1
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Sun Y, Li T, Guo Y, Sun P, Wu J, Pan C, Wang H, Zhu L. A Click-Type Enzymatic Method for Antigen-Adjuvant Conjugation. SMALL METHODS 2024:e2401116. [PMID: 39177201 DOI: 10.1002/smtd.202401116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Indexed: 08/24/2024]
Abstract
The Toll-like receptor 9 (TLR9) stimulator, CpG oligodeoxynucleotide, has emerged as a potent enhancer of protein subunit vaccines. Incorporating the protein antigen directly with the CpG adjuvant presents a novel strategy to significantly reduce the required dosage of CpG compared to traditional methods that use separate components. In contrast to existing chemical conjugation methods, this study introduces an enzymatic approach for antigen-adjuvant coupling using a recombinant endonuclease DCV fused with SpyTag. This fusion protein catalyzes the covalent linkage between itself and the CpG adjuvant under mild conditions. These conjugates can be further linked with target protein antigens containing the SpyCatcher sequence, yielding stable, covalently-linked antigen-adjuvant complexes. The corresponding complex utilizing the receptor-binding domain (RBD) of SARS-CoV-2 spike protein as the model antigen, elicits high-titer, specific antibody production in mice via both subcutaneous administration and intratracheal inoculation. Notably, the tumor vaccine candidate fabricated by this method has also shown significant inhibition of cancer progression after intratracheal administration. The technique ensures precise, site-specific coupling and preserves the antigen's structural integrity due to the post-purification coupling strategy that simplifies manufacturing and aids in developing inhalable vaccines.
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Affiliation(s)
- Yange Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Ting Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Peng Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Jun Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Chao Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Hengliang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
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2
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Soxpollard N, Strauss S, Jungmann R, MacPherson IS. Selection of antibody-binding covalent aptamers. Commun Chem 2024; 7:174. [PMID: 39117896 PMCID: PMC11310417 DOI: 10.1038/s42004-024-01255-7] [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: 10/10/2023] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Aptamers are oligonucleotides with antibody-like binding function, selected from large combinatorial libraries. In this study, we modified a DNA aptamer library with N-hydroxysuccinimide esters, enabling covalent conjugation with cognate proteins. We selected for the ability to bind to mouse monoclonal antibodies, resulting in the isolation of two distinct covalent binding motifs. The covalent aptamers are specific for the Fc region of mouse monoclonal IgG1 and are cross-reactive with mouse IgG2a and other IgGs. Investigation into the covalent conjugation of the aptamers revealed a dependence on micromolar concentrations of Cu2+ ions which can be explained by residual catalyst remaining after modification of the aptamer library. The aptamers were successfully used as adapters in the formation of antibody-oligonucleotide conjugates (AOCs) for use in detection of HIV protein p24 and super-resolution imaging of actin. This work introduces a new method for the site-specific modification of native monoclonal antibodies and may be useful in applications requiring AOCs or other antibody conjugates.
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Affiliation(s)
- Noah Soxpollard
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawaii, Honolulu, HI, 96813, USA
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Iain S MacPherson
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawaii, Honolulu, HI, 96813, USA.
