1
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García-Chamé M, Wadhwani P, Pfeifer J, Schepers U, Niemeyer CM, Domínguez CM. A Versatile Microfluidic Platform for Extravasation Studies Based on DNA Origami-Cell Interactions. Angew Chem Int Ed Engl 2024; 63:e202318805. [PMID: 38687094 DOI: 10.1002/anie.202318805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
The adhesion of circulating tumor cells (CTCs) to the endothelial lumen and their extravasation to surrounding tissues are crucial in the seeding of metastases and remain the most complex events of the metastatic cascade to study. Integrins expressed on CTCs are major regulators of the extravasation process. This knowledge is primarily derived from animal models and biomimetic systems based on artificial endothelial layers, but these methods have ethical or technical limitations. We present a versatile microfluidic device to study cancer cell extravasation that mimics the endothelial barrier by using a porous membrane functionalized with DNA origami nanostructures (DONs) that display nanoscale patterns of adhesion peptides to circulating cancer cells. The device simulates physiological flow conditions and allows direct visualization of cell transmigration through microchannel pores using 3D confocal imaging. Using this system, we studied integrin-specific adhesion in the absence of other adhesive events. Specifically, we show that the transmigration ability of the metastatic cancer cell line MDA-MB-231 is influenced by the type, distance, and density of adhesion peptides present on the DONs. Furthermore, studies with mixed ligand systems indicate that integrins binding to RGD (arginine-glycine-aspartic acid) and IDS (isoleucine-aspartic acid-serine) did not synergistically enhance the extravasation process of MDA-MB-231 cells.
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Affiliation(s)
- Miguel García-Chamé
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 2 (IBG 2), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Juliana Pfeifer
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Carmen M Domínguez
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
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2
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Chen K, Mao M, Huo L, Wang G, Pu Z, Zhang Y. Flexible DNA Nanoclaws Offer Multivalent and Powerful Spatial Pattern-Recognition for Tumor Cells. ACS APPLIED MATERIALS & INTERFACES 2024; 16:29760-29769. [PMID: 38813974 DOI: 10.1021/acsami.4c03382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Multivalent receptor-ligand interactions (RLIs) exhibit excellent affinity for binding when targeting cell membrane receptors with low expression. However, existing strategies only allow for limited control of the valency and spacing of ligands for a certain receptor, lacking recognition patterns for multiple interested receptors with complex spatial distributions. Here, we developed flexible DNA nanoclaws with multivalent aptamers to achieve powerful cell recognition by controlling the spacing of aptamers to match the spatial patterns of receptors. The DNA nanoclaw with spacing-controllable binding sites was constructed via hybrid chain reaction (HCR), enabling dual targeting of HER2 and EpCAM molecules. The results demonstrate that the binding affinity of multivalent DNA nanoclaws to tumor cells is enhanced. We speculate that the flexible structure may conform better to irregularly shaped membrane surfaces, increasing the probability of intermolecular contact. The capture efficiency of circulating tumor cells successfully verified the high affinity and selectivity of this spatial pattern. This strategy will further promote the potential application of DNA frameworks in future disease diagnosis and treatment.
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Affiliation(s)
- Kang Chen
- Department of Laboratory Medicine, Zhongshan City People's Hospital, 528403 Zhongshan, Guangdong, China
| | - Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Lian Huo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Guanzhao Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Zhe Pu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
| | - Yuanqing Zhang
- Department of Laboratory Medicine, Zhongshan City People's Hospital, 528403 Zhongshan, Guangdong, China
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, Guangdong, China
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3
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Shahrokhtash A, Sutherland DS. Smart Biointerfaces via Click Chemistry-Enabled Nanopatterning of Multiple Bioligands and DNA Force Sensors. ACS APPLIED MATERIALS & INTERFACES 2024; 16:21534-21545. [PMID: 38634566 PMCID: PMC11073048 DOI: 10.1021/acsami.4c00831] [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: 01/15/2024] [Revised: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Nanoscale biomolecular placement is crucial for advancing cellular signaling, sensor technology, and molecular interaction studies. Despite this, current methods fall short in enabling large-area nanopatterning of multiple biomolecules while minimizing nonspecific interactions. Using bioorthogonal tags at a submicron scale, we introduce a novel hole-mask colloidal lithography method for arranging up to three distinct proteins, DNA, or peptides on large, fully passivated surfaces. The surfaces are compatible with single-molecule fluorescence microscopy and microplate formats, facilitating versatile applications in cellular and single-molecule assays. We utilize fully passivated and transparent substrates devoid of metals and nanotopographical features to ensure accurate patterning and minimize nonspecific interactions. Surface patterning is achieved using bioorthogonal TCO-tetrazine (inverse electron-demand Diels-Alder, IEDDA) ligation, DBCO-azide (strain-promoted azide-alkyne cycloaddition, SPAAC) click chemistry, and biotin-avidin interactions. These are arranged on surfaces passivated with dense poly(ethylene glycol) PEG brushes crafted through the selective and stepwise removal of sacrificial metallic and polymeric layers, enabling the directed attachment of biospecific tags with nanometric precision. In a proof-of-concept experiment, DNA tension gauge tether (TGT) force sensors, conjugated to cRGD (arginylglycylaspartic acid) in nanoclusters, measured fibroblast integrin tension. This novel application enables the quantification of forces in the piconewton range, which is restricted within the nanopatterned clusters. A second demonstration of the platform to study integrin and epidermal growth factor (EGF) proximal signaling reveals clear mechanotransduction and changes in the cellular morphology. The findings illustrate the platform's potential as a powerful tool for probing complex biochemical pathways involving several molecules arranged with nanometer precision and cellular interactions at the nanoscale.
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Affiliation(s)
- Ali Shahrokhtash
- Interdisciplinary
Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000Aarhus C, Denmark
- The
Centre for Cellular Signal Patterns (CellPAT), Gustav Wieds Vej 14, 8000 Aarhus C ,Denmark
| | - Duncan S. Sutherland
- Interdisciplinary
Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000Aarhus C, Denmark
- The
Centre for Cellular Signal Patterns (CellPAT), Gustav Wieds Vej 14, 8000 Aarhus C ,Denmark
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4
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Mayer I, Karimian T, Gordiyenko K, Angelin A, Kumar R, Hirtz M, Mikut R, Reischl M, Stegmaier J, Zhou L, Ma R, Nienhaus GU, Rabe KS, Lanzerstorfer P, Domínguez CM, Niemeyer CM. Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation. NANO LETTERS 2024; 24:1611-1619. [PMID: 38267020 PMCID: PMC10853960 DOI: 10.1021/acs.nanolett.3c04272] [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: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The nanoscale arrangement of ligands can have a major effect on the activation of membrane receptor proteins and thus cellular communication mechanisms. Here we report on the technological development and use of tailored DNA origami-based molecular rulers to fabricate "Multiscale Origami Structures As Interface for Cells" (MOSAIC), to enable the systematic investigation of the effect of the nanoscale spacing of epidermal growth factor (EGF) ligands on the activation of the EGF receptor (EGFR). MOSAIC-based analyses revealed that EGF distances of about 30-40 nm led to the highest response in EGFR activation of adherent MCF7 and Hela cells. Our study emphasizes the significance of DNA-based platforms for the detailed investigation of the molecular mechanisms of cellular signaling cascades.
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Affiliation(s)
- Ivy Mayer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tina Karimian
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Klavdiya Gordiyenko
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Michael Hirtz
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Imaging and Computer Vision, RWTH Aachen
University, 52074 Aachen, Germany
| | - Lu Zhou
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Rui Ma
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
- Institute
of Biological and Chemical Systems (IBCS) and Institute of Nanotechnology
(INT), Karlsruhe Institute of Technology
(KIT), 76021 Karlsruhe, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kersten S. Rabe
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Peter Lanzerstorfer
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Carmen M. Domínguez
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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5
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Martynenko IV, Erber E, Ruider V, Dass M, Posnjak G, Yin X, Altpeter P, Liedl T. Site-directed placement of three-dimensional DNA origami. NATURE NANOTECHNOLOGY 2023; 18:1456-1462. [PMID: 37640908 PMCID: PMC7616159 DOI: 10.1038/s41565-023-01487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.
