1
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Jäkel AC, Aufinger L, Simmel FC. Steady-State Operation of a Cell-Free Genetic Band-Detection Circuit. ACS Synth Biol 2022; 11:3273-3284. [PMID: 36095299 DOI: 10.1021/acssynbio.2c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pattern formation processes play a decisive role during embryogenesis and involve the precise spatial and temporal orchestration of intricate gene regulatory processes. Synthetic gene circuits modeled after their biological counterparts can be used to investigate such processes under well-controlled conditions and may, in the future, be utilized for autonomous position determination in synthetic biological materials. Here, we investigated a three-node feed-forward gene regulatory circuit in vitro that generates three distinct fluorescent outputs in response to varying concentrations of a single externally supplied morphogen. The circuit acts as a band detector for the morphogen concentration and, in a spatial context, could serve as a stripe-forming gene circuit. We simulated the behavior of the genetic circuit in the presence of a morphogen gradient using a system of ordinary differential equations and determined optimal parameters for stripe-pattern formation using an evolutionary algorithm. To analyze the subcircuits of the system, we conducted cell-free characterization experiments and finally tested the whole genetic circuit in nanoliter-scale microfluidic flow reactors that provided a continuous supply of cell extract and metabolites and allowed removal of degradation products. To make use of the widely employed promoters PLlacO-1 and PLtetO-1 in our design, we removed LacI from our bacterial cell extract by genome engineering Escherichia coli using a pORTMAGE workflow. Our results show that the band-detector works as designed when operated out of equilibrium within the flow reactors. On the other hand, subcircuits of the system and the whole circuit fail to generate the desired gene expression response when operated in a closed reactor. Our work thus underlines the importance of out-of-equilibrium operation of complex gene circuits, which cannot settle to a steady-state expression pattern within the finite lifetime of a cell-free expression system.
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Affiliation(s)
- Anna C Jäkel
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching D-85748, Germany
| | - Lukas Aufinger
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching D-85748, Germany
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching D-85748, Germany
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2
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Nguindjel ADC, de Visser PJ, Winkens M, Korevaar PA. Spatial programming of self-organizing chemical systems using sustained physicochemical gradients from reaction, diffusion and hydrodynamics. Phys Chem Chem Phys 2022; 24:23980-24001. [PMID: 36172850 PMCID: PMC9554936 DOI: 10.1039/d2cp02542f] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022]
Abstract
Living organisms employ chemical self-organization to build structures, and inspire new strategies to design synthetic systems that spontaneously take a particular form, via a combination of integrated chemical reactions, assembly pathways and physicochemical processes. However, spatial programmability that is required to direct such self-organization is a challenge to control. Thermodynamic equilibrium typically brings about a homogeneous solution, or equilibrium structures such as supramolecular complexes and crystals. This perspective addresses out-of-equilibrium gradients that can be driven by coupling chemical reaction, diffusion and hydrodynamics, and provide spatial differentiation in the self-organization of molecular, ionic or colloidal building blocks in solution. These physicochemical gradients are required to (1) direct the organization from the starting conditions (e.g. a homogeneous solution), and (2) sustain the organization, to prevent it from decaying towards thermodynamic equilibrium. We highlight four different concepts that can be used as a design principle to establish such self-organization, using chemical reactions as a driving force to sustain the gradient and, ultimately, program the characteristics of the gradient: (1) reaction-diffusion coupling; (2) reaction-convection; (3) the Marangoni effect and (4) diffusiophoresis. Furthermore, we outline their potential as attractive pathways to translate chemical reactions and molecular/colloidal assembly into organization of patterns in solution, (dynamic) self-assembled architectures and collectively moving swarms at the micro-, meso- and macroscale, exemplified by recent demonstrations in the literature.
