Entropy-driven DNA logic circuits regulated by DNAzyme

Yang, Jing; Wu, Ranfeng; Li, Yifan; Wang, Zhiyu; Pan, Linqiang; Zhang, Qiang; Lu, Zhiyong; Zhang, Cheng

doi:10.1093/nar/gky663

Cited by 90 publications

(43 citation statements)

References 44 publications

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“…This patterning would be an integral component of complex, biochip-based spatially organized genetic circuits. In addition, cascading nucleic acid computing circuits based on programmable and targeted substrate cleavage can be achieved with selective nucleases such as RNase H and HII, which can be triggered to cleave at specific locations and release specific sequences for triggering, e.g., downstream logic gates 8,52 .…”

Section: Discussionmentioning

confidence: 99%

Multi-level patterning nucleic acid photolithography

et al. 2019

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The versatile and tunable self-assembly properties of nucleic acids and engineered nucleic acid constructs make them invaluable in constructing microscale and nanoscale devices, structures and circuits. Increasing the complexity, functionality and ease of assembly of such constructs, as well as interfacing them to the macroscopic world requires a multifaceted and programmable fabrication approach that combines efficient and spatially resolved nucleic acid synthesis with multiple post-synthetic chemical and enzymatic modifications. Here we demonstrate a multi-level photolithographic patterning approach that starts with large-scale in situ surface synthesis of natural, modified or chimeric nucleic acid molecular structures and is followed by chemical and enzymatic nucleic acid modifications and processing. The resulting high-complexity, micrometer-resolution nucleic acid surface patterns include linear and branched structures, multi-color fluorophore labeling and programmable targeted oligonucleotide immobilization and cleavage.

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Section: Discussionmentioning

confidence: 99%

Multi-level patterning nucleic acid photolithography

et al. 2019

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“…tremendously accelerates the process of branch migration and provides a reliable support for large biochemical reaction circuits. The introduction of toeholds guides a wide variety of biochemical reaction networks, including entropy-driven reactions and DNA-catalyzed networks [30], DNAzymerelated logic circuits [31], nonlinear hybridization chain reactions [32], DNA logic gate platform for miRNA analysis [33] and deoxyribozyme-based molecular automaton [34].…”

Section: Introductionmentioning

confidence: 99%

Biochemical Logic Circuits Based on DNA Combinatorial Displacement

2020

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DNA, as an excellent nano-engineering material, contributes to a new computing model, namely, DNA computing. This model is a type of biological computing, which takes advantage of the high density and high parallelism of molecules. One of the current methods of implementing DNA computing is to construct DNA circuits, among which the toehold-mediated DNA strand displacement technique is an important method. The hybridization of toehold domains provides the start position and accelerates the branch migration process. Toehold-based DNA combinatorial displacement is a practical method for designing and implementing DNA circuits. In this paper, we designed and simulated a multiplexer using the DNA combinatorial displacement mechanism to verify its practicability. Additionally, we improved and optimized the existing logic INHIBIT gate by leveraging the DNA combinatorial displacement mechanism so that the DNA strands in the entire chemical reaction network (CRN) system are capable of coexisting in large quantities. Moreover, we applied this improvement to the demultiplexer. Our method provides more capabilities to larger and more complicated DNA integrated circuits. INDEX TERMS Combinatorial strand displacement, logic gate, CRN, DNA computing.

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“…logarithms Network [20], Enzymatic reaction Network, and other networks are outstanding works [21]- [24].…”

Section: Introductionmentioning

confidence: 99%

DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement

et al. 2020

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Since the discovery of the DNA Strand Displacement mechanism, researchers have implemented a lot of applications, such as DNA computing, DNA Circuits, Logic gates, and Chemical Reaction network. To achieve those functions, a well-designed system is essential, among which the toehold domains and migration domains play a vital role. In this paper, we designed three basic logic gates based on the toehold mediates DNA strand displacement mechanism, and utilized them to struct a three-layer multiplexer DNA logic circuit. However, the traditional INHIBIT gate annihilated all the inputs strands which obscure the multiplexer in further applications. Therefore, we improved the INHIBIT gate, so the desired input strand can be selected, and the corresponding output strand can be identified. Lastly, we adjusted the multiplexer and realized a cyclic DNA circuit. The simulation results verified the efficiency and reliability of our multiplexer DNA logic circuits. Our method has the ability in architecting complex DNA integrated circuits.INDEX TERMS DNA strand displacement, logic circuits, INHIBIT gate, demultiplexer.

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Entropy-driven DNA logic circuits regulated by DNAzyme

Cited by 90 publications

References 44 publications

Multi-level patterning nucleic acid photolithography

Multi-level patterning nucleic acid photolithography

Biochemical Logic Circuits Based on DNA Combinatorial Displacement

DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement

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