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Affiliation(s)
- Irina V Martynenko
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| | - Elisabeth Erber
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Xin Yin
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Philipp Altpeter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
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6
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Majkowska A, Inostroza-Brito KE, Gonzalez M, Redondo-Gómez C, Rice A, Rodriguez-Cabello JC, Del Rio Hernandez AE, Mata A. Peptide-Protein Coassemblies into Hierarchical and Bioactive Tubular Membranes. Biomacromolecules 2023; 24:4419-4429. [PMID: 36696687 PMCID: PMC10565817 DOI: 10.1021/acs.biomac.2c01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/16/2022] [Indexed: 01/26/2023]
Abstract
Multicomponent self-assembly offers opportunities for the design of complex and functional biomaterials with tunable properties. Here, we demonstrate how minor modifications in the molecular structures of peptide amphiphiles (PAs) and elastin-like recombinamers (ELs) can be used to generate coassembling tubular membranes with distinct structures, properties, and bioactivity. First, by introducing minor modifications in the charge density of PA molecules (PAK2, PAK3, PAK4), different diffusion-reaction processes can be triggered, resulting in distinct membrane microstructures. Second, by combining different types of these PAs prior to their coassembly with ELs, further modifications can be achieved, tuning the structures and properties of the tubular membranes. Finally, by introducing the cell adhesive peptide RGDS in either the PA or EL molecules, it is possible to harness the different diffusion-reaction processes to generate tubular membranes with distinct bioactivities. The study demonstrates the possibility to trigger and achieve minor but crucial differences in coassembling processes and tune material structure and bioactivity. The study demonstrates the possibility to use minor, yet crucial, differences in coassembling processes to tune material structure and bioactivity.
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Affiliation(s)
- Anna Majkowska
- William
Harvey Research Institute, Queen Mary University
of London, London EC1M 6BQ, U.K.
- Institute
of Bioengineering, Queen Mary University
of London, London E1 4NS, U.K.
- School
of Engineering and Materials Science, Queen
Mary University of London, London E1 4NS, U.K.
| | - Karla E. Inostroza-Brito
- School
of Engineering and Materials Science, Queen
Mary University of London, London E1 4NS, U.K.
| | - Mariel Gonzalez
- School
of Engineering and Materials Science, Queen
Mary University of London, London E1 4NS, U.K.
| | - Carlos Redondo-Gómez
- Institute
of Bioengineering, Queen Mary University
of London, London E1 4NS, U.K.
- School
of Engineering and Materials Science, Queen
Mary University of London, London E1 4NS, U.K.
| | - Alistair Rice
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
| | | | | | - Alvaro Mata
- Institute
of Bioengineering, Queen Mary University
of London, London E1 4NS, U.K.
- School
of Engineering and Materials Science, Queen
Mary University of London, London E1 4NS, U.K.
- School
of
Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
- Biodiscovery
Institute, University of Nottingham, Nottingham NG7 2RD, U.K.
- Department
of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K.
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7
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Li L, Wang Z, Guo H, Lin Q. Nanomaterials: a promising multimodal theranostics platform for thyroid cancer. J Mater Chem B 2023; 11:7544-7566. [PMID: 37439780 DOI: 10.1039/d3tb01175e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Thyroid cancer is the most prevalent malignant neoplasm of the cervical region and endocrine system, characterized by a discernible upward trend in incidence over recent years. Ultrasound-guided fine needle aspiration is the current standard for preoperative diagnosis of thyroid cancer, albeit with limitations and a certain degree of false-negative outcomes. Although differentiated thyroid carcinoma generally exhibits a favorable prognosis, dedifferentiation is associated with an unfavorable clinical course. Anaplastic thyroid cancer, characterized by high malignancy and aggressiveness, remains an unmet clinical need with no effective treatments available. The emergence of nanomedicine has opened new avenues for cancer theranostics. The unique features of nanomaterials, including multifunctionality, modifiability, and various detection modes, enable non-invasive and convenient thyroid cancer diagnosis through multimodal imaging. For thyroid cancer treatment, nanomaterial-based photothermal therapy or photodynamic therapy, combined with chemotherapy, radiotherapy, or gene therapy, holds promise in reducing invasiveness and prolonging patient survival or alleviating pain in individuals with anaplastic thyroid carcinoma. Furthermore, nanomaterials enable simultaneous diagnosis and treatment of thyroid cancer. This review aims to provide a comprehensive survey of the latest developments in nanomaterials for thyroid cancer diagnosis and treatment and encourage further research in developing innovative and effective theranostic approaches for thyroid cancer.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
- Department of Endocrinology, Lequn Branch, The First Hospital of Jilin University, Changchun, 130031, China.
| | - Ze Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
| | - Hui Guo
- Department of Endocrinology, Lequn Branch, The First Hospital of Jilin University, Changchun, 130031, China.
| | - Quan Lin
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
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8
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Toledo E, Iraqi M, Pandey A, Tzadka S, Le Saux G, Porgador A, Schvartzman M. Multifunctional Nanoscale Platform for the Study of T Cell Receptor Segregation. ACS OMEGA 2023; 8:28968-28975. [PMID: 37599975 PMCID: PMC10433356 DOI: 10.1021/acsomega.2c08194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/10/2023] [Indexed: 08/22/2023]
Abstract
T cells respond not only to biochemical stimuli transmitted through their activating, costimulatory, and inhibitory receptors but also to biophysical aspects of their environment, including the receptors' spatial arrangement. While these receptors form nanoclusters that can either colocalize or segregate, the roles of these colocalization and segregation remain unclear. Deciphering these roles requires a nanoscale platform with independent and simultaneous spatial control of multiple types of receptors. Herein, using a straightforward and modular fabrication process, we engineered a tunable nanoscale chip used as a platform for T cell stimulation, allowing spatial control over the clustering and segregation of activating, costimulatory, and inhibitory receptors. Using this platform, we showed that, upon blocked inhibition, cells became sensitive to changes in the nanoscale ligand configuration. The nanofabrication methodology described here opens a pathway to numerous studies, which will produce an important insight into the molecular mechanism of T cell activation. This insight is essential for the fundamental understanding of our immune system as well as for the rational design of future immunotherapies.
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Affiliation(s)
- Esti Toledo
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Muhammed Iraqi
- The
Shraga Segal Department of Microbiology, Immunology, and Genetics,
Faculty of Health Science, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
| | - Ashish Pandey
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Sivan Tzadka
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Guillaume Le Saux
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Angel Porgador
- The
Shraga Segal Department of Microbiology, Immunology, and Genetics,
Faculty of Health Science, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
| | - Mark Schvartzman
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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9
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Zhang Y, Tian X, Wang Z, Wang H, Liu F, Long Q, Jiang S. Advanced applications of DNA nanostructures dominated by DNA origami in antitumor drug delivery. Front Mol Biosci 2023; 10:1239952. [PMID: 37609372 PMCID: PMC10440542 DOI: 10.3389/fmolb.2023.1239952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
DNA origami is a cutting-edge DNA self-assembly technique that neatly folds DNA strands and creates specific structures based on the complementary base pairing principle. These innovative DNA origami nanostructures provide numerous benefits, including lower biotoxicity, increased stability, and superior adaptability, making them an excellent choice for transporting anti-tumor agents. Furthermore, they can considerably reduce side effects and improve therapy success by offering precise, targeted, and multifunctional drug delivery system. This comprehensive review looks into the principles and design strategies of DNA origami, providing valuable insights into this technology's latest research achievements and development trends in the field of anti-tumor drug delivery. Additionally, we review the key function and major benefits of DNA origami in cancer treatment, some of these approaches also involve aspects related to DNA tetrahedra, aiming to provide novel ideas and effective solutions to address drug delivery challenges in cancer therapy.