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Affiliation(s)
| | - Pieter J de Visser
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Mitch Winkens
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Peter A Korevaar
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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3
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Dupin A, Aufinger L, Styazhkin I, Rothfischer F, Kaufmann BK, Schwarz S, Galensowske N, Clausen-Schaumann H, Simmel FC. Synthetic cell-based materials extract positional information from morphogen gradients. SCIENCE ADVANCES 2022; 8:eabl9228. [PMID: 35394842 PMCID: PMC8993112 DOI: 10.1126/sciadv.abl9228] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/17/2022] [Indexed: 05/19/2023]
Abstract
Biomaterials composed of synthetic cells have the potential to adapt and differentiate guided by physicochemical environmental cues. Inspired by biological systems in development, which extract positional information (PI) from morphogen gradients in the presence of uncertainties, we here investigate how well synthetic cells can determine their position within a multicellular structure. To calculate PI, we created and analyzed a large number of synthetic cellular assemblies composed of emulsion droplets connected via lipid bilayer membranes. These droplets contained cell-free feedback gene circuits that responded to gradients of a genetic inducer acting as a morphogen. PI is found to be limited by gene expression noise and affected by the temporal evolution of the morphogen gradient and the cell-free expression system itself. The generation of PI can be rationalized by computational modeling of the system. We scale our approach using three-dimensional printing and demonstrate morphogen-based differentiation in larger tissue-like assemblies.
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Affiliation(s)
- Aurore Dupin
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | - Lukas Aufinger
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | - Igor Styazhkin
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | | | - Benedikt K. Kaufmann
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
- Heinz-Nixdorf-Chair of Biomedical Electronics, TranslaTUM, TU Munich, 81675 Munich, Germany
| | - Sascha Schwarz
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
| | | | - Hauke Clausen-Schaumann
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
| | - Friedrich C. Simmel
- Physics Department (E14), TU Munich, 85748 Garching, Germany
- Corresponding author.
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4
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Dúzs B, Szalai I. Reaction-diffusion phenomena in antagonistic bipolar diffusion fields. Phys Chem Chem Phys 2022; 24:1814-1820. [PMID: 34986213 DOI: 10.1039/d1cp04662d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Operating natural or artificial chemical systems requires nonequilibrium conditions under which temporal and spatial control of the process is realizable. Open reaction-diffusion systems provide a general way to create such conditions. A key issue is the proper design of reactors in which the nonequilibrium conditions can be maintained. A hydrogel with flow-through channels is a simple, flexible, and easy-to-make device in which chemical reactions are performed in the diffusion field of localized separated sources of reactants. Two reactants separated in two channels create a bipolar antagonistic diffusion field, where the reaction intermediates firmly separate in space. Numerical simulations and corresponding experiments are performed to present this inhomogeneous diffusion field-induced chemical separation in sequential reactions. A remarkable result of this bipolar spatial control is localized wave phenomena in a nonlinear activatory-inhibitory reaction. These findings may help design functioning artificial nonequilibrium systems with the desired spatial separation of chemicals.
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Affiliation(s)
- Brigitta Dúzs
- Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, Hungary.
| | - István Szalai
- Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, Hungary.
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5
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Abe K, Murata S, Kawamata I. Cascaded pattern formation in hydrogel medium using the polymerisation approach. SOFT MATTER 2021; 17:6160-6167. [PMID: 34085082 DOI: 10.1039/d1sm00296a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.
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Affiliation(s)
- Keita Abe
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan.
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan.
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Japan. and Natural Science Division, Faculty of Core Research, Ochanomizu University, Japan
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6
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Dúzs B, Szalai I. A simple hydrogel device with flow-through channels to maintain dissipative non-equilibrium phenomena. Commun Chem 2020; 3:168. [PMID: 36703396 PMCID: PMC9814359 DOI: 10.1038/s42004-020-00420-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/21/2020] [Indexed: 01/29/2023] Open
Abstract
The development of autonomous chemical systems that could imitate the properties of living matter, is a challenging problem at the meeting point of materials science and nonequilibrium chemistry. Here we design a multi-channel gel reactor in which out-of-equilibrium conditions are maintained by antagonistic chemical gradients. Our device is a rectangular hydrogel with two or more channels for the flows of separated reactants, which diffuse into the gel to react. The relative position of the channels acts as geometric control parameters, while the concentrations of the chemicals in the channels and the variable composition of the hydrogel, which affects the diffusivity of the chemicals, can be used as chemical control parameters. This flexibility allows finding easily the optimal conditions for the development of nonequilibrium phenomena. We demonstrate this straightforward operation by generating diverse spatiotemporal patterns in different chemical reactions. The use of additional channels can create interacting reaction zones.
