Fuel‐Selective Transient Activation of Nanosystems for Signal Generation

Sala, Flavio della; Maiti, Subhabrata; Bonanni, Andrea; Scrimin, Paolo; Prins, Leonard J.

doi:10.1002/ange.201711964

Cited by 33 publications

(4 citation statements)

References 41 publications

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“…The difficulty in implementing such a concept in synthetic system is related to the need for highest levels of programmability and ability for deterministic autonomous reconfiguration leading to multiple transient dynamic steady-state (DySS) structures, which is a profound challenge in supramolecular chemistry. [24][25][26] On the contrary, DNA shows great potential to program reaction networks and pathways for self-assemblies in a systems chemistry approach. [27][28][29] Herein, we demonstrate pathway complexity in ATP-fueled transient DNA polymerizations from a species pool realizing autonomous and transient multiple DySS structures (Figure 1a,b).…”

Section: Introductionmentioning

confidence: 99%

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

Deng

Walther

2020

J. Am. Chem. Soc.

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We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization systems, achieving autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomers of dimers to randomized polymer structures 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 in the structure-forming step and which are reconfigured in an enzymatic reaction network. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.Nature relies on non-equilibrium structures and processes to perform work by dissipating energy stored in ATP or GTP. 1-4 Pathway complexity plays a pivotal role to associate those dynamic structures and thus realize a living system. For instance, intracellular signaling networks involve multiple steps of ATP/GTP-powered phosphorylation and enzyme activation for downstream regulations. 5-8 Thus far, synthetic systems with fuel-driven transient properties are developed in the fields of systems chemistry, materials science and synthetic biology. 4,[9][10][11][12] Synthetic systems requiring continuous energy influx have extended the features and functions of present-day functional materials. [13][14] Most presently existing fuel-driven systems show single trajectories of their non-equilibrium states, such as helical structure switching, 15 supramolecular polymerization, 14, 16 nanoreactors, 13, 17 transient hydrogels, [18][19] and photonic materials. 20 On the contrary, in classical supramolecular chemistry, pathway complexity is regularly exploited to transiently pass energetically downhill from metastable structures to equilibrium. 21-22 A relevant example showing multiple states in an autonomous fashion is the case of supramolecular helicity switching coupled to hydrolysis of environmental ATP to ADP, AMP, and to adenosine. 15 In directly chemically driven systems, Boekhoven and coworkers recently showed that small fuel amounts allowed the formation of reversibly assembling transient clusters, while large fuel amounts lead to a trapping of aggregates in a non-transient fashion. 23 Critically, pathway-controlled uphill fuel-driven systems involving multiple building blocks with an autonomous structural reconfiguration of multiple dynamic transient states have not been shown by any previous report. Such a concept would however be very valuable to promote a further integration of systems chemistry concepts with reaction networks and dissipative and transient structure formation.The difficulty in implementing such a concept in synthetic system is related to the need for highest levels of programmability and ability for deterministic autonomous reconfiguration leading to multiple transient dynamic steady-state (DySS) structures, which is a profound challenge in supramolecular chemistry. 24-26 On the contrary, DNA ...

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Section: Introductionmentioning

confidence: 99%

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

Deng

Walther

2020

J. Am. Chem. Soc.

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“…AP cleaves monophosphate nucleosides in nucleoside and inorganic phosphate, which have a lower templating ability. 27,32 Consequently, the addition of nucleotide under dissipative conditions installed by the presence of enzyme results in templated self-assembly with a lifetime that is determined by the rate at which the template is cleaved.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Chemical Information Processing by a Responsive Chemical System

Gabrielli,

Goldin,

Chandrabhas

et al. 2024

J. Am. Chem. Soc.

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Nature has an extraordinary capacity to precisely regulate the chemical reactivity in a highly complex mixture of molecules that is present in the cell. External stimuli lead to transient up-and downregulation of chemical reactions and provide a means for a cell to process information arriving from the environment. The development of synthetic chemical systems with life-like properties requires strategies that allow likewise control over chemical reactivity in a complex environment. Here, we show a synthetic system that mimics the initial steps that take place when a natural signal transduction pathway is activated. Monophosphate nucleosides act as chemical triggers for the self-assembly of nanoreactors that upregulate chemical reactions between reagents present at low micromolar concentrations. Different nucleotides template different assemblies and hence activate different pathways, thus establishing a distinct connection between input and output molecules. Trigger-induced upregulation of chemical reactivity occurs for only a limited amount of time because the chemical triggers are gradually removed from the system by enzymes. It is shown that the same system transiently produces different output molecules depending on the chemical input that is provided.

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“…Nanozymes are functional nanomaterials with emerging enzyme-like activities. − Because of their much more stable catalytic activities and lower cost compared with those of natural enzymes, they have recently been developed for wide applications, including biosensing. − A few pioneering studies have shown that the nanozyme sensor arrays composed of gold or iron oxide nanoparticles could be used for protein discrimination. − Inspired by these, we envisaged that 2D-MOF nanozymes are good alternatives to gold or iron oxide nanoparticles for sensor arrays because of their tailorable structures and catalytic activities as well as their highly exposed surfaces and active sites . In this work, we demonstrated that the peroxidase-mimicking activities of a series of 2D-MOF nanozymes could be modulated by various phosphates, forming the basis of the designed sensor arrays for phosphate discrimination.…”

mentioning

confidence: 99%

2D-Metal–Organic-Framework-Nanozyme Sensor Arrays for Probing Phosphates and Their Enzymatic Hydrolysis

et al. 2018

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The detection of phosphates and their enzymatic hydrolysis is of great importance because of their essential roles in various biological processes and numerous diseases. Compared with individual sensors for detecting one given phosphate at a time, sensor arrays are able to discriminate multiple phosphates simultaneously. Although nanomaterial-based sensor arrays have shown great promise for the discrimination of phosphates, very few of them have been explored for probing phosphates involved enzymatic hydrolysis. To fill this gap, herein we fabricated two-dimensional-metal-organic-framework (2D-MOF)-nanozyme-based sensor arrays by modulating their peroxidase-mimicking activity with various phosphates, including AMP, ADP, ATP, pyrophosphate (PPi), and phosphate (Pi). The sensor arrays were used to successfully discriminate the five phosphates not only in aqueous solutions but also in biological samples. The practical application of the sensor arrays was then validated with blind samples, where 30 unknown samples containing phosphates were accurately identified. Moreover, the sensor arrays were successfully applied to probing hydrolytic processes involving ATP and PPi that are catalyzed by apyrase and PPase, respectively. This work demonstrates a nanozyme-based sensor array as a convenient and reliable analytical platform for probing phosphates and their related enzymatic processes, which could be applied to other analytes and enzymatic reactions.

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Fuel‐Selective Transient Activation of Nanosystems for Signal Generation

Cited by 33 publications

References 41 publications

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

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

Chemical Information Processing by a Responsive Chemical System

2D-Metal–Organic-Framework-Nanozyme Sensor Arrays for Probing Phosphates and Their Enzymatic Hydrolysis

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