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Affiliation(s)
- Yiming Zhang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Zijian Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Haochen Wang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Qipeng Long
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
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10
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Cervantes-Salguero K, Gutiérrez Fosado YA, Megone W, Gautrot JE, Palma M. Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization. Molecules 2023; 28:molecules28093686. [PMID: 37175096 PMCID: PMC10180480 DOI: 10.3390/molecules28093686] [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: 03/03/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
DNA is programmed to hierarchically self-assemble into superstructures spanning from nanometer to micrometer scales. Here, we demonstrate DNA nanosheets assembled out of a rationally designed flexible DNA unit (F-unit), whose shape resembles a Feynman diagram. F-units were designed to self-assemble in two dimensions and to display a high DNA density of hydrophobic moieties. oxDNA simulations confirmed the planarity of the F-unit. DNA nanosheets with a thickness of a single DNA duplex layer and with large coverage (at least 30 μm × 30 μm) were assembled from the liquid phase at the solid/liquid interface, as unambiguously evidenced by atomic force microscopy imaging. Interestingly, single-layer nanodiscs formed in solution at low DNA concentrations. DNA nanosheet superstructures were further assembled at liquid/liquid interfaces, as demonstrated by the fluorescence of a double-stranded DNA intercalator. Moreover, the interfacial mechanical properties of the nanosheet superstructures were measured as a response to temperature changes, demonstrating the control of interfacial shear mechanics based on DNA nanostructure engineering. The rational design of the F-unit, along with the presented results, provide an avenue toward the controlled assembly of reconfigurable/responsive nanosheets and membranes at liquid/liquid interfaces, to be potentially used in the characterization of biomechanical processes and materials transport.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - William Megone
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Julien E Gautrot
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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11
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Schneider L, Rabe KS, Domínguez CM, Niemeyer CM. Hapten-Decorated DNA Nanostructures Decipher the Antigen-Mediated Spatial Organization of Antibodies Involved in Mast Cell Activation. ACS NANO 2023; 17:6719-6730. [PMID: 36990450 PMCID: PMC10100567 DOI: 10.1021/acsnano.2c12647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The immunological response of mast cells is controlled by the multivalent binding of antigens to immunoglobulin E (IgE) antibodies bound to the high-affinity receptor FcεRI on the cell membrane surface. However, the spatial organization of antigen-antibody-receptor complexes at the nanometer scale and the structural constraints involved in the initial events at the cell surface are not yet fully understood. For example, it is unclear what influence the affinity and nanoscale distance between the binding partners involved have on the activation of mast cells to degranulate inflammatory mediators from storage granules. We report the use of DNA origami nanostructures (DON) functionalized with different arrangements of the haptenic 2,4-dinitrophenyl (DNP) ligand to generate multivalent artificial antigens with full control over valency and nanoscale ligand architecture. To investigate the spatial requirements for mast cell activation, the DNP-DON complexes were initially used in surface plasmon resonance (SPR) analysis to study the binding kinetics of isolated IgE under physiological conditions. The most stable binding was observed in a narrow window of approximately 16 nm spacing between haptens. In contrast, affinity studies with FcεRI-linked IgE antibodies on the surface of rat basophilic leukemia cells (RBL-2H3) indicated virtually no distance-dependent variations in the binding of the differently structured DNP-DON complexes but suggested a supramolecular oligovalent nature of the interaction. Finally, the use of DNP-DON complexes for mast cell activation revealed that antigen-directed tight assembly of antibody-receptor complexes is the critical factor for triggering degranulation, even more critical than ligand valence. Our study emphasizes the significance of DNA nanostructures for the study of fundamental biological processes.
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12
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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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13
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Hawkes W, Marhuenda E, Reynolds P, O'Neill C, Pandey P, Samuel Wilson DG, Freeley M, Huang D, Hu J, Gondarenko S, Hone J, Gadegaard N, Palma M, Iskratsch T. Regulation of cardiomyocyte adhesion and mechanosignalling through distinct nanoscale behaviour of integrin ligands mimicking healthy or fibrotic extracellular matrix. Philos Trans R Soc Lond B Biol Sci 2022; 377:20220021. [PMID: 36189804 PMCID: PMC9527911 DOI: 10.1098/rstb.2022.0021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/12/2022] [Indexed: 12/21/2022] Open
Abstract
The stiffness of the cardiovascular environment changes during ageing and in disease and contributes to disease incidence and progression. Changing collagen expression and cross-linking regulate the rigidity of the cardiac extracellular matrix (ECM). Additionally, basal lamina glycoproteins, especially laminin and fibronectin regulate cardiomyocyte adhesion formation, mechanics and mechanosignalling. Laminin is abundant in the healthy heart, but fibronectin is increasingly expressed in the fibrotic heart. ECM receptors are co-regulated with the changing ECM. Owing to differences in integrin dynamics, clustering and downstream adhesion formation this is expected to ultimately influence cardiomyocyte mechanosignalling; however, details remain elusive. Here, we sought to investigate how different cardiomyocyte integrin/ligand combinations affect adhesion formation, traction forces and mechanosignalling, using a combination of uniformly coated surfaces with defined stiffness, polydimethylsiloxane nanopillars, micropatterning and specifically designed bionanoarrays for precise ligand presentation. Thereby we found that the adhesion nanoscale organization, signalling and traction force generation of neonatal rat cardiomyocytes (which express both laminin and fibronectin binding integrins) are strongly dependent on the integrin/ligand combination. Together our data indicate that the presence of fibronectin in combination with the enhanced stiffness in fibrotic areas will strongly impact on the cardiomyocyte behaviour and influence disease progression. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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Affiliation(s)
- William Hawkes
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Emilie Marhuenda
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Paul Reynolds
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, UK
| | - Caoimhe O'Neill
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Pragati Pandey
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | | | - Mark Freeley
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Da Huang
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Junquiang Hu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Sasha Gondarenko
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - James Hone
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | | | - Matteo Palma
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Thomas Iskratsch
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
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14
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Handrea-Dragan IM, Botiz I, Tatar AS, Boca S. Patterning at the micro/nano-scale: Polymeric scaffolds for medical diagnostic and cell-surface interaction applications. Colloids Surf B Biointerfaces 2022; 218:112730. [DOI: 10.1016/j.colsurfb.2022.112730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022]
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15
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Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Bioactive Fibronectin-III 10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. ACS APPLIED BIO MATERIALS 2022; 5:10.1021/acsabm.2c00303. [PMID: 36108278 PMCID: PMC10014493 DOI: 10.1021/acsabm.2c00303] [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] [Indexed: 11/30/2022]
Abstract
The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.
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Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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16
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Cervantes-Salguero K, Freeley M, Gwyther REA, Jones DD, Chávez JL, Palma M. Single molecule DNA origami nanoarrays with controlled protein orientation. BIOPHYSICS REVIEWS 2022; 3:031401. [PMID: 38505279 PMCID: PMC10903486 DOI: 10.1063/5.0099294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/20/2022] [Indexed: 03/21/2024]
Abstract
The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.
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Affiliation(s)
- K. Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - M. Freeley
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - R. E. A. Gwyther
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - D. D. Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - J. L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio 45433-7901, USA
| | - M. Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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17
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Domínguez CM, García-Chamé M, Müller U, Kraus A, Gordiyenko K, Itani A, Haschke H, Lanzerstorfer P, Rabe KS, Niemeyer CM. Linker Engineering of Ligand-Decorated DNA Origami Nanostructures Affects Biological Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202704. [PMID: 35934828 DOI: 10.1002/smll.202202704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/11/2022] [Indexed: 06/15/2023]
Abstract
News from an old acquaintance: The streptavidin (STV)-biotin binding system is frequently used for the decoration of DNA origami nanostructures (DON) to study biological systems. Here, a surprisingly high dynamic of the STV/DON interaction is reported, which is affected by the structure of the DNA linker system. Analysis of different mono- or bi-dentate linker architectures on DON with a novel high-speed atomic force microscope (HS-AFM) enabling acquisition times as short as 50 ms per frame gave detailed insights into the dynamics of the DON/STV interaction, revealing dwell times in the sub-100 millisecond range. The linker systems are also used to present biotinylated epidermal growth factor on DON to study the activation of the epidermal growth factor receptor signaling cascade in HeLa cells. The studies confirm that cellular activation correlated with the binding properties of linker-specific STV/DON interactions observed by HS-AFM. This work sheds more light on the commonly used STV/DON system and will help to further standardize the use of DNA nanostructures for the study of biological processes.
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Affiliation(s)
- Carmen M Domínguez
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Miguel García-Chamé
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ulrike Müller
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Andreas Kraus
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Klavdiya Gordiyenko
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ahmad Itani
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Heiko Haschke
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Peter Lanzerstorfer
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
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18
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Fang Q, Guo P, Zeng Y, Wang C, Jiang T, Jiang Y. Design of high-avidity multivalent ligand structures that target cells with high ligand economy. Chem Commun (Camb) 2022; 58:9802-9805. [PMID: 35971899 DOI: 10.1039/d2cc03296a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel cell-targeting ligand structures are constructed with a spikey core scaffold, where multiple copies of coiled-coil peptide nanorods are conjugated on the surface of a peptide nanosheet. Clustering of carbohydrate and aptamer ligands at the end of the coiled coils optimizes ligand accessibility to cell-surface receptors. Display of the ligand-coil conjugates on the nanosheet generates a patchy ligand pattern bearing two levels of multivalency. With the ligand-scaffold system, high-avidity cell targeting is realized using fewer ligands than ever, which facilitates future applications in cell detection and drug delivery.
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Affiliation(s)
- Qingqing Fang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China.
| | - Pan Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China.
| | - Yiting Zeng
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China.
| | - Chenru Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China.
| | - Tao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China. .,Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Yunbao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China. .,Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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19
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Sun Y, Yan L, Sun J, Xiao M, Lai W, Song G, Li L, Fan C, Pei H. Nanoscale organization of two-dimensional multimeric pMHC reagents with DNA origami for CD8 + T cell detection. Nat Commun 2022; 13:3916. [PMID: 35798752 PMCID: PMC9263106 DOI: 10.1038/s41467-022-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2022] [Indexed: 11/08/2022] Open
Abstract
Peptide-MHC (pMHC) multimers have excelled in the detection of antigen-specific T cells and have allowed phenotypic analysis using other reagents, but their use for detection of low-affinity T cells remains a challenge. Here we develop a multimeric T cell identifying reagent platform using two-dimensional DNA origami scaffolds to spatially organize pMHCs (termed as dorimers) with nanoscale control. We show that these dorimers enhance the binding avidity for low-affinity antigen-specific T cell receptors (TCRs). The dorimers are able to detect more antigen-specific T cells in mouse CD8+ T cells and early-stage CD4+CD8+ double-positive thymocytes that express less dense TCRs, compared with the equivalent tetramers and dextramers. Moreover, we demonstrate dorimer function in the analysis of autoimmune CD8+ T cells that express low-affinity TCRs, which are difficult to detect using tetramers. We anticipate that dorimers could contribute to the investigation of antigen-specific T cells in immune T cell function or immunotherapy applications.
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Affiliation(s)
- Yueyang Sun
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Lu Yan
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Jiajia Sun
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Guangqi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, 200241, Shanghai, China.
- Institute of Eco-Chongming, 202162, Shanghai, China.
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20
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Wang C, Chen X, Su Y, Wang H, Li D. Precise Regulating T Cell Activation Signaling with Spatial Controllable Positioning of Receptors on DNA Origami. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
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22
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DNA nanotechnology-facilitated ligand manipulation for targeted therapeutics and diagnostics. J Control Release 2021; 340:292-307. [PMID: 34748871 DOI: 10.1016/j.jconrel.2021.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022]
Abstract
Ligands, mostly binding to proteins to form complexes and catalyze chemical reactions, can serve as drug and probe molecules, as well as sensing elements. DNA nanotechnology can integrate the high editability of DNA nanostructures and the biological activity of ligands into functionalized DNA nanostructures in a manner of controlled ligand stoichiometry, type, and arrangement, which provides significant advantages for targeted therapeutics and diagnostics. As therapeutic agents, multiple- and multivalent-ligands functionalized DNA nanostructures increase ligand-receptor affinity and activate multivalent ligand-receptor interactions, enabling improved regulation of cell signaling and enhanced control of cell behavior. As diagnostic agents, multiple ligands interaction via DNA nanostructures endows DNA nanosensors with high sensitivity and excellent signal transduction capability. Herein, we review the principles and advantages of using DNA nanostructures to manipulate ligands for targeted therapeutics and diagnostics and provide future perspectives.
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23
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Sethi S, Sugiyama H, Endo M. Biomimetic DNA Nanotechnology to Understand and Control Cellular Responses. Chembiochem 2021; 23:e202100446. [PMID: 34664334 DOI: 10.1002/cbic.202100446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Indexed: 12/15/2022]
Abstract
At the cellular level, numerous nanocues guide the cells to adhere, interact, proliferate, differentiate, etc. Understanding and manipulating the cellular functions in vitro, necessitates the elucidation of these nanocues provided to the cells by the extracellular matrix (ECM), neighbouring cells or in the form of ligands. DNA nanotechnology is a biocompatible, flexible and a promising molecular level toolkit for mimicking cell-cell and cell-matrix interactions. In this review, we summarize various advances in cell-matrix, cell-cell and cell receptor-ligand interactions using DNA nanotechnology as a tool. We also provide a brief outlook on the current challenges and the future potentials of these DNA-based nanostructures so as to inspire novel innovations in the field.
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Affiliation(s)
- Soumya Sethi
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, 564-8680, Japan
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24
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He Q, Liu Y, Li K, Wu Y, Wang T, Tan Y, Jiang T, Liu X, Liu Z. Deoxyribonucleic acid anchored on cell membranes for biomedical application. Biomater Sci 2021; 9:6691-6717. [PMID: 34494042 DOI: 10.1039/d1bm01057c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
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Affiliation(s)
- Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China. .,Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, P. R. China
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25
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Swiatlowska P, Iskratsch T. Tools for studying and modulating (cardiac muscle) cell mechanics and mechanosensing across the scales. Biophys Rev 2021; 13:611-623. [PMID: 34765044 PMCID: PMC8553672 DOI: 10.1007/s12551-021-00837-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022] Open
Abstract
Cardiomyocytes generate force for the contraction of the heart to pump blood into the lungs and body. At the same time, they are exquisitely tuned to the mechanical environment and react to e.g. changes in cell and extracellular matrix stiffness or altered stretching due to reduced ejection fraction in heart disease, by adapting their cytoskeleton, force generation and cell mechanics. Both mechanical sensing and cell mechanical adaptations are multiscale processes. Receptor interactions with the extracellular matrix at the nanoscale will lead to clustering of receptors and modification of the cytoskeleton. This in turn alters mechanosensing, force generation, cell and nuclear stiffness and viscoelasticity at the microscale. Further, this affects cell shape, orientation, maturation and tissue integration at the microscale to macroscale. A variety of tools have been developed and adapted to measure cardiomyocyte receptor-ligand interactions and forces or mechanics at the different ranges, resulting in a wealth of new information about cardiomyocyte mechanobiology. Here, we take stock at the different tools for exploring cardiomyocyte mechanosensing and cell mechanics at the different scales from the nanoscale to microscale and macroscale.
