1
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Yu S, Shi T, Li C, Xie C, Wang F, Liu X. Programming DNA Nanoassemblies into Polyvalent Lysosomal Degraders for Potent Degradation of Pathogenic Membrane Proteins. NANO LETTERS 2024; 24:11573-11580. [PMID: 39225423 DOI: 10.1021/acs.nanolett.4c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Lysosome-targeting chimera (LYTAC) shows great promise for protein-based therapeutics by targeted degradation of disease-associated membrane or extracellular proteins, yet its efficiency is constrained by the limited binding affinity between LYTAC reagents and designated proteins. Here, we established a programmable and multivalent LYTAC system by tandem assembly of DNA into a high-affinity protein degrader, a heterodimer aptamer nanostructure targeting both pathogenic membrane protein and lysosome-targeting receptor (insulin-like growth factor 2 receptor, IGF2R) with adjustable spatial distribution or organization pattern. The DNA-based multivalent LYTACs showed enhanced efficacy in removing immune-checkpoint protein programmable death-ligand 1 (PD-L1) and vascular endothelial growth factor receptor 2 (VEGFR2) in tumor cell membrane that respectively motivated a significant increase in T cell activity and a potent effect on cancer cell growth inhibition. With high programmability and versatility, this multivalent LYTAC system holds considerable promise for realizing protein therapeutics with enhanced activity.
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Affiliation(s)
- Shuyi Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Tianhui Shi
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chenbiao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chongyu Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Beijing Life Science Academy, Beijing 102209, China
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2
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Dong Y, Guo C, Wang J, Ye C, Min Q. Recent Advances in DNA Nanotechnology-Based Sensing Platforms for Rapid Virus Detection. Chembiochem 2024; 25:e202400230. [PMID: 38825565 DOI: 10.1002/cbic.202400230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/04/2024]
Abstract
Several major viral pandemics in history have significantly impacted the public health of human beings. The COVID-19 pandemic has further underscored the critical need for early detection and screening of infected individuals. However, current detection techniques are confronted with deficiencies in sensitivity and accuracy, restricting the capability of detecting trace amounts of viruses in human bodies and in the environments. The advent of DNA nanotechnology has opened up a feasible solution for rapid and sensitive virus determination. By harnessing the designability and addressability of DNA nanostructures, a range of rapid virus sensing platforms have been proposed. This review overviewed the recent progress, application, and prospect of DNA nanotechnology-based rapid virus detection platforms. Furthermore, the challenges and developmental prospects in this field were discussed.
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Affiliation(s)
- Yuxiang Dong
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Cheng Guo
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Jialing Wang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Changqing Ye
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, P. R. China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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3
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Huang K, Yang Q, Bao M, Wang S, Zhao L, Shi Q, Yang Y. Modulated Cell Internalization Behavior of Icosahedral DNA Framework with Programmable Surface Modification. J Am Chem Soc 2024; 146:21442-21452. [PMID: 39038211 DOI: 10.1021/jacs.4c04106] [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: 07/24/2024]
Abstract
Surface modification could enhance the cell internalization efficiency of nanovehicles for targeted gene or drug delivery. However, the influence of surface modification parameters, including recognition manners, valences, and patterns, is often clouded, especially for the endocytosis of DNA nanostructures in customized shapes. Focusing on an icosahedral DNA framework, we systematically programmed three distinct types of ligands with diverse valence and spatial distribution on their outer surface to study the internalization efficiency, endocytic pathways, and postinternalization fate. The comparison in different aspects of parameters deepens our understanding of the intricate relationship between surface modification and cell entry behavior, offering insights crucial for designing and optimizing DNA framework nanostructures for potent cell-targeted purposes.
