1
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Li L, Yin J, Ma W, Tang L, Zou J, Yang L, Du T, Zhao Y, Wang L, Yang Z, Fan C, Chao J, Chen X. A DNA origami device spatially controls CD95 signalling to induce immune tolerance in rheumatoid arthritis. NATURE MATERIALS 2024; 23:993-1001. [PMID: 38594486 DOI: 10.1038/s41563-024-01865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
DNA origami is capable of spatially organizing molecules into sophisticated geometric patterns with nanometric precision. Here we describe a reconfigurable, two-dimensional DNA origami with geometrically patterned CD95 ligands that regulates immune cell signalling to alleviate rheumatoid arthritis. In response to pH changes, the device reversibly transforms from a closed to an open configuration, displaying a hexagonal pattern of CD95 ligands with ~10 nm intermolecular spacing, precisely mirroring the spatial arrangement of CD95 receptor clusters on the surface of immune cells. In a collagen-induced arthritis mouse model, DNA origami elicits robust and selective activation of CD95 death-inducing signalling in activated immune cells located in inflamed synovial tissues. Such localized immune tolerance ameliorates joint damage with no noticeable side effects. This device allows for the precise spatial control of cellular signalling, expanding our understanding of ligand-receptor interactions and is a promising platform for the development of pharmacological interventions targeting these interactions.
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Affiliation(s)
- Ling Li
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Jue Yin
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Wen Ma
- Strait Laboratory of Flexible Electronics, Fujian Key Laboratory of Flexible Electronics, Strait Institute of Flexible Electronics, Fujian Normal University, Fuzhou, China
| | - Longguang Tang
- Department of Pharmacy, Center for Regeneration and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Jianhua Zou
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Linzi Yang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Ting Du
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yi Zhao
- Strait Laboratory of Flexible Electronics, Fujian Key Laboratory of Flexible Electronics, Strait Institute of Flexible Electronics, Fujian Normal University, Fuzhou, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zhen Yang
- Strait Laboratory of Flexible Electronics, Fujian Key Laboratory of Flexible Electronics, Strait Institute of Flexible Electronics, Fujian Normal University, Fuzhou, 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, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China.
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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2
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Sülzle J, Elfeky L, Manley S. Surface passivation and functionalisation for mass photometry. J Microsc 2024; 295:14-20. [PMID: 38606461 DOI: 10.1111/jmi.13302] [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: 11/30/2023] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
Interferometric scattering (iSCAT) microscopy enables the label-free observation of biomolecules. Consequently, single-particle imaging and tracking with the iSCAT-based method known as mass photometry (MP) is a growing area of study. However, establishing reliable cover glass passivation and functionalisation methods is crucial to reduce nonspecific binding and prepare surfaces for in vitro single-molecule binding experiments. Existing protocols for fluorescence microscopy can contain strongly scattering or mobile components, which make them impractical for MP-based microscopy. In this study, we characterise several different surface coatings using MP. We present approaches for cover glass passivation using 3-aminopropyltriethoxysilane (APTES) and polyethylene glycol (PEG, 2k) along with functionalisation via a maleimide-thiol linker. These coatings are compatible with water or salt buffers, and show low background scattering; thus, we are able to measure proteins as small as 60 kDa. In this technical note, we offer a surface preparation suitable for in vitro experiments with MP.
