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.

A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme

“…DNAzyme [ 28 ] is a kind of functional nucleic acid with a special sequence. It has the characteristics of easy synthesis, efficient catalysis, and specific recognition, and it has been widely applied in nanodevices [ 29 , 30 ], logic computing [ 31 , 32 , 33 , 34 , 35 ], dynamic reaction networks [ 36 , 37 , 38 , 39 , 40 , 41 ], and self-assembly [ 42 , 43 ]. In the study of DNAzyme, the programmable regulation of conformation has always been the focus of research.…”

Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits

“…1,2 Based on the principle of complementary base pairing, DNA molecules are being used in frontier areas such as neural networks, 3,4 information encryption 5,6 disease detection 7,8 and DNA storage. [9][10][11] With great potential for information transfer and processing, DNA molecules enable molecular logic circuits, [12][13][14] tiles, [15][16][17] walker machines, [18][19][20] and protein interaction. 21 Molecular logic circuits are circuits that perform basic logic operations, and they are often used to implement functions such as parity checking, 22,23 logic computations, 24,25 drug delivery 26,27 and biosensing.…”