Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

10.26434/chemrxiv.10059131.v2 ◽

2019 ◽

Author(s):

Jie Deng ◽

Andreas Walther

Keyword(s):

Molecular Recognition ◽

Enzymatic Reaction ◽

Reaction Network ◽

Steady States ◽

Hierarchical Level ◽

Dna Nanostructures ◽

Structural Dynamic ◽

Systems Chemistry ◽

Sticky End ◽

Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

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Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

10.26434/chemrxiv.10059131 ◽

2019 ◽

Author(s):

Jie Deng ◽

Andreas Walther

Keyword(s):

Molecular Recognition ◽

Enzymatic Reaction ◽

Reaction Network ◽

Steady States ◽

Hierarchical Level ◽

Dna Nanostructures ◽

Structural Dynamic ◽

Systems Chemistry ◽

Sticky End ◽

Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

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Programmable Dynamic Steady States in ATP-Driven Non-Equilibrium DNA Systems

10.26434/chemrxiv.7964489.v1 ◽

2019 ◽

Author(s):

Laura Heinen ◽

Andreas Walther

Keyword(s):

Self Assembly ◽

Soft Matter ◽

Enzymatic Reaction ◽

Reaction Network ◽

Steady States ◽

Supramolecular Systems ◽

Kinetics Of ◽

Average Bond ◽

Full Synchronization ◽

Non Equilibrium

<div><div><div><p>Inspired by the dynamics of the dissipative self-assembly of microtubules, chemically fueled synthetic systems with transient lifetimes are emerging for non-equilibrium materials design. However, realizing programmable or even adaptive structural dynamics has proven challenging because it requires synchronization of energy uptake and dissipation events within true steady states, which remains difficult to orthogonally control in supramolecular systems. Here, we demonstrate full synchronization of both events by ATP-fueled activation and dynamization of covalent DNA bonds via an enzymatic reaction network of concurrent ligation and cleavage. Critically, the average bond ratio and the frequency of bond exchange are imprinted into the energy dissipation kinetics of the network and tunable through its constituents. We introduce temporally and structurally programmable dynamics by polymerization of transient, dynamic covalent DNA polymers with adaptive steady-state properties in dependence of ATP fuel and enzyme concentrations. This approach enables generic access to non-equilibrium soft matter systems with adaptive and programmable dynamics.</p></div></div></div>

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Programmable dynamic steady states in ATP-driven nonequilibrium DNA systems

Science Advances ◽

10.1126/sciadv.aaw0590 ◽

2019 ◽

Vol 5 (7) ◽

pp. eaaw0590 ◽

Cited By ~ 40

Author(s):

Laura Heinen ◽

Andreas Walther

Keyword(s):

Self Assembly ◽

Soft Matter ◽

Enzymatic Reaction ◽

Reaction Network ◽

Steady States ◽

Supramolecular Systems ◽

Dissipation Kinetics ◽

Kinetics Of ◽

Average Bond ◽

Full Synchronization

Inspired by the dynamics of the dissipative self-assembly of microtubules, chemically fueled synthetic systems with transient lifetimes are emerging for nonequilibrium materials design. However, realizing programmable or even adaptive structural dynamics has proven challenging because it requires synchronization of energy uptake and dissipation events within true steady states, which remains difficult to orthogonally control in supramolecular systems. Here, we demonstrate full synchronization of both events by ATP-fueled activation and dynamization of covalent DNA bonds via an enzymatic reaction network of concurrent ligation and cleavage. Critically, the average bond ratio and the frequency of bond exchange are imprinted into the energy dissipation kinetics of the network and tunable through its constituents. We introduce temporally and structurally programmable dynamics by polymerization of transient, dynamic covalent DNA polymers with adaptive steady-state properties in dependence of ATP fuel and enzyme concentrations. This approach enables generic access to nonequilibrium soft matter systems with adaptive and programmable dynamics.

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Programmable Dynamic Steady States in ATP-Driven Non-Equilibrium DNA Systems

10.26434/chemrxiv.7964489 ◽

2019 ◽

Author(s):

Laura Heinen ◽

Andreas Walther

Keyword(s):

Self Assembly ◽

Soft Matter ◽

Enzymatic Reaction ◽

Reaction Network ◽

Steady States ◽

Supramolecular Systems ◽

Kinetics Of ◽

Average Bond ◽

Full Synchronization ◽

Non Equilibrium

<div><div><div><p>Inspired by the dynamics of the dissipative self-assembly of microtubules, chemically fueled synthetic systems with transient lifetimes are emerging for non-equilibrium materials design. However, realizing programmable or even adaptive structural dynamics has proven challenging because it requires synchronization of energy uptake and dissipation events within true steady states, which remains difficult to orthogonally control in supramolecular systems. Here, we demonstrate full synchronization of both events by ATP-fueled activation and dynamization of covalent DNA bonds via an enzymatic reaction network of concurrent ligation and cleavage. Critically, the average bond ratio and the frequency of bond exchange are imprinted into the energy dissipation kinetics of the network and tunable through its constituents. We introduce temporally and structurally programmable dynamics by polymerization of transient, dynamic covalent DNA polymers with adaptive steady-state properties in dependence of ATP fuel and enzyme concentrations. This approach enables generic access to non-equilibrium soft matter systems with adaptive and programmable dynamics.</p></div></div></div>

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Zero Eigenvalue Analysis for the Determination of Multiple Steady States in Reaction Networks

Zeitschrift für Naturforschung A ◽

10.1515/zna-1998-3-411 ◽

1998 ◽

Vol 53 (3-4) ◽

pp. 171-177

Author(s):

Hsing-Ya Li

Keyword(s):

Steady State ◽

Rate Constants ◽

Reaction Network ◽

Steady States ◽

Eigenvalue Analysis ◽

Zero Eigenvalue ◽

Positive Steady State ◽

Positive Steady States ◽

Positive Rate ◽

System Of Inequalities

Abstract A chemical reaction network can admit multiple positive steady states if and only if there exists a positive steady state having a zero eigenvalue with its eigenvector in the stoichiometric subspace. A zero eigenvalue analysis is proposed which provides a necessary and sufficient condition to determine the possibility of the existence of such a steady state. The condition forms a system of inequalities and equations. If a set of solutions for the system is found, then the network under study is able to admit multiple positive steady states for some positive rate constants. Otherwise, the network can exhibit at most one steady state, no matter what positive rate constants the system might have. The construction of a zero-eigenvalue positive steady state and a set of positive rate constants is also presented. The analysis is demonstrated by two examples.

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