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3
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Ang YS, Yung LYL. Protein-DNA Conjugates with a Discrete Number of Oligonucleotide Strands for Highly Reproducible Protein Quantification by the DNA Proximity Assay. Anal Chem 2023; 95:12071-12079. [PMID: 37523447 DOI: 10.1021/acs.analchem.3c02033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Protein-oligonucleotide conjugates are increasingly used as detection probes in biological applications such as proximity sensing and spatial biology. The preparation of high-quality conjugate probes as starting reagents is critical for achieving good and consistent performance, which we demonstrate via the DNA proximity assay (DPA) for the one-pot quantification of protein targets. We first established a complete conjugation and anion-exchange chromatography purification workflow to reproducibly obtain pure subpopulations of protein probes carrying a discrete number of oligonucleotide strands. A systematic study using the purified conjugate sub-populations confirmed that the order of conjugate (number of oligonucleotides per protein) and its purity (the absence of the unconjugated antibody) were important for ensuring optimal and reproducible assay performance. The streamlined workflow was then successfully used to conjugate a pair of universal DPA initiator oligonucleotides onto a wide range of binders including antibodies, nanobodies, and antigens which enabled the versatile detection of different types of proteins such as cytokines, total antibodies, and specific antibody isotypes. The good assay robustness (the inter-assay coefficient of variation lower than 5%) and linear calibration curve was achieved across all targets with just a single mix-and-incubate reaction step and a short reaction time of 30 min. We anticipate the streamlined protein-oligonucleotide probe preparation workflow developed in this work to have broad utility across applications leveraging the specificity of protein bio-recognition with the programmability of DNA hybridization.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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4
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Genet SAAM, Wolfs JRE, Vu CBAK, Wolter M, Broeren MAC, van Dongen J, Brunsveld L, Scharnhorst V, van de Kerkhof D. Analysis of Neuron-Specific enolase isozymes in human serum using immunoaffinity purification and liquid chromatography-tandem mass spectrometry quantification. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1223:123701. [PMID: 37086508 DOI: 10.1016/j.jchromb.2023.123701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/24/2023]
Abstract
Neuron-specific enolase (NSE) is a promising small-cell lung cancer (SCLC) biomarker composed of αγ and γγ isozyme dimers. As the conventional immunoassays are prone to interferences and cannot differentiate between the isozymes, we developed a multiplex immunoaffinity (IA) liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for the quantification of NSEα and NSEγ in human serum. A calibrator was prepared by performing cold denaturation of recombinantly expressed αα and γγ enolase dimers to induce a new dimer equilibrium that was determined to be approximately 1αγ:1γγ:1αα. Selective sample purification was achieved by performing IA extraction using an antibody specific towards NSEγ. The isolated αγ and γγ dimers were denatured and trypsin digested to allow quantification of the selected signature peptides and their corresponding isotopically labelled peptide internal standard. The obtained linear dynamic ranges were determined to be 1.5-56 ng/mL and 0.64-167 ng/mL for NSEα and NSEγ (R2 = 0.88 and 0.97 respectively). Validation of the assay showed acceptable accuracy and precision for NSEα and NSEγ. The method was successfully applied to patient serum in which both isozymes were detected. Compared to the conventional immunoassay, substantially lower total NSE concentrations were measured in IA LC-MS/MS. With this multiplex IA LC-MS/MS assay, the clinical value of quantifying the individual isozymes can be explored. In addition, together with the calibrator described here, it may be applied to standardize NSE immunoassays across different platforms.
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Affiliation(s)
- Sylvia A A M Genet
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Catharina Hospital Eindhoven, Eindhoven, the Netherlands; Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Jur R E Wolfs
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Chris B A K Vu
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Maarten A C Broeren
- Máxima Medical Center, Eindhoven/Veldhoven, the Netherlands; Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Joost van Dongen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Volkher Scharnhorst
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Catharina Hospital Eindhoven, Eindhoven, the Netherlands; Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Daan van de Kerkhof
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Catharina Hospital Eindhoven, Eindhoven, the Netherlands; Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands.
