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License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.2020.7
URN: urn:nbn:de:0030-drops-129602
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2020/12960/
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Lankinen, Antti ; Mullor Ruiz, Ismael ; Ouldridge, Thomas E.

Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts

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LIPIcs-DNA-2020-7.pdf (0.7 MB)

Abstract

DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct "catalyst" strand from the one that triggered the reaction. These facts make emulation of the out-of-equilibrium catalytic circuitry of living cells more difficult. Here, we propose a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC). ACDC components are all double-stranded complexes, with reactions occurring through 4-way strand exchange. Catalysts directly bind to their substrates, and the "identity" strand of the catalyst recovered at the end of a reaction is the same molecule as the one that initiated it. We analyse the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells. We also propose two methods of systematically introducing mismatches within DNA strands to avoid leak reactions and introduce driving through net base pair formation. We then combine these results into a compiler to automate the process of designing DNA strands that realise any catalytic network allowed by our framework.

BibTeX - Entry

@InProceedings{lankinen_et_al:LIPIcs:2020:12960,
  author =	{Antti Lankinen and Ismael Mullor Ruiz and Thomas E. Ouldridge},
  title =	{{Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{7:1--7:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Cody Geary and Matthew J. Patitz},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2020/12960},
  URN =		{urn:nbn:de:0030-drops-129602},
  doi =		{10.4230/LIPIcs.DNA.2020.7},
  annote =	{Keywords: DNA strand displacement, Catalysis, Information-processing networks}
}

Keywords: DNA strand displacement, Catalysis, Information-processing networks
Collection: 26th International Conference on DNA Computing and Molecular Programming (DNA 26)
Issue Date: 2020
Date of publication: 04.09.2020
Supplementary Material: A compiler to generate optimal sequences for each strand in any allowed catalytic network is available at https://zenodo.org/record/3948343.

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