Abstract
Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network’s various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.
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Data availability
The data associated with this manuscript are available at: https://doi.org/10.7281/T1/UBSZF1.
Code availability
The general genelet model code, including scripts for the main text simulations, is available at: https://github.com/sschaff6/general-genelet-model.git.
Change history
08 September 2022
A Correction to this paper has been published: https://doi.org/10.1038/s41557-022-01058-0
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Acknowledgements
The authors thank E. Franco, E. Nakamura, M. Rubanov and P. Moerman for insightful conversations and comments on the manuscript. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under grant number DGE-1232825 to S.W.S. This work was principally supported by the Department of Energy under award number DE-SC001 0426 to R.S. K.C. was supported by National Science Foundation award number EFRI-1830893 and Army Research Office award W911NF2010057. This work was also supported by the University of Chicago Materials Research Science and Engineering Center, which is funded by the National Science Foundation under award number DMR-2011854 to J.O. and A.M. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
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S.W.S and R.S. designed the research. S.W.S conducted most of the experiments and simulations. K.C. performed the experiments presented in Supplementary Information, sections 11, 3.4 and 4.6. M.N. performed preliminary experiments for the study. J.O. and A.M. conducted the multistability simulations and analysis. S.W.S and R.S. wrote the paper with feedback from the other authors.
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Schaffter, S.W., Chen, KL., O’Brien, J. et al. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nat. Chem. 14, 1224–1232 (2022). https://doi.org/10.1038/s41557-022-01001-3
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DOI: https://doi.org/10.1038/s41557-022-01001-3
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