1
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Hou Y, Treanor B. DNA origami: Interrogating the nano-landscape of immune receptor activation. Biophys J 2024; 123:2211-2223. [PMID: 37838832 PMCID: PMC11331043 DOI: 10.1016/j.bpj.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
The immune response is orchestrated by elaborate protein interaction networks that interweave ligand-mediated receptor reorganization with signaling cascades. While the biochemical processes have been extensively investigated, delineating the biophysical principles governing immune receptor activation has remained challenging due to design limitations of traditional ligand display platforms. These constraints have been overcome by advances in DNA origami nanotechnology, enabling unprecedented control over ligand geometry on configurable scaffolds. It is now possible to systematically dissect the independent roles of ligand stoichiometry, spatial distribution, and rigidity in immune receptor activation, signaling, and cooperativity. In this review, we highlight pioneering efforts in manipulating the ligand presentation landscape to understand immune receptor triggering and to engineer functional immune responses.
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Affiliation(s)
- Yuchen Hou
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario.
| | - Bebhinn Treanor
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario; Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario; Department of Immunology, University of Toronto, Toronto, Ontario.
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2
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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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3
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Li Z, Wang J, O’Hagan MP, Huang F, Xia F, Willner I. Dynamic Fusion of Nucleic Acid Functionalized Nano-/Micro-Cell-Like Containments: From Basic Concepts to Applications. ACS NANO 2023; 17:15308-15327. [PMID: 37549398 PMCID: PMC10448756 DOI: 10.1021/acsnano.3c04415] [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: 05/17/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.
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Affiliation(s)
- Zhenzhen Li
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael P. O’Hagan
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, People’s Republic of China
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, People’s Republic of China
| | - Itamar Willner
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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4
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Joshi H, Li CY, Aksimentiev A. All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores. Methods Mol Biol 2023; 2639:113-128. [PMID: 37166714 DOI: 10.1007/978-1-0716-3028-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.
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Affiliation(s)
- Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Chen-Yu Li
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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5
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Khmelinskaia A, Schwille P, Franquelim HG. Binding and Characterization of DNA Origami Nanostructures on Lipid Membranes. Methods Mol Biol 2023; 2639:231-255. [PMID: 37166721 DOI: 10.1007/978-1-0716-3028-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA origami is an extremely versatile nanoengineering tool with widespread applicability in various fields of research, including membrane physiology and biophysics. The possibility to easily modify DNA strands with lipophilic moieties enabled the recent development of a variety of membrane-active DNA origami devices. Biological membranes, as the core barriers of the cells, display vital structural and functional roles. Therefore, lipid bilayers are widely popular targets of DNA origami nanotechnology for synthetic biology and biomedical applications. In this chapter, we summarize the typical experimental methods used to investigate the interaction of DNA origami with synthetic membrane models. Herein, we present detailed protocols for the production of lipid model membranes and characterization of membrane-targeted DNA origami nanostructures using different microscopy approaches.
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Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry, Munich, Germany
- Institute of Protein Design, University of Washington, Seattle, WA, USA
- Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | | | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Munich, Germany.
- Interfaculty Centre for Bioactive Matter (b-ACTmatter), Leipzig University, Leipzig, Germany.
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6
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Liu L, Xiong Q, Xie C, Pincet F, Lin C. Actuating tension-loaded DNA clamps drives membrane tubulation. SCIENCE ADVANCES 2022; 8:eadd1830. [PMID: 36223466 PMCID: PMC9555772 DOI: 10.1126/sciadv.add1830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Membrane dynamics in living organisms can arise from proteins adhering to, assembling on, and exerting force on cell membranes. Programmable synthetic materials, such as self-assembled DNA nanostructures, offer the capability to drive membrane-remodeling events that resemble protein-mediated dynamics but with user-defined outcomes. An illustrative example is the tubular deformation of liposomes by DNA nanostructures with purposely designed shapes, surface modifications, and self-assembling properties. However, stimulus-responsive membrane tubulation mediated by DNA reconfiguration remains challenging. Here, we present the triggered formation of membrane tubes in response to specific DNA signals that actuate membrane-bound DNA clamps from an open state to various predefined closed states, releasing prestored energy to activate membrane deformation. We show that the timing and efficiency of vesicle tubulation, as well as the membrane tube widths, are modulated by the conformational change of DNA clamps, marking a solid step toward spatiotemporal control of membrane dynamics in an artificial system.
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Affiliation(s)
- Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chun Xie
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Laboratoire de Physique de l’Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
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7
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Paez-Perez M, Russell IA, Cicuta P, Di Michele L. Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition. SOFT MATTER 2022; 18:7035-7044. [PMID: 36000473 PMCID: PMC9516350 DOI: 10.1039/d2sm00863g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Membrane fusion is a ubiquitous phenomenon linked to many biological processes, and represents a crucial step in liposome-based drug delivery strategies. The ability to control, ever more precisely, membrane fusion pathways would thus be highly valuable for next generation nano-medical solutions and, more generally, the design of advanced biomimetic systems such as synthetic cells. In this article, we present fusogenic nanostructures constructed from synthetic DNA which, different from previous solutions, unlock routes for modulating the rate of fusion and making it conditional to the presence of soluble DNA molecules, thus demonstrating how membrane fusion can be controlled through simple DNA-based molecular circuits. We then systematically explore the relationship between lipid-membrane composition, its biophysical properties, and measured fusion efficiency, linking our observations to the stability of transition states in the fusion pathway. Finally, we observe that specific lipid compositions lead to the emergence of complex bilayer architectures in the fusion products, such as nested morphologies, which are accompanied by alterations in biophysical behaviour. Our findings provide multiple, orthogonal strategies to program lipid-membrane fusion, which leverage the design of either the fusogenic DNA constructs or the physico/chemical properties of the membranes, and could thus be valuable in applications where some design parameters are constrained by other factors such as material cost and biocompatibility, as it is often the case in biotechnological applications.
