1
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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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2
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Walczak M, Mancini L, Xu J, Raguseo F, Kotar J, Cicuta P, Di Michele L. A Synthetic Signaling Network Imitating the Action of Immune Cells in Response to Bacterial Metabolism. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2301562. [PMID: 37156014 DOI: 10.1002/adma.202301562] [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: 02/17/2023] [Revised: 04/16/2023] [Indexed: 05/10/2023]
Abstract
State-of-the-art bottom-up synthetic biology allows to replicate many basic biological functions in artificial-cell-like devices. To mimic more complex behaviors, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here, a sophisticated biological response is considered, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. A consortium consisting of two synthetic agents is designed-responsive DNA-based particles and antibiotic-loaded lipid vesicles-whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilization and exposure to antibiotics. The results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.
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Affiliation(s)
- Michal Walczak
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Leonardo Mancini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Jiayi Xu
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Federica Raguseo
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Jurij Kotar
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
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3
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Rubio-Sánchez R, Mognetti BM, Cicuta P, Di Michele L. DNA-Origami Line-Actants Control Domain Organization and Fission in Synthetic Membranes. J Am Chem Soc 2023; 145:11265-11275. [PMID: 37163977 DOI: 10.1021/jacs.3c01493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cells can precisely program the shape and lateral organization of their membranes using protein machinery. Aiming to replicate a comparable degree of control, here we introduce DNA-origami line-actants (DOLAs) as synthetic analogues of membrane-sculpting proteins. DOLAs are designed to selectively accumulate at the line-interface between coexisting domains in phase-separated lipid membranes, modulating the tendency of the domains to coalesce. With experiments and coarse-grained simulations, we demonstrate that DOLAs can reversibly stabilize two-dimensional analogues of Pickering emulsions on synthetic giant liposomes, enabling dynamic programming of membrane lateral organization. The control afforded over membrane structure by DOLAs extends to three-dimensional morphology, as exemplified by a proof-of-concept synthetic pathway leading to vesicle fission. With DOLAs we lay the foundations for mimicking, in synthetic systems, some of the critical membrane-hosted functionalities of biological cells, including signaling, trafficking, sensing, and division.
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Affiliation(s)
- Roger Rubio-Sánchez
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Bortolo Matteo Mognetti
- Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, Boulevard du Triomphe, B-1050 Brussels, Belgium
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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4
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Maingi V, Zhang Z, Thachuk C, Sarraf N, Chapman ER, Rothemund PWK. Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Nat Commun 2023; 14:1532. [PMID: 36941256 PMCID: PMC10027858 DOI: 10.1038/s41467-023-36996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Interactions between membrane proteins are essential for cell survival but are often poorly understood. Even the biologically functional ratio of components within a multi-subunit membrane complex-the native stoichiometry-is difficult to establish. Here we demonstrate digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors (modelling membrane proteins). Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence, which in principle is generalizable to any ratio. Similar single-molecule-in-bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.
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Affiliation(s)
- Vishal Maingi
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
| | - Zhao Zhang
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA
| | - Chris Thachuk
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
| | - Namita Sarraf
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
| | - Paul W K Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation & Neural Systems, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation + Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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5
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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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6
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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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7
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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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8
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Li L, Kamal MA, Stumpf BH, Thibaudau F, Sengupta K, Smith AS. Biomechanics as driver of aggregation of tethers in adherent membranes. SOFT MATTER 2021; 17:10101-10107. [PMID: 34723306 DOI: 10.1039/d1sm00921d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell adhesion is an important cellular process and is mediated by adhesion proteins residing on the cell membrane. Sometimes, two types of linker proteins are involved in adhesion, and they can segregate to form domains through a poorly understood size-exclusion process. We present an experimental and theoretical study of adhesion via linkers of two different sizes, realised in a mimetic model-system, based on giant unilamellar vesicles interacting with supported lipid bilayers. Here, adhesion is mediated by DNA linkers with two different lengths, but with the same binding enthalpy. We study the organisation of these linkers into domains as a function of relative fraction of long and short DNA constructs. Experimentally, we find that, irrespective of the composition, the adhesion domains are uniform with coexisting DNA bridge types, despite their relative difference in length of 9 nm. However, simulations suggest formation of nanodomains of the minority fraction at short length scales, which is below the optical resolution of the microscope. The nano-aggregation is more significant for long bridges, which are also more stable.
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Affiliation(s)
- Long Li
- PULS Group, Institut for Theoretical Physics and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstrasse 3, Erlangen, 91058, Germany.
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Mohammad Arif Kamal
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), 13009 Marseille, France.
| | - Bernd Henning Stumpf
- PULS Group, Institut for Theoretical Physics and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstrasse 3, Erlangen, 91058, Germany.
| | - Franck Thibaudau
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), 13009 Marseille, France.
| | - Kheya Sengupta
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), 13009 Marseille, France.
| | - Ana-Sunčana Smith
- PULS Group, Institut for Theoretical Physics and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstrasse 3, Erlangen, 91058, Germany.
