Massively Parallel DNA Computing Based on Domino DNA Strand Displacement Logic Gates

Abstract

DNA computing has gained considerable attention due to the characteristics of high-density information storage and high parallel computing for solving computational problems. Building addressable logic gates with biomolecules is the basis for establishing biological computers. In the current calculation model, the multiinput AND operation often needs to be realized through a multilevel cascade between logic gates. Through experiments, it was found that the multilevel cascade causes signal leakage and affects the stability of the system. Using DNA strand displacement technology, we constructed a domino-like multiinput AND gate computing system instead of a cascade of operations, realizing multiinput AND computing on one logic gate and abandoning the traditional multilevel cascade of operations. Fluorescence experiments demonstrated that our methods significantly reduce system construction costs and improve the stability and robustness of the system. Finally, we proved stability and robustness of the domino AND gate by simulating the tic-tac-toe process with a massively parallel computing strategy.

Recent progress in stimuli‐responsive DNA‐based logic gates: Design, working principles and biological applications

“…Over the past years, many biological gates have been created by comprising various biomolecules including DNA, RNA, proteins and signaling molecules. [100,101] Among the biomolecular candidates, DNA has the merits of high programmability and structural predictability, so it is capable of processing complex logic operations, [102][103][104] making it favorable to be adopted in developing biological gates. Chen and co-workers utilized DNA strand displacement to engineer synthetic protein switches to control the proximity of two proteins dynamically and logically.…”

A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems

“…It can be achieved at room temperature. Currently, DNA molecule displacement reactions have been widely used in fields such as logic computation, [3][4][5][6][7] biosensors, [8][9][10] molecular robotics, [11][12][13] information encryption, [14][15][16][17] and medical diagnosis. [18][19][20][21] The emergence of complex biomolecular circuits facilitated the survival of cells with intelligent behavior, predating the evolution of neural brains.…”

“…It can be achieved at room temperature. Currently, DNA molecule displacement reactions have been widely used in fields such as logic computation, 3–7 biosensors, 8–10 molecular robotics, 11–13 information encryption, 14–17 and medical diagnosis. 18–21…”

Rapid microRNA detection method based on DNA strand displacement for ovarian cancer cells

“…So far, TSDRs have been applied in various fields, including biocomputing systems [24][25][26][27], artificial neuro systems [28,29], bio-electronical circuits [30,31], and biosensors [32,33]. In the field of biosensors, many remarkable works have been accomplished.…”