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5
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Banerjee A, Anand M, Ganji M. Labeling approaches for DNA-PAINT super-resolution imaging. NANOSCALE 2023; 15:6563-6580. [PMID: 36942769 DOI: 10.1039/d2nr06541j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
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6
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Mechanistic Approaches to the Application of Nano-Zinc in the Poultry and Biomedical Industries: A Comprehensive Review of Future Perspectives and Challenges. Molecules 2023; 28:molecules28031064. [PMID: 36770731 PMCID: PMC9921179 DOI: 10.3390/molecules28031064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Bio-fortification is a new, viable, cost-effective, and long-term method of administering crucial minerals to a populace with limited exposure to diversified foods and other nutritional regimens. Nanotechnology entities aid in the improvement of traditional nutraceutical absorption, digestibility, and bio-availability. Nano-applications are employed in poultry systems utilizing readily accessible instruments and processes that have no negative impact on animal health and welfare. Nanotechnology is a sophisticated innovation in the realm of biomedical engineering that is used to diagnose and cure various poultry ailments. In the 21st century, zinc nanoparticles had received a lot of considerable interest due to their unusual features. ZnO NPs exhibit antibacterial properties; however, the qualities of nanoparticles (NPs) vary with their size and structure, rendering them adaptable to diverse uses. ZnO NPs have shown remarkable promise in bio-imaging and drug delivery due to their high bio-compatibility. The green synthesized nanoparticles have robust biological activities and are used in a variety of biological applications across industries. The current review also discusses the formulation and recent advancements of zinc oxide nanoparticles from plant sources (such as leaves, stems, bark, roots, rhizomes, fruits, flowers, and seeds) and their anti-cancerous activities, activities in wound healing, and drug delivery, followed by a detailed discussion of their mechanisms of action.
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7
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Riera R, Archontakis E, Cremers G, de Greef T, Zijlstra P, Albertazzi L. Precision and Accuracy of Receptor Quantification on Synthetic and Biological Surfaces Using DNA-PAINT. ACS Sens 2023; 8:80-93. [PMID: 36655822 PMCID: PMC9887648 DOI: 10.1021/acssensors.2c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Characterization of the number and distribution of biological molecules on 2D surfaces is of foremost importance in biology and biomedicine. Synthetic surfaces bearing recognition motifs are a cornerstone of biosensors, while receptors on the cell surface are critical/vital targets for the treatment of diseases. However, the techniques used to quantify their abundance are qualitative or semi-quantitative and usually lack sensitivity, accuracy, or precision. Detailed herein a simple and versatile workflow based on super-resolution microscopy (DNA-PAINT) was standardized to improve the quantification of the density and distribution of molecules on synthetic substrates and cell membranes. A detailed analysis of accuracy and precision of receptor quantification is presented, based on simulated and experimental data. We demonstrate enhanced accuracy and sensitivity by filtering out non-specific interactions and artifacts. While optimizing the workflow to provide faithful counting over a broad range of receptor densities. We validated the workflow by specifically quantifying the density of docking strands on a synthetic sensor surface and the densities of PD1 and EGF receptors (EGFR) on two cellular models.
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Affiliation(s)
- Roger Riera
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, Netherlands
| | - Emmanouil Archontakis
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, Netherlands
| | - Glenn Cremers
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, The Netherlands,Computational
Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology,
P.O. Box 513, Eindhoven5600 MB, The Netherlands
| | - Tom de Greef
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, The Netherlands,Computational
Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology,
P.O. Box 513, Eindhoven5600 MB, The Netherlands,Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, AJ Nijmegen6525, The Netherlands
| | - Peter Zijlstra
- Department
of Applied Physics and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, The Netherlands,
| | - Lorenzo Albertazzi
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, Netherlands,Nanoscopy
for Nanomedicine, Institute for Bioengineering
of Catalonia, Barcelona08028, Spain,
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8
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Woythe L, Tholen MME, Rosier BJHM, Albertazzi L. Single-Particle Functionality Imaging of Antibody-Conjugated Nanoparticles in Complex Media. ACS APPLIED BIO MATERIALS 2023; 6:171-181. [PMID: 36594422 PMCID: PMC9846673 DOI: 10.1021/acsabm.2c00830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The properties of nanoparticles (NPs) can change upon contact with serum components, occluding the NP surface by forming a biomolecular corona. It is believed that targeted NPs can lose their functionality due to this biological coating, thus losing specificity and selectivity toward target cells and leading to poor therapeutic efficiency. A better understanding of how the biomolecular corona affects NP ligand functionality is needed to maintain NP targeting capabilities. However, techniques that can quantify the functionality of NPs at a single-particle level in a complex medium are limited and often laborious in sample preparation, measurement, and analysis. In this work, the influence of serum exposure on the functionality of antibody-functionalized NPs was quantified using a straightforward total internal reflection fluorescence (TIRF) microscopy method and evaluated in cell uptake studies. The single-particle resolution of TIRF reveals the interparticle functionality heterogeneity and the substantial differences between NPs conjugated with covalent and noncovalent methods. Notably, only NPs covalently conjugated with a relatively high amount of antibodies maintain their functionality to a certain extent and still showed cell specificity and selectivity toward high receptor density cells after incubation in full serum. The presented study emphasizes the importance of single-particle functional characterization of NPs in complex media, contributing to the understanding and design of targeted NPs that retain their cell specificity and selectivity in biologically relevant conditions.