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Affiliation(s)
- Kui Huang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiulan Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Bao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shengwen Wang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Luming Zhao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Shi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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4
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Zhang J, Xu Y, Chen M, Wang S, Lin G, Huang Y, Yang C, Yang Y, Song Y. Spatial Engineering of Heterotypic Antigens on a DNA Framework for the Preparation of Mosaic Nanoparticle Vaccines with Enhanced Immune Activation against SARS-CoV-2 Variants. Angew Chem Int Ed Engl 2024:e202412294. [PMID: 39030890 DOI: 10.1002/anie.202412294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/22/2024]
Abstract
Mosaic nanoparticle vaccines with heterotypic antigens exhibit broad-spectrum antiviral capabilities, but the impact of antigen proportions and distribution patterns on vaccine-induced immunity remains largely unexplored. Here, we present a DNA nanotechnology-based strategy for spatially assembling heterotypic antigens to guide the rational design of mosaic nanoparticle vaccines. By utilizing two aptamers with orthogonal selectivity for the original SARS-CoV-2 spike trimer and Omicron receptor-binding domain (RBD), along with a DNA soccer-ball framework, we precisely manipulate the spacing, stoichiometry, and overall distribution of heterotypic antigens to create mosaic nanoparticles with average, bipolar, and unipolar antigen distributions. Systematic in vitro and in vivo immunological investigations demonstrate that 30 heterotypic antigens in equivalent proportions, with an average distribution, lead to higher production of broad-spectrum neutralizing antibodies compared to the bipolar and unipolar distributions. Furthermore, the precise assembly utilizing our developed methodology reveals that a mere increment of five Omicron RBD antigens on a nanoparticle (from 15 to 20) not only diminishes neutralization against the Omicron variant but also triggers excessive inflammation. This work provides a unique perspective on the rational design of mosaic vaccines by highlighting the significance of the spatial placement and proportion of heterotypic antigens in their structure-activity mechanisms.
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Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mingying Chen
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen University, Xiamen, Fujian, 361005, China
| | - Shengwen Wang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200234, China
| | - Guihong Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen University, Xiamen, Fujian, 361005, China
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen University, Xiamen, Fujian, 361005, China
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5
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Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024; 53:6830-6859. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [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: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
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Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
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6
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Willner E, Kolbe F, Momburg F, Protzer U, Dietz H. Hepatitis B Virus Neutralization with DNA Origami Nanoshells. ACS APPLIED MATERIALS & INTERFACES 2024; 16:25836-25842. [PMID: 38728653 PMCID: PMC11129107 DOI: 10.1021/acsami.4c03700] [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: 03/05/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
We demonstrate the use of DNA origami to create virus-trapping nanoshells that efficiently neutralize hepatitis B virus (HBV) in cell culture. By modification of the shells with a synthetic monoclonal antibody that binds to the HBV envelope, the effective neutralization potency per antibody is increased by approximately 100 times compared to using free antibodies. The improvements in neutralizing the virus are attributed to two factors: first, the shells act as a physical barrier that blocks the virus from interacting with host cells; second, the multivalent binding of the antibodies inside the shells lead to stronger attachment to the trapped virus, a phenomenon known as avidity. Pre-incubation of shells with HBV and simultaneous addition of both components separately to cells lead to comparable levels of neutralization, indicating rapid trapping of the virions by the shells. Our study highlights the potential of the DNA shell system to rationally create antivirals using components that, when used individually, show little to no antiviral effectiveness.
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Affiliation(s)
- Elena
M. Willner
- Department
of Biosciences, School of Natural Sciences and Munich Institute of
Biomedical Engineering, Technical University
of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Fenna Kolbe
- Institute
of Virology, School of Medicine & Health, Technical University of Munich and Helmholtz Munich, Trogerstraße 30, 81675 Munich, Germany
| | - Frank Momburg
- Translational
Immunity Unit, German Cancer Research Center
(DKFZ), Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Ulrike Protzer
- Institute
of Virology, School of Medicine & Health, Technical University of Munich and Helmholtz Munich, Trogerstraße 30, 81675 Munich, Germany
- German
Center for Infection Research (DZIF),
Munich Partner Site, 81675 Munich, Germany
| | - Hendrik Dietz
- Department
of Biosciences, School of Natural Sciences and Munich Institute of
Biomedical Engineering, Technical University
of Munich, Boltzmannstraße 11, 85748 Garching, Germany
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7
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Liu H, Matthies M, Russo J, Rovigatti L, Narayanan RP, Diep T, McKeen D, Gang O, Stephanopoulos N, Sciortino F, Yan H, Romano F, Šulc P. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Science 2024; 384:776-781. [PMID: 38753798 DOI: 10.1126/science.adl5549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
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Affiliation(s)
- Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Thong Diep
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Flavio Romano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30171 Venezia-Mestre, Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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8
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Wang X, Kang H, Huang K, Guo M, Wu Y, Ying T, Liu Y, Wei D. Antibody Nanotweezer Constructing Bivalent Transistor-Biomolecule Interface with Spatial Tolerance. NANO LETTERS 2024; 24:3914-3921. [PMID: 38513214 DOI: 10.1021/acs.nanolett.3c05140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Establishing a multivalent interface between the biointerface of a living system and electronic device is vital to building intelligent bioelectronic systems. How to achieve multivalent binding with spatial tolerance at the nanoscale remains challenging. Here, we report an antibody nanotweezer that is a self-adaptive bivalent nanobody enabling strong and resilient binding between transistor and envelope proteins at biointerfaces. The antibody nanotweezer is constructed by a DNA framework, where the nanoscale patterning of nanobodies along with their local spatial adaptivity enables simultaneous recognition of target epitopes without binding stress. As such, effective binding affinity increases by 1 order of magnitude compared with monovalent antibody. The antibody nanotweezer operating on transistor offers enhanced signal transduction, which is implemented to detect clinical pathogens, showing ∼100% overall agreement with PCR results. This work provides a perspective of engineering multivalent interfaces between biosystems with solid-state devices, holding great potential for organoid intelligence on a chip.
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Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Hua Kang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Keke Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Mingquan Guo
- Shanghai Institute of Phage, Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yanling Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
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9
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Guo Y, Song W, Dong Y, Wang X, Nie G, Li F. A Poly Aptamer Encoded DNA Nanocatcher Informs Efficient Virus Trapping. NANO LETTERS 2024; 24:3614-3623. [PMID: 38497742 DOI: 10.1021/acs.nanolett.3c04510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Broad-spectrum antiviral platforms are always desired but still lack the ability to cope with the threats to global public health. Herein, we develop a poly aptamer encoded DNA nanocatcher platform that can trap entire virus particles to inhibit infection with a broad antiviral spectrum. Ultralong single-stranded DNA (ssDNA) containing repeated aptamers was synthesized as the scaffold of a nanocatcher via a biocatalytic process, wherein mineralization of magnesium pyrophosphate on the ssDNA could occur and consequently lead to the formation of nanocatcher with interfacial nanocaves decorated with virus-binding aptamers. Once the viruses were recognized by the apatmers, they would be captured and trapped in the nanocaves via multisite synergistic interactions. Meanwhile, the size of nanocatchers was optimized to prevent their cellular uptake, which further guaranteed inhibition of virus infection. By taking SARS-CoV-2 variants as a model target, we demonstrated the broad virus-trapping capability of a DNA nanocatcher in engulfing the variants and blocking the infection to host cells.
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Affiliation(s)
- Yunhua Guo
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenzhe Song
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xuejun Wang
- Bioinformatics Center of AMMS, Taiping Rd, Haidian District, Beijing, 100850, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
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10
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Gao R, Xu X, Kumar P, Liu Y, Zhang H, Guo X, Sun M, Colombari FM, de Moura AF, Hao C, Ma J, Turali Emre ES, Cha M, Xu L, Kuang H, Kotov NA, Xu C. Tapered chiral nanoparticles as broad-spectrum thermally stable antivirals for SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2024; 121:e2310469121. [PMID: 38502692 PMCID: PMC10990083 DOI: 10.1073/pnas.2310469121] [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: 07/21/2023] [Accepted: 01/19/2024] [Indexed: 03/21/2024] Open
Abstract
The incessant mutations of viruses, variable immune responses, and likely emergence of new viral threats necessitate multiple approaches to novel antiviral therapeutics. Furthermore, the new antiviral agents should have broad-spectrum activity and be environmentally stable. Here, we show that biocompatible tapered CuS nanoparticles (NPs) efficiently agglutinate coronaviruses with binding affinity dependent on the chirality of surface ligands and particle shape. L-penicillamine-stabilized NPs with left-handed curved apexes display half-maximal inhibitory concentrations (IC50) as low as 0.66 pM (1.4 ng/mL) and 0.57 pM (1.2 ng/mL) for pseudo-type SARS-CoV-2 viruses and wild-type Wuhan-1 SARS-CoV-2 viruses, respectively, which are about 1,100 times lower than those for antibodies (0.73 nM). Benefiting from strong NPs-protein interactions, the same particles are also effective against other strains of coronaviruses, such as HCoV-HKU1, HCoV-OC43, HCoV-NL63, and SARS-CoV-2 Omicron variants with IC50 values below 10 pM (21.8 ng/mL). Considering rapid response to outbreaks, exposure to elevated temperatures causes no change in the antiviral activity of NPs while antibodies are completely deactivated. Testing in mice indicates that the chirality-optimized NPs can serve as thermally stable analogs of antiviral biologics complementing the current spectrum of treatments.
