51
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Dorsey PJ, Rubanov M, Wang W, Schulman R. Digital Maskless Photolithographic Patterning of DNA-Functionalized Poly(ethylene glycol) Diacrylate Hydrogels with Visible Light Enabling Photodirected Release of Oligonucleotides. ACS Macro Lett 2019; 8:1133-1140. [PMID: 35619455 DOI: 10.1021/acsmacrolett.9b00450] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Soft biomaterials possessing structural hierarchy have growing applications in lab-on-chip devices, artificial tissues, and micromechanical and chemomechanical systems. The ability to integrate sets of biomolecules, specifically DNA, within hydrogel substrates at precise locations could offer the potential to form and modulate complex biochemical processes with DNA-based molecular switches in such materials and provide a means of creating dynamic spatial patterns, thus enabling spatiotemporal control of a wide array of reaction-diffusion phenomena prevalent in biological systems. Here we develop a means of photopatterning two-dimensional DNA-functionalized poly(ethylene glycol) diacrylate (PEGDA) hydrogel architectures with an aim toward these applications. While PEGDA photopatterning methods are well-established for the fabrication of hydrogels, including those containing oligonucleotides, the photoinitiators typically used have significant crosstalk with many UV-photoswitchable chemistries including nitrobenzyl derivatives. We demonstrate the digital photopatterning of PEGDA-co-DNA hydrogels using a blue light-absorbing (470 nm peak) photoinitiator system and macromer comprised of camphorquinone, triethanolamine, and poly(ethylene glycol) diacrylate (Mn = 575) that minimizes absorption in the UV-A wavelength range commonly used to trigger photoswitchable chemistries. We demonstrate this method using digital maskless photolithography within microfluidic devices that allows for the reliable construction of multidomain structures. The method achieves feature resolutions as small as 25 μm, and the resulting materials allow for lateral isotropic bulk diffusion of short single-stranded (ss) DNA oligonucleotides. Finally, we show how the use of these photoinitiators allows for orthogonal control of photopolymerization and UV-photoscission of acrylate-modified DNA containing a 1-(2-nitrophenyl) ethyl spacer to selectively cleave DNA from regions of a PEGDA substrate.
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52
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Schaffter SW, Schulman R. Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules. Nat Chem 2019; 11:829-838. [PMID: 31427767 DOI: 10.1038/s41557-019-0292-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/13/2019] [Indexed: 02/04/2023]
Abstract
The regulation of cellular dynamics and responses to stimuli by genetic regulatory networks suggests how in vitro chemical reaction networks might analogously direct the dynamics of synthetic materials or chemistries. A key step in developing genetic regulatory network analogues capable of this type of sophisticated regulation is the integration of multiple coordinated functions within a single network. Here, we demonstrate how such functional integration can be achieved using in vitro transcriptional genelet circuits that emulate essential features of cellular genetic regulatory networks. By successively incorporating functional genelet modules into a bistable circuit, we construct an integrated regulatory network that dynamically changes its state in response to upstream stimuli and coordinates the timing of downstream signal expression. We use quantitative models to guide module integration and develop strategies to mitigate undesired interactions between network components that arise as the size of the network increases. This approach could enable the construction of in vitro networks capable of multifaceted chemical and material regulation.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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53
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Aufinger L, Simmel FC. Establishing Communication Between Artificial Cells. Chemistry 2019; 25:12659-12670. [DOI: 10.1002/chem.201901726] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/23/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Lukas Aufinger
- Physics Department and ZNNTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Friedrich C. Simmel
- Physics Department and ZNNTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
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54
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Urtel G, Van Der Hofstadt M, Galas JC, Estevez-Torres A. rEXPAR: An Isothermal Amplification Scheme That Is Robust to Autocatalytic Parasites. Biochemistry 2019; 58:2675-2681. [PMID: 31074259 PMCID: PMC6562758 DOI: 10.1021/acs.biochem.9b00063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/29/2019] [Indexed: 11/30/2022]
Abstract
In the absence of DNA, a solution containing the four deoxynucleotidetriphosphates (dNTPs), a DNA polymerase, and a nicking enzyme generates a self-replicating mixture of DNA species called parasite. Parasites are problematic in template-based isothermal amplification schemes such as EXPAR as well as in related molecular programming approaches, such as the PEN DNA toolbox. Here we show that using a nicking enzyme with only three letters (C, G, T) in the top strand of its recognition site, such as Nb.BssSI, allows us to change the sequence design of EXPAR templates in a way that prevents the formation of parasites when dATP is removed from the solution. This method allows us to make the EXPAR reaction robust to parasite contamination, a common feature in the laboratory, while keeping it compatible with PEN programs, which we demonstrate by engineering a parasite-proof bistable reaction network.