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Affiliation(s)
- Pamela Swiatlowska
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Thomas Iskratsch
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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26
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Hellmeier J, Platzer R, Mühlgrabner V, Schneider MC, Kurz E, Schütz GJ, Huppa JB, Sevcsik E. Strategies for the Site-Specific Decoration of DNA Origami Nanostructures with Functionally Intact Proteins. ACS NANO 2021; 15:15057-15068. [PMID: 34463486 PMCID: PMC8482763 DOI: 10.1021/acsnano.1c05411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
DNA origami structures provide flexible scaffolds for the organization of single biomolecules with nanometer precision. While they find increasing use for a variety of biological applications, the functionalization with proteins at defined stoichiometry, high yield, and under preservation of protein function remains challenging. In this study, we applied single molecule fluorescence microscopy in combination with a cell biological functional assay to systematically evaluate different strategies for the site-specific decoration of DNA origami structures, focusing on efficiency, stoichiometry, and protein functionality. Using an activating ligand of the T-cell receptor (TCR) as the protein of interest, we found that two commonly used methodologies underperformed with regard to stoichiometry and protein functionality. While strategies employing tetravalent wildtype streptavidin for coupling of a biotinylated TCR-ligand yielded mixed populations of DNA origami structures featuring up to three proteins, the use of divalent (dSAv) or DNA-conjugated monovalent streptavidin (mSAv) allowed for site-specific attachment of a single biotinylated TCR-ligand. The most straightforward decoration strategy, via covalent DNA conjugation, resulted in a 3-fold decrease in ligand potency, likely due to charge-mediated impairment of protein function. Replacing DNA with charge-neutral peptide nucleic acid (PNA) in a ligand conjugate emerged as the coupling strategy with the best overall performance in our study, as it produced the highest yield with no multivalent DNA origami structures and fully retained protein functionality. With our study we aim to provide guidelines for the stoichiometrically defined, site-specific functionalization of DNA origami structures with proteins of choice serving a wide range of biological applications.
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Affiliation(s)
| | - René Platzer
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Vanessa Mühlgrabner
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | | | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, Oxford, OX3 7FY, U.K.
| | | | - Johannes B. Huppa
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Eva Sevcsik
- Institute
of Applied Physics, TU Wien, Vienna, 1060, Austria
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27
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Sethi S, Hidaka K, Sugiyama H, Endo M. Non‐invasive Regulation of Cellular Morphology Using a Photoswitchable Mechanical DNA Polymer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Soumya Sethi
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Kumi Hidaka
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences Kyoto University Japan
| | - Masayuki Endo
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences Kyoto University Japan
- Organization for Research and Development of Innovative Science and Technology Kansai University Japan
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28
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Sethi S, Hidaka K, Sugiyama H, Endo M. Non-invasive Regulation of Cellular Morphology Using a Photoswitchable Mechanical DNA Polymer. Angew Chem Int Ed Engl 2021; 60:20342-20349. [PMID: 33987972 DOI: 10.1002/anie.202105425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Indexed: 01/08/2023]
Abstract
The extracellular matrix (ECM) in which the cells reside provides a dynamic and reversible environment. Spatiotemporal cues are essential when cells are undergoing morphogenesis, repair and differentiation. Emulation of such an intricate system with reversible presentation of nanoscale cues can help us better understand cellular processes and can allow the precise manipulation of cell function in vitro. Herein, we formulated a photoswitchable DNA mechanical nanostructure containing azobenzene moieties and dynamically regulated the spatial distance between adhesion peptides using a photoswitchable DNA polymer with photoirradiation. We found that the DNA polymer reversibly forms two different structures, a relaxed linear and shrunken compact form, observed by AFM. Using the mechanical properties of this DNA polymer, UV and visible light irradiation induced a significant morphology change of the cells between a round shape and spindle shape, thus providing a tool to decipher the language of the ECM better.
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Affiliation(s)
- Soumya Sethi
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Japan.,Organization for Research and Development of Innovative Science and Technology, Kansai University, Japan
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29
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Kocabey S, Ekim Kocabey A, Schneiter R, Rüegg C. Membrane-Interacting DNA Nanotubes Induce Cancer Cell Death. NANOMATERIALS 2021; 11:nano11082003. [PMID: 34443832 PMCID: PMC8397952 DOI: 10.3390/nano11082003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology offers to build nanoscale structures with defined chemistries to precisely position biomolecules or drugs for selective cell targeting and drug delivery. Owing to the negatively charged nature of DNA, for delivery purposes, DNA is frequently conjugated with hydrophobic moieties, positively charged polymers/peptides and cell surface receptor-recognizing molecules or antibodies. Here, we designed and assembled cholesterol-modified DNA nanotubes to interact with cancer cells and conjugated them with cytochrome c to induce cancer cell apoptosis. By flow cytometry and confocal microscopy, we observed that DNA nanotubes efficiently bound to the plasma membrane as a function of the number of conjugated cholesterol moieties. The complex was taken up by the cells and localized to the endosomal compartment. Cholesterol-modified DNA nanotubes, but not unmodified ones, increased membrane permeability, caspase activation and cell death. Irreversible inhibition of caspase activity with a caspase inhibitor, however, only partially prevented cell death. Cytochrome c-conjugated DNA nanotubes were also efficiently taken up but did not increase the rate of cell death. These results demonstrate that cholesterol-modified DNA nanotubes induce cancer cell death associated with increased cell membrane permeability and are only partially dependent on caspase activity, consistent with a combined form of apoptotic and necrotic cell death. DNA nanotubes may be further developed as primary cytotoxic agents, or drug delivery vehicles, through cholesterol-mediated cellular membrane interactions and uptake.
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Affiliation(s)
- Samet Kocabey
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
- Correspondence: (S.K.); (C.R.)
| | - Aslihan Ekim Kocabey
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 10, PER05, 1700 Fribourg, Switzerland; (A.E.K.); (R.S.)
| | - Roger Schneiter
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 10, PER05, 1700 Fribourg, Switzerland; (A.E.K.); (R.S.)
| | - Curzio Rüegg
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
- Correspondence: (S.K.); (C.R.)
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30
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Sala L, Zerolová A, Rodriguez A, Reimitz D, Davídková M, Ebel K, Bald I, Kočišek J. Folding DNA into origami nanostructures enhances resistance to ionizing radiation. NANOSCALE 2021; 13:11197-11203. [PMID: 34142687 PMCID: PMC8247635 DOI: 10.1039/d1nr02013g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/04/2021] [Indexed: 05/22/2023]
Abstract
We report experimental results on damage induced by ionizing radiation to DNA origami triangles which are commonly used prototypes for scaffolded DNA origami nanostructures. We demonstrate extreme stability of DNA origami upon irradiation, which is caused by (i) the multi-row design holding the shape of the origami even after severe damage to the scaffold DNA and (ii) the reduction of damage to the scaffold DNA due to the protective effect of the folded structure. With respect to damage induced by ionizing radiation, the protective effect of the structure is superior to that of a naturally paired DNA double helix. Present results allow estimating the stability of scaffolded DNA origami nanostructures in applications such as nanotechnology, pharmacy or in singulo molecular studies where they are exposed to ionizing radiation from natural and artificial sources. Additionally, possibilities are opened for scaffolded DNA use in the design of radiation-resistant and radio-sensitive materials.