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Affiliation(s)
- Miguel Paez-Perez
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.
- fabriCELL, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.
- fabriCELL, Imperial College London, Wood Lane, London, W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
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8
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Baumann KN, Schröder T, Ciryam PS, Morzy D, Tinnefeld P, Knowles TPJ, Hernández-Ainsa S. DNA-Liposome Hybrid Carriers for Triggered Cargo Release. ACS APPLIED BIO MATERIALS 2022; 5:3713-3721. [PMID: 35838663 PMCID: PMC9382633 DOI: 10.1021/acsabm.2c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The design of simple and versatile synthetic routes to
accomplish
triggered-release properties in carriers is of particular interest
for drug delivery purposes. In this context, the programmability and
adaptability of DNA nanoarchitectures in combination with liposomes
have great potential to render biocompatible hybrid carriers for triggered
cargo release. We present an approach to form a DNA mesh on large
unilamellar liposomes incorporating a stimuli-responsive DNA building
block. Upon incubation with a single-stranded DNA trigger sequence,
a hairpin closes, and the DNA building block is allowed to self-contract.
We demonstrate the actuation of this building block by single-molecule
Förster resonance energy transfer (FRET), fluorescence recovery
after photobleaching, and fluorescence quenching measurements. By
triggering this process, we demonstrate the elevated release of the
dye calcein from the DNA–liposome hybrid carriers. Interestingly,
the incubation of the doxorubicin-laden active hybrid carrier with
HEK293T cells suggests increased cytotoxicity relative to a control
carrier without the triggered-release mechanism. In the future, the
trigger could be provided by peritumoral nucleic acid sequences and
lead to site-selective release of encapsulated chemotherapeutics.
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Affiliation(s)
- Kevin N Baumann
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Prashanth S Ciryam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Diana Morzy
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Silvia Hernández-Ainsa
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.,Government of Aragon, ARAID Foundation, Zaragoza 50018, Spain
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9
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Romero-Sanchez IC, Castellano LE, Laurati M. Tuning the Effective Interactions between Spherical Double-Stranded DNA Brushes. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivany C. Romero-Sanchez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, 47150 León, Mexico
- Dipartimento di Chimica & CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy
| | - Laura E. Castellano
- División de Ciencias e Ingenierías, Universidad de Guanajuato, 47150 León, Mexico
| | - Marco Laurati
- Dipartimento di Chimica & CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy
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10
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Suzuki Y, Kawamata I, Watanabe K, Mano E. Lipid bilayer-assisted dynamic self-assembly of hexagonal DNA origami blocks into monolayer crystalline structures with designed geometries. iScience 2022; 25:104292. [PMID: 35573202 PMCID: PMC9097702 DOI: 10.1016/j.isci.2022.104292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/18/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
The DNA origami technique is used to construct custom-shaped nanostructures that can be used as components of two-dimensional crystalline structures with user-defined structural patterns. Here, we designed an Mg2+-responsive hexagonal 3D DNA origami block with self-shape-complementary ruggedness on the sides. Hexagonal DNA origami blocks were electrostatically adsorbed onto a fluidic lipid bilayer membrane surface to ensure lateral diffusion. A subsequent increase in the Mg2+ concentration in the surrounding environment induced the self-assembly of the origami blocks into lattices with prescribed geometries based on a self-complementary shape fit. High-speed atomic force microscopy (HS-AFM) images revealed dynamic events involved in the self-assembly process, including edge reorganization, defect splitting, diffusion, and filling, which provide a glimpse into how the lattice structures are self-improved. Lipid bilayer-assisted self-assembly of 3D DNA origami blocks was achieved Time-lapse AFM imaging of the self-assembly processes was performed Different assembly patterns were achieved from a single DNA origami design
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8578, Japan
- Corresponding author
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kotaro Watanabe
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Eriko Mano
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8578, Japan
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11
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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12
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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13
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Morzy D, Joshi H, Sandler SE, Aksimentiev A, Keyser UF. Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure. NANO LETTERS 2021; 21:9789-9796. [PMID: 34767378 DOI: 10.1021/acs.nanolett.1c03791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improvement. Here, we demonstrate an approach to overcoming the unfavorable DNA-lipid interactions that hinder the formation of a stable transmembrane pore. Our all-atom MD simulations and experiments show that the insertion-driving cholesterol modifications can cause fraying of terminal base pairs of nicked DNA constructs, distorting them when embedded in a lipid bilayer. Importantly, we show that DNA nanostructures with no backbone discontinuities form more stable conductive pores and insert into membranes with a higher efficiency than the equivalent nicked constructs. Moreover, lack of nicks allows design and maintenance of membrane-spanning helices in a tilted orientation within the lipid bilayer. Thus, reducing the conformational degrees of freedom of the DNA nanostructures enables better control over their function as synthetic ion channels.
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Affiliation(s)
- Diana Morzy
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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14
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Maffeis V, Belluati A, Craciun I, Wu D, Novak S, Schoenenberger CA, Palivan CG. Clustering of catalytic nanocompartments for enhancing an extracellular non-native cascade reaction. Chem Sci 2021; 12:12274-12285. [PMID: 34603657 PMCID: PMC8480338 DOI: 10.1039/d1sc04267j] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/14/2021] [Indexed: 01/10/2023] Open
Abstract
Compartmentalization is fundamental in nature, where the spatial segregation of biochemical reactions within and between cells ensures optimal conditions for the regulation of cascade reactions. While the distance between compartments or their interaction are essential parameters supporting the efficiency of bio-reactions, so far they have not been exploited to regulate cascade reactions between bioinspired catalytic nanocompartments. Here, we generate individual catalytic nanocompartments (CNCs) by encapsulating within polymersomes or attaching to their surface enzymes involved in a cascade reaction and then, tether the polymersomes together into clusters. By conjugating complementary DNA strands to the polymersomes' surface, DNA hybridization drove the clusterization process of enzyme-loaded polymersomes and controlled the distance between the respective catalytic nanocompartments. Owing to the close proximity of CNCs within clusters and the overall stability of the cluster architecture, the cascade reaction between spatially segregated enzymes was significantly more efficient than when the catalytic nanocompartments were not linked together by DNA duplexes. Additionally, residual DNA single strands that were not engaged in clustering, allowed for an interaction of the clusters with the cell surface as evidenced by A549 cells, where clusters decorating the surface endowed the cells with a non-native enzymatic cascade. The self-organization into clusters of catalytic nanocompartments confining different enzymes of a cascade reaction allows for a distance control of the reaction spaces which opens new avenues for highly efficient applications in domains such as catalysis or nanomedicine.