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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9
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Liu G, Huang S, Liu X, Chen W, Ma X, Cao S, Wang L, Chen L, Yang H. DNA-Based Artificial Signaling System Mimicking the Dimerization of Receptors for Signal Transduction and Amplification. Anal Chem 2021; 93:13807-13814. [PMID: 34613712 DOI: 10.1021/acs.analchem.1c02405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transmembrane signal transduction is of profound significance in many biological processes. The dimerization of cell-surface receptors is one prominent mechanism by which signals are transmitted across the membrane and trigger intracellular cascade amplification reactions. Recreating such processes in artificial systems has potential applications in sensing, drug delivery, bioengineering, and providing a new route for a deep understanding of fundamental biological processes. However, it remains a challenge to design artificial signal transduction systems working by the receptor dimerization mechanism in a predictable and smart manner. Here, benefitting from DNA with features of programmability, controllability, and flexible design, we use DNA as a building material to construct an artificial system mimicking dimerization of receptors for signal transduction and cascade amplification. DNA-based membrane-spanning receptor analogues are designed to recognize external signals, which drives two receptors into close spatial proximity to activate DNAzymes inside the cell-mimicking system. The activation of the DNAzyme initiates the catalyzed cleavage of encapsulated substrates and leads to the release of fluorescent second messengers for signal amplification. Such an artificial signal transduction system extends the range of biomimetic DNA-based signaling systems, providing a new avenue to study natural cell signaling processes and artificially regulate biological processes.
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Affiliation(s)
- Guo Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Shan Huang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Xiaochen Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Wanzhen Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Xin Ma
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Shuang Cao
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Liping Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
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10
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Rubio-Sánchez R, Barker SE, Walczak M, Cicuta P, Michele LD. A Modular, Dynamic, DNA-Based Platform for Regulating Cargo Distribution and Transport between Lipid Domains. NANO LETTERS 2021; 21:2800-2808. [PMID: 33733783 PMCID: PMC8050828 DOI: 10.1021/acs.nanolett.0c04867] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/03/2021] [Indexed: 05/04/2023]
Abstract
Cell membranes regulate the distribution of biological machinery between phase-separated lipid domains to facilitate key processes including signaling and transport, which are among the life-like functionalities that bottom-up synthetic biology aims to replicate in artificial-cellular systems. Here, we introduce a modular approach to program partitioning of amphiphilic DNA nanostructures in coexisting lipid domains. Exploiting the tendency of different hydrophobic "anchors" to enrich different phases, we modulate the lateral distribution of our devices by rationally combining hydrophobes and by changing nanostructure size and topology. We demonstrate the functionality of our strategy with a bioinspired DNA architecture, which dynamically undergoes ligand-induced reconfiguration to mediate cargo transport between domains via lateral redistribution. Our findings pave the way to next-generation biomimetic platforms for sensing, transduction, and communication in synthetic cellular systems.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Simone Eizagirre Barker
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Michal Walczak
- 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
- Molecular
Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
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11
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Zhu J, Bošković F, Nguyen BNT, Nitschke JR, Keyser UF. Kinetics of Toehold-Mediated DNA Strand Displacement Depend on Fe II4L 4 Tetrahedron Concentration. NANO LETTERS 2021; 21:1368-1374. [PMID: 33508195 PMCID: PMC7886027 DOI: 10.1021/acs.nanolett.0c04125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/29/2020] [Indexed: 06/12/2023]
Abstract
The toehold-mediated strand displacement reaction (SDR) is a powerful enzyme-free tool for molecular manipulation, DNA computing, signal amplification, etc. However, precise modulation of SDR kinetics without changing the original design remains a significant challenge. We introduce a new means of modulating SDR kinetics using an external stimulus: a water-soluble FeII4L4 tetrahedral cage. Our results show that the presence of a flexible phosphate group and a minimum toehold segment length are essential for FeII4L4 binding to DNA. SDRs mediated by toehold ends in different lengths (3-5) were investigated as a function of cage concentration. Their reaction rates all first increased and then decreased as cage concentration increased. We infer that cage binding on the toehold end slows SDR, whereas the stabilization of intermediates that contain two overhangs accelerates SDR. The tetrahedral cage thus serves as a versatile tool for modulation of SDR kinetics.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of
Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Filip Bošković
- Cavendish Laboratory, University of
Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Bao-Nguyen T. Nguyen
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Jonathan R. Nitschke
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of
Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United
Kingdom
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Mohajeri N, Imani M, Akbarzadeh A, Sadighi A, Zarghami N. An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities. Biosens Bioelectron 2019; 144:111633. [DOI: 10.1016/j.bios.2019.111633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
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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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