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Affiliation(s)
- Jenny Sülzle
- Laboratory of Experimental Biophysics (LEB), Institute of Physics and Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laila Elfeky
- Laboratory of Experimental Biophysics (LEB), Institute of Physics and Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics (LEB), Institute of Physics and Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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3
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Cao X, Li M, Li Q, Fan C, Sun J, Gao Z. Single-molecule localization microscopy at 2.4-fold resolution improvement with optical lattice pattern illumination. OPTICS EXPRESS 2024; 32:20218-20229. [PMID: 38859137 DOI: 10.1364/oe.514937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/27/2024] [Indexed: 06/12/2024]
Abstract
Traditional camera-based single-molecule localization microscopy (SMLM), with its high imaging resolution and localization throughput, has made significant advancements in biological and chemical researches. However, due to the limitation of the fluorescence signal-to-noise ratio (SNR) of a single molecule, its resolution is difficult to reach to 5 nm. Optical lattice produces a nondiffracting beam pattern that holds the potential to enhance microscope performance through its high contrast and penetration depth. Here, we propose a new method named LatticeFLUX which utilizes the wide-field optical lattice pattern illumination for individual molecule excitation and localization. We calculated the Cramér-Rao lower bound of LatticeFLUX resolution and proved that our method can improve the single molecule localization precision by 2.4 times compared with the traditional SMLM. We propose a scheme using 9-frame localization, which solves the problem of uneven lattice light illumination. Based on the experimental single-molecule fluorescence SNR, we coded the image reconstruction software to further verify the resolution enhancement capability of LatticeFLUX on simulated punctate DNA origami, line pairs, and cytoskeleton. LatticeFLUX confirms the feasibility of using 2D structured light illumination to obtain high single-molecule localization precision under high localization throughput. It paves the way for further implementation of ultra-high resolution full 3D structured-light-illuminated SMLM.
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4
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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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5
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Neyra K, Everson HR, Mathur D. Dominant Analytical Techniques in DNA Nanotechnology for Various Applications. Anal Chem 2024; 96:3687-3697. [PMID: 38353660 PMCID: PMC11261746 DOI: 10.1021/acs.analchem.3c04176] [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: 03/06/2024]
Abstract
DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.
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Affiliation(s)
- Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Heather R Everson
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
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6
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Paloja K, Weiden J, Hellmeier J, Eklund AS, Reinhardt SCM, Parish IA, Jungmann R, Bastings MMC. Balancing the Nanoscale Organization in Multivalent Materials for Functional Inhibition of the Programmed Death-1 Immune Checkpoint. ACS NANO 2024; 18:1381-1395. [PMID: 38126310 PMCID: PMC10795474 DOI: 10.1021/acsnano.3c06552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Dendritic cells (DCs) regulate immune priming by expressing programmed death ligand 1 (PD-L1) and PD-L2, which interact with the inhibitory receptor PD-1 on activated T cells. PD-1 signaling regulates T cell effector functions and limits autoimmunity. Tumor cells can hijack this pathway by overexpressing PD-L1 to suppress antitumor T cell responses. Blocking this inhibitory pathway has been beneficial for the treatment of various cancer types, although only a subset of patients responds. A deepened understanding of the spatial organization and molecular interplay between PD-1 and its ligands may inform the design of more efficacious nanotherapeutics. We visualized the natural molecular PD-L1 organization on DCs by DNA-PAINT microscopy and created a template to engineer DNA-based nanoclusters presenting PD-1 at defined valencies, distances, and patterns. These multivalent nanomaterials were examined for their cellular binding and blocking ability. Our data show that PD-1 nano-organization has profound effects on ligand interaction and that the valency of PD-1 molecules modulates the effectiveness in restoring T cell function. This work highlights the power of spatially controlled functional materials to unravel the importance of multivalent patterns in the PD-1 pathway and presents alternative design strategies for immune-engineering.