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Affiliation(s)
- Rui Gao
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Xinxin Xu
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Prashant Kumar
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
| | - Ye Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan650000, People’s Republic of China
| | - Hongyu Zhang
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Xiao Guo
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Maozhong Sun
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Felippe Mariano Colombari
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo13083-100, Brazil
| | - André F. de Moura
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo13565-905, Brazil
| | - Changlong Hao
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Jessica Ma
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
- NSF Center for Complex Particles and Particle Systems (COMPASS), University of Michigan, Ann Arbor, MI48109
| | - Emine Sumeyra Turali Emre
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
- NSF Center for Complex Particles and Particle Systems (COMPASS), University of Michigan, Ann Arbor, MI48109
| | - Minjeong Cha
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
| | - Liguang Xu
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Nicholas A. Kotov
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
- NSF Center for Complex Particles and Particle Systems (COMPASS), University of Michigan, Ann Arbor, MI48109
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
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11
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
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12
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Song T, Cooper L, Galván Achi J, Wang X, Dwivedy A, Rong L, Wang X. Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition. J Am Chem Soc 2024; 146:5894-5900. [PMID: 38408177 PMCID: PMC10965196 DOI: 10.1021/jacs.3c11760] [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] [Indexed: 02/28/2024]
Abstract
Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.
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Affiliation(s)
- Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jazmin Galván Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xiaojing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Chen Z, Sun Q, Yang Y, Nie X, Xiang W, Ren Y, Le T. Aptamer-based diagnostic and therapeutic approaches for animal viruses: A review. Int J Biol Macromol 2024; 257:128677. [PMID: 38072350 DOI: 10.1016/j.ijbiomac.2023.128677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
Animal diseases often have significant consequences due to the unclear and time-consuming diagnosis process. Furthermore, the emergence of new viral infections and drug-resistant pathogens has further complicated the diagnosis and treatment of viral diseases. Aptamers, which are obtained through systematic evolution of ligands by exponential enrichment (SELEX) technology, provide a promising solution as they enable specific identification and binding to targets, facilitating pathogen detection and the development of novel therapeutics. This review presented an overview of aptasensors for animal virus detection, discussed the antiviral activity and mechanisms of aptamers, and highlighted advancements in aptamer-based antiviral research following the COVID-19 pandemic. Additionally, the challenges and prospects of aptamer-based virus diagnosis and treatment research were explored. Although this review was not exhaustive, it offered valuable insights into the progress of aptamer-based antiviral drug research, target mechanisms, as well as the development of novel antiviral drugs and biosensors.
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Affiliation(s)
- Zhuoer Chen
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Qi Sun
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Ying Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Xunqing Nie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Wenyu Xiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Yueyang Ren
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Tao Le
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China.
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14
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Dhar A, Gupta SL, Saini P, Sinha K, Khandelwal A, Tyagi R, Singh A, Sharma P, Jaiswal RK. Nanotechnology-based theranostic and prophylactic approaches against SARS-CoV-2. Immunol Res 2024; 72:14-33. [PMID: 37682455 DOI: 10.1007/s12026-023-09416-x] [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: 03/19/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023]
Abstract
SARS-CoV-2 (COVID-19) pandemic has been an unpredicted burden on global healthcare system by infecting over 700 million individuals, with approximately 6 million deaths worldwide. COVID-19 significantly impacted all sectors, but it very adversely affected the healthcare system. These effects were much more evident in the resource limited part of the world. Individuals with acute conditions were also severely impacted. Although classical COVID-19 diagnostics such as RT-PCR and rapid antibody testing have played a crucial role in reducing the spread of infection, these diagnostic techniques are associated with certain limitations. For instance, drawback of RT-PCR diagnostics is that due to degradation of viral RNA during shipping, it can give false negative results. Also, rapid antibody testing majorly depends on the phase of infection and cannot be performed on immune compromised individuals. These limitations in current diagnostic tools require the development of nanodiagnostic tools for early detection of COVID-19 infection. Therefore, the SARS-CoV-2 outbreak has necessitated the development of specific, responsive, accurate, rapid, low-cost, and simple-to-use diagnostic tools at point of care. In recent years, early detection has been a challenge for several health diseases that require prompt attention and treatment. Disease identification at an early stage, increased imaging of inner health issues, and ease of diagnostic processes have all been established using a new discipline of laboratory medicine called nanodiagnostics, even before symptoms have appeared. Nanodiagnostics refers to the application of nanoparticles (material with size equal to or less than 100 nm) for medical diagnostic purposes. The special property of nanomaterials compared to their macroscopic counterparts is a lesser signal loss and an enhanced electromagnetic field. Nanosize of the detection material also enhances its sensitivity and increases the signal to noise ratio. Microchips, nanorobots, biosensors, nanoidentification of single-celled structures, and microelectromechanical systems are some of the most modern nanodiagnostics technologies now in development. Here, we have highlighted the important roles of nanotechnology in healthcare sector, with a detailed focus on the management of the COVID-19 pandemic. We outline the different types of nanotechnology-based diagnostic devices for SARS-CoV-2 and the possible applications of nanomaterials in COVID-19 treatment. We also discuss the utility of nanomaterials in formulating preventive strategies against SARS-CoV-2 including their use in manufacture of protective equipment, formulation of vaccines, and strategies for directly hindering viral infection. We further discuss the factors hindering the large-scale accessibility of nanotechnology-based healthcare applications and suggestions for overcoming them.
