DNA‐Mediated Proximity‐Based Assembly Circuit for Actuation of Biochemical Reactions

Oh, Sung Won; Pereira, Adriana; Zhang, Ting; Li, Tianran; Lane, Ariel; Fu, Jinglin

doi:10.1002/ange.201806749

Cited by 2 publications

(6 citation statements)

References 33 publications

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“…Fu's group fabricated a DNA-regulated proximity-based logic circuit for modulation of biochemical reactions, Figure 17B. [113] The circuit consisted of a hairpin-locked catalytic cofactor with prohibited activity. In the presence of specific inputs, the TMSD reaction and aptamer/target interaction will induce a conformational change of DNA lock.…”

Section: Dna Logic-based Intelligent Bioanalysismentioning

confidence: 99%

Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio‐Applications

Fan

Wang

et al. 2020

Advanced Science

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DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

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Section: Dna Logic-based Intelligent Bioanalysismentioning

confidence: 99%

Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio‐Applications

Fan

Wang

et al. 2020

Advanced Science

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“…GOx/HRP cascade) are not sensitive to enzyme proximity, as discussed previously [92], only small differences of enzyme cascade activities were observed for these four conformations of DNA tweezers. In contrast, DNA nanomachines were more efficient in regulating enzyme/cofactor pairs (which do rely on proximity interaction), with enhanced activities ranging from a few fold up to 100-fold or more [48,49].…”

Section: Regulation Of Proximity Interactions In Biochemical Reactionsmentioning

confidence: 99%

“…Another commonly used crosslinker is disuccinimidyl suberate (DSS) in which the double succinimide ends can react with two primary amines to link them together [47]. DSS is especially useful for conjugating amine-modified ssDNA with organic cofactors, such as NAD or ATP [47][48][49]. Considerable progress has been made over the past two decades to improve the site-specificity of DNA-protein crosslinking.…”

Section: Protein-dna Bioconjugationmentioning

confidence: 99%

“…Using a simpler approach, Fu and coworkers reported a method of using a DNA hairpin structure to mediate the proximity assembly of biochemical reactions (Fig. 18a) [49]. The self-folded DNA hairpin carried a cofactor that was not able to interact with its partner enzyme, resulting in very low catalytic activity.…”

Section: Regulation Of Proximity Interactions In Biochemical Reactionsmentioning

confidence: 99%

mentioning

confidence: 99%

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DNA-Scaffolded Proximity Assembly and Confinement of Multienzyme Reactions

Wang

Liang

et al. 2020

Top Curr Chem (Z)

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Cellular functions rely on a series of organized and regulated multienzyme cascade reactions. The catalytic efficiencies of these cascades depend on the precise spatial organization of the constituent enzymes, which is optimized to facilitate substrate transport and regulate activities. Mimicry of this organization in a non-living, artificial system would be very useful in a broad range of applications-with impacts on both the scientific community and society at large. Self-assembled DNA nanostructures are promising applications to organize biomolecular components into prescribed, multidimensional patterns. In this review, we focus on recent progress in the field of DNA-scaffolded assembly and confinement of multienzyme reactions. DNA self-assembly is exploited to build spatially organized multienzyme cascades with control over their relative distance, substrate diffusion paths, compartmentalization and activity actuation. The combination of addressable DNA assembly and multienzyme cascades can deliver breakthroughs toward the engineering of novel synthetic and biomimetic reactors.

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DNA‐Mediated Proximity‐Based Assembly Circuit for Actuation of Biochemical Reactions

Cited by 2 publications

References 33 publications

Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio‐Applications

Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio‐Applications

DNA-Scaffolded Proximity Assembly and Confinement of Multienzyme Reactions

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