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Affiliation(s)
- Brigitta Dúzs
- grid.5591.80000 0001 2294 6276Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - István Szalai
- grid.5591.80000 0001 2294 6276Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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7
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Affiliation(s)
- Phillip James Dorsey
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
| | - Dominic Scalise
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
- Department of Computer Science Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
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8
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Dorsey PJ, Scalise D, Schulman R. DNA Reaction–Diffusion Attractor Patterns. Angew Chem Int Ed Engl 2020; 60:338-344. [DOI: 10.1002/anie.202009756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/25/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Phillip James Dorsey
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
| | - Dominic Scalise
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
- Department of Computer Science Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
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9
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Rogers WB. A mean-field model of linker-mediated colloidal interactions. J Chem Phys 2020; 153:124901. [DOI: 10.1063/5.0020578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- W. Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, 02453, USA
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10
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Accelerating the Finite-Element Method for Reaction-Diffusion Simulations on GPUs with CUDA. MICROMACHINES 2020; 11:mi11090881. [PMID: 32971889 PMCID: PMC7569852 DOI: 10.3390/mi11090881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling waves. The Finite Element Method (FEM) is a standard tool to simulate the physics of such systems where boundary conditions play a crucial role. However, a fine discretization in time and space is required for complex geometries (like sharp corners) and highly nonlinear chemistry. Graphical Processing Units (GPUs) are increasingly used to speed up scientific computing, but their application to accelerate simulations of reaction-diffusion in DNA nanotechnology has been little investigated. Here we study reaction-diffusion equations (a DNA-based predator-prey system) in a tortuous geometry (a maze), which was shown experimentally to generate subtle geometric effects. We solve the partial differential equations on a GPU, demonstrating a speedup of ∼100 over the same resolution on a 20 cores CPU.
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11
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Abstract
In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.
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Affiliation(s)
- Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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12
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Chen S, Seelig G. Programmable patterns in a DNA-based reaction-diffusion system. SOFT MATTER 2020; 16:3555-3563. [PMID: 32219296 DOI: 10.1039/c9sm02413a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biology offers compelling proof that macroscopic "living materials" can emerge from reactions between diffusing biomolecules. Here, we show that molecular self-organization could be a similarly powerful approach for engineering functional synthetic materials. We introduce a programmable DNA embedded hydrogel that produces tunable patterns at the centimeter length scale. We generate these patterns by implementing chemical reaction networks through synthetic DNA complexes, embedding the complexes in the hydrogel, and triggering with locally applied input DNA strands. We first demonstrate ring pattern formation around a circular input cavity and show that the ring width and intensity can be predictably tuned. Then, we create patterns of increasing complexity, including concentric rings and non-isotropic patterns. Finally, we show "destructive" and "constructive" interference patterns, by combining several ring-forming modules in the gel and triggering them from multiple sources. We further show that computer simulations based on the reaction-diffusion model can predict and inform the programming of target patterns.