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Affiliation(s)
- Atika Dhar
- National Institute of Immunology, New Delhi, India, 110067
| | | | - Pratima Saini
- National Institute of Immunology, New Delhi, India, 110067
| | - Kirti Sinha
- Department of Zoology, Patna Science College, Patna University, Patna, Bihar, India
| | | | - Rohit Tyagi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alka Singh
- Department of Chemistry, Feroze Gandhi College, Raebareli, U.P, India, 229001
| | - Priyanka Sharma
- Department of Zoology, Patna Science College, Patna University, Patna, Bihar, India.
| | - Rishi Kumar Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, 60153, USA.
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15
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Yu X, Wang Y, Wang K, Zhu Z, Xiao L, Huang Y, Song Y, Liu D. Enhanced portable detection for Sars-CoV-2 utilizing DNA tetrahedron-tethered aptamers and a pressure meter. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:639-644. [PMID: 38205650 DOI: 10.1039/d3ay02100a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Tethering oligonucleotide aptamers to a DNA tetrahedron structure can enhance the recognition of SARS-CoV-2 spike protein to effectively overcome challenges with its detection in current diagnostic assays. Building on this framework, we have developed a unique portable detection method for COVID-19 that provides exceptional sensitivity and selectivity via pressure meter readout. This innovative assay streamlines the detection process, providing a rapid, sensitive, cost-effective, and user-friendly diagnostic tool. This point-of-care test exhibits high sensitivity and specificity, achieving an impressive detection limit of 0.1 pg mL-1 for the spike protein. The effectiveness of this method was validated using pseudoviruses and oropharyngeal swab samples, and its utility for environmental monitoring is demonstrated by testing sewage samples. With a wide linear range and strong potential for clinical or home application, our assay represents a major innovation in point-of-care diagnostics and provides a vital contribution to the current toolkit for controlling the impacts of COVID-19.
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Affiliation(s)
- Xingbo Yu
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, China.
| | - Ying Wang
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, China.
| | - Kun Wang
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, China.
| | - Ziyuan Zhu
- Institute of Analytical Technology and Smart Instruments, Xiamen Key Laboratory of Food and Drug Safety, College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China.
| | - Lu Xiao
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, China.
| | - Yishun Huang
- Institute of Analytical Technology and Smart Instruments, Xiamen Key Laboratory of Food and Drug Safety, College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China.
| | - Yanling Song
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Dan Liu
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, China.
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16
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Li D, Sun C, Zhuang P, Mei X. Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods. Talanta 2024; 266:124937. [PMID: 37481886 DOI: 10.1016/j.talanta.2023.124937] [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: 03/08/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.
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Affiliation(s)
- Dan Li
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co., Ltd., Shenyang, China
| | - Pengfei Zhuang
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Key Laboratory of Medical Tissue Engineering of Liaoning Province, Jinzhou Medical University, Jinzhou, Liaoning, China.
