Programmable DNA Nanoindicator‐Based Platform for Large‐Scale Square Root Logic Biocomputing

Abstract

The prospect of programming molecular computing systems to realize complex autonomous tasks has advanced the design of synthetic biochemical logic circuits. One way to implement digital and analog integrated circuits is to use noncovalent hybridization and strand displacement reactions in cell‐free and enzyme‐free nucleic acid systems. To date, DNA‐based circuits involving tens of logic gates capable of implementing basic and complex logic functions have been demonstrated experimentally. However, most of these circuits are still incapable of realizing complex mathematical operations, such as square root logic operations, which can only be carried out with 4 bit binary numbers. A high‐capacity DNA biocomputing system is demonstrated through the development of a 10 bit square root logic circuit. It can calculate the square root of a 10 bit binary number (within the decimal integer 900) by designing DNA sequences and programming DNA strand displacement reactions. The input signals are optimized through the output feedback to improve performance in more complex logical operations. This study provides a more universal approach for applications in biotechnology and bioengineering.

Constructing DNA logic circuits based on the toehold preemption mechanism

“…8 Because of its programmability, addressability, and specicity, DNA 9,10 has been one of the ideal materials for nanotechnology. It has been used to construct a wide variety of highly robust nanodevices, such as DNA circuits, [11][12][13][14][15][16] arithmetic computing systems, 17 biosensors, 18,19 nanomachines, 20 and probes. 21,22 Among them, the DNA logic circuit, which can be used as the basis for the development of biological computers, has attracted extensive attention.…”

“…The scalability and accuracy of DNA logic circuits in molecular computing and information processing have been extensively demonstrated. [11][12][13][14][15][16][17][42][43][44] Especially, nucleic acid-based constitutional dynamic networks provide versatile means to design computing circuits of enhanced complexity and advance the processing and scaling of DNA computing systems. 45 However, existing circuits have some problems that cannot be ignored.…”

Engineering the Stability of Nanozyme-Catalyzed Product for Colorimetric Logic Gate Operations

“…On the other hand, great progress has been made in the construction of logic gates and biochemical computation based on DNA [19][20][21], enzymes [16,[22][23][24][25], or complex biochemical systems [26]. For example, like computer devices, the use of natural enzymes for the construction of different Boolean logic systems has aroused people's wide concern due to a huge number of enzyme-based biocatalytic processes in living organisms (plants, animals, microorganisms) [25].…”

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

“…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.…”