A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides
In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across sp...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
The Royal Society
2022-08-01
|
| Series: | Royal Society Open Science |
| Subjects: | |
| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsos.220200 |
| _version_ | 1797840249770999808 |
|---|---|
| author | Phillip J. Dorsey Dominic Scalise Rebecca Schulman |
| author_facet | Phillip J. Dorsey Dominic Scalise Rebecca Schulman |
| author_sort | Phillip J. Dorsey |
| collection | DOAJ |
| description | In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction–diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions. |
| first_indexed | 2024-04-09T16:11:51Z |
| format | Article |
| id | doaj.art-0288e349eac24c3b8257765f0f4b2a31 |
| institution | Directory Open Access Journal |
| issn | 2054-5703 |
| language | English |
| last_indexed | 2024-04-09T16:11:51Z |
| publishDate | 2022-08-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Royal Society Open Science |
| spelling | doaj.art-0288e349eac24c3b8257765f0f4b2a312023-04-24T09:17:22ZengThe Royal SocietyRoyal Society Open Science2054-57032022-08-019810.1098/rsos.220200A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguidesPhillip J. Dorsey0Dominic Scalise1Rebecca Schulman2Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USADepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USADepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USAIn multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction–diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions.https://royalsocietypublishing.org/doi/10.1098/rsos.220200chemical reaction networksDNA nanotechnologyreaction–diffusion systems |
| spellingShingle | Phillip J. Dorsey Dominic Scalise Rebecca Schulman A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides Royal Society Open Science chemical reaction networks DNA nanotechnology reaction–diffusion systems |
| title | A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides |
| title_full | A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides |
| title_fullStr | A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides |
| title_full_unstemmed | A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides |
| title_short | A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides |
| title_sort | model of spatio temporal regulation within biomaterials using dna reaction diffusion waveguides |
| topic | chemical reaction networks DNA nanotechnology reaction–diffusion systems |
| url | https://royalsocietypublishing.org/doi/10.1098/rsos.220200 |
| work_keys_str_mv | AT phillipjdorsey amodelofspatiotemporalregulationwithinbiomaterialsusingdnareactiondiffusionwaveguides AT dominicscalise amodelofspatiotemporalregulationwithinbiomaterialsusingdnareactiondiffusionwaveguides AT rebeccaschulman amodelofspatiotemporalregulationwithinbiomaterialsusingdnareactiondiffusionwaveguides AT phillipjdorsey modelofspatiotemporalregulationwithinbiomaterialsusingdnareactiondiffusionwaveguides AT dominicscalise modelofspatiotemporalregulationwithinbiomaterialsusingdnareactiondiffusionwaveguides AT rebeccaschulman modelofspatiotemporalregulationwithinbiomaterialsusingdnareactiondiffusionwaveguides |