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17
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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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18
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Lei Y, Fei X, Ding Y, Zhang J, Zhang G, Dong L, Song J, Zhuo Y, Xue W, Zhang P, Yang C. Simultaneous subset tracing and miRNA profiling of tumor-derived exosomes via dual-surface-protein orthogonal barcoding. SCIENCE ADVANCES 2023; 9:eadi1556. [PMID: 37792944 PMCID: PMC10550235 DOI: 10.1126/sciadv.adi1556] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
The clinical potential of miRNA-based liquid biopsy has been largely limited by the heterogeneous sources in plasma and tedious assay processes. Here, we develop a precise and robust one-pot assay called dual-surface-protein-guided orthogonal recognition of tumor-derived exosomes and in situ profiling of microRNAs (SORTER) to detect tumor-derived exosomal miRNAs and enhance the diagnostic accuracy of prostate cancer (PCa). The SORTER uses two allosteric aptamers against exosomal marker CD63 and tumor marker EpCAM to create an orthogonal labeling barcode and achieve selective sorting of tumor-specific exosome subtypes. Furthermore, the labeled barcode on tumor-derived exosomes initiated targeted membrane fusion with liposome probes to import miRNA detection reagents, enabling in situ sensitive profiling of tumor-derived exosomal miRNAs. With a signature of six miRNAs, SORTER differentiated PCa and benign prostatic hyperplasia with an accuracy of 100%. Notably, the diagnostic accuracy reached 90.6% in the classification of metastatic and nonmetastatic PCa. We envision that the SORTER will promote the clinical adaptability of miRNA-based liquid biopsy.
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Affiliation(s)
- Yanmei Lei
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaochen Fei
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yue Ding
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianhui Zhang
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Guihua Zhang
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liang Dong
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jia Song
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, 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, China
| | - Wei Xue
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Peng Zhang
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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19
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Xu Y, Zheng R, Prasad A, Liu M, Wan Z, Zhou X, Porter RM, Sample M, Poppleton E, Procyk J, Liu H, Li Y, Wang S, Yan H, Sulc P, Stephanopoulos N. High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558353. [PMID: 37790307 PMCID: PMC10542138 DOI: 10.1101/2023.09.18.558353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody ("nano-synbody") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.
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20
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Zhang YP, Wang ZG, Tian YF, Jiang LH, Zhao L, Kong DM, Li X, Pang DW, Liu SL. In Situ Self-Assembly of Fluorogenic RNA Nanozipper Enables Real-Time Imaging of Single Viral mRNA Translation. Angew Chem Int Ed Engl 2023; 62:e202217230. [PMID: 37082873 DOI: 10.1002/anie.202217230] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/22/2023]
Abstract
Real-time visualization of individual viral mRNA translation activities in live cells is essential to obtain critical details of viral mRNA dynamics and to detect its transient responses to environmental stress. Fluorogenic RNA aptamers are powerful tools for real-time imaging of mRNA in live cells, but monitoring the translation activity of individual mRNAs remains a challenge due to their intrinsic photophysical properties. Here, we develop a genetically encoded turn-on 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI)-binding RNA nanozipper with superior brightness and high photostability by in situ self-assembly of multiple nanozippers along single mRNAs. The nanozipper enables real-time imaging of the mobility and dynamic translation of individual viral mRNAs in live cells, providing information on the spatial dynamics and translational elongation rate of viral mRNAs.
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Affiliation(s)
- Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yi-Fan Tian
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Lin-Han Jiang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Liang Zhao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Xing Li
- Beijing Institutes of Life Science, Chinese Academy of Science, Beijing, 100101, China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Engineering Research Center of Nano Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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21
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Mao M, Lin Z, Chen L, Zou Z, Zhang J, Dou Q, Wu J, Chen J, Wu M, Niu L, Fan C, Zhang Y. Modular DNA-Origami-Based Nanoarrays Enhance Cell Binding Affinity through the "Lock-and-Key" Interaction. J Am Chem Soc 2023; 145:5447-5455. [PMID: 36812464 DOI: 10.1021/jacs.2c13825] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Surface proteins of cells are generally recognized through receptor-ligand interactions (RLIs) in disease diagnosis, but their nonuniform spatial distribution and higher-order structure lead to low binding affinity. Constructing nanotopologies that match the spatial distribution of membrane proteins to improve the binding affinity remains a challenge. Inspired by the multiantigen recognition of immune synapses, we developed modular DNA-origami-based nanoarrays with multivalent aptamers. By adjusting the valency and interspacing of the aptamers, we constructed specific nanotopology to match the spatial distribution of target protein clusters and avoid potential steric hindrance. We found that the nanoarrays significantly enhanced the binding affinity of target cells and synergistically recognized low-affinity antigen-specific cells. In addition, DNA nanoarrays used for the clinical detection of circulating tumor cells successfully verified their precise recognition ability and high-affinity RLIs. Such nanoarrays will further promote the potential application of DNA materials in clinical detection and even cell membrane engineering.
