Development of a neuron model based on DNAzyme regulation

Chen, Cong; Wu, Ranfeng; Wang, Bin

doi:10.1039/d0ra10515e

Cited by 4 publications

(3 citation statements)

References 52 publications

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“…Similarly, DNAzyme and ASO associations that we have reported before have analyte recognizing modules that activate the associations′ RNA cleaving functions only after selective interaction with the analyte sequence [14,20,21,30] . Such dynamic DNA associations, that owe their responsiveness to DNA's inherent traits such as complementarity, can become intrinsic building blocks to DNA nanotechnology and molecular computational circuits [31–33] . Binary DNAzymes’ separated analyte recognition and target cleavage modules can be tailored to perfect their functionality independently from each other.…”

Section: Discussionmentioning

confidence: 91%

“…[14,20,21,30] Such dynamic DNA associations, that owe their responsiveness to DNA's inherent traits such as complementarity, can become intrinsic building blocks to DNA nanotechnology and molecular computational circuits. [31][32][33] Binary DNAzymes' separated analyte recognition and target cleavage modules can be tailored to perfect their functionality independently from each other. This feature makes them advantageous for molecular computation as they can be potentially designed to analyze complex molecular environments and perform complex logical operations.…”

Section: Discussionmentioning

confidence: 99%

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Thresholding DNA Nanomachine as a Highly Cooperative and Efficient Enzyme‐Like System for Controlled RNA Cleavage

Patra

ELdeeb

2023

ChemMedChem

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Therapeutic nucleic acid agents (TNA) can be activated by a marker RNA sequence followed by initiation of targeted RNA cleavage. This property can be used in conditional cell suppression, e. g., cancer marker‐dependent cell death. However, healthy cells often express lower levels of cancer markers, thus jeopardizing TNA activation exclusively in cancer cells. Earlier, we developed a conditionally activated split deoxyribozyme construct (DNA thresholder or DTh) that can be activated by high but not by low concentrations of cancer markers. It's activity, however, was suppressed by very high marker concentrations. Herein, we combine the DTh functional units in a single DNA association (Thresholding DNA nanomachine or Th‐DNM). Th‐DNM maintains a high level of RNA cleavage activity in the presence of marker concentrations above the threshold level. Th‐DNM differentiated fully complementary miR17 markers sequence from double base mismatched miR‐20. Th‐DNM can become a building block of DNA nanorobots for cancer treatment.

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Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Thresholding DNA Nanomachine as a Highly Cooperative and Efficient Enzyme‐Like System for Controlled RNA Cleavage

Patra

ELdeeb

2023

ChemMedChem

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“…Dediu et al [ 15 ] simulated the Boolean circuit using contextual hypergraph grammars techniques and further constructed the self-assembly of DNA tiles. In addition, half adder and half subtractor [ 16 , 17 , 18 ], full adder and full subtractor [ 19 , 20 , 21 ], encoder decoder [ 22 , 23 ], square root calculation [ 24 ], and neuron calculation model [ 25 ] have emerged. Qian and Winfree et al [ 26 ] proposed a “seesaw door” DNA motif based on DNA strand displacement technology, and on this basis, they further constructed a four-neuron Hopfield neural network computing model that can realize “heart guessing” [ 27 ] and winner-take-all neural network model [ 28 ]; this was breakthrough research in the field of molecular intelligent computing.…”

Section: Introductionmentioning

confidence: 99%

DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate

Liu

Zhou

et al. 2021

Biomolecules

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Numerical computation is a focus of DNA computing, and matrix operations are among the most basic and frequently used operations in numerical computation. As an important computing tool, matrix operations are often used to deal with intensive computing tasks. During calculation, the speed and accuracy of matrix operations directly affect the performance of the entire computing system. Therefore, it is important to find a way to perform matrix calculations that can ensure the speed of calculations and improve the accuracy. This paper proposes a DNA matrix operation method based on the mechanism of the DNAzyme binding to auxiliary strands to cleave the substrate. In this mechanism, the DNAzyme binding substrate requires the connection of two auxiliary strands. Without any of the two auxiliary strands, the DNAzyme does not cleave the substrate. Based on this mechanism, the multiplication operation of two matrices is realized; the two types of auxiliary strands are used as elements of the two matrices, to participate in the operation, and then are combined with the DNAzyme to cut the substrate and output the result of the matrix operation. This research provides a new method of matrix operations and provides ideas for more complex computing systems.

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Synthetic biological neural networks: From current implementations to future perspectives

Halužan Vasle,

Moškon

2024

BioSystems

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Development of a neuron model based on DNAzyme regulation

Abstract: The neuron model regulated by DNAzymes is simple to construct and possesses strong scalability, having great potential for use in the construction of large neural networks.

Cited by 4 publications

References 52 publications

Thresholding DNA Nanomachine as a Highly Cooperative and Efficient Enzyme‐Like System for Controlled RNA Cleavage

Thresholding DNA Nanomachine as a Highly Cooperative and Efficient Enzyme‐Like System for Controlled RNA Cleavage

DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate

Synthetic biological neural networks: From current implementations to future perspectives

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