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Affiliation(s)
- Leo Sala
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Agnes Zerolová
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic. and Department of Chemistry, Technical University of Liberec, 46117, Liberec, Czech Republic
| | - Alvaro Rodriguez
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Dan Reimitz
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Prague, Czech Republic
| | - Kenny Ebel
- Institute of Chemistry-Physical Chemistry, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam, Germany
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
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31
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Toledo E, Le Saux G, Edri A, Li L, Rosenberg M, Keidar Y, Bhingardive V, Radinsky O, Hadad U, Di Primo C, Buffeteau T, Smith AS, Porgador A, Schvartzman M. Molecular-scale spatio-chemical control of the activating-inhibitory signal integration in NK cells. SCIENCE ADVANCES 2021; 7:7/24/eabc1640. [PMID: 34117052 PMCID: PMC8195486 DOI: 10.1126/sciadv.abc1640] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/21/2021] [Indexed: 05/13/2023]
Abstract
The role of juxtaposition of activating and inhibitory receptors in signal inhibition of cytotoxic lymphocytes remains strongly debated. The challenge lies in the lack of tools that allow simultaneous spatial manipulation of signaling molecules. To circumvent this, we produced a nanoengineered multifunctional platform with molecular-scale spatial control of ligands, which was applied to elucidate KIR2DL1-mediated inhibition of NKG2D signaling-receptors of natural killer cells. This platform was conceived by bimetallic nanodot patterning with molecular-scale registry, followed by a ternary functionalization with distinct moieties. We found that a 40-nm gap between activating and inhibitory ligands provided optimal inhibitory conditions. Supported by theoretical modeling, we interpret these findings as a consequence of the size mismatch and conformational flexibility of ligands in their spatial interaction. This highly versatile approach provides an important insight into the spatial mechanism of inhibitory immune checkpoints, which is essential for the rational design of future immunotherapies.
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Affiliation(s)
- Esti Toledo
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Avishay Edri
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Long Li
- Department of Physics, IZNF, FAU Erlangen-Nürnberg, Erlangen 91058, Germany
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Maor Rosenberg
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Yossi Keidar
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Viraj Bhingardive
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Olga Radinsky
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Uzi Hadad
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Carmelo Di Primo
- University of Bordeaux, INSERM U1212, UMR CNRS 5320, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | | | - Ana-Sunčana Smith
- Department of Physics, IZNF, FAU Erlangen-Nürnberg, Erlangen 91058, Germany
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Angel Porgador
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Mark Schvartzman
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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32
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Liu Y, Wijesekara P, Kumar S, Wang W, Ren X, Taylor RE. The effects of overhang placement and multivalency on cell labeling by DNA origami. NANOSCALE 2021; 13:6819-6828. [PMID: 33885483 PMCID: PMC8161690 DOI: 10.1039/d0nr09212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Through targeted binding to the cell membrane, structural DNA nanotechnology has the potential to guide and affix biomolecules such as drugs, growth factors and nanobiosensors to the surfaces of cells. In this study, we investigated the targeted binding efficiency of three distinct DNA origami shapes to cultured endothelial cells via cholesterol anchors. Our results showed that the labeling efficiency is highly dependent on the shape of the origami as well as the number and the location of the binding overhangs. With a uniform surface spacing of binding overhangs, 3D isotropic nanospheres and 1D anisotropic nanorods labeled cells effectively, and the isotropic nanosphere labeling fit well with an independent binding model. Face-decoration and edge-decoration of the anisotropic nanotile were performed to investigate the effects of binding overhang location on cell labeling, and only the edge-decorated nanotiles were successful at labeling cells. Edge proximity studies demonstrated that the labeling efficiency can be modulated in both nanotiles and nanorods by moving the binding overhangs towards the edges and vertices, respectively. Furthermore, we demonstrated that while double-stranded DNA (dsDNA) bridge tethers can rescue the labeling efficiency of the face-decorated rectangular plate, this effect is also dependent on the proximity of bridge tethers to the edges or vertices of the nanostructures. A final comparison of all three nanoshapes revealed that the end-labeled nanorod and the nanosphere achieved the highest absolute labeling intensities, but the highest signal-to-noise ratio, calculated as the ratio of overall labeling to initiator-free background labeling, was achieved by the end-labeled nanorod, with the edge-labeled nanotile coming in second place slightly ahead of the nanosphere. The findings from this study can help us further understand the factors that affect membrane attachment using cholesterol anchors, thus providing guidelines for the rational design of future functional DNA nanostructures.
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Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, USA.
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33
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Cervantes-Salguero K, Freeley M, Chávez JL, Palma M. Single-molecule DNA origami aptasensors for real-time biomarker detection. J Mater Chem B 2021; 8:6352-6356. [PMID: 32716449 DOI: 10.1039/d0tb01291b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we report the use of DNA nanostructures as platforms to monitor the inherent conformational changes of aptamers upon analyte binding, with single-molecule resolution and real-time capability. An aptasensor designed to sense cortisol was found to suffer from instability in solution, but this was reconciled via a rational design of a single-molecule sensing platform. In this regard, DNA origami was employed to immobilise individual aptasensors on a glass surface and to ensure adequate interaction with their environment, for single-molecule analysis. The strategy presented here can be applied to any aptamer obtained by the destabilisation of a duplex in a SELEX process, and hence employed in the rational design of single-molecule biosensors.
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Affiliation(s)
- Keitel Cervantes-Salguero
- School of Biological and Chemical Sciences and Materials Research Institute, Queen Mary University of London, London, UK.
| | - Mark Freeley
- School of Biological and Chemical Sciences and Materials Research Institute, Queen Mary University of London, London, UK.
| | - Jorge L Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio, USA.
| | - Matteo Palma
- School of Biological and Chemical Sciences and Materials Research Institute, Queen Mary University of London, London, UK.
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34
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Fang T, Alvelid J, Spratt J, Ambrosetti E, Testa I, Teixeira AI. Spatial Regulation of T-Cell Signaling by Programmed Death-Ligand 1 on Wireframe DNA Origami Flat Sheets. ACS NANO 2021; 15:3441-3452. [PMID: 33556239 PMCID: PMC7905882 DOI: 10.1021/acsnano.0c10632] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Programmed Death-1 (PD-1) is a coinhibitory receptor expressed on activated T cells that suppresses T-cell signaling and effector functions. It has been previously shown that binding to its ligand PD-L1 induces a spatial reorganization of PD-1 receptors into microclusters on the cell membrane. However, the roles of the spatial organization of PD-L1 on PD-1 clustering and T-cell signaling have not been elucidated. Here, we used DNA origami flat sheets to display PD-L1 ligands at defined nanoscale distances and investigated their ability to inhibit T-cell activation in vitro. We found that DNA origami flat sheets modified with CD3 and CD28 activating antibodies (FS-α-CD3-CD28) induced robust T-cell activation. Co-treatment with flat sheets presenting PD-L1 ligands separated by ∼200 nm (FS-PD-L1-200), but not 13 nm (FS-PD-L1-13) or 40 nm (FS-PD-L1-40), caused an inhibition of T-cell signaling, which increased with increasing molar ratio of FS-PD-L1-200 to FS-α-CD3-CD28. Furthermore, FS-PD-L1-200 induced the formation of smaller PD-1 nanoclusters and caused a larger reduction in IL-2 expression compared to FS-PD-L1-13. Together, these findings suggest that the spatial organization of PD-L1 determines its ability to regulate T-cell signaling and may guide the development of future nanomedicine-based immunomodulatory therapies.
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Affiliation(s)
- Trixy Fang
- Department
of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Jonatan Alvelid
- Department
of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Joel Spratt
- Department
of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Elena Ambrosetti
- Department
of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Ilaria Testa
- Department
of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Ana I. Teixeira
- Department
of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
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35
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Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041885] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.
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36
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Amoroso G, Sapelkin A, Ye Q, Araullo-Peters V, Cecconello A, Fernandez G, Palma M. DNA-driven dynamic assembly of MoS 2 nanosheets. Faraday Discuss 2021; 227:233-244. [PMID: 33404023 DOI: 10.1039/c9fd00118b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlling the assembly of molybdenum disulfide (MoS2) layers into static and dynamic superstructures can impact on their use in optoelectronics, energy, and drug delivery. Toward this goal, we present a strategy to drive the assembly of MoS2 layers via the hybridization of complementary DNA linkers. By functionalizing the MoS2 surface with thiolated DNA, MoS2 nanosheets were assembled into mulitlayered superstructures, and the complementary DNA strands were used as linkers. A disassembly process was triggered by the formation of an intramolecular i-motif structure at a cystosine-rich sequence in the DNA linker at acidic pH values. We tested the versatility of our approach by driving the disassembly of the MoS2 superstructures through a different DNA-based mechanism, namely strand displacement. This study demonstrates how DNA can be employed to drive the static and dynamic assembly of MoS2 nanosheets in aqueous solution.
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Affiliation(s)
- Giuseppe Amoroso
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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Dems D, Freeman R, Riker KD, Coradin T, Stupp SI, Aimé C. Multivalent Clustering of Adhesion Ligands in Nanofiber-Nanoparticle Composites. Acta Biomater 2021; 119:303-311. [PMID: 33171314 DOI: 10.1016/j.actbio.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/17/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023]
Abstract
Because the positioning and clustering of biomolecules within the extracellular matrix dictates cell behaviors, the engineering of biomaterials incorporating bioactive epitopes with spatial organization tunable at the nanoscale is of primary importance. Here we used a highly modular composite approach combining peptide amphiphile (PA) nanofibers and silica nanoparticles, which are both easily functionalized with one or several bioactive signals. We show that the surface of silica nanoparticles allows the clustering of RGDS bioactive signals leading to improved adhesion and spreading of fibroblast cells on composite hydrogels at an epitope concentration much lower than in PA-only based matrices. Most importantly, by combining the two integrin-binding sequences RGDS and PHSRN on nanoparticle surfaces, we improved cell adhesion on the PA nanofiber/particle composite hydrogels, which is attributed to synergistic interactions known to be effective only for peptide intermolecular distance of ca. 5 nm. Such composites with soft and hard nanostructures offer a strategy for the design of advanced scaffolds to display multiple signals and control cell behavior.
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Affiliation(s)
- Dounia Dems
- Sorbonne Université, CNRS, Collège de France, Laboratoire de Chimie de la Matière Condensée de Paris, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Ronit Freeman
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.; Department of Applied Physical Sciences, University of North Carolina, 121 South Rd, Chapel Hill, North Carolina, 27514, United States
| | - Kyle D Riker
- Department of Applied Physical Sciences, University of North Carolina, 121 South Rd, Chapel Hill, North Carolina, 27514, United States
| | - Thibaud Coradin
- Sorbonne Université, CNRS, Collège de France, Laboratoire de Chimie de la Matière Condensée de Paris, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Samuel I Stupp
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.; Department of Materials and Science & Engineering; Department of Chemistry; Department of Biomedical Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States; Department of Medicine, Northwestern University, 676 North St. Clair Street, Chicago, Illinois 60611, United States
| | - Carole Aimé
- Sorbonne Université, CNRS, Collège de France, Laboratoire de Chimie de la Matière Condensée de Paris, 4 place Jussieu, 75252 Paris cedex 05, France.
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Karagöz Z, Rijns L, Dankers PY, van Griensven M, Carlier A. Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks. Comput Struct Biotechnol J 2020; 19:303-314. [PMID: 33425258 PMCID: PMC7779863 DOI: 10.1016/j.csbj.2020.12.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The interactions between cells and their extracellular matrix (ECM) are critically important for homeostatic control of cell growth, proliferation, differentiation and apoptosis. Transmembrane integrin molecules facilitate the communication between ECM and the cell. Since the characterization of integrins in the late 1980s, there has been great advancement in understanding the function of integrins at different subcellular levels. However, the versatility in molecular pathways integrins are involved in, the high diversity in their interaction partners both outside and inside the cell as well as on the cell membrane and the short lifetime of events happening at the cell-ECM interface make it difficult to elucidate all the details regarding integrin function experimentally. To overcome the experimental challenges and advance the understanding of integrin biology, computational modeling tools have been used extensively. In this review, we summarize the computational models of integrin signaling while we explain the function of integrins at three main subcellular levels (outside the cell, cell membrane, cytosol). We also discuss how these computational modeling efforts can be helpful in other disciplines such as biomaterial design. As such, this review is a didactic modeling summary for biomaterial researchers interested in complementing their experimental work with computational tools or for seasoned computational scientists that would like to advance current in silico integrin models.
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Affiliation(s)
- Zeynep Karagöz
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - Laura Rijns
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands
| | - Patricia Y.W. Dankers
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands
| | - Martijn van Griensven
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - Aurélie Carlier
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
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Wang W, Arias DS, Deserno M, Ren X, Taylor RE. Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng 2020; 4:041507. [PMID: 33344875 PMCID: PMC7725538 DOI: 10.1063/5.0027022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
DNA nanotechnology has proven exceptionally apt at probing and manipulating biological environments as it can create nanostructures of almost arbitrary shape that permit countless types of modifications, all while being inherently biocompatible. Emergent areas of particular interest are applications involving cellular membranes, but to fully explore the range of possibilities requires interdisciplinary knowledge of DNA nanotechnology, cell and membrane biology, and biophysics. In this review, we aim for a concise introduction to the intersection of these three fields. After briefly revisiting DNA nanotechnology, as well as the biological and mechanical properties of lipid bilayers and cellular membranes, we summarize strategies to mediate interactions between membranes and DNA nanostructures, with a focus on programmed delivery onto, into, and through lipid membranes. We also highlight emerging applications, including membrane sculpting, multicell self-assembly, spatial arrangement and organization of ligands and proteins, biomechanical sensing, synthetic DNA nanopores, biological imaging, and biomelecular sensing. Many critical but exciting challenges lie ahead, and we outline what strikes us as promising directions when translating DNA nanostructures for future in vitro and in vivo membrane applications.
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Affiliation(s)
- Weitao Wang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - D. Sebastian Arias
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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40
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Maynard SA, Winter CW, Cunnane EM, Stevens MM. Advancing Cell-Instructive Biomaterials Through Increased Understanding of Cell Receptor Spacing and Material Surface Functionalization. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2020; 7:553-547. [PMID: 34805482 PMCID: PMC8594271 DOI: 10.1007/s40883-020-00180-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract Regenerative medicine is aimed at restoring normal tissue function and can benefit from the application of tissue engineering and nano-therapeutics. In order for regenerative therapies to be effective, the spatiotemporal integration of tissue-engineered scaffolds by the native tissue, and the binding/release of therapeutic payloads by nano-materials, must be tightly controlled at the nanoscale in order to direct cell fate. However, due to a lack of insight regarding cell–material interactions at the nanoscale and subsequent downstream signaling, the clinical translation of regenerative therapies is limited due to poor material integration, rapid clearance, and complications such as graft-versus-host disease. This review paper is intended to outline our current understanding of cell–material interactions with the aim of highlighting potential areas for knowledge advancement or application in the field of regenerative medicine. This is achieved by reviewing the nanoscale organization of key cell surface receptors, the current techniques used to control the presentation of cell-interactive molecules on material surfaces, and the most advanced techniques for characterizing the interactions that occur between cell surface receptors and materials intended for use in regenerative medicine. Lay Summary The combination of biology, chemistry, materials science, and imaging technology affords exciting opportunities to better diagnose and treat a wide range of diseases. Recent advances in imaging technologies have enabled better understanding of the specific interactions that occur between human cells and their immediate surroundings in both health and disease. This biological understanding can be used to design smart therapies and tissue replacements that better mimic native tissue. Here, we discuss the advances in molecular biology and technologies that can be employed to functionalize materials and characterize their interaction with biological entities to facilitate the design of more sophisticated medical therapies.
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Affiliation(s)
- Stephanie A. Maynard
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ UK
| | - Charles W. Winter
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ UK
| | - Eoghan M. Cunnane
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ UK
| | - Molly M. Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ UK
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41
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Zhang Z, Ma J, Zhang G, Ding X, Zhang R, Zhou T, Wang X, Wang F. Large-Scale DNA Nanoarrays with a Controllable Fluorescence Switch Constructed by RCA Simplified Origami. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10989-10995. [PMID: 32838532 DOI: 10.1021/acs.langmuir.0c01821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The manufacture of large-scale and highly ordered fluorescent assemblies has received more and more scientific attention in recent years. An ingenious and low-cost strategy for constructing large-scale DNA nanoarrays by rolling circle amplification (RCA) and a simplified DNA origami technique is proposed in this study. Thrombins are used to trigger the excitation of the fluorescent groups modified on the aptamer staple strands of nanoladders, which leads to the delicate construction of millimeter large-scale fluorescent nanoarrays, whose fluorescence intensity could be effectively regulated by the concentration of thrombin. The above fluorescent nanoarrays will generate a potential application value in the fields of biosensors, super-resolution imaging, and novel light-emitting devices.
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Affiliation(s)
- Zhiqing Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jie Ma
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Guodong Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiaoyan Ding
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ruyan Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ting Zhou
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiufeng Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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42
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Hawkes W, Huang D, Reynolds P, Hammond L, Ward M, Gadegaard N, Marshall JF, Iskratsch T, Palma M. Probing the nanoscale organisation and multivalency of cell surface receptors: DNA origami nanoarrays for cellular studies with single-molecule control. Faraday Discuss 2020; 219:203-219. [PMID: 31314021 DOI: 10.1039/c9fd00023b] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nanoscale organisation of receptor ligands has become an important approach to study the clustering behaviour of cell-surface receptors. Biomimetic substrates fabricated via different nanopatterning strategies have so far been applied to investigate specific integrins and cell types, but without multivalent control. Here we use DNA origami to surpass the limits of current approaches and fabricate nanoarrays to study different cell adhesion processes, with nanoscale spatial resolution and single-molecule control. Notably, DNA nanostructures enable the display of receptor ligands in a highly customisable manner, with modifiable parameters including ligand number, ligand spacing and most importantly, multivalency. To test the adaptability and robustness of the system we combined it with focused ion beam and electron-beam lithography nanopatterning to additionally control the distance between the origami structures (i.e. receptor clusters). Moreover, we demonstrate how the platform can be used to interrogate two different biological questions: (1) the cooperative effect of integrin and growth factor receptor in cancer cell spreading, and (2) the role of integrin clustering in cardiomyocyte adhesion and maturation. Thereby we find previously unknown clustering behaviour of different integrins, further outlining the importance for such customisable platforms for future investigations of specific receptor organisation at the nanoscale.
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Affiliation(s)
- William Hawkes
- Randall Centre of Cell and Molecular Biophysics, King's College London, UK
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43
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Xin Y, Kielar C, Zhu S, Sikeler C, Xu X, Möser C, Grundmeier G, Liedl T, Heuer-Jungemann A, Smith DM, Keller A. Cryopreservation of DNA Origami Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905959. [PMID: 32130783 DOI: 10.1002/smll.201905959] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Although DNA origami nanostructures have found their way into numerous fields of fundamental and applied research, they often suffer from rather limited stability when subjected to environments that differ from the employed assembly conditions, that is, suspended in Mg2+ -containing buffer at moderate temperatures. Here, means for efficient cryopreservation of 2D and 3D DNA origami nanostructures and, in particular, the effect of repeated freezing and thawing cycles are investigated. It is found that, while the 2D DNA origami nanostructures maintain their structural integrity over at least 32 freeze-thaw cycles, ice crystal formation makes the DNA origami gradually more sensitive toward harsh sample treatment conditions. Whereas no freeze damage could be detected in 3D DNA origami nanostructures subjected to 32 freeze-thaw cycles, 1000 freeze-thaw cycles result in significant fragmentation. The cryoprotectants glycerol and trehalose are found to efficiently protect the DNA origami nanostructures against freeze damage at concentrations between 0.2 × 10-3 and 200 × 10-3 m and without any negative effects on DNA origami shape. This work thus provides a basis for the long-term storage of DNA origami nanostructures, which is an important prerequisite for various technological and medical applications.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Christoph Sikeler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Christin Möser
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103, Leipzig, Germany
- Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476, Potsdam, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Amelie Heuer-Jungemann
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - David M Smith
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103, Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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Modulating Tumor Cell Functions by Tunable Nanopatterned Ligand Presentation. NANOMATERIALS 2020; 10:nano10020212. [PMID: 31991896 PMCID: PMC7074906 DOI: 10.3390/nano10020212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022]
Abstract
Cancer comprises a large group of complex diseases which arise from the misrouted interplay of mutated cells with other cells and the extracellular matrix. The extracellular matrix is a highly dynamic structure providing biochemical and biophysical cues that regulate tumor cell behavior. While the relevance of biochemical signals has been appreciated, the complex input of biophysical properties like the variation of ligand density and distribution is a relatively new field in cancer research. Nanotechnology has become a very promising tool to mimic the physiological dimension of biophysical signals and their positive (i.e., growth-promoting) and negative (i.e., anti-tumoral or cytotoxic) effects on cellular functions. Here, we review tumor-associated cellular functions such as proliferation, epithelial-mesenchymal transition (EMT), invasion, and phenotype switch that are regulated by biophysical parameters such as ligand density or substrate elasticity. We also address the question of how such factors exert inhibitory or even toxic effects upon tumor cells. We describe three principles of nanostructured model systems based on block copolymer nanolithography, electron beam lithography, and DNA origami that have contributed to our understanding of how biophysical signals direct cancer cell fate.
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45
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Yeldell SB, Seitz O. Nucleic acid constructs for the interrogation of multivalent protein interactions. Chem Soc Rev 2020; 49:6848-6865. [DOI: 10.1039/d0cs00518e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence-programmed self-assembly provides multivalent nucleic acid–ligand constructs used as tailor-made probes for unravelling and exploiting the mechanisms of multivalency-enhanced interactions on protein receptors.
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Affiliation(s)
- Sean B. Yeldell
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
| | - Oliver Seitz
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
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46
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Mishra S, Feng Y, Endo M, Sugiyama H. Advances in DNA Origami–Cell Interfaces. Chembiochem 2019; 21:33-44. [DOI: 10.1002/cbic.201900481] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Shubham Mishra
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Yihong Feng
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Masayuki Endo
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
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47
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Jahanban-Esfahlan R, Seidi K, Jahanban-Esfahlan A, Jaymand M, Alizadeh E, Majdi H, Najjar R, Javaheri T, Zare P. Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications. Nanotechnol Sci Appl 2019; 12:25-46. [PMID: 31686793 PMCID: PMC6800557 DOI: 10.2147/nsa.s227193] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
Among the various nano/biomaterials used in cancer treatment, the beauty and benefits of DNA nanocomposites are outstanding. The specificity and programmability of the base pairing of DNA strands, together with their ability to conjugate with different types of functionalities have realized unsurpassed potential for the production of two- and three-dimensional nano-sized structures in any shape, size, surface chemistry and functionality. This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and dendrimer as young but promising platforms for cancer theranostics. The utility and potential of the individual formats in biomedical science and especially in cancer therapy will be discussed.
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Affiliation(s)
- Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center (NDDRC), Kermanshah University of Medical Sciences, Kermanshah9883, Iran
| | - Effat Alizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Hasan Majdi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Reza Najjar
- Polymer Research Laboratory, Faculty of Chemistry, University of Tabriz, Tabriz9841, Iran
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, Vienna1090, Austria
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw01-938, Poland
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48
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Wang W, Yu S, Huang S, Bi S, Han H, Zhang JR, Lu Y, Zhu JJ. Bioapplications of DNA nanotechnology at the solid-liquid interface. Chem Soc Rev 2019; 48:4892-4920. [PMID: 31402369 PMCID: PMC6746594 DOI: 10.1039/c8cs00402a] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.
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Affiliation(s)
- Wenjing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.
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