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Affiliation(s)
- Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Zhengyu Zou
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Jie Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Quanhao Dou
- Joint Laboratory of Optofluidic Technology and Systems, National Center for International Research on Green Optoelectronics, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, Guangdong 510006, China
| | - Jiacheng Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Jinglin Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Minhao Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Li Niu
- Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, Guangdong 510006, 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, Shanghai 200240, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
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22
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Yang D, Yang L, Wang P. Nucleic Acid Molecular Systems for In Vitro Detection of Biomolecules. ACS MATERIALS AU 2023; 3:83-87. [PMID: 38089727 PMCID: PMC9999474 DOI: 10.1021/acsmaterialsau.2c00056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 09/15/2024]
Abstract
Molecular systems composed of information-rich nucleic acids have emerged as one of the most robust materials due to their programmability, editability, and designability. Among their various applications, the specific and sensitive in vitro detection of biomolecules for the purpose of disease diagnosis has attracted increasing attention from both fundamental and translational researchers. In this perspective, we introduce the basic design principles for nucleic acid molecular systems toward in vitro detection of biomolecules, accompanied by representative examples from reported works. The perspective concludes with perspectives and outlooks to tackle a variety of technical hurdles for the development and practical translation of nucleic acid molecular systems for biomolecule detection.
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Affiliation(s)
- Donglei Yang
- Institute of Molecular Medicine,
Department
of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry
and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lijiao Yang
- Institute of Molecular Medicine,
Department
of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry
and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine,
Department
of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry
and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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23
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Chen J, Li Y, Liu Z. Functional nucleic acids as potent therapeutics against SARS-CoV-2 infection. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101249. [PMID: 36714073 PMCID: PMC9869493 DOI: 10.1016/j.xcrp.2023.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The COVID-19 pandemic has posed a severe threat to human life and the global economy. Although conventional treatments, including vaccines, antibodies, and small-molecule inhibitors, have been broadly developed, they usually fall behind the constant mutation of SARS-CoV-2, due to the long screening process and high production cost. Functional nucleic acid (FNA)-based therapeutics are a newly emerging promising means against COVID-19, considering their timely adaption to different mutants and easy design for broad-spectrum virus inhibition. In this review, we survey typical FNA-related therapeutics against SARS-CoV-2 infection, including aptamers, aptamer-integrated DNA frameworks, functional RNA, and CRISPR-Cas technology. We first introduce the pathogenesis, transmission, and evolution of SARS-CoV-2, then analyze the existing therapeutic and prophylactic strategies, including their pros and cons. Subsequently, the FNAs are recommended as potent alternative therapeutics from their screening process and controllable engineering to effective neutralization. Finally, we put forward the remaining challenges of the existing field and sketch out the future development directions.
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Affiliation(s)
- Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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24
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Shi Q, Wu Y, Xu Y, Bao M, Chen X, Huang K, Yang Q, Yang Y. Virus Mimetic Framework DNA as a Non-LNP Gene Carrier for Modulated Cell Endocytosis and Apoptosis. ACS NANO 2023; 17:2460-2471. [PMID: 36693051 DOI: 10.1021/acsnano.2c09772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mimicking the size and shape of spherical viruses, we constructed a soccer-ball shaped virus-inspired DNA origami (ViDO) framework as a programmable non-LNP (lipid nanoparticle) gene carrier. The DNA framework was decorated with precisely controlled recognition molecules outside and loaded with adequate genetic molecules inside. Five variants were constructed to systematically investigate their cell uptake and modulated gene silencing efficiency. Cellular uptake was enhanced with an increasing number of aptamers, while with a median number of aptamer supply, dispersed distribution performed better than the clustered pattern. Intriguingly, the transfection efficiency was maximized using the ViDO with clustered five aptamers, which exhibited a competitive RNA silencing effect induced by Lipo2000 with low cytotoxicity. Our results revealed the effects of aptamer distribution patterns on endocytosis and transfection, thus providing a programmable platform for meticulous optimization of the gene delivery system.
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Affiliation(s)
- Qian Shi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuanyuan Wu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Bao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao Chen
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Kui Huang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiulan Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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25
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Li J, Zhang Z, Gu J, Amini R, Mansfield AG, Xia J, White D, Stacey HD, Ang JC, Panesar G, Capretta A, Filipe CDM, Mossman K, Salena BJ, Gubbay JB, Balion C, Soleymani L, Miller MS, Yamamura D, Brennan JD, Li Y. Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer. J Am Chem Soc 2022; 144:23465-23473. [PMID: 36520671 PMCID: PMC9762500 DOI: 10.1021/jacs.2c09870] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 12/23/2022]
Abstract
Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva with a limit of detection as low as 6.3 × 103 copies/mL. The ELABA was also used to test 50 SARS-CoV-2-positive and 60 SARS-CoV-2-negative patient saliva samples, providing sensitivity and specificity values of 84.0 and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.
