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Published July 13, 2022 | Published + Supplemental Material
Journal Article Open

DNA Strand-Displacement Temporal Logic Circuits

Abstract

Molecular circuits capable of processing temporal information are essential for complex decision making in response to both the presence and history of a molecular environment. A particular type of temporal information that has been recognized to be important is the relative timing of signals. Here we demonstrate the strategy of temporal memory combined with logic computation in DNA strand-displacement circuits capable of making decisions based on specific combinations of inputs as well as their relative timing. The circuit encodes the timing information on inputs in a set of memory strands, which allows for the construction of logic gates that act on current and historical signals. We show that mismatches can be employed to reduce the complexity of circuit design and that shortening specific toeholds can be useful for improving the robustness of circuit behavior. We also show that a detailed model can provide critical insights for guiding certain aspects of experimental investigations that an abstract model cannot. We envision that the design principles explored in this study can be generalized to more complex temporal logic circuits and incorporated into other types of circuit architectures, including DNA-based neural networks, enabling the implementation of timing-dependent learning rules and opening up new opportunities for embedding intelligent behaviors into artificial molecular machines.

Additional Information

© 2022 The Authors. Published by American Chemical Society. Attribution 4.0 International (CC BY 4.0). Received: April 22, 2022; Published: July 2, 2022. A.P.L. and N.S. were supported by Caltech internal funds for BE/CS 196, a course on design and construction of programmable molecular systems. N.S. was also supported by an NIH/NRSA training grant (T32 GM07616). L.Q. was supported by an NSF award (1813550). Author Contributions. A.P.L. and N.S. contributed equally. The authors declare no competing financial interest.

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Supplemental Material - ja2c04325_si_001.pdf

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Additional details

Created:
August 22, 2023
Modified:
December 22, 2023