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Affiliation(s)
- Georg Urtel
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
| | - Marc Van Der Hofstadt
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
| | - Jean-Christophe Galas
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
| | - André Estevez-Torres
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
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55
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Lovrak M, Hendriksen WE, Kreutzer MT, van Steijn V, Eelkema R, van Esch JH. Control over the formation of supramolecular material objects using reaction-diffusion. SOFT MATTER 2019; 15:4276-4283. [PMID: 31038130 DOI: 10.1039/c8sm02588f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Controlled diffusion, reaction and assembly of hydrogelator precursors can be used to create soft hydrogel objects of defined shape and size. In this study we show that controlling local reaction kinetics by means of pH, diffusion length and the concentrations of reactants allows control over the dimensions of formed supramolecular structures. By correlating a reaction diffusion model to experimental results, we show that the influence of all these control parameters can be unified using the Damköhler number, thus providing an easy-to-use relation between experimental parameters and structure dimensions. Finally, our study suggests that control over concentration gradients and chemical reactivity in combination with supramolecular chemistry is a promising platform for the design of soft matter objects of defined sizes, a concept that has received little attention up until now.
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Affiliation(s)
- Matija Lovrak
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Wouter E Hendriksen
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Michiel T Kreutzer
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Volkert van Steijn
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Jan H van Esch
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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56
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Jeong D, Klocke M, Agarwal S, Kim J, Choi S, Franco E, Kim J. Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems. Methods Protoc 2019; 2:E39. [PMID: 31164618 PMCID: PMC6632179 DOI: 10.3390/mps2020039] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/12/2019] [Accepted: 05/08/2019] [Indexed: 01/07/2023] Open
Abstract
Synthetic biology brings engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription-translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.
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Affiliation(s)
- Dohyun Jeong
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Melissa Klocke
- Department of Mechanical Engineering, University of California at Riverside, 900 University Ave, Riverside, CA 92521, USA.
| | - Siddharth Agarwal
- Department of Mechanical Engineering, University of California at Riverside, 900 University Ave, Riverside, CA 92521, USA.
| | - Jeongwon Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Seungdo Choi
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Jongmin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
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57
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Sato Y, Takinoue M. Creation of Artificial Cell-Like Structures Promoted by Microfluidics Technologies. MICROMACHINES 2019; 10:E216. [PMID: 30934758 PMCID: PMC6523379 DOI: 10.3390/mi10040216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
Abstract
The creation of artificial cells is an immensely challenging task in science. Artificial cells contribute to revealing the mechanisms of biological systems and deepening our understanding of them. The progress of versatile biological research fields has clarified many biological phenomena, and various artificial cell models have been proposed in these fields. Microfluidics provides useful technologies for the study of artificial cells because it allows the fabrication of cell-like compartments, including water-in-oil emulsions and giant unilamellar vesicles. Furthermore, microfluidics also allows the mimicry of cellular functions with chip devices based on sophisticated chamber design. In this review, we describe contributions of microfluidics to the study of artificial cells. Although typical microfluidic methods are useful for the creation of artificial-cell compartments, recent methods provide further benefits, including low-cost fabrication and a reduction of the sample volume. Microfluidics also allows us to create multi-compartments, compartments with artificial organelles, and on-chip artificial cells. We discuss these topics and the future perspective of microfluidics for the study of artificial cells and molecular robotics.