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Affiliation(s)
- Kaltrina Paloja
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale
de Lausanne, Lausanne 1015, Switzerland
| | - Jorieke Weiden
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale
de Lausanne, Lausanne 1015, Switzerland
| | | | | | - Susanne C. M. Reinhardt
- Max
Planck Institute of Biochemistry, Planegg 82152, Germany
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich 80539, Germany
| | - Ian A. Parish
- Peter
MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir
Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3128, Australia
| | - Ralf Jungmann
- Max
Planck Institute of Biochemistry, Planegg 82152, Germany
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich 80539, Germany
| | - Maartje M. C. Bastings
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale
de Lausanne, Lausanne 1015, Switzerland
- Interfaculty
Bioengineering Institute, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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7
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Wang WX, Douglas TR, Zhang H, Bhattacharya A, Rothenbroker M, Tang W, Sun Y, Jia Z, Muffat J, Li Y, Chou LYT. Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamiFISH. NATURE NANOTECHNOLOGY 2024; 19:58-69. [PMID: 37500778 DOI: 10.1038/s41565-023-01449-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
Structural DNA nanotechnology enables the fabrication of user-defined DNA origami nanostructures (DNs) for biological applications. However, the role of DN design during cellular interactions and subsequent biodistribution remain poorly understood. Current methods for tracking DN fates in situ, including fluorescent-dye labelling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for the single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction probes to achieve 1,000-fold signal amplification. We identify cell-type- and DN shape-specific spatiotemporal distribution patterns within a minute of uptake and at picomolar DN concentrations, 10,000× lower than field standards. We additionally optimize compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo-/vibratome sections, slice cultures and whole-mount organoids. Together, origamiFISH enables the accurate mapping of DN distribution across subcellular and tissue barriers for guiding the development of DN-based therapeutics.
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Affiliation(s)
- Wendy Xueyi Wang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Travis R Douglas
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Haiwang Zhang
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Afrin Bhattacharya
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Wentian Tang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Yu Sun
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Zhengping Jia
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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8
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Rodríguez-Franco HJ, Weiden J, Bastings MMC. Stabilizing Polymer Coatings Alter the Protein Corona of DNA Origami and Can Be Engineered to Bias the Cellular Uptake. ACS POLYMERS AU 2023; 3:344-353. [PMID: 37576710 PMCID: PMC10416322 DOI: 10.1021/acspolymersau.3c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 08/15/2023]
Abstract
With DNA-based nanomaterials being designed for applications in cellular environments, the need arises to accurately understand their surface interactions toward biological targets. As for any material exposed to protein-rich cell culture conditions, a protein corona will establish around DNA nanoparticles, potentially altering the a-priori designed particle function. Here, we first set out to identify the protein corona around DNA origami nanomaterials, taking into account the application of stabilizing block co-polymer coatings (oligolysine-1kPEG or oligolysine-5kPEG) widely used to ensure particle integrity. By implementing a label-free methodology, the distinct polymer coating conditions show unique protein profiles, predominantly defined by differences in the molecular weight and isoelectric point of the adsorbed proteins. Interestingly, none of the applied coatings reduced the diversity of the proteins detected within the specific coronae. We then biased the protein corona through pre-incubation with selected proteins and show significant changes in the cell uptake. Our study contributes to a deeper understanding of the complex interplay between DNA nanomaterials, proteins, and cells at the bio-interface.
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Affiliation(s)
- Hugo J. Rodríguez-Franco
- Programmable Biomaterials Laboratory,
Institute of Materials, Interfaculty Bioengineering Institute, School
of Engineering, Ecole Polytechnique Fédérale
Lausanne, Lausanne 1015, Switzerland
| | - Jorieke Weiden
- Programmable Biomaterials Laboratory,
Institute of Materials, Interfaculty Bioengineering Institute, School
of Engineering, Ecole Polytechnique Fédérale
Lausanne, Lausanne 1015, Switzerland
| | - Maartje M. C. Bastings
- Programmable Biomaterials Laboratory,
Institute of Materials, Interfaculty Bioengineering Institute, School
of Engineering, Ecole Polytechnique Fédérale
Lausanne, Lausanne 1015, Switzerland
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9
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Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
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Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
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10
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Reinhardt SCM, Masullo LA, Baudrexel I, Steen PR, Kowalewski R, Eklund AS, Strauss S, Unterauer EM, Schlichthaerle T, Strauss MT, Klein C, Jungmann R. Ångström-resolution fluorescence microscopy. Nature 2023; 617:711-716. [PMID: 37225882 PMCID: PMC10208979 DOI: 10.1038/s41586-023-05925-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/07/2023] [Indexed: 05/26/2023]
Abstract
