Implementing non-equilibrium networks with active circuits of duplex catalysts
File(s)LIPIcs-DNA-2020-7.pdf (1.14 MB)
Published version
Author(s)
Lankinen, Antti
Ruiz, Ismael Mullor
Ouldridge, Thomas E
Type
Conference Paper
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 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.
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 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.
Date Issued
2020-09-04
Date Acceptance
2020-09-01
Citation
2020, pp.1-25
Publisher
Schloss Dagstuhl--Leibniz-Zentrum
Start Page
1
End Page
25
Copyright Statement
© Antti Lankinen, Ismael Mullor Ruiz, and Thomas E. Ouldridge;
licensed under Creative Commons License CC-BY https://creativecommons.org/licenses/by/3.0/
licensed under Creative Commons License CC-BY https://creativecommons.org/licenses/by/3.0/
License URL
Sponsor
The Royal Society
The Royal Society
The Royal Society
Identifier
http://arxiv.org/abs/2005.11433v1
Grant Number
UF150067
RG160606
RGF\EA\180281
Source
26th International Conference on DNA Computing and Molecular Programming (DNA 26)
Subjects
q-bio.MN
q-bio.MN
q-bio.BM
Start Date
2020-09-14
Finish Date
2020-09-17
Coverage Spatial
Oxford, UK
Date Publish Online
2020-09-04