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Affiliation(s)
- Yusuke Sato
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
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58
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Wang SS, Ellington AD. Pattern Generation with Nucleic Acid Chemical Reaction Networks. Chem Rev 2019; 119:6370-6383. [DOI: 10.1021/acs.chemrev.8b00625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Siyuan S. Wang
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
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59
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Dúzs B, De Kepper P, Szalai I. Turing Patterns and Waves in Closed Two-Layer Gel Reactors. ACS OMEGA 2019; 4:3213-3219. [PMID: 31459538 PMCID: PMC6648942 DOI: 10.1021/acsomega.8b02997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/10/2019] [Indexed: 05/07/2023]
Abstract
Reaction-diffusion waves and stationary Turing patterns are observed in closed two-layer gel reactors, where the two compartments are initially filled with complementary sets of reactants of the chlorine dioxide-iodine-malonic acid-poly(vinyl alcohol) reaction. The asymmetrical loading generates concentration gradients and the patterns form at the interface between the two parts. These easy-to-perform experiments allow us to study a wide range of dynamical phenomena without requiring a specific reactor design or the use of sophisticated equipment. To get complementary information on pattern formation in parallel and perpendicular to the direction of the concentration gradients, two geometrically different configurations of compartments are presented. We demonstrate that three variants of the initial distribution of the chemicals can be equally applied, and this flexibility provides a way to introduce additional reagents to perturb the dynamics of the systems. A noticeable increase in the wavelength of Turing patterns and in the period of waves has been induced by adding bromide ions. The interaction of Turing and Hopf modes has been observed as a result of not only the variation of the initial poly(vinyl alcohol) concentration but that of the gradients as well.
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Affiliation(s)
- Brigitta Dúzs
- Institute
of Chemistry, Eötvös Loránd
University, Pázmány
Péter s. 1/A, H-1117 Budapest, Hungary
| | - Patrick De Kepper
- Centre
de Recherche Paul Pascal, CNRS, University of Bordeaux I, Avenue Schweitzer, F-33600 Pessac, France
| | - István Szalai
- Institute
of Chemistry, Eötvös Loránd
University, Pázmány
Péter s. 1/A, H-1117 Budapest, Hungary
- E-mail: (I.S.)
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60
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Aufinger L, Simmel FC. Artificial Gel-Based Organelles for Spatial Organization of Cell-Free Gene Expression Reactions. Angew Chem Int Ed Engl 2018; 57:17245-17248. [PMID: 30394633 PMCID: PMC6640049 DOI: 10.1002/anie.201809374] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/10/2018] [Indexed: 11/11/2022]
Abstract
Gel-based artificial organelles have been developed that enable sequence-specific and programmable localization of cell-free transcription and translation reactions inside an artificial cellular system. To this end, we utilize agarose microgels covalently modified with DNA templates coding for various functions and encapsulate them into emulsion droplets. We show that RNA signals transcribed from transcription organelles can be specifically targeted to capture organelles via hybridization to the corresponding DNA addresses. We also demonstrate that mRNA molecules, produced from transcription organelles and controlled by toehold switch riboregulators, are only translated in translation organelles containing their cognate DNA triggers. Spatial confinement of transcription and translation in separate organelles is thus superficially similar to gene expression in eukaryotic cells. Combining communicating gel spheres with specialized functions opens up new possibilities for programming artificial cellular systems at the organelle level.
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Affiliation(s)
- Lukas Aufinger
- Physics-Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Friedrich C. Simmel
- Physics-Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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61
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Chatterjee G, Chen YJ, Seelig G. Nucleic Acid Strand Displacement with Synthetic mRNA Inputs in Living Mammalian Cells. ACS Synth Biol 2018; 7:2737-2741. [PMID: 30441897 DOI: 10.1021/acssynbio.8b00288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Strand displacement reactions are widely used in DNA nanotechnology as a building block for engineering molecular computers and machines. Here, we demonstrate that strand displacement-based probes can be triggered by RNA expressed in mammalian cells, thus taking a step toward adapting the DNA nanotechnology toolbox to a cellular environment. We systematically compare different probe architectures in order to identify a design that works robustly in living cells. Our optimized strand displacement probe combines chemically modified nucleic acids that enhance stability to degradation by cellular nucleases with structural elements that improve probe retention in the cytoplasm. We visualize probe binding to individual mRNA carrying 96 repeats of a target sequence in the 3'UTR. We find that RNA counts based on live cell imaging using a strand displacement probe are comparable to counts from independent measurement based on fluorescence in situ hybridization experiments. We used probes with scrambled toeholds and scrambled binding domains to demonstrate that target recognition indeed occurs through toehold-mediated strand displacement. Our results demonstrate that strand displacement probes can work reliably in mammalian cells and lay the groundwork for future applications of such probes for live-cell imaging and molecular computing.
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Affiliation(s)
- Gourab Chatterjee
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Yuan-Jyue Chen
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, United States
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62
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Santos‐Moreno J, Schaerli Y. Using Synthetic Biology to Engineer Spatial Patterns. ACTA ACUST UNITED AC 2018; 3:e1800280. [DOI: 10.1002/adbi.201800280] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/14/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Javier Santos‐Moreno
- Department of Fundamental MicrobiologyUniversity of LausanneBiophore Building 1015 Lausanne Switzerland
| | - Yolanda Schaerli
- Department of Fundamental MicrobiologyUniversity of LausanneBiophore Building 1015 Lausanne Switzerland
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63
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Niederholtmeyer H, Chaggan C, Devaraj NK. Communication and quorum sensing in non-living mimics of eukaryotic cells. Nat Commun 2018; 9:5027. [PMID: 30487584 PMCID: PMC6261949 DOI: 10.1038/s41467-018-07473-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 01/22/2023] Open
Abstract
Cells in tissues or biofilms communicate with one another through chemical and mechanical signals to coordinate collective behaviors. Non-living cell mimics provide simplified models of natural systems; however, it has remained challenging to implement communication capabilities comparable to living cells. Here we present a porous artificial cell-mimic containing a nucleus-like DNA-hydrogel compartment that is able to express and display proteins, and communicate with neighboring cell-mimics through diffusive protein signals. We show that communication between cell-mimics allows distribution of tasks, quorum sensing, and cellular differentiation according to local environment. Cell-mimics can be manufactured in large quantities, easily stored, chemically modified, and spatially organized into diffusively connected tissue-like arrangements, offering a means for studying communication in large ensembles of artificial cells. Cells communicate through chemical and mechanical signals but emulating these in non-living mimics has been challenging. Here the authors present a porous mimic with a DNA-hydrogel ‘nucleus’ that can communicate through diffusive protein signals.
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Affiliation(s)
- Henrike Niederholtmeyer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Cynthia Chaggan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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64
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Aufinger L, Simmel FC. Künstliche, gelbasierte Organellen für die räumliche Organisation von zellfreien Genexpressionsreaktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lukas Aufinger
- Physik-Department und ZNN Technische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Friedrich C. Simmel
- Physik-Department und ZNN Technische Universität München Am Coulombwall 4a 85748 Garching Deutschland
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65
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Dupin A, Simmel FC. Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat Chem 2018; 11:32-39. [PMID: 30478365 PMCID: PMC6298583 DOI: 10.1038/s41557-018-0174-9] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/19/2018] [Indexed: 01/18/2023]
Abstract
Multicellularity enables the growth of complex life forms as it allows for specialization of cell types, differentiation, and large scale spatial organization. In a similar way, modular construction of synthetic multicellular systems will lead to dynamic biomimetic materials that can respond to their environment in complex ways. In order to achieve this goal, artificial cellular communication and developmental programs still have to be established. Here, we create geometrically controlled spatial arrangements of emulsion-based artificial cellular compartments containing synthetic in vitro gene circuitry, separated by lipid bilayer membranes. We quantitatively determine the membrane pore-dependent response of the circuits to artificial morphogen gradients, which are established via diffusion from dedicated organizer cells. Utilizing different types of feed-forward and feedback in vitro gene circuits, we then implement artificial signaling and differentiation processes, demonstrating the potential for the realization of complex spatiotemporal dynamics in artificial multicellular systems.
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Affiliation(s)
- Aurore Dupin
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany.