Fluorescence microscopy, with its molecular specificity, is one of the major characterization methods used in the life sciences to understand complex biological systems. Super-resolution approaches1-6 can achieve resolution in cells in the range of 15 to 20 nm, but interactions between individual biomolecules occur at length scales below 10 nm and characterization of intramolecular structure requires Ångström resolution. State-of-the-art super-resolution implementations7-14 have demonstrated spatial resolutions down to 5 nm and localization precisions of 1 nm under certain in vitro conditions. However, such resolutions do not directly translate to experiments in cells, and Ångström resolution has not been demonstrated to date. Here we introdue a DNA-barcoding method, resolution enhancement by sequential imaging (RESI), that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents. By sequentially imaging sparse target subsets at moderate spatial resolutions of >15 nm, we demonstrate that single-protein resolution can be achieved for biomolecules in whole intact cells. Furthermore, we experimentally resolve the DNA backbone distance of single bases in DNA origami with Ångström resolution. We use our method in a proof-of-principle demonstration to map the molecular arrangement of the immunotherapy target CD20 in situ in untreated and drug-treated cells, which opens possibilities for assessing the molecular mechanisms of targeted immunotherapy. These observations demonstrate that, by enabling intramolecular imaging under ambient conditions in whole intact cells, RESI closes the gap between super-resolution microscopy and structural biology studies and thus delivers information key to understanding complex biological systems.
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Affiliation(s)
- Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | | | - Isabelle Baudrexel
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Philipp R Steen
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Alexandra S Eklund
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Thomas Schlichthaerle
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Maximilian T Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Christian Klein
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
- Roche Innovation Center Zurich, Roche Pharma Research and Early Development, Schlieren, Switzerland
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany.
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany.
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11
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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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12
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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13
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Morzy D, Tekin C, Caroprese V, Rubio-Sánchez R, Di Michele L, Bastings MMC. Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes. NANOSCALE 2023; 15:2849-2859. [PMID: 36688792 PMCID: PMC9909679 DOI: 10.1039/d2nr05368c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electrostatics surely play a pivotal role in interactions between them. Here we discuss how each component of a DNA/ion/lipid system determines its electrostatic attachment. We examine membrane binding of a library of DNA molecules varying from nanoengineered DNA origami through plasmids to short DNA domains, demonstrating the interplay between the molecular structure of the nucleic acid and the phase of lipid bilayers. Furthermore, the magnitude of DNA/lipid interactions is tuned by varying the concentration of magnesium ions in the physiologically relevant range. Notably, we observe that the structural and mechanical properties of DNA are critical in determining its attachment to lipid bilayers and demonstrate that binding is correlated positively with the size, and negatively with the flexibility of the nucleic acid. The findings are utilized in a proof-of-concept comparison of membrane interactions of two DNA origami designs - potential nanotherapeutic platforms - showing how the results can have a direct impact on the choice of DNA geometry for biotechnological applications.
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Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Cem Tekin
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Vincenzo Caroprese
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Roger Rubio-Sánchez
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
- Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland
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14
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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15
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2023; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam
- Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
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16
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Bila H, Paloja K, Caroprese V, Kononenko A, Bastings MM. Multivalent Pattern Recognition through Control of Nano-Spacing in Low-Valency Super-Selective Materials. J Am Chem Soc 2022; 144:21576-21586. [DOI: 10.1021/jacs.2c08529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Hale Bila
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Kaltrina Paloja
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Vincenzo Caroprese
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Artem Kononenko
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Maartje M.C. Bastings
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
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17
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Liu J, Li M, Zuo X. DNA Nanotechnology-Empowered Live Cell Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204711. [PMID: 36124715 DOI: 10.1002/smll.202204711] [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] [Received: 08/01/2022] [Revised: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The systematic analysis and precise manipulation of a variety of biomolecules should lead to unprecedented findings in fundamental biology. However, conventional technology cannot meet the current requirements. Despite this, there has been progress as DNA nanotechnology has evolved to generate DNA nanostructures and circuits over the past four decades. Many potential applications of DNA nanotechnology for live cell measurements have begun to emerge owing to the biocompatibility, nanometer addressability, and stimulus responsiveness of DNA. In this review, the DNA nanotechnology-empowered live cell measurements which are currently available are summarized. The stability of the DNA nanostructures, in a cellular microenvironment, which is crucial for accomplishing precise live cell measurements, is first summarized. Thereafter, measurements in the extracellular and intracellular microenvironment, in live cells, are introduced. Finally, the challenges that are innate to, and the further developments that are possible in this nascent field are discussed.
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Affiliation(s)
- Jiangbo Liu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- 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
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18
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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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19
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Koga MM, Comberlato A, Rodríguez-Franco HJ, Bastings MMC. Strategic Insights into Engineering Parameters Affecting Cell Type-Specific Uptake of DNA-Based Nanomaterials. Biomacromolecules 2022; 23:2586-2594. [PMID: 35641881 PMCID: PMC9198982 DOI: 10.1021/acs.biomac.2c00282] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
DNA-based nanomaterials are gaining popularity as uniform and programmable bioengineering tools as a result of recent solutions to their weak stability under biological conditions. The DNA nanotechnology platform uniquely allows decoupling of engineering parameters to comprehensively study the effect of each upon cellular encounter. We here present a systematic analysis of the effect of surface parameters of DNA-based nanoparticles on uptake in three different cell models: tumor cells, macrophages, and dendritic cells. The influence of surface charge, stabilizing coating, fluorophore types, functionalization technique, and particle concentration employed is found to cause significant differences in material uptake among these cell types. We therefore provide new insights into the large variance in cell type-specific uptake, highlighting the necessity of proper engineering and careful assay development when DNA-based materials are used as tools in bioengineering and as future nanotherapeutic agents.
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Affiliation(s)
- Marianna M Koga
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Alice Comberlato
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Hugo J Rodríguez-Franco
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
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21
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Comberlato A, Koga MM, Nüssing S, Parish IA, Bastings MMC. Spatially Controlled Activation of Toll-like Receptor 9 with DNA-Based Nanomaterials. NANO LETTERS 2022; 22:2506-2513. [PMID: 35266392 PMCID: PMC8949768 DOI: 10.1021/acs.nanolett.2c00275] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
First evidence of geometrical patterns and defined distances of biomolecules as fundamental parameters to regulate receptor binding and cell signaling have emerged recently. Here, we demonstrate the importance of controlled nanospacing of immunostimulatory agents for the activation of immune cells by exploiting DNA-based nanomaterials and pre-existing crystallography data. We created DNA origami nanoparticles that present CpG-motifs in rationally designed spatial patterns to activate Toll-like Receptor 9 in RAW 264.7 macrophages. We demonstrated that stronger immune activation is achieved when active molecules are positioned at the distance of 7 nm, matching the active dimer structure of the receptor. Moreover, we show how the introduction of linkers between particle and ligand can influence the spatial tolerance of binding. These findings are fundamental for a fine-tuned manipulation of the immune system, considering the importance of spatially controlled presentation of therapeutics to increase efficacy and specificity of immune-modulating nanomaterials where multivalent binding is involved.
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Affiliation(s)
- Alice Comberlato
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Marianna M. Koga
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Simone Nüssing
- Peter
MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir
Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ian A. Parish
- Peter
MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir
Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Maartje M. C. Bastings
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
- Interfaculty
Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
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22
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Heuer-Jungemann A, Linko V. Engineering Inorganic Materials with DNA Nanostructures. ACS CENTRAL SCIENCE 2021; 7:1969-1979. [PMID: 34963890 PMCID: PMC8704036 DOI: 10.1021/acscentsci.1c01272] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 05/25/2023]
Abstract
Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.
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Affiliation(s)
- Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center
for Nanoscience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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