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Affiliation(s)
- Viviana Maffeis
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
| | - Andrea Belluati
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Ioana Craciun
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Dalin Wu
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Samantha Novak
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel Mattenstrasse 24a, BPR 1096 4058 Basel Switzerland .,NCCR-Molecular Systems Engineering BPR 1095, Mattenstrasse 24a CH-4058 Basel Switzerland
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15
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Beltrán SM, Slepian MJ, Taylor RE. Extending the Capabilities of Molecular Force Sensors via DNA Nanotechnology. Crit Rev Biomed Eng 2021; 48:1-16. [PMID: 32749116 DOI: 10.1615/critrevbiomedeng.2020033450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
At the nanoscale, pushing, pulling, and shearing forces drive biochemical processes in development and remodeling as well as in wound healing and disease progression. Research in the field of mechanobiology investigates not only how these loads affect biochemical signaling pathways but also how signaling pathways respond to local loading by triggering mechanical changes such as regional stiffening of a tissue. This feedback between mechanical and biochemical signaling is increasingly recognized as fundamental in embryonic development, tissue morphogenesis, cell signaling, and disease pathogenesis. Historically, the interdisciplinary field of mechanobiology has been driven by the development of technologies for measuring and manipulating cellular and molecular forces, with each new tool enabling vast new lines of inquiry. In this review, we discuss recent advances in the manufacturing and capabilities of molecular-scale force and strain sensors. We also demonstrate how DNA nanotechnology has been critical to the enhancement of existing techniques and to the development of unique capabilities for future mechanosensor assembly. DNA is a responsive and programmable building material for sensor fabrication. It enables the systematic interrogation of molecular biomechanics with forces at the 1- to 200-pN scale that are needed to elucidate the fundamental means by which cells and proteins transduce mechanical signals.
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Affiliation(s)
- Susana M Beltrán
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Marvin J Slepian
- Department of Medicine and Sarver Heart Center, University of Arizona, Tucson; Department of Biomedical Engineering, University of Arizona, Tucson; Department of Materials Science and Engineering, University of Arizona, Tucson
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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16
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Responsive core-shell DNA particles trigger lipid-membrane disruption and bacteria entrapment. Nat Commun 2021; 12:4743. [PMID: 34362911 PMCID: PMC8346484 DOI: 10.1038/s41467-021-24989-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
Biology has evolved a variety of agents capable of permeabilizing and disrupting lipid membranes, from amyloid aggregates, to antimicrobial peptides, to venom compounds. While often associated with disease or toxicity, these agents are also central to many biosensing and therapeutic technologies. Here, we introduce a class of synthetic, DNA-based particles capable of disrupting lipid membranes. The particles have finely programmable size, and self-assemble from all-DNA and cholesterol-DNA nanostructures, the latter forming a membrane-adhesive core and the former a protective hydrophilic corona. We show that the corona can be selectively displaced with a molecular cue, exposing the 'sticky' core. Unprotected particles adhere to synthetic lipid vesicles, which in turn enhances membrane permeability and leads to vesicle collapse. Furthermore, particle-particle coalescence leads to the formation of gel-like DNA aggregates that envelop surviving vesicles. This response is reminiscent of pathogen immobilisation through immune cells secretion of DNA networks, as we demonstrate by trapping E. coli bacteria.
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17
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Sabir F, Zeeshan M, Laraib U, Barani M, Rahdar A, Cucchiarini M, Pandey S. DNA Based and Stimuli-Responsive Smart Nanocarrier for Diagnosis and Treatment of Cancer: Applications and Challenges. Cancers (Basel) 2021; 13:3396. [PMID: 34298610 PMCID: PMC8307033 DOI: 10.3390/cancers13143396] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/19/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
The rapid development of multidrug co-delivery and nano-medicines has made spontaneous progress in tumor treatment and diagnosis. DNA is a unique biological molecule that can be tailored and molded into various nanostructures. The addition of ligands or stimuli-responsive elements enables DNA nanostructures to mediate highly targeted drug delivery to the cancer cells. Smart DNA nanostructures, owing to their various shapes, sizes, geometry, sequences, and characteristics, have various modes of cellular internalization and final disposition. On the other hand, functionalized DNA nanocarriers have specific receptor-mediated uptake, and most of these ligand anchored nanostructures able to escape lysosomal degradation. DNA-based and stimuli responsive nano-carrier systems are the latest advancement in cancer targeting. The data exploration from various studies demonstrated that the DNA nanostructure and stimuli responsive drug delivery systems are perfect tools to overcome the problems existing in the cancer treatment including toxicity and compromised drug efficacy. In this light, the review summarized the insights about various types of DNA nanostructures and stimuli responsive nanocarrier systems applications for diagnosis and treatment of cancer.
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Affiliation(s)
- Fakhara Sabir
- Faculty of Pharmacy, Institute of Pharmaceutical Technology and Regulatory Affairs, University of Szeged, Eötvös u. 6, H-6720 Szeged, Hungary;
| | - Mahira Zeeshan
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Ushna Laraib
- Department of Pharmacy, College of Pharmacy, University of Sargodha, Sargodha 40100, Pakistan;
| | - Mahmood Barani
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman 76169-13555, Iran;
| | - Abbas Rahdar
- Department of Physics, Faculty of Science, University of Zabol, Zabol 98615-538, Iran;
| | - Magali Cucchiarini
- Center of Experimental Orthopaedics, Saarland University Medical Center, 66421 Homburg, Germany
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Science, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Korea
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18
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Jones S, Joshi H, Terry SJ, Burns JR, Aksimentiev A, Eggert US, Howorka S. Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes. J Am Chem Soc 2021; 143:8305-8313. [PMID: 34015219 PMCID: PMC8193631 DOI: 10.1021/jacs.0c13235] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA-membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures.
