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

Shaoxia  Xu; Yuan  Liu; Shihua Zhou; Qiang  Zhang; Nikola Kasabov

doi:10.3390/biom11121797

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

Shaoxia Xu
, Yuan Liu
, Shihua Zhou
, Qiang Zhang
, Nikola Kasabov

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

110 Downloads (Pure)

Abstract

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.

Original language	English
Article number	1797
Pages (from-to)	1-16
Number of pages	16
Journal	Biomolecules
Volume	11
Issue number	12
Early online date	30 Nov 2021
DOIs	https://doi.org/10.3390/biom11121797
Publication status	Published online - 30 Nov 2021

Bibliographical note

Funding Information:
This work is supported by the National Key Technology R&D Program of China (No.2018YFC0910500), the National Natural Science Foundation of China (Nos. 61425002, 61751203, 61772100, 61972266, 61802040), Liao Ning Revitalization Talents Program (No. XLYC2008017), the Innovation and Entrepreneurship Team of Dalian University (No. XQN202008), Natural Science Foundation of Liaoning Province (No. 2021MS344), Scientific Research Fund of Liaoning Provincial Education Department (No. LJKZ1186), Dalian University Scientific Research Platform Program (No. 202101YB02).

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Funding

Funding Information: This work is supported by the National Key Technology R&D Program of China (No.2018YFC0910500), the National Natural Science Foundation of China (Nos. 61425002, 61751203, 61772100, 61972266, 61802040), Liao Ning Revitalization Talents Program (No. XLYC2008017), the Innovation and Entrepreneurship Team of Dalian University (No. XQN202008), Natural Science Foundation of Liaoning Province (No. 2021MS344), Scientific Research Fund of Liaoning Provincial Education Department (No. LJKZ1186), Dalian University Scientific Research Platform Program (No. 202101YB02). Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 9 Industry, Innovation, and Infrastructure

Keywords

DNA computing
numerical computation
DNAzyme
matrix operations

Access to Document

10.3390/biom11121797Licence: CC BY

Zhou et al MDPI biomolecules-11-01797-v2Final published version, 3.87 MBLicence: CC BY

Cite this

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title = "DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate",

abstract = "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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AU - Kasabov, Nikola

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N2 - 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.

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

Abstract

Bibliographical note

Funding

UN SDGs

Keywords

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