Transient self-organisation of DNA coated colloids directed by enzymatic reactions

Dehne, H.; Reitenbach, A.; Bausch, Andreas R.

doi:10.1038/s41598-019-43720-7

Cited by 22 publications

(32 citation statements)

References 36 publications

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“…Additionally, assembly (kinetics) can be controlled spatially by fuel diffusion, for example, from a high-concentration reservoir. 119 , 132 − 134 Finally, the rate of fuel consumption and hence assembly kinetics can be regulated by relying on catalytic fuel-converting processes. 135 − 138 However, the use of fuels is typically associated with an accumulation of waste products in the system ( Figure 1 ).…”

Section: Fuel-mediated Out-of-equilibrium Assemblymentioning

confidence: 99%

“…coupled the transient clustering of micrometer-sized DNA coated colloids with a competing antagonistic enzymatic reaction of RNA polymerization and degradation. 119 The system comprises two types of colloidal particles ( Figure 11 , red and green) both decorated with noncomplementary single-stranded DNA segments. In equilibrium, both types of colloids are mutually repelling due to the electrosteric repulsion of the DNA corona, resulting in a stable dispersion.…”

Section: Fuel-mediated Out-of-equilibrium Assemblymentioning

confidence: 99%

Section: Fuel-mediated Out-of-equilibrium Assemblymentioning

confidence: 99%

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Out-of-Equilibrium Colloidal Assembly Driven by Chemical Reaction Networks

et al. 2020

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Transient assembled structures play an indispensable role in a wide variety of processes fundamental to living organisms including cellular transport, cell motility, and proliferation. Typically, the formation of these transient structures is driven by the consumption of molecular fuels via dissipative reaction networks. In these networks, building blocks are converted from inactive precursor states to active (assembling) states by (a set of) irreversible chemical reactions. Since the activated state is intrinsically unstable and can be maintained only in the presence of sufficient fuel, fuel depletion results in the spontaneous disintegration of the formed superstructures. Consequently, the properties and behavior of these assembled structures are governed by the kinetics of fuel consumption rather than by their thermodynamic stability. This fuel dependency endows biological systems with unprecedented spatiotemporal adaptability and inherent self-healing capabilities. Fascinated by these unique material characteristics, coupling the assembly behavior to molecular fuel or light-driven reaction networks was recently implemented in synthetic (supra)molecular systems. In this invited feature article, we discuss recent studies demonstrating that dissipative assembly is not limited to the molecular world but can also be translated to building blocks of colloidal dimensions. We highlight crucial guiding principles for the successful design of dissipative colloidal systems and illustrate these with the current state of the art. Finally, we present our vision on the future of the field and how marrying nonequilibrium self-assembly with the functional properties associated with colloidal building blocks presents a promising route for the development of next-generation materials.

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Section: Fuel-mediated Out-of-equilibrium Assemblymentioning

confidence: 99%

Section: Fuel-mediated Out-of-equilibrium Assemblymentioning

confidence: 99%

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Out-of-Equilibrium Colloidal Assembly Driven by Chemical Reaction Networks

et al. 2020

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“…In previous studies, RNA strands were utilized as a fuel to drive the formation of polymeric colloid assemblies, DNA nanotubes, and a molecular device . The advantage of using RNA fuel within mixed RNA/DNA assemblies is the easy control over the selectivity of fuel consumption by RNases while maintaining DNA strands as structural elements within the assemblies.…”

Section: Figurementioning

confidence: 99%

Four‐Dimensional Deoxyribonucleic Acid–Gold Nanoparticle Assemblies

et al. 2020

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Organization of gold nanoobjects by oligonucleotides has resulted in many three‐dimensional colloidal assemblies with diverse size, shape, and complexity; nonetheless, autonomous and temporal control during formation remains challenging. In contrast, living systems temporally and spatially self‐regulate formation of functional structures by internally orchestrating assembly and disassembly kinetics of dissipative biomacromolecular networks. We present a novel approach for fabricating four‐dimensional gold nanostructures by adding an additional dimension: time. The dissipative character of our system is achieved using exonuclease III digestion of deoxyribonucleic acid (DNA) fuel as an energy‐dissipating pathway. Temporal control over amorphous clusters composed of spherical gold nanoparticles (AuNPs) and well‐defined core–satellite structures from gold nanorods (AuNRs) and AuNPs is demonstrated. Furthermore, the high specificity of DNA hybridization allowed us to demonstrate selective activation of the evolution of multiple architectures of higher complexity in a single mixture containing small and larger spherical AuNPs and AuNRs.

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“…However, so far most examples of DNA-based molecular motors 32 , walkers 33 , or transport systems 34 – 36 are thermodynamically down-hill, and only few studies focused on fuel-driven non-equilibrium self-assembled DNA structures using temporary up-hill process, which, however, is essential for programming transient autonomous lifecycles and adaptive steady-states 37 . Most notable examples include enzyme-assisted transcription/degradation machineries that allow transient structures 38 , 39 or other reaction networks 40 . We recently demonstrated ATP-fueled dynamization of a covalent DNA bond via an enzymatic reaction network (ERN) of concurrent ligation and cleavage, and reported details on engineering the adaptiveness of the dynamics, pathway complexity, and light-modulated behaviors on a polymer level 41 – 43 .…”

Section: Introductionmentioning

confidence: 99%

ATP-powered molecular recognition to engineer transient multivalency and self-sorting 4D hierarchical systems

Deng

Walther

2020

Nat Commun

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Biological systems organize multiple hierarchical structures in parallel, and create dynamic assemblies and functions by energy dissipation. In contrast, emerging artificial nonequilibrium self-assembling systems have remained relatively simplistic concerning hierarchical design, and non-equilibrium multi-component systems are uncharted territory. Here we report a modular DNA toolbox allowing to program transient non-equilibrium multicomponent systems across hierarchical length scales by introducing chemically fueled molecular recognition orchestrated by reaction networks of concurrent ATP-powered ligation and cleavage of freely programmable DNA building blocks. Going across hierarchical levels, we demonstrate transient side-chain functionalized nucleic acid polymers, and further introduce the concept of transient cooperative multivalency as a key to bridge length scales to pioneer fuel-driven encapsulation, self-assembly of colloids, and non-equilibrium transient narcissistic colloidal self-sorting on a systems level. The fully programmable and functionalizable DNA components pave the way to design chemically fueled 4D (3 space, 1 time) molecular multicomponent systems and autonomous materials.

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Transient self-organisation of DNA coated colloids directed by enzymatic reactions

Cited by 22 publications

References 36 publications

Out-of-Equilibrium Colloidal Assembly Driven by Chemical Reaction Networks

Out-of-Equilibrium Colloidal Assembly Driven by Chemical Reaction Networks

Four‐Dimensional Deoxyribonucleic Acid–Gold Nanoparticle Assemblies

ATP-powered molecular recognition to engineer transient multivalency and self-sorting 4D hierarchical systems

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