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Affiliation(s)
- Sioned
F. Jones
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
| | - Himanshu Joshi
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen J. Terry
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
- UCL
Ear Institute, London WC1X 8EE, United Kingdom
| | - Jonathan R. Burns
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Aleksei Aksimentiev
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ulrike S. Eggert
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
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19
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Zuraw-Weston SE, Siavashpouri M, Moustaka ME, Gerling T, Dietz H, Fraden S, Ribbe AE, Dinsmore AD. Membrane Remodeling by DNA Origami Nanorods: Experiments Exploring the Parameter Space for Vesicle Remodeling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6219-6231. [PMID: 33983740 DOI: 10.1021/acs.langmuir.1c00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Inspired by the ability of cell membranes to alter their shape in response to bound particles, we report an experimental study of long, slender nanorods binding to lipid bilayer vesicles and altering the membrane shape. Our work illuminates the role of particle concentration, adhesion strength, and membrane tension in determining the membrane morphology. We combined giant unilamellar vesicles with oppositely charged nanorods, carefully tuning the adhesion strength, membrane tension, and particle concentration. With increasing adhesion strength, the primary behaviors observed were membrane deformation, vesicle-vesicle adhesion, and vesicle rupture. These behaviors were observed in well-defined regions in the parameter space with sharp transitions between them. We observed the deformation of the membrane resulting in tubulation, textured surfaces, and small and large lipid-particle aggregates. These responses are robust and repeatable and provide a new physical understanding of the dependence on the shape, binding affinity, and particle concentration in membrane remodeling. The design principles derived from these experiments may lead to new bioinspired membrane-based materials.
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Affiliation(s)
- Sarah E Zuraw-Weston
- Department of Physics, University of Massachusetts Amherst, Hasbrouck Lab, 666 North Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Mahsa Siavashpouri
- Department of Physics, Brandeis University, Abelson-Bass-Yalem, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Maria E Moustaka
- Department of Physics, Brandeis University, Abelson-Bass-Yalem, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Thomas Gerling
- Department of Physics, Technical University of Munich, James-Franck-Str., 1, Garching D-85748, Germany
| | - Hendrik Dietz
- Department of Physics, Technical University of Munich, James-Franck-Str., 1, Garching D-85748, Germany
| | - Seth Fraden
- Department of Physics, Brandeis University, Abelson-Bass-Yalem, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Alexander E Ribbe
- Department of Polymer Science and Engineering, Silvio O. Conte National Center for Polymer Research, University of Massachusetts Amherst, 120 Governors Drive, Amherst, Massachusetts 01003, United States
| | - Anthony D Dinsmore
- Department of Physics, University of Massachusetts Amherst, Hasbrouck Lab, 666 North Pleasant Street, Amherst, Massachusetts 01002, United States
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20
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Dai Z, Wang L, Wang Z. Functional Immunostimulating DNA Materials: The Rising Stars for Cancer Immunotherapy. Macromol Biosci 2021; 21:e2100083. [PMID: 33896107 DOI: 10.1002/mabi.202100083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/29/2021] [Indexed: 12/13/2022]
Abstract
Cancer immunotherapy has risen as a promising method in clinical practice for cancer treatment and DNA-based immune intervention materials, along with DNA nanotechnology, have obtained increasing importance in this field. In this review, various immunostimulating DNA materials are introduced and the mechanisms via which they exerted an immune effect are explained. Then, representative examples in which DNA is used as the leading component for anticancer applications through immune stimulation are provided and their efficacy is evaluated. Finally, the challenges for those materials in clinical applications are discussed and suggestions for possible further research directions are also put forward.
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Affiliation(s)
- Ziwen Dai
- College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518055, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Lei Wang
- College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518055, China
| | - Zhigang Wang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518055, China
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21
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Jahnke K, Grubmüller H, Igaev M, Göpfrich K. Choice of fluorophore affects dynamic DNA nanostructures. Nucleic Acids Res 2021; 49:4186-4195. [PMID: 33784399 PMCID: PMC8053122 DOI: 10.1093/nar/gkab201] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modelling, we demonstrate for 12 different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation-without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.
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Affiliation(s)
- Kevin Jahnke
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Department of Theoretical and Computational Biophysics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Maxim Igaev
- Max Planck Institute for Biophysical Chemistry, Department of Theoretical and Computational Biophysics, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kerstin Göpfrich
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
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22
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Franquelim HG, Dietz H, Schwille P. Reversible membrane deformations by straight DNA origami filaments. SOFT MATTER 2021; 17:276-287. [PMID: 32406895 DOI: 10.1039/d0sm00150c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membrane-active cytoskeletal elements, such as FtsZ, septin or actin, form filamentous polymers able to induce and stabilize curvature on cellular membranes. In order to emulate the characteristic dynamic self-assembly properties of cytoskeletal subunits in vitro, biomimetic synthetic scaffolds were here developed using DNA origami. In contrast to our earlier work with pre-curved scaffolds, we specifically assessed the potential of origami mimicking straight filaments, such as actin and microtubules, by origami presenting cholesteryl anchors for membrane binding and additional blunt end stacking interactions for controllable polymerization into linear filaments. By assessing the interaction of our DNA nanostructures with model membranes using fluorescence microscopy, we show that filaments can be formed, upon increasing MgCl2 in solution, for structures displaying blunt ends; and can subsequently depolymerize, by decreasing the concentration of MgCl2. Distinctive spike-like membrane protrusions were generated on giant unilamellar vesicles at high membrane-bound filament densities, and the presence of such deformations was reversible and shown to correlate with the MgCl2-triggered polymerization of DNA origami subunits into filamentous aggregates. In the end, our approach reveals the formation of membrane-bound filaments as a minimal requirement for membrane shaping by straight cytoskeletal-like objects.