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Affiliation(s)
- Laura Woythe
- Department
of Biomedical Engineering, Institute for Complex Molecular systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands
| | - Marrit M. E. Tholen
- Department
of Biomedical Engineering, Institute for Complex Molecular systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands
| | - Bas J. H. M. Rosier
- Department
of Biomedical Engineering, Institute for Complex Molecular systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands
| | - Lorenzo Albertazzi
- Department
of Biomedical Engineering, Institute for Complex Molecular systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands,Institute
of Bioengineering of Catalonia (IBEC), The
Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain,
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9
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Rajwar A, Shetty SR, Vaswani P, Morya V, Barai A, Sen S, Sonawane M, Bhatia D. Geometry of a DNA Nanostructure Influences Its Endocytosis: Cellular Study on 2D, 3D, and in Vivo Systems. ACS NANO 2022; 16:10496-10508. [PMID: 35715010 DOI: 10.1021/acsnano.2c01382] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between the cell membrane and different topologies of 3D DNA nanostructures are crucial for designing efficient tools for interfacing DNA devices with biological systems. The practical applications of these DNA nanocages are still limited in cellular and biological systems owing to the limited understanding of their interaction with the cell membrane and endocytic pathway. The correlation between the geometry of DNA nanostructures and their internalization efficiency remains elusive. We investigated the influence of the shape and size of 3D DNA nanostructures on their cellular internalization efficiency. We found that one particular geometry, i.e., the tetrahedral shape, is more favored over other designed geometries for their cellular uptake in 2D and 3D cell models. This is also replicable for cellular processes like cell invasion assays in a 3D spheroid model, and passing the epithelial barriers in in vivo zebrafish model systems. Our work provides detailed information for the rational design of DNA nanodevices for their upcoming biological and biomedical applications.
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Affiliation(s)
- Anjali Rajwar
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Shravani Reddy Shetty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Payal Vaswani
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Vinod Morya
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Amlan Barai
- Bioscience and Bioengineering Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shamik Sen
- Bioscience and Bioengineering Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mahendra Sonawane
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
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10
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Dai Z, Xie X, Gao Z, Li Q. DNA‐PAINT Super‐Resolution Imaging for Characterization of Nucleic Acid Nanostructures. Chempluschem 2022; 87:e202200127. [DOI: 10.1002/cplu.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zheze Dai
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiaodong Xie
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Zhaoshuai Gao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Road 800中国 200240 Shanghai CHINA
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11
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Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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12
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Harish V, Tewari D, Gaur M, Yadav AB, Swaroop S, Bechelany M, Barhoum A. Review on Nanoparticles and Nanostructured Materials: Bioimaging, Biosensing, Drug Delivery, Tissue Engineering, Antimicrobial, and Agro-Food Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:457. [PMID: 35159802 PMCID: PMC8839643 DOI: 10.3390/nano12030457] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 01/27/2023]
Abstract
In the last few decades, the vast potential of nanomaterials for biomedical and healthcare applications has been extensively investigated. Several case studies demonstrated that nanomaterials can offer solutions to the current challenges of raw materials in the biomedical and healthcare fields. This review describes the different nanoparticles and nanostructured material synthesis approaches and presents some emerging biomedical, healthcare, and agro-food applications. This review focuses on various nanomaterial types (e.g., spherical, nanorods, nanotubes, nanosheets, nanofibers, core-shell, and mesoporous) that can be synthesized from different raw materials and their emerging applications in bioimaging, biosensing, drug delivery, tissue engineering, antimicrobial, and agro-foods. Depending on their morphology (e.g., size, aspect ratio, geometry, porosity), nanomaterials can be used as formulation modifiers, moisturizers, nanofillers, additives, membranes, and films. As toxicological assessment depends on sizes and morphologies, stringent regulation is needed from the testing of efficient nanomaterials dosages. The challenges and perspectives for an industrial breakthrough of nanomaterials are related to the optimization of production and processing conditions.
