C-I oxidative addition to Pt(0)(PPh3)4. First, the synthesis was performed with protected nucleosides to generate complexes 1 and 2, which were deprotected under basic conditions, affording complexes 3 and 4 in good yields. The synthesis with the unprotected nucleosides was also performed and provided complexes 3 and 4 effectively. Base pairing interactions were measured for complex 1, either for self-base pairing or for the Watson-Crick base pair. Complex 1 undergoes self-base pairing in CDCl3, and this aggregation was found not to be dependent on metalation. Contrastingly, for the Watson-Crick base pair with adenine, base pairing was also observed, but metalation was found to affect hydrogen bonding considerably. Complexes 3 and 4 and the corresponding ligand precursors were evaluated for their antiproliferative activity against human glioblastoma cell line U-251. The compounds showed IC50 values of 3.30 (3) and 1.84 (4) μM but are also toxic for nontumorous cell lines.
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Affiliation(s)
- Maria Inês P S Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da Republica, 2780-157 Oeiras, Portugal
| | - Giulia Orsini
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da Republica, 2780-157 Oeiras, Portugal
| | - Fernanda Murtinheira
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Dep. Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Clara S B Gomes
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO and i4HB - Applied Molecular Biosciences Unit and Institute for Health and Bioeconomy, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Federico Herrera
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Dep. Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Ana Petronilho
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da Republica, 2780-157 Oeiras, Portugal
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Zuo L, Ren K, Guo X, Pokhrel P, Pokhrel B, Hossain MA, Chen ZX, Mao H, Shen H. Amalgamation of DNAzymes and Nanozymes in a Coronazyme. J Am Chem Soc 2023; 145:5750-5758. [PMID: 36795472 PMCID: PMC10325850 DOI: 10.1021/jacs.2c12367] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Artificial enzymes such as nanozymes and DNAzymes are economical and stable alternatives to natural enzymes. By coating Au nanoparticles (AuNPs) with a DNA corona (AuNP@DNA), we amalgamated nanozymes and DNAzymes into a new artificial enzyme with catalytic efficiency 5 times higher than AuNP nanozymes, 10 times higher than other nanozymes, and significantly greater than most of the DNAzymes on the same oxidation reaction. The AuNP@DNA demonstrates excellent specificity as its reactivity on a reduction reaction does not change with respect to pristine AuNP. Single-molecule fluorescence and force spectroscopies and density functional theory (DFT) simulations indicate a long-range oxidation reaction initiated by radical production on the AuNP surface, followed by radical transport to the DNA corona, where the binding and turnover of substrates take place. The AuNP@DNA is named coronazyme because of its natural enzyme mimicking capability through the well-orchestrated structures and synergetic functions. By incorporating different nanocores and corona materials beyond DNAs, we anticipate that the coronazymes represent generic enzyme mimics to carry out versatile reactions in harsh environments.
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Affiliation(s)
- Li Zuo
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Xianming Guo
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Bishal Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | | | - Zhao-Xu Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
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Ouyang X, Wu Y, Gao Y, Li L, Li L, Liu T, Jing X, Fu Y, Luo J, Xie G, Jia S, Li M, Li Q, Fan C, Liu X. Micron-Scale Fabrication of Ultrathin Amorphous Copper Nanosheets Templated by DNA Scaffolds. J Am Chem Soc 2023; 145:4553-4563. [PMID: 36802526 DOI: 10.1021/jacs.2c12009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Two-dimensional (2D) amorphous materials could outperform their crystalline counterparts toward various applications because they have more defects and reactive sites and thus could exhibit a unique surface chemical state and provide an advanced electron/ion transport path. Nevertheless, it is challenging to fabricate ultrathin and large-sized 2D amorphous metallic nanomaterials in a mild and controllable manner due to the strong metallic bonds between metal atoms. Here, we reported a simple yet fast (10 min) DNA nanosheet (DNS)-templated method to synthesize micron-scale amorphous copper nanosheets (CuNSs) with a thickness of 1.9 ± 0.4 nm in aqueous solution at room temperature. We demonstrated the amorphous feature of the DNS/CuNSs by transmission electron microscopy (TEM) and X-ray diffraction (XRD). Interestingly, we found that they could transform to crystalline forms under continuous electron beam irradiation. Of note, the amorphous DNS/CuNSs exhibited much stronger photoemission (∼62-fold) and photostability than dsDNA-templated discrete Cu nanoclusters due to the elevation of both the conduction band (CB) and valence band (VB). Such ultrathin amorphous DNS/CuNSs hold great potential for practical applications in biosensing, nanodevices, and photodevices.
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Affiliation(s)
- Xiangyuan Ouyang
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Yongli Wu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Yanjing Gao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyun Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Le Li
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Ting Liu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Xinxin Jing
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Fu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Jing Luo
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Gang Xie
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Sisi Jia
- Zhangjiang Laboratory, 100 Haike Road, Shanghai 201210, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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