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

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>

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

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>

scholarly journals Programmable dynamic steady states in ATP-driven nonequilibrium DNA systems

2019 ◽  
Vol 5 (7) ◽  
pp. eaaw0590 ◽  
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.

scholarly journals Controlling the Kinetics of an Enzymatic Reaction through Enzyme or Substrate Confinement into Lipid Mesophases with Tunable Structural Parameters

2020 ◽  
Vol 21 (14) ◽  
pp. 5116
Author(s):  
Marco Mendozza ◽  
Arianna Balestri ◽  
Costanza Montis ◽  
Debora Berti
Keyword(s):  
Reaction Kinetics ◽  
Self Assembly ◽  
Liquid Crystalline ◽  
Structural Parameters ◽  
Enzymatic Reaction ◽  
X Ray Scattering ◽  
Nitrophenyl Phosphate ◽  
Vis Spectroscopy ◽  
Kinetics Of ◽  
Enzyme Alkaline Phosphatase

Lipid liquid crystalline mesophases, resulting from the self-assembly of polymorphic lipids in water, have been widely explored as biocompatible drug delivery systems. In this respect, non-lamellar structures are particularly attractive: they are characterized by complex 3D architectures, with the coexistence of hydrophobic and hydrophilic regions that can conveniently host drugs of different polarities. The fine tunability of the structural parameters is nontrivial, but of paramount relevance, in order to control the diffusive properties of encapsulated active principles and, ultimately, their pharmacokinetics and release. In this work, we investigate the reaction kinetics of p-nitrophenyl phosphate conversion into p-nitrophenol, catalysed by the enzyme Alkaline Phosphatase, upon alternative confinement of the substrate and of the enzyme into liquid crystalline mesophases of phytantriol/H2O containing variable amounts of an additive, sucrose stearate, able to swell the mesophase. A structural investigation through Small-Angle X-ray Scattering, revealed the possibility to finely control the structure/size of the mesophases with the amount of the included additive. A UV–vis spectroscopy study highlighted that the enzymatic reaction kinetics could be controlled by tuning the structural parameters of the mesophase, opening new perspectives for the exploitation of non-lamellar mesophases for confinement and controlled release of therapeutics.

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

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.

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

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.

scholarly journals On the use of catalysis to bias reaction pathways in out-of-equilibrium systems

2021 ◽  
Author(s):  
Michelle P. van der Helm ◽  
Tuanke de Beun ◽  
Rienk Eelkema
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Steady States ◽  
Chemical Reaction Network ◽  
Reaction Pathways ◽  
Maximum Conversion ◽  
Equilibrium Chemical Reaction ◽  
Equilibrium Chemical ◽  
Non Equilibrium

We show, via simulations, how catalytic control over individual paths in a fuel-driven non-equilibrium chemical reaction network in batch or flow gives rise to responses in maximum conversion, lifetime and steady states.

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

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.

In situ Time-Resolved Small-Angle X-ray Scattering Reveals the Formation Kinetics of Polyelectrolyte Complex Micelles

2019 ◽  
Author(s):  
Hao Wu ◽  
Jeffrey Ting ◽  
Siqi Meng ◽  
Matthew Tirrell
Keyword(s):  
Small Angle ◽  
Self Assembly ◽  
Electrostatic Interactions ◽  
Polyelectrolyte Complex ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Kinetics Of ◽  
Ray Scattering

We have directly observed the <i>in situ</i> self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. This work has elucidated one general kinetic pathway for the process of PEC micelle formation, which provides useful physical insights for increasing our fundamental understanding of complexation and self-assembly dynamics driven by electrostatic interactions that occur on ultrafast timescales.

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