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Affiliation(s)
- Sifang Chen
- Department of Physics, University of Washington, USA
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13
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Urtel G, Estevez-Torres A, Galas JC. DNA-based long-lived reaction-diffusion patterning in a host hydrogel. SOFT MATTER 2019; 15:9343-9351. [PMID: 31693052 DOI: 10.1039/c9sm01786k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The development of living organisms is a source of inspiration for the creation of synthetic life-like materials. Embryo development is divided into three stages that are inextricably linked: patterning, differentiation and growth. During patterning, sustained out-of-equilibrium molecular programs interpret underlying molecular cues to create well-defined concentration profiles. Implementing this patterning stage in an autonomous synthetic material is a challenge that at least requires a programmable and long-lasting out-of-equilibrium chemistry compatible with a host material. Here, we show that DNA/enzyme reactions can create reaction-diffusion patterns that are extraordinarily long-lasting both in solution and inside an autonomous hydrogel. The life-time and stability of these patterns - here, traveling fronts and two-band patterns - are significantly increased by blocking parasitic side reactions and by dramatically reducing the diffusion coefficient of specific DNA strands. Immersed in oil, hydrogels pattern autonomously with limited evaporation, but can also exchange chemical information with other gels when brought into contact. Providing a certain degree of autonomy and being capable of interacting with each other, we believe these out-of-equilibrium hydrogels open the way for the rational design of primitive metabolic materials.
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Affiliation(s)
- Georg Urtel
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France.
| | - André Estevez-Torres
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France.
| | - Jean-Christophe Galas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France.
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14
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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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15
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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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16
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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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17
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Bánsági T, Taylor AF. Switches induced by quorum sensing in a model of enzyme-loaded microparticles. J R Soc Interface 2018. [PMID: 29514986 DOI: 10.1098/rsif.2017.0945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Quorum sensing refers to the ability of bacteria and other single-celled organisms to respond to changes in cell density or number with population-wide changes in behaviour. Here, simulations were performed to investigate quorum sensing in groups of diffusively coupled enzyme microparticles using a well-characterized autocatalytic reaction which raises the pH of the medium: hydrolysis of urea by urease. The enzyme urease is found in both plants and microorganisms, and has been widely exploited in engineering processes. We demonstrate how increases in group size can be used to achieve a sigmoidal switch in pH at high enzyme loading, oscillations in pH at intermediate enzyme loading and a bistable, hysteretic switch at low enzyme loading. Thus, quorum sensing can be exploited to obtain different types of response in the same system, depending on the enzyme concentration. The implications for microorganisms in colonies are discussed, and the results could help in the design of synthetic quorum sensing for biotechnology applications such as drug delivery.
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Affiliation(s)
- Tamás Bánsági
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Annette F Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
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18
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Cervantes-Salguero K, Kawamata I, Nomura SIM, Murata S. Unzipping and shearing DNA with electrophoresed nanoparticles in hydrogels. Phys Chem Chem Phys 2017; 19:13414-13418. [PMID: 28513698 DOI: 10.1039/c7cp02214j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show electric control of unzipping and shearing dehybridization of a DNA duplex anchored to a hydrogel. Tensile force is applied by electrophoresing (25 V cm-1) gold nanoparticles pulling the DNA duplex. The pulled DNA strand is gradually released from the hydrogel. The unzipping release rate is faster than shearing; for example, 3-fold for a 15 base pair duplex, which helps to design electrically driven DNA devices.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-1 Aobayama, Sendai 980-8579, Japan.
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19
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Khodadadi J, Mirabbaszadeh K, Yarmohammadi M. Sequence dependency of the thermodynamic properties of long DNA double-strands. RSC Adv 2017. [DOI: 10.1039/c7ra05974d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Temperature and sequence dependency of the Pauli paramagnetic susceptibility (PMS) and electronic heat capacity (EHC) of selected configurations are investigated for π-electrons within a ladder model of long DNA double-strands acting as semiconducting nanowires.
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Affiliation(s)
- Jabbar Khodadadi
- Department of Energy Engineering and Physics
- Amirkabir University of Technology
- Tehran
- Iran
| | - Kavoos Mirabbaszadeh
- Department of Energy Engineering and Physics
- Amirkabir University of Technology
- Tehran
- Iran
| | - Mohsen Yarmohammadi
- Young Researchers and Elite Club
- Kermanshah Branch
- Islamic Azad University
- Kermanshah
- Iran
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