1 Search Results for "Lankinen, Antti"


Document
Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts

Authors: Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)


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.

Cite as

Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge. Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 7:1-7:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


Copy BibTex To Clipboard

@InProceedings{lankinen_et_al:LIPIcs.DNA.2020.7,
  author =	{Lankinen, Antti and Mullor Ruiz, Ismael and Ouldridge, Thomas E.},
  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 =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.7},
  URN =		{urn:nbn:de:0030-drops-129602},
  doi =		{10.4230/LIPIcs.DNA.2020.7},
  annote =	{Keywords: DNA strand displacement, Catalysis, Information-processing networks}
}
  • Refine by Author
  • 1 Lankinen, Antti
  • 1 Mullor Ruiz, Ismael
  • 1 Ouldridge, Thomas E.

  • Refine by Classification
  • 1 Hardware → Biology-related information processing

  • Refine by Keyword
  • 1 Catalysis
  • 1 DNA strand displacement
  • 1 Information-processing networks

  • Refine by Type
  • 1 document

  • Refine by Publication Year
  • 1 2020

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail