Dissipative operation of pH-responsive DNA-based nanodevices

Mariottini, Davide; Ercolani, Gianfranco; Stefano, Stefano Di; Ricci, Francesco

doi:10.1039/d1sc03435a

Cited by 36 publications

(32 citation statements)

References 65 publications

(40 reference statements)

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“…In Ricci's group, a dissipative system with pH‐controlling ability was constructed with carboxylic acid derivatives (Figure 3C, left panel). [ 34 ] The initial addition of 2‐cyanopropanoic acid (CPA) led to a pH drop and the gradual decarboxylation of the CPA restored the pH. Instead of a DNA i‐motif, a pH‐sensitive DNA sequence that could form an intramolecular triplex via Hoogsteen interactions was used and it was functionalized with both a fluorescent probe and a quencher.…”

Section: Chemically Fueled Dna‐based Dissipative Assemblymentioning

confidence: 99%

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DNA‐Based Dissipative Assembly toward Nanoarchitectonics

Liu

et al. 2022

Adv Funct Materials

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Figure 4. Dissipative DNA assemblies fueled by redox reactions. A) Left panel: The reversible release of a ligand from a DNA sequence fueled by a redox reaction. Right panel: The fluorescence evolution upon the repeated addition of the disulfide-linked DNA modulator. Reproduced with permission. [36] Copyright 2020, Wiley-VCH. B) Top left panel: Schematic illustration of the transient self-assembly of DNA nanotubes activated by disulfide-containing DNA. Top middle panel: The measured DNT formation in the presence of disulfide activators with various lengths at 1 and 24 h. Top right panel: Fluorescence microscopy images of transient DNA nanotubes in the presence of Act_16. Bottom left panel: Schematic illustration of the transient selfassembly of DNA nanotubes inhibited by disulfide-containing DNA. Bottom middle panel: The measured DNA nanotube formation in the presence of disulfide inhibitors with various lengths at 1 and 24 h. Bottom right panel: Fluorescence microscopy images of transient DNA nanotubes in the presence of Inhib_14. Reproduced with permission. [37] Copyright 2020, Wiley-VCH.

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Section: Chemically Fueled Dna‐based Dissipative Assemblymentioning

confidence: 99%

“…Middle and right panel: The evolution of pH (left) and fluorescence intensity (right) upon the addition of 2-cyanopropanoic acid. Reproduced with permission [34]. Copyright 2021, Royal Society of Chemistry.…”

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confidence: 99%

DNA‐Based Dissipative Assembly toward Nanoarchitectonics

Liu

et al. 2022

Adv Funct Materials

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“…Later, Di Stefano and Ricci further employed the time‐programmable modulation of pH by activated carboxylic acids to control the operation of DNA‐based nanodevices, which undergo duplex‐triplex transitions at acidic pH [60b] . The pH‐responsiveness is given by the number of cytosine bases in the engineered oligonucleotide sequences, which are prone to form an intramolecular triplex at low pH through Hoogsteen interactions between complementary C‐G base pairs.…”

Section: Chemical Tools For the Temporal Control Of Water Solution Phmentioning

confidence: 99%

Chemical Tools for the Temporal Control of Water Solution pH and Applications in Dissipative Systems

2022

Self Cite

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The chemical reagents used to achieve a predictable and programmable time control of the pH of water solutions are reviewed with the purpose to present a toolbox of instruments to be used when a precise pH vs time profile is needed. These tools are particularly useful in view of the growing interest on dissipative systems, many of which operate in water solutions, under the action of reagents (chemical fuels) that allow for programmed pH evolution. After a brief introduction describing the importance of such tools for the operation of dissipative systems in water, five sections follow, which illustrate the different method used so far to temporally control the pH of a water solution. In particular, time‐programmable pH variations based on: 1) bubbling of gases (CO2, N2, Air), 2) hydrolysis of esters, lactones and sultones, 3) enzymatic and biocatalytic networks, 4) decarboxylation reaction of activated carboxylic acids, and 5) pH‐oscillators are described together with selected examples of application.

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“…Such a dynamics is considered a dissipative process, of high current interest in relation to transient supramolecular assemblies. [30][31][32][33][34][35][36][37][38] Engineering a dissipative dynamics in a crown ether rotaxane is challenging, because it is known that subtle changes in stopper structure lead to large changes in the threading/dethreading kinetics, resulting in a sharp transition from pseudorotaxane to rotaxane-like character of the complex, an effect termed "all-ornothing" substituent effect. [39,40] So far, studies that approached self-assembly kinetics investigated the threading processes affording thermodynamically stable complexes, whereas the dethreading kinetics from high-energy states -which are expected to be significantly different -remained essentially unexplored.…”

Section: Introductionmentioning

confidence: 99%

Control on dissipative kinetics reveals the entropically-dominated essence of interlocked molecular machines

Noja

Garrido

Gualandi

et al. 2022

Preprint

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The operation of nanomachines is fundamentally different from that of their macroscopic counterparts. In particular, the role of solvent is critical, yet rarely associated with machine functionality. Here we study a minimal model of one of the most advanced molecular machines, to gain control on its operation by engineering components and the employed solvent. Operation kinetics was modulated over more than four orders of magnitude, and could be fine-tuned. Leveraging solvent properties, it was possible to realize multiple cycles of the molecular machine operation while monitoring it. Our work expands the capabilities of acid-base powered molecular machines, contributing to the development of systems that leverage solvent properties to expand their functionality.

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Dissipative operation of pH-responsive DNA-based nanodevices

Abstract: We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the...

Cited by 36 publications

References 65 publications

DNA‐Based Dissipative Assembly toward Nanoarchitectonics

DNA‐Based Dissipative Assembly toward Nanoarchitectonics

Chemical Tools for the Temporal Control of Water Solution pH and Applications in Dissipative Systems

Control on dissipative kinetics reveals the entropically-dominated essence of interlocked molecular machines

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