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Affiliation(s)
| | - Hendrik Dietz
- Technical University of Munich, Garching Near Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried near Munich, Germany.
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23
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Bhatia D, Wunder C, Johannes L. Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications. Chembiochem 2021; 22:763-778. [PMID: 32961015 DOI: 10.1002/cbic.202000372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/19/2020] [Indexed: 12/28/2022]
Abstract
The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.
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Affiliation(s)
- Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, 382330, Gandhinagar, India
| | - Christian Wunder
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
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24
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Rajwar A, Morya V, Kharbanda S, Bhatia D. DNA Nanodevices to Probe and Program Membrane Organization, Dynamics, and Applications. J Membr Biol 2020; 253:577-587. [DOI: 10.1007/s00232-020-00154-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/07/2020] [Indexed: 12/18/2022]
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25
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Dolder N, von Ballmoos C. Bifunctional DNA Duplexes Permit Efficient Incorporation of pH Probes into Liposomes. Chembiochem 2020; 21:2219-2224. [PMID: 32181556 DOI: 10.1002/cbic.202000146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 11/10/2022]
Abstract
Enzyme-mediated proton transport across biological membranes is critical for many vital cellular processes. pH-sensitive fluorescent dyes are an indispensable tool for investigating the molecular mechanism of proton-translocating enzymes. Here, we present a novel strategy to entrap pH-sensitive probes in the lumen of liposomes that has several advantages over the use of soluble or lipid-coupled probes. In our approach, the pH sensor is linked to a DNA oligomer with a sequence complementary to a second oligomer modified with a lipophilic moiety that anchors the DNA conjugate to the inner and outer leaflets of the lipid bilayer. The use of DNA as a scaffold allows subsequent selective enzymatic removal of the probe in the outer bilayer leaflet. The method shows a high yield of insertion and is compatible with reconstitution of membrane proteins by different methods. The usefulness of the conjugate for time-resolved proton pumping measurements was demonstrated by using two large membrane protein complexes.
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Affiliation(s)
- Nicolas Dolder
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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26
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Liu J, Craciun I, Belluati A, Wu D, Sieber S, Einfalt T, Witzigmann D, Chami M, Huwyler J, Palivan CG. DNA-directed arrangement of soft synthetic compartments and their behavior in vitro and in vivo. NANOSCALE 2020; 12:9786-9799. [PMID: 32328600 DOI: 10.1039/d0nr00361a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA has been widely used as a key tether to promote self-organization of super-assemblies with emergent properties. However, control of this process is still challenging for compartment assemblies and to date the resulting assemblies have unstable membranes precluding in vitro and in vivo testing. Here we present our approach to overcome these limitations, by manipulating molecular factors such as compartment membrane composition and DNA surface density, thereby controlling the size and stability of the resulting DNA-linked compartment clusters. The soft, flexible character of the polymer membrane and low number of ssDNA remaining exposed after cluster formation determine the interaction of these clusters with the cell surface. These clusters exhibit in vivo stability and lack of toxicity in a zebrafish model. To display the breadth of therapeutic applications attainable with our system, we encapsulated the medically established enzyme laccase within the inner compartment and demonstrated its activity within the clustered compartments. Most importantly, these clusters can interact selectively with different cell lines, opening a new strategy to modify and expand cellular functions by attaching such pre-organized soft DNA-mediated compartment clusters on cell surfaces for cell engineering or therapeutic applications.
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Affiliation(s)
- Juan Liu
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Ioana Craciun
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Andrea Belluati
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Dalin Wu
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Sandro Sieber
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Tomaz Einfalt
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Dominik Witzigmann
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Mohamed Chami
- BioEM lab, Biozentrum, University of Basel, Mattenstrasse 26, Basel-4058, Switzerland
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
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27
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Shen Q, Grome MW, Yang Y, Lin C. Engineering Lipid Membranes with Programmable DNA Nanostructures. ADVANCED BIOSYSTEMS 2020; 4:1900215. [PMID: 31934608 PMCID: PMC6957268 DOI: 10.1002/adbi.201900215] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/18/2022]
Abstract
Lipid and DNA are abundant biomolecules with critical functions in cells. The water-insoluble, amphipathic lipid molecules are best known for their roles in energy storage (e.g. as triglyceride), signaling (e.g. as sphingolipid), and compartmentalization (e.g. by forming membrane-enclosed bodies). The soluble, highly negatively charged DNA, which stores cells' genetic information, has proven to be an excellent material for constructing programmable nanostructures in vitro thanks to its self-assembling capabilities. These two seemingly distant molecules make contact within cell nuclei, often via lipidated proteins, with proposed functions of modulating chromatin structures. Carefully formulated lipid/DNA complexes are promising reagents for gene therapy. The past few years saw an emerging research field of interfacing DNA nanostructures with lipid membranes, with an overarching goal of generating DNA/lipid hybrid materials that possess novel and controllable structure, dynamics, and function. An arsenal of DNA-based tools has been created to coat, mold, deform, and penetrate lipid bilayers, affording us the ability to manipulate membranes with nanoscopic precision. These membrane engineering methods not only enable quantitative biophysical studies, but also open new opportunities in synthetic biology (e.g. artificial cells) and therapeutics (e.g. drug delivery).
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Affiliation(s)
- Qi Shen
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Michael W Grome
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Yang Yang
- Department of Cell Biology and Nanobiology Institute, Yale University
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chenxiang Lin
- Department of Cell Biology and Nanobiology Institute, Yale University
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28
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Ohmann A, Göpfrich K, Joshi H, Thompson RF, Sobota D, Ranson NA, Aksimentiev A, Keyser UF. Controlling aggregation of cholesterol-modified DNA nanostructures. Nucleic Acids Res 2019; 47:11441-11451. [PMID: 31642494 PMCID: PMC6868430 DOI: 10.1093/nar/gkz914] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022] Open
Abstract
DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure-function relationship of membrane-interfacing DNA constructs - a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.
