Chemically Fueled Self‐Assembly in Biology and Chemistry

Das, Krishnendu; Gabrielli, Luca; Prins, Leonard J.

doi:10.1002/ange.202100274

Cited by 41 publications

(34 citation statements)

References 180 publications

(256 reference statements)

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“…In a wider perspective of systems chemistry, this work adds another layer of complexity compared to typically operated individual cyclic reaction networks 10,14,30 which are important for the design of autonomous systems and more intelligent materials. Even though biological machinery and enzymes are robust tools for the implementation of such a communication and cross-regulation behavior, we believe that the guidelines provided here are also relevant to improve fully man-made regulatory networks in supramolecular chemistry, or even classic polymer chemistry.…”

Section: Discussionmentioning

confidence: 99%

Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks

Sun

Deng

Walther

2021

Preprint

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Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. In contrast, emerging artificial fuel-driven systems most-ly focus on a single CRN and their implementation to direct self-assembly or material responses. In this work, we introduce a facile example of communication and cross-regulation among multiple DNA-based ERNs regulated by a concatenated RNA transcription regulator. For this purpose, we run two fuel-driven DNA-based ERNs by concurrent NAD+-fueled ligation and restriction via endo-nucleases (REases) in parallel. ERN one allows for the dynamic steady-state formation of the promoter sequence for T7 RNA poly-merase, which activates RNA transcription. The produced RNA regulator can repress or promote the second ERN via RNA-mediated strand displacement. Furthermore, adding RNase H to degrade the produced RNA can restart the reaction or tune the lag time of two ERNs, giving rise to a repression-recovery and promotion-stop processes. We believe that concatenation of multiple CRNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.

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Section: Discussionmentioning

confidence: 99%

Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks

Sun

Deng

Walther

2021

Preprint

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“…Unlike biology, synthetic chemists are not restricted to natural fuels like ATP and GTP, amino acid building blocks, or even to aqueous solvents. The past decade has seen an exploration of suitable chemistries, switches, and monomers that can reproduce some aspects of dissipative self-assembly that make microtubules so mesmerizing (see recent reviews ) [5][6][7][8][9] .…”

Section: Inspiration From Naturementioning

confidence: 99%

“…In recent years, 'toy models' [21][22][23][24] that consider the steady-state dimerization of species have been put forward to classify dissipative self-assembly based on how chemical energy is stored in thermodynamically unfavorable states (inspired by energy/information ratchets in biological systems 25,26 ; see also work on molecular motors 21 ). In addition, several numerical studies have been devoted to this topic 27,28 as well as perspectives 8,[29][30][31][32][33][34] .…”

Section: Aimmentioning

confidence: 99%

Insights into chemically-fueled supramolecular polymers

Sharko

Livitz

Piccoli

et al. 2022

Preprint

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Supramolecular polymerization can be controlled in space and time by chemical fuels. A non-assembled monomer is activated by the fuel and subsequently self-assembles into a polymer. Deactivation of the molecule either in solution or inside the polymer leads to disassembly. Whereas biology has already mastered this approach, fully artificial examples have only appeared in the past decade. Here, we map the available literature examples into four distinct regimes depending on their activation/deactivation rates and the equivalents of deactivating fuel. We present increasingly complex mathematical models, first considering only the chemical activation/deactivation rates (i.e., Transient Activation), and later including the full details of the isodesmic or cooperative supramolecular processes (i.e., Transient Self-assembly). We finish by showing that sustained oscillations are possible in chemically fueled cooperative supramolecular polymerization and provide mechanistic insights. We hope our models encourage the exact quantification of activation, deactivation, assembly, and disassembly kinetics in future studies.

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“…The nonequilibrium assembly in nature is a common and essential process. [1][2][3][4][5] The dissipative self-assembling systems always run at high energy states and maintain the active structures by consuming chemical fuels, which are the basis for living organisms to perform their complex functions. 4,6,7 Diverse transient assembly processes exist in life forms on both micro and macroscales.…”

Section: Introductionmentioning

confidence: 99%

“…[1][2][3][4][5] The dissipative self-assembling systems always run at high energy states and maintain the active structures by consuming chemical fuels, which are the basis for living organisms to perform their complex functions. 4,6,7 Diverse transient assembly processes exist in life forms on both micro and macroscales. 8,9 Learning from nature, the dissipative assembly of synthetic molecules driven by chemical fuels was suggested in 2010 by Boekhoven et al 10 Now, scientists have successfully constructed diverse nonequilibrium systems by adopting various types of microscopic building blocks, such as small molecules, [11][12][13][14] synthetic polymers, 15,16 biomacromolecules, 17,18 and nanoparticles.…”

Section: Introductionmentioning

confidence: 99%

Nonequilibrium Regulation of Interfacial Chemistry for Dissipative Supramolecular Assembly of Macroscopic Hydrogels

Zhao

Yuyu

Cui

et al. 2022

Preprint

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The nonequilibrium assembly in nature exists at the microscopic and macroscopic scales, and represents the most common way to regulate object motions by consuming chemical fuels. In artificial nonequilibrium systems, most of the work has focused on the microscopic dissipative assembly, whereas the investigation on nonequilibrium assembly of macroscopic building blocks is rarely reported. Here, we present an efficient strategy to dynamically mediate the interfacial chemistry of pH-responsive polyelectrolyte hydrogels, thereby regulating their macroscopic nonequilibrium assembly. The driving force for the assembly is the transient electrostatic attraction, which is regulated by the biocatalytic feedback-driven temporal programming of the pH of the system. The dissipative assembly process can be controlled by adjusting the hydrogel parameters and fuel composition and it can be repeated by refueling the system. Most importantly, the ordered sewing of complementary hydrogels promotes the precise nonequilibrium supramolecular assembly to yield transient macroscopic supramolecular devices potentially useful for timed release.

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Chemically Fueled Self‐Assembly in Biology and Chemistry

Cited by 41 publications

References 180 publications

Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks

Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks

Insights into chemically-fueled supramolecular polymers

Nonequilibrium Regulation of Interfacial Chemistry for Dissipative Supramolecular Assembly of Macroscopic Hydrogels

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