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66
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Kurylo I, Gines G, Rondelez Y, Coffinier Y, Vlandas A. Spatiotemporal control of DNA-based chemical reaction network via electrochemical activation in microfluidics. Sci Rep 2018; 8:6396. [PMID: 29686392 PMCID: PMC5913268 DOI: 10.1038/s41598-018-24659-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/26/2018] [Indexed: 11/09/2022] Open
Abstract
In recent years, DNA computing frameworks have been developed to create dynamical systems which can be used for information processing. These emerging synthetic biochemistry tools can be leveraged to gain a better understanding of fundamental biology but can also be implemented in biosensors and unconventional computing. Most of the efforts so far have focused on changing the topologies of DNA molecular networks or scaling them up. Several issues have thus received little attention and remain to be solved to turn them into real life technologies. In particular, the ability to easily interact in real-time with them is a key requirement. The previous attempts to achieve this aim have used microfluidic approaches, such as valves, which are cumbersome. We show that electrochemical triggering using DNA-grafted micro-fabricated gold electrodes can be used to give instructions to these molecular systems. We demonstrate how this approach can be used to release at specific times and locations DNA- based instructions. In particular, we trigger reaction-diffusion autocatalytic fronts in microfluidic channels. While limited by the stability of the Au-S bond, this easy to implement, versatile and scalable technique can be used in any biology laboratory to provide new ways to interact with any DNA-based computing framework.
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Affiliation(s)
- Ievgen Kurylo
- BioMEMS, Univ. Lille, CNRS, ISEN, UMR 8520 - IEMN, F-59000, Lille, France
| | - Guillaume Gines
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Yannick Coffinier
- NanoBioInterfaces, Univ. Lille, CNRS, ISEN, UMR 8520 - IEMN, F-59000, Lille, France
| | - Alexis Vlandas
- BioMEMS, Univ. Lille, CNRS, ISEN, UMR 8520 - IEMN, F-59000, Lille, France.
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67
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Dúzs B, Szalai I. Design of localized spatiotemporal pH patterns by means of antagonistic chemical gradients. RSC Adv 2018; 8:41756-41761. [PMID: 35558810 PMCID: PMC9091980 DOI: 10.1039/c8ra08028c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Spatially localized moving and stationary pH patterns are generated in two-side-fed reaction-diffusion systems. The patterns are sandwiched between two quiescent zones and positioned by the antagonistic gradients of the reactants of the self-activatory process. Spatial bistability, spatiotemporal oscillations, and formation of stationary Turing patterns have been predicted by numerical simulations and observed in experiments performed by using different hydrogen ion autocatalytic chemical systems. The formation of stationary patterns due to long-range inhibition is promoted by a large molecular weight hydrogen ion binding polymer. Spatially localized moving and stationary pH patterns are generated in two-side-fed reaction-diffusion systems.![]()
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Affiliation(s)
- Brigitta Dúzs
- Institute of Chemistry
- Eötvös Loránd University
- Budapest
- Hungary
| | - István Szalai
- Institute of Chemistry
- Eötvös Loránd University
- Budapest
- Hungary
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68
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Synchrony and pattern formation of coupled genetic oscillators on a chip of artificial cells. Proc Natl Acad Sci U S A 2017; 114:11609-11614. [PMID: 29078346 PMCID: PMC5676917 DOI: 10.1073/pnas.1710620114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Understanding how biochemical networks lead to large-scale nonequilibrium self-organization and pattern formation in life is a major challenge, with important implications for the design of programmable synthetic systems. Here, we assembled cell-free genetic oscillators in a spatially distributed system of on-chip DNA compartments as artificial cells, and measured reaction-diffusion dynamics at the single-cell level up to the multicell scale. Using a cell-free gene network we programmed molecular interactions that control the frequency of oscillations, population variability, and dynamical stability. We observed frequency entrainment, synchronized oscillatory reactions and pattern formation in space, as manifestation of collective behavior. The transition to synchrony occurs as the local coupling between compartments strengthens. Spatiotemporal oscillations are induced either by a concentration gradient of a diffusible signal, or by spontaneous symmetry breaking close to a transition from oscillatory to nonoscillatory dynamics. This work offers design principles for programmable biochemical reactions with potential applications to autonomous sensing, distributed computing, and biomedical diagnostics.
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