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Enzyme-Free Nucleic Acid Dynamical Systems

Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik
doi: https://doi.org/10.1101/138420
Niranjan Srinivas
California Institute of Technology;
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James Parkin
California Institute of Technology;
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Georg Seelig
University of Washington;
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Erik Winfree
California Institute of Technology;
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David Soloveichik
UT Austin
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  • For correspondence: david.soloveichik@utexas.edu
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Abstract

Chemistries exhibiting complex dynamics - from inorganic oscillators to gene regulatory networks - have been long known but either cannot be reprogrammed at will, or rely on the sophisticated chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract coupled chemical reactions have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems, identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base pairing interactions alone suffice for arbitrarily complex dynamics. Our results argue that autonomous molecular systems that interact with and control their chemical environment can be designed via molecular programming languages.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 29, 2017.
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Enzyme-Free Nucleic Acid Dynamical Systems
Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik
bioRxiv 138420; doi: https://doi.org/10.1101/138420
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Enzyme-Free Nucleic Acid Dynamical Systems
Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik
bioRxiv 138420; doi: https://doi.org/10.1101/138420

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