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Affiliation(s)
- Vancha Harish
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144401, India; (V.H.); (D.T.)
| | - Devesh Tewari
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144401, India; (V.H.); (D.T.)
| | - Manish Gaur
- Centre of Biotechnology, University of Allahabad, Prayagraj, Uttar Pradesh 211002, India;
| | - Awadh Bihari Yadav
- Centre of Biotechnology, University of Allahabad, Prayagraj, Uttar Pradesh 211002, India;
| | - Shiv Swaroop
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India;
| | - Mikhael Bechelany
- Institut Européen des Membranes, IEM UMR 5635, University Montpellier, ENSCM, CNRS, 34730 Montpellier, France
| | - Ahmed Barhoum
- NanoStruc Research Group, Chemistry Department, Faculty of Science, Ain Helwan, Cairo 11795, Egypt
- National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, D09 Y074 Dublin, Ireland
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13
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Arista-Romero M, Delcanale P, Pujals S, Albertazzi L. Nanoscale Mapping of Recombinant Viral Proteins: From Cells to Virus-Like Particles. ACS PHOTONICS 2022; 9:101-109. [PMID: 35083366 PMCID: PMC8778639 DOI: 10.1021/acsphotonics.1c01154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 05/17/2023]
Abstract
Influenza recombinant proteins and virus-like particles (VLPs) play an important role in vaccine development (e.g., CadiFlu-S). However, their production from mammalian cells suffers from low yields and lack of control of the final VLPs. To improve these issues, characterization techniques able to visualize and quantify the different steps of the process are needed. Fluorescence microscopy represents a powerful tool able to image multiple protein targets; however, its limited resolution hinders the study of viral constructs. Here, we propose the use of super-resolution microscopy and in particular of DNA-point accumulation for imaging in nanoscale topography (DNA-PAINT) microscopy as a characterization method for recombinant viral proteins on both cells and VLPs. We were able to quantify the amount of the three main influenza proteins (hemagglutinin (HA), neuraminidase (NA), and ion channel matrix protein 2 (M2)) per cell and per VLP with nanometer resolution and single-molecule sensitivity, proving that DNA-PAINT is a powerful technique to characterize recombinant viral constructs.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
| | - Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco area delle Scienze 7/A, 43124 Parma, Italy
| | - Silvia Pujals
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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14
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Tas RP, Albertazzi L, Voets IK. Small Peptide-Protein Interaction Pair for Genetically Encoded, Fixation Compatible Peptide-PAINT. NANO LETTERS 2021; 21:9509-9516. [PMID: 34757759 PMCID: PMC8631740 DOI: 10.1021/acs.nanolett.1c02895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/01/2021] [Indexed: 05/08/2023]
Abstract
Super-resolution microscopy via PAINT has been widely adopted in life sciences to interrogate the nanoscale architecture of many cellular structures. However, obtaining quantitative information in fixed cellular samples remains challenging because control of labeling stoichiometry is hampered in current approaches due to click-chemistry and additional targeting probes. To overcome these challenges, we have identified a small, PDZ-based, peptide-protein interaction pair that is genetically encodable and compatible with super-resolution imaging upon cellular fixation without additional labeling. Stoichiometric labeling control by genetic incorporation of this probe into the cellular vimentin network and mitochondria resulted in super-resolved 3D reconstructions with high specificity and spatial resolution. Further characterization reveals that this peptide-protein interaction is compatible with quantitative PAINT and that its binding kinetics remains unaltered upon fixation. Finally, by fusion of our probe to nanobodies against conventional expression markers, we show that this approach provides a versatile addition to the super-resolution toolbox.
