DNAzyme- and light-induced dissipative and gated DNA networks

Wang, Jianbang; Li, Zhenzhen; Zhou, Zhixin; Ouyang, Yu; Zhang, Junji; Ma, Xiang; Tian, He; Willner, Itamar

doi:10.1039/d1sc02091a

Cited by 37 publications

(49 citation statements)

References 91 publications

(40 reference statements)

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“…In addition, enzyme-guided transient release and uptake of loads and DNA ligation ( 43 , 44 ) and transient enzyme-driven aggregation of nanoparticles and control over their optical properties were demonstrated ( 45 ). All-DNA DNAzyme-driven transient systems and gated transient networks and control over transient catalytic processes were reported ( 46 ). Mimicking complex biological networks by artificial circuits is, however, at its infancy, and transcriptional circuits acting as transcriptional oscillators ( 47 , 48 ) or transcriptional switches ( 49 ) and bistable regulatory networks ( 50 ) were reported.…”

Section: Introductionmentioning

confidence: 99%

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

Wang

Willner

2022

Sci. Adv.

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Following transient spatiotemporal misregulation of gene expression programs by native transcription machineries, we introduce a versatile biomimetic concept to design transient dynamic transcription machineries, revealing gated and cascaded temporal transcription of RNAs. The concept is based on the engineering of the reaction module consisting of malachite green (MG) and/or DFHBI {(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4 H -imidazol-4-one} DNA scaffolds, T7 RNA polymerase (RNAP) aptamer transcription scaffold, and the inhibited T7 RNAP-aptamer complex. In the presence of the counter RNAP aptamer strand and ribonucleoside triphosphates, the triggered activation of the three transcription scaffolds are activated, leading to the transcription of the MG and/or DFHBI RNA aptamer and to the transcription of the RNAP aptamer acting as an autoinhibitor that leads to the transient temporal, dissipative, and blockage of all transcription. By appropriate design of the transcription scaffolds and the inhibitors/coupler, transient gated and cascaded transcription processes are demonstrated, and a bimodal transcription module synthesizing a transient operating ribozyme is introduced.

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Section: Introductionmentioning

confidence: 99%

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

Wang

Willner

2022

Sci. Adv.

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“…These photoswitchable binding affinities of azobenzene compounds were applied to develop DNA-based switches, [150][151][152] machines, [153][154][155] and nanoscale devices. [156][157] In fact, transazobenzene is photoisomerized to cis-azobenzene, illumination [149] Copyright 2021, Royal Society of Chemistry.…”

Section: Photochemically-driven Transient Dna-based Network and Struc...mentioning

confidence: 99%

“…The ligated domains include the BamHI cleavage site, resulting in the cleavage of the duplex G/P into the parent deprotected units, while the ATP fuel is being consumed, Figure 14C. Thus, the light-triggered release of the [149] Copyright 2021, Royal Society of Chemistry.…”

Section: Photochemically-driven Transient Dna-based Network and Struc...mentioning

confidence: 99%

Transient Out‐of‐Equilibrium Nucleic Acid‐Based Dissipative Networks and Their Applications

Wang

Willner

2022

Adv Funct Materials

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Dynamic, dissipative reactions play important roles in biological processes, and emulating such biological processes by artificial circuits and networks is a challenging topic in the area of Systems Chemistry. The present article summarizes efforts to apply the information encoded in the base sequence of nucleic acids to assemble transient, dissipative DNA‐based networks mimicking natural processes. The design principles of the transient nucleic acid‐based systems are introduced. Triggered reaction moduli lead to a transient intermediary constituent recovered to the parent moduli by enzymes, DNAzyme, or light as control units are described. Transient DNA‐based circuitries of enhanced complexities revealing temporal gated or cascaded transformations are demonstrated. Different applications of dynamically triggered transient circuits are introduced, including the temporal aggregation and deaggregation of plasmonic nanoparticles or semiconductor quantum dots and the control over their optical properties, the transient release and uptake of loads by aptamer scaffolds, and the transient reconfiguration of constitutional dynamic networks and the control over emergent catalytic functions. The future perspectives of dissipative nucleic acid‐based networks and their potential future applications are discussed.

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“…In addition, the recognition and catalytic properties of nucleic acid and their responsiveness to auxiliary enzymes, such as nicking enzymes or endonucleases, provide versatile means to design dynamic, transient, out-of-equilibrium systems (43)(44)(45). These included the fuel-driven transient DNA strand displacement circuitry with self-resetting functions (46), dissipative DNA-based aptamers for the transient loading and release of cargoes (47), the assembly of bistable genetic regulatory networks (48,49), the design of in vitro transcriptional oscillators (50,51), the design of transient nucleic acid structures controlled by redox inputs (52), and the assembly of dynamic DNAzyme-based circuitries (53). In addition, enzymeguided activation of transient nucleic acid-based networks was demonstrated, including the nicking enzyme-activated dissipative gated and cascaded DNA network operations (54), the nicking enzyme-guided transient reconfiguration of constitutional dynamic networks (55), the nicking enzyme-activated transient control of the optical properties of Au nanoparticles and semiconductor quantum dots, through their dynamic dissipative aggregation and deaggregation by bridging nucleic acids (56), and the adenosine triphosphatedriven ligation of toehold-modified duplex nucleic acids and their dissipative separation by endonucleases (57).…”

Section: Introductionmentioning

confidence: 99%

Dissipative biocatalytic cascades and gated transient biocatalytic cascades driven by nucleic acid networks

2022

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Living systems consist of complex transient cellular networks guiding structural, catalytic, and switchable functions driven by auxiliary triggers, such as chemical or light energy inputs. We introduce two different transient, dissipative, biocatalytic cascades, the coupled glucose oxidase (GOx)/horseradish peroxidase (HRP) glucose–driven oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS 2− ) to the radical anion (ABTS •− ) and the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD + ) lactate–driven reduction of NAD + to NADH. The transient biocatalytic systems are driven by nucleic acid reaction modules using a nucleic acid fuel strand L 1 ′ and a nicking enzyme, Nt.BbvCI, as fuel-degrading catalyst, leading to the dynamic spatiotemporal transient formation of structurally proximate biocatalysts activating the biocatalytic cascades and transient coupled processes, including the generation of chemiluminescence and the synthesis of alanine. Subjecting the mixture of biocatalysts to selective inhibitors allows the gated transient operation of the biocatalysts. The kinetics of transient biocatalytic cascades are accompanied by kinetic models and computational simulations.

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DNAzyme- and light-induced dissipative and gated DNA networks

Abstract: Nucleic acid-based dissipative, out-of-equilibrium systems are introduced as functional assemblies emulating transient dissipative biological transformations. One system involves a Pb2+-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of...

Cited by 37 publications

References 91 publications

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

Transient Out‐of‐Equilibrium Nucleic Acid‐Based Dissipative Networks and Their Applications

Dissipative biocatalytic cascades and gated transient biocatalytic cascades driven by nucleic acid networks

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