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Affiliation(s)
- Alexander Ohmann
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Kerstin Göpfrich
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | | | - Diana Sobota
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Neil A Ranson
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
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29
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Jia H, Schwille P. Bottom-up synthetic biology: reconstitution in space and time. Curr Opin Biotechnol 2019; 60:179-187. [DOI: 10.1016/j.copbio.2019.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 05/07/2019] [Indexed: 01/30/2023]
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30
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Grupi A, Ashur I, Degani-Katzav N, Yudovich S, Shapira Z, Marzouq A, Morgenstein L, Mandel Y, Weiss S. Interfacing the Cell with "Biomimetic Membrane Proteins". SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1903006. [PMID: 31765076 DOI: 10.1002/smll.201903006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Integral membrane proteins mediate a myriad of cellular processes and are the target of many therapeutic drugs. Enhancement and extension of the functional scope of membrane proteins can be realized by membrane incorporation of engineered nanoparticles designed for specific diagnostic and therapeutic applications. In contrast to hydrophobic insertion of small amphiphilic molecules, delivery and membrane incorporation of particles on the nanometric scale poses a crucial barrier for technological development. In this perspective, the transformative potential of biomimetic membrane proteins (BMPs), current state of the art, and the barriers that need to be overcome in order to advance the field are discussed.
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Affiliation(s)
- Asaf Grupi
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Idan Ashur
- Agricultural Research Organization, The Volcani Center, Institute of Agricultural Engineering, Rishon LeZion, 7505101, Israel
| | - Nurit Degani-Katzav
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shimon Yudovich
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Zehavit Shapira
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Adan Marzouq
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Lion Morgenstein
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yossi Mandel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- School of Optometry and Vision Science, Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shimon Weiss
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
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31
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DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
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Mognetti BM, Cicuta P, Di Michele L. Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:116601. [PMID: 31370052 DOI: 10.1088/1361-6633/ab37ca] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes where, among other functions, they control cell adhesion, motility and tissue formation. Besides being central to several biological processes, multivalent interactions mediated by reactive linkers confined to deformable substrates underpin the design of synthetic-biological platforms and advanced biomimetic materials. Here we review recent advances on the experimental study and theoretical modelling of a heterogeneous class of biomimetic systems in which synthetic linkers mediate multivalent interactions between fluid and deformable colloidal units, including lipid vesicles and emulsion droplets. Linkers are often prepared from synthetic DNA nanostructures, enabling full programmability of the thermodynamic and kinetic properties of their mutual interactions. The coupling of the statistical effects of multivalent interactions with substrate fluidity and deformability gives rise to a rich emerging phenomenology that, in the context of self-assembled soft materials, has been shown to produce exotic phase behaviour, stimuli-responsiveness, and kinetic programmability of the self-assembly process. Applications to (synthetic) biology will also be reviewed.
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Affiliation(s)
- Bortolo Matteo Mognetti
- Université libre de Bruxelles (ULB), Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Campus Plaine, CP 231, Blvd. du Triomphe, B-1050 Brussels, Belgium
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33
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Artificial cells containing sustainable energy conversion engines. Emerg Top Life Sci 2019; 3:573-578. [DOI: 10.1042/etls20190103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 11/17/2022]
Abstract
Living cells naturally maintain a variety of metabolic reactions via energy conversion mechanisms that are coupled to proton transfer across cell membranes, thereby producing energy-rich compounds. Until now, researchers have been unable to maintain continuous biochemical reactions in artificially engineered cells, mainly due to the lack of mechanisms that generate energy-rich resources, such as adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide (NADH). If these metabolic activities in artificial cells are to be sustained, reliable energy transduction strategies must be realized. In this perspective, this article discusses the development of an artificially engineered cell containing a sustainable energy conversion process.
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34
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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35
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Shen H, Wang Y, Wang J, Li Z, Yuan Q. Emerging Biomimetic Applications of DNA Nanotechnology. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13859-13873. [PMID: 29939004 DOI: 10.1021/acsami.8b06175] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Re-engineering cellular components and biological processes has received great interest and promised compelling advantages in applications ranging from basic cell biology to biomedicine. With the advent of DNA nanotechnology, the programmable self-assembly ability makes DNA an appealing candidate for rational design of artificial components with different structures and functions. This Forum Article summarizes recent developments of DNA nanotechnology in mimicking the structures and functions of existing cellular components. We highlight key successes in the achievements of DNA-based biomimetic membrane proteins and discuss the assembly behavior of these artificial proteins. Then, we focus on the construction of higher-order structures by DNA nanotechnology to recreate cell-like structures. Finally, we explore the current challenges and speculate on future directions of DNA nanotechnology in biomimetics.