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Affiliation(s)
- Jiuxing Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Zijie Zhang
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jimmy Gu
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Ryan Amini
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alexandria G. Mansfield
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jianrun Xia
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Dawn White
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
| | - Hannah D. Stacey
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jann C. Ang
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Gurpreet Panesar
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alfredo Capretta
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Carlos D. M. Filipe
- Department
of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Karen Mossman
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Bruno J. Salena
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | | | - Cynthia Balion
- Department
of Pathology and Molecular Medicine, McMaster
University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Leyla Soleymani
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School
of Biomedical Engineering, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Matthew S. Miller
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Deborah Yamamura
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Pathology and Molecular Medicine, McMaster
University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
| | - Yingfu Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School
of Biomedical Engineering, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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26
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Xu F, Xia Q, Ye J, Dong L, Yang D, Xue W, Wang P. Programming DNA Aptamer Arrays of Prescribed Spatial Features with Enhanced Bioavailability and Cell Growth Modulation. NANO LETTERS 2022; 22:9935-9942. [PMID: 36480429 DOI: 10.1021/acs.nanolett.2c03377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Epithelial cell adhesion molecules (EpCAMs) play pivotal roles in tumorigenesis in many cancer types, which is reported to reside within nano- to microscale membrane domains, forming small clusters. We propose that building multivalent ligands that spatially patch to EpCAM clusters may largely enhance their targeting capability. Herein, we assembled EpCAM aptamers into nanoscale arrays of prescribed valency and spatial arrangements by using a rectangular DNA pegboard. Our results revealed that EpCAM aptamer arrays exhibited significantly higher binding avidity to MCF-7 cells than free monovalent aptamers, which was affected by both valency and spatial arrangement of aptamers. Furthermore, EpCAM aptamer arrays showed improved tolerance against competing targets in an extracellular environment and potent bioavailability and targeting specificity in a xenograft tumor model in mice. This work may shed light on rationally designing multivalent ligand complexes of defined parameters with optimized binding avidity and targeting capability toward various applications in the biomedical fields.
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Affiliation(s)
- Fan Xu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qing Xia
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jing Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liang Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Xue
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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27
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Zhang J, Xu Y, Chen M, Huang Y, Song T, Yang C, Yang Y, Song Y. Elucidating the Effect of Nanoscale Receptor-Binding Domain Organization on SARS-CoV-2 Infection and Immunity Activation with DNA Origami. J Am Chem Soc 2022; 144:21295-21303. [DOI: 10.1021/jacs.2c09229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mingying Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Ting Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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28
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Qu Y, Shen F, Zhang Z, Wang Q, Huang H, Xu Y, Li Q, Zhu X, Sun L. Applications of Functional DNA Materials in Immunomodulatory Therapy. ACS APPLIED MATERIALS & INTERFACES 2022; 14:45079-45095. [PMID: 36171537 DOI: 10.1021/acsami.2c13768] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In recent years, nanoscale or microscale functional materials derived from DNA have shown great potential for immunotherapy as superior delivery carriers. DNA nanostructures with excellent programmability and addressability enable the precise assembly of molecules or nanoparticles. DNA hydrogels have predictable structures and adjustable mechanical strength, thus being advantageous in controllable release of cargos. In addition, utilizing systematic evolution of ligands by exponential enrichment technology, a variety of DNA aptamers have been screened for specific recognition of ions, molecules, and even cells. Moreover, a wide variety of chemical modifications can further enrich the function of DNA. The unique advantages of functional DNA materials make them extremely attractive in immunomodulation. Recently, functional DNA materials-based immunotherapy has shown great potential in fighting against many diseases like cancer, viral infection, and inflammation. Therefore, in this review, we focus on discussing the progress of the applications of functional DNA materials in immunotherapy; before that, we also summarize the characteristics of the functional DNA materials descried above. Finally, we discuss the challenges and future opportunities of functional DNA materials in immunomodulatory therapy.
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Affiliation(s)
- Yanfei Qu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Fengyun Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ziyi Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qi Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Hao Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yufei Xu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Lele Sun
- School of Life Sciences, Shanghai University, Shanghai 200444, China
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