scholarly journals Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

10.3791/53087 ◽  
2015 ◽  
Author(s):  
Yuan-Jyue Chen ◽  
Sundipta D. Rao ◽  
Georg Seelig
Keyword(s):  
Chemical Reaction ◽  
Chemical Reaction Networks ◽  
Reaction Networks ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

scholarly journals Autonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther
Keyword(s):  
Chemical Reaction ◽  
Self Assembly ◽  
Structural Complexity ◽  
Hierarchical Structures ◽  
Chemical Reaction Networks ◽  
Reaction Networks ◽  
Dna Nanostructures ◽  
Dna Strand Displacement ◽  
Energy Gains ◽  
Dna Strand

AbstractConcatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. Here, to provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds. This allows to achieve hierarchical non-equilibrium systems by concurrent ATP-powered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. We introduce indirect and direct activation of DNT self-assemblies, and orthogonal molecular recognition allows ATP-fueled self-sorting of transient multicomponent DNTs. Coupling ATP dissipation to DNA nanostructures via programmable DSD is a generic concept which should be widely applicable to organize other DNA nanostructures, and enable the design of automatons and life-like systems of higher structural complexity.

scholarly journals Less haste, less waste: on recycling and its limits in strand displacement systems

2012 ◽  
Vol 2 (4) ◽  
pp. 512-521 ◽  
Author(s):  
Anne Condon ◽  
Alan J. Hu ◽  
Ján Maňuch ◽  
Chris Thachuk
Keyword(s):  
Chemical Reaction ◽  
Polynomial Function ◽  
Gray Code ◽  
Strand Displacement ◽  
Reaction Systems ◽  
Chemical Reaction Systems ◽  
Binary Counter ◽  
Dna Strand Displacement ◽  
Dna Strands ◽  
Dna Strand

We study the potential for molecule recycling in chemical reaction systems and their DNA strand displacement realizations. Recycling happens when a product of one reaction is a reactant in a later reaction. Recycling has the benefits of reducing consumption, or waste, of molecules and of avoiding fuel depletion. We present a binary counter that recycles molecules efficiently while incurring just a moderate slowdown compared with alternative counters that do not recycle strands. This counter is an n -bit binary reflecting Gray code counter that advances through 2 n states. In the strand displacement realization of this counter, the waste—total number of nucleotides of the DNA strands consumed—is polynomial in n , the number of bits of the counter, while the waste of alternative counters grows exponentially in n . We also show that our n -bit counter fails to work correctly when many ( Θ ( n )) copies of the species that represent the bits of the counter are present initially. The proof applies more generally to show that in chemical reaction systems where all but one reactant of each reaction are catalysts, computations longer than a polynomial function of the size of the system are not possible when there are polynomially many copies of the system present.

scholarly journals Visual synchronization of two 3-variable Lotka–Volterra oscillators based on DNA strand displacement

RSC Advances ◽  
2018 ◽  
Vol 8 (37) ◽  
pp. 20941-20951 ◽  
Author(s):  
Chengye Zou ◽  
Xiaopeng Wei ◽  
Qiang Zhang
Keyword(s):  
Reaction Networks ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

DNA strand displacement as a theoretic foundation is helpful in constructing reaction networks and DNA circuits.

scholarly journals Reachability bounds for chemical reaction networks and strand displacement systems

2013 ◽  
Vol 13 (4) ◽  
pp. 499-516 ◽  
Author(s):  
Anne Condon ◽  
Bonnie Kirkpatrick ◽  
Ján Maňuch
Keyword(s):  
Chemical Reaction ◽  
Chemical Reaction Networks ◽  
Reaction Networks ◽  
Strand Displacement

An Observer for Mass-action Chemical Reaction Networks

2009 ◽  
Vol 15 (5) ◽  
pp. 578-597
Author(s):  
Marcello Farina ◽  
Sergio Bittanti
Keyword(s):  
Chemical Reaction ◽  
Chemical Reaction Networks ◽  
Mass Action ◽  
Reaction Networks

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of
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