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Affiliation(s)
- Roderick P. Tas
- Laboratory
of Self-Organizing Soft Matter, Institute for Complex Molecular Systems
and Department of Chemical Engineering and Chemistry, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
| | - Lorenzo Albertazzi
- Laboratory
of Nanoscopy for Nanomedicine, Institute for Complex Molecular Systems
and Department of Biomedical Engineering, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
| | - Ilja K. Voets
- Laboratory
of Self-Organizing Soft Matter, Institute for Complex Molecular Systems
and Department of Chemical Engineering and Chemistry, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
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15
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von Witting E, Hober S, Kanje S. Affinity-Based Methods for Site-Specific Conjugation of Antibodies. Bioconjug Chem 2021; 32:1515-1524. [PMID: 34369763 PMCID: PMC8377709 DOI: 10.1021/acs.bioconjchem.1c00313] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conjugation of various reagents to antibodies has long been an elegant way to combine the superior binding features of the antibody with other desired but non-natural functions. Applications range from labels for detection in different analytical assays to the creation of new drugs by conjugation to molecules which improves the pharmaceutical effect. In many of these applications, it has been proven advantageous to control both the site and the stoichiometry of the conjugation to achieve a homogeneous product with predictable, and often also improved, characteristics. For this purpose, many research groups have, during the latest decade, reported novel methods and techniques, based on small molecules, peptides, and proteins with inherent affinity for the antibody, for site-specific conjugation of antibodies. This review provides a comprehensive overview of these methods and their applications and also describes a historical perspective of the field.
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Affiliation(s)
- Emma von Witting
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Centre, SE-114 19, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Centre, SE-114 19, Stockholm, Sweden
| | - Sara Kanje
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Centre, SE-114 19, Stockholm, Sweden
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16
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Cremers GAO, Rosier BJHM, Meijs A, Tito NB, van Duijnhoven SMJ, van Eenennaam H, Albertazzi L, de Greef TFA. Determinants of Ligand-Functionalized DNA Nanostructure-Cell Interactions. J Am Chem Soc 2021; 143:10131-10142. [PMID: 34180666 PMCID: PMC8283757 DOI: 10.1021/jacs.1c02298] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Synthesis of ligand-functionalized
nanomaterials with control over
size, shape, and ligand orientation facilitates the design of targeted
nanomedicines for therapeutic purposes. DNA nanotechnology has emerged
as a powerful tool to rationally construct two- and three-dimensional
nanostructures, enabling site-specific incorporation of protein ligands
with control over stoichiometry and orientation. To efficiently target
cell surface receptors, exploration of the parameters that modulate
cellular accessibility of these nanostructures is essential. In this
study, we systematically investigate tunable design parameters of
antibody-functionalized DNA nanostructures binding to therapeutically
relevant receptors, including the programmed cell death protein 1,
the epidermal growth factor receptor, and the human epidermal growth
factor receptor 2. We show that, although the native affinity of antibody-functionalized
DNA nanostructures remains unaltered, the absolute number of bound
surface receptors is lower compared to soluble antibodies due to receptor
accessibility by the nanostructure. We explore structural determinants
of this phenomenon to improve efficiency, revealing that receptor
binding is mainly governed by nanostructure size and DNA handle location.
The obtained results provide key insights in the ability of ligand-functionalized
DNA nanostructures to bind surface receptors and yields design rules
for optimal cellular targeting.
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Affiliation(s)
- Glenn A O Cremers
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ab Meijs
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Nicholas B Tito
- Electric Ant Lab, Science Park 106, 1098 XG Amsterdam, The Netherlands
| | | | - Hans van Eenennaam
- Aduro Biotech Europe B.V., Kloosterstraat 9, 5349 AB Oss, The Netherlands
| | - Lorenzo Albertazzi
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Molecular Biosensing for Medical Diagnostics, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, 5600 MB Eindhoven, The Netherlands
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17
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Ahn SY, Liu J, Vellampatti S, Wu Y, Um SH. DNA Transformations for Diagnosis and Therapy. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2008279. [PMID: 33613148 PMCID: PMC7883235 DOI: 10.1002/adfm.202008279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Indexed: 05/03/2023]
Abstract
Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.
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Affiliation(s)
- So Yeon Ahn
- School of Chemical EngineeringSungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
| | - Jin Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Srivithya Vellampatti
- Institute of Convergent Chemical Engineering and TechnologySungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Present address:
Progeneer, Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Soong Ho Um
- School of Chemical EngineeringSKKU Advanced Institute of Nanotechnology (SAINT)Biomedical Institute for Convergence at SKKU (BICS) and Institute of Quantum Biophysics (IQB)Sungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Progeneer Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
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18
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Ko J, Wang Y, Carlson JCT, Marquard A, Gungabeesoon J, Charest A, Weitz D, Pittet MJ, Weissleder R. Single Extracellular Vesicle Protein Analysis Using Immuno-Droplet Digital Polymerase Chain Reaction Amplification. ADVANCED BIOSYSTEMS 2020; 4:e1900307. [PMID: 33274611 PMCID: PMC8491538 DOI: 10.1002/adbi.201900307] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/04/2020] [Accepted: 02/20/2020] [Indexed: 11/08/2022]
Abstract
There is a need for novel analytical techniques to study the composition of single extracellular vesicles (EV). Such techniques are required to improve the understanding of heterogeneous EV populations, to allow identification of unique subpopulations, and to enable earlier and more sensitive disease detection. Because of the small size of EV and their low protein content, ultrahigh sensitivity technologies are required. Here, an immuno-droplet digital polymerase chain reaction (iddPCR) amplification method is described that allows multiplexed single EV protein profiling. Antibody-DNA conjugates are used to label EV, followed by stochastic microfluidic incorporation of single EV into droplets. In situ PCR with fluorescent reporter probes converts and amplifies the barcode signal for subsequent read-out by droplet imaging. In these proof-of-principle studies, it is shown that multiplex protein analysis is possible in single EV, opening the door for future analyses.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Yongcheng Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Jonathan CT Carlson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Angela Marquard
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Jeremy Gungabeesoon
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Alain Charest
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | - David Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA 02138
| | - Mikael J. Pittet
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115
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19
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Stiller C, Aghelpasand H, Frick T, Westerlund K, Ahmadian A, Karlström AE. Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates. Bioconjug Chem 2019; 30:2790-2798. [PMID: 31609586 DOI: 10.1021/acs.bioconjchem.9b00548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Antibody-DNA conjugates are powerful tools for DNA-assisted protein analysis. Growing usage of these methods demands efficient production of high-quality conjugates. We developed an easy and fast synthesis route yielding covalent antibody-DNA conjugates with a defined conjugation site and low batch-to-batch variability. We utilize the Z domain from protein A, containing the unnatural amino acid 4-benzoylphenylalanine (BPA) for photoaffinity labeling of the antibodies' Fc region. Z(xBPA) domains are C-terminally modified with triple-glycine (G3)-modified DNA-oligonucleotides via enzymatic Sortase A coupling. We show reliable modification of the most commonly used IgG's. To prove our conjugates' functionality, we detected antibody-antigen binding events in an assay called Droplet Barcode Sequencing for Protein analysis (DBS-Pro). It confirms not only retained functionality for both conjugate parts but also the potential of using DBS-Pro for quantifying protein abundances. As intermediates are easily storable and our approach is modular, it offers a convenient strategy for screening various antibody-DNA conjugates using the same starting material.
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Affiliation(s)
- Christiane Stiller
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
| | - Hooman Aghelpasand
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Tobias Frick
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Kristina Westerlund
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
| | - Afshin Ahmadian
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
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