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Affiliation(s)
- Haijing Shen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Yingqian Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
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36
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Kaufhold WT, Brady RA, Tuffnell JM, Cicuta P, Di Michele L. Membrane Scaffolds Enhance the Responsiveness and Stability of DNA-Based Sensing Circuits. Bioconjug Chem 2019; 30:1850-1859. [PMID: 30865433 DOI: 10.1021/acs.bioconjchem.9b00080] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Will T. Kaufhold
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ryan A. Brady
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Joshua M. Tuffnell
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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37
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Lanfranco R, Jana PK, Tunesi L, Cicuta P, Mognetti BM, Di Michele L, Bruylants G. Kinetics of Nanoparticle-Membrane Adhesion Mediated by Multivalent Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2002-2012. [PMID: 30636419 DOI: 10.1021/acs.langmuir.8b02707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multivalent adhesive interactions mediated by a large number of ligands and receptors underpin many biological processes, including cell adhesion and the uptake of particles, viruses, parasites, and nanomedical vectors. In materials science, multivalent interactions between colloidal particles have enabled unprecedented control over the phase behavior of self-assembled materials. Theoretical and experimental studies have pinpointed the relationship between equilibrium states and microscopic system parameters such as the ligand-receptor binding strength and their density. In regimes of strong interactions, however, kinetic factors are expected to slow down equilibration and lead to the emergence of long-lived out-of-equilibrium states that may significantly influence the outcome of self-assembly experiments and the adhesion of particles to biological membranes. Here we experimentally investigate the kinetics of adhesion of nanoparticles to biomimetic lipid membranes. Multivalent interactions are reproduced by strongly interacting DNA constructs, playing the role of both ligands and receptors. The rate of nanoparticle adhesion is investigated as a function of the surface density of membrane-anchored receptors and the bulk concentration of nanoparticles and is observed to decrease substantially in regimes where the number of available receptors is limited compared to the overall number of ligands. We attribute such peculiar behavior to the rapid sequestration of available receptors after initial nanoparticle adsorption. The experimental trends and the proposed interpretation are supported by numerical simulations.
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Affiliation(s)
- Roberta Lanfranco
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
- Université Libre de Bruxelles (ULB) , Engineering of Molecular NanoSystems , 50 av. F.D. Roosevelt , 1050 Brussels , Belgium
| | - Pritam Kumar Jana
- Université Libre de Bruxelles (ULB) , Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Campus Plaine , CP 231, Blvd. du Triomphe , B-1050 Brussels , Belgium
| | - Lucia Tunesi
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Bortolo Matteo Mognetti
- Université Libre de Bruxelles (ULB) , Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Campus Plaine , CP 231, Blvd. du Triomphe , B-1050 Brussels , Belgium
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Gilles Bruylants
- Université Libre de Bruxelles (ULB) , Engineering of Molecular NanoSystems , 50 av. F.D. Roosevelt , 1050 Brussels , Belgium
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38
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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39
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Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF. Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions. J Am Chem Soc 2018; 141:1100-1108. [DOI: 10.1021/jacs.8b11898] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Dillon McCarthy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Xin Luo
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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40
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Wu N, Chen F, Zhao Y, Yu X, Wei J, Zhao Y. Functional and Biomimetic DNA Nanostructures on Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14721-14730. [PMID: 30044097 DOI: 10.1021/acs.langmuir.8b01818] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sophisticated and dynamic membrane-anchored DNA nanostructures were developed to mimic a variety of membrane proteins, which play crucial roles in cellular functions. DNA biomimetic constructions bound on membranes are capable of modulating the morphologies, physical properties, and functions of lipid membranes, via mobility on membranes and/or inherent architectural features. This inspired young field of DNA-lipid-based nanobiomimetic systems is on the foundation of DNA nanotechnology. In this review, we highlight key successes in the development of structural DNA nanotechnology and demonstrate some typical static and dynamic complex DNA nanostructures first. Then, we discuss the biophysical properties of lipid membranes. Primary approaches are shown to attach hydrophilic DNA to hydrophobic lipid membranes. With appropriate designs, membrane-floating DNA nanostructures assemble and disassemble on membranes, modulated by external stimuluses. The aggregation of DNA nanostructures could influence the physical properties of lipid membranes. We also summarize artificial nanochannels made of DNA, analogous to transmembrane proteins. Transformations of DNA nanopores might be achieved under certain conditions and realize the transport of small molecules across membranes. Next, we focus on membrane-shaping functions of membrane-anchored DNA nanostructures. Curvature of the membrane is closely related to the rich diversity of cellular functions. Mimicking membrane-sculpting proteins, such as BAR family domains and SNARE proteins etc., DNA biomimetic nanostructures induce the transformations of lipid membranes and modulate membrane adhesion and membrane fusion processes. Although recent studies in DNA nanostructure-lipid membrane biomimetic nanosystems have made great progress, this field is still facing many challenges. In the future, the designs of more elaborated DNA architectures will be explored. Sophisticated dynamic DNA nanostructures inspired by natural membrane machines will be driven by the synergistic effect of multiple interactions, including hydrophobic force, electrostatic force, and ligand-receptor interactions by chemical modifications on bases, to expand their applications in vivo from model membrane to cell membrane to karyotheca.
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Affiliation(s)
- Na Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Xu Yu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
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41
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Khmelinskaia A, Mücksch J, Petrov EP, Franquelim HG, Schwille P. Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14921-14931. [PMID: 30253101 DOI: 10.1021/acs.langmuir.8b01850] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA origami nanotechnology is being increasingly used to mimic membrane-associated biophysical phenomena. Although a variety of DNA origami nanostructures has already been produced to target lipid membranes, the requirements for membrane binding have so far not been systematically assessed. Here, we used a set of elongated DNA origami structures with varying placement and number of cholesteryl-based membrane anchors to compare different strategies for their incorporation. Single and multiple cholesteryl anchors were attached to DNA nanostructures using single- and double-stranded DNA spacers of varying length. The produced DNA nanostructures were studied in terms of their membrane binding and diffusion. Our results show that the location and number of anchoring moieties play a crucial role for membrane binding of DNA nanostructures mainly if the cholesteryl anchors are in close proximity to the bulky DNA nanostructures. Moreover, the use of DNA spacers largely overcomes local steric hindrances and thus enhances membrane binding. Fluorescence correlation spectroscopy measurements demonstrate that the distinct physical properties of single- and double-stranded DNA spacers control the interaction of the amphipathic DNA nanostructures with lipid membranes. Thus, we provide a rational basis for the design of amphipathic DNA origami nanostructures to efficiently bind lipid membranes in various environments.
