CaltechAUTHORS
  A Caltech Library Service

Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides

Dorsey, Phillip J. and Scalise, Dominic and Schulman, Rebecca (2022) Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20220301-560251000

[img] PDF - Submitted Version
See Usage Policy.

9MB
[img] PDF - Supplemental Material
See Usage Policy.

1MB

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20220301-560251000

Abstract

In multicellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning microns to meters. Endowing 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 signaling and electronic circuitry to design a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide can 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 show how a sink reaction 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 programs triggered by changing environmental conditions.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2022.02.26.482105DOIDiscussion Paper
ORCID:
AuthorORCID
Dorsey, Phillip J.0000-0002-0711-4428
Scalise, Dominic0000-0001-8218-1797
Schulman, Rebecca0000-0003-4555-3162
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This work was supported by NSF SHF grant no. 1161941, Department of Energy grant no. DE-SC0015906, and a Johns Hopkins Catalyst Award. Authors’ contributions: PJD and DS conceived of and designed the study. PJD designed and executed the simulations and experimental work. DS and RS provided technical guidance and analysis. All authors gave final approval for publication and agree to held accountable for the work performed therein. Data accessibility. Datasets and MATLAB code supporting this article are available in Dryad Repository through the following link. The authors have declared no competing interest.
Funders:
Funding AgencyGrant Number
NSFCCF-1161941
Department of Energy (DOE)DE-SC0015906
Johns Hopkins UniversityUNSPECIFIED
Subject Keywords:chemical reaction networks, DNA nanotechnology, reaction-diffusion systems
DOI:10.1101/2022.02.26.482105
Record Number:CaltechAUTHORS:20220301-560251000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220301-560251000
Official Citation:Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides Phillip J Dorsey, Dominic Scalise, Rebecca Schulman bioRxiv 2022.02.26.482105; doi: https://doi.org/10.1101/2022.02.26.482105
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:113661
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:01 Mar 2022 20:23
Last Modified:01 Mar 2022 20:23

Repository Staff Only: item control page