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Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Eugene P Petrov
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
- Faculty of Physics , Ludwig Maximilian University of Munich , Geschwister-Scholl-Platz 1 , 80539 Munich , Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
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42
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Yewdall NA, Mason AF, van Hest JCM. The hallmarks of living systems: towards creating artificial cells. Interface Focus 2018; 8:20180023. [PMID: 30443324 PMCID: PMC6227776 DOI: 10.1098/rsfs.2018.0023] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 01/01/2023] Open
Abstract
Despite the astonishing diversity and complexity of living systems, they all share five common hallmarks: compartmentalization, growth and division, information processing, energy transduction and adaptability. In this review, we give not only examples of how cells satisfy these requirements for life and the ways in which it is possible to emulate these characteristics in engineered platforms, but also the gaps that remain to be bridged. The bottom-up synthesis of life-like systems continues to be driven forward by the advent of new technologies, by the discovery of biological phenomena through their transplantation to experimentally simpler constructs and by providing insights into one of the oldest questions posed by mankind, the origin of life on Earth.
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Affiliation(s)
| | | | - Jan C. M. van Hest
- Eindhoven University of Technology, PO Box 513 (STO 3.31), Eindhoven, MB, The Netherlands
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43
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Whitfield CJ, Little RC, Khan K, Ijiro K, Connolly BA, Tuite EM, Pike AR. Self-Priming Enzymatic Fabrication of Multiply Modified DNA. Chemistry 2018; 24:15267-15274. [PMID: 29931815 DOI: 10.1002/chem.201801976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/19/2018] [Indexed: 12/15/2022]
Abstract
The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex "oligoseeds" provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC]5 /[GATC]5 and [A4 G]4 /[CT4 ]4 . The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing). Nucleobase modifications that lie in the major groove were reliably read and written by the polymerase during the extension reaction, even when bulky or in contiguous sequences. Repeat sequence DNA over 500 bp long, bearing four different modified units was produced by this method. The number, position and type of modification, as well as the overall length of the DNA can be controlled to yield designer DNA that offers sequence-determined sites for further chemical adaptations, targeted small molecule binding studies, or sensing and sequencing applications.
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Affiliation(s)
- Colette J Whitfield
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Rachel C Little
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kasid Khan
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kuniharu Ijiro
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Bernard A Connolly
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Eimer M Tuite
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew R Pike
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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Biswas KH, Cho NJ, Groves JT. Fabrication of Multicomponent, Spatially Segregated DNA and Protein-Functionalized Supported Membrane Microarray. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9781-9788. [PMID: 30032610 DOI: 10.1021/acs.langmuir.8b01364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Deoxyribonucleic acid (DNA) has been used as a material for a variety of applications, including surface functionalization for cell biological or in vitro reconstitution studies. Use of DNA-based surface functionalization eliminates limitations of multiplexing posed by traditionally used methods in applications requiring spatially segregated surface functionalization. Recently, we have reported a stochastic, membrane fusion-based strategy to fabricate multicomponent membrane array substrates displaying spatially segregated protein ligands using biotin-streptavidin and Ni-NTA-polyhistidine interactions. Here, we report the delivery of DNA oligonucleotide-conjugated lipid molecules to membrane corrals, allowing spatially segregated membrane corral functionalization in a membrane microarray. Incubation of microbeads coated with the supported membrane resulted in an exchange of lipid contents with planar membrane corrals present on a micropatterned substrate. Increases in the system temperature and membrane corral size resulted in alterations in the rate constant of lipid exchange, which are in agreement with our previously developed analytical model and further confirm that lipid exchange is a diffusion-based process that takes place after the formation of a long "fusion-stalk" between the two membranes. We take advantage of the physical dimensions of the fusion-stalk with a large aspect ratio to deliver DNA oligonucleotide-conjugated lipid molecules to membrane corrals. We believe that the ability to functionalize membrane corrals with DNA oligonucleotides significantly increases the utility of the stochastic fusion-mediated lipid delivery strategy in the functionalization of biomolecules such as DNA or DNA-conjugated protein ligands.
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Affiliation(s)
- Kabir H Biswas
- Mechanobiology Institute , National University of Singapore , Singapore 117411 , Singapore
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798 , Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798 , Singapore
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive , Singapore 637459 , Singapore
| | - Jay T Groves
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798 , Singapore
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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Chidchob P, Sleiman HF. Recent advances in DNA nanotechnology. Curr Opin Chem Biol 2018; 46:63-70. [PMID: 29751162 DOI: 10.1016/j.cbpa.2018.04.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/14/2018] [Accepted: 04/20/2018] [Indexed: 12/28/2022]
Abstract
DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use. Recent work on incorporating blunt-end stacking and hydrophobic interactions as orthogonal instruction rules in DNA assembly, and several emerging applications of DNA nanomaterials will also be highlighted.
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Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada.
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Structural polymorphism of a cytosine-rich DNA sequence forming i-motif structure: Exploring pH based biosensors. Int J Biol Macromol 2018; 111:455-461. [DOI: 10.1016/j.ijbiomac.2018.01.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 11/15/2022]
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48
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Grome MW, Zhang Z, Pincet F, Lin C. Vesicle Tubulation with Self-Assembling DNA Nanosprings. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Michael W. Grome
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Frédéric Pincet
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
- Laboratoire de Physique Statistique; Ecole Normale Supérieure; PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS; 24 rue Lhomond 75005 Paris France
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
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Grome MW, Zhang Z, Pincet F, Lin C. Vesicle Tubulation with Self-Assembling DNA Nanosprings. Angew Chem Int Ed Engl 2018; 57:5330-5334. [PMID: 29575478 DOI: 10.1002/anie.201800141] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/23/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Michael W. Grome
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Frédéric Pincet
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
- Laboratoire de Physique Statistique; Ecole Normale Supérieure; PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS; 24 rue Lhomond 75005 Paris France
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
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50
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Joshi H, Maiti PK. Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes. Nucleic Acids Res 2018; 46:2234-2242. [PMID: 29136243 PMCID: PMC5861442 DOI: 10.1093/nar/gkx1078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/25/2017] [Accepted: 11/03/2017] [Indexed: 01/18/2023] Open
Abstract
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.
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Affiliation(s)
- Himanshu Joshi
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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