Molecular Logic Gates Based on Localized DNA Strand Displacement

2016 ◽  
Vol 13 (6) ◽  
pp. 3948-3952 ◽  
Author(s):  
Yanfeng Wang ◽  
Wenwen Zhang ◽  
Xing Li ◽  
Guangzhao Cui
Keyword(s):  
Logic Gates ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Molecular Logic Gates ◽  
Dna Strand Displacement ◽  
Dna Strand

Molecular Logic Gate Based on DNA Strand Displacement Reaction

2021 ◽  
Vol 16 (6) ◽  
pp. 974-977
Author(s):  
Jingjing Ma
Keyword(s):  
Logic Gate ◽  
Logic Gates ◽  
Displacement Reaction ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Molecular Logic Gates ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Biochemical Experiment ◽  
Strand Displacement Reaction

In this paper, I construct an XOR logic gate based on DNA strand displacement reaction, and verify our design through corresponding biochemical experiment. I designed several different DNA strands. Based on two basic DNA strand displacement reaction mechanisms, by adding different input strands and taking the signal of FAM fluorescent group as the output, the XOR logic gate is realized. The result shows that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.

scholarly journals 8-Bit Adder and Subtractor with Domain Label Based on DNA Strand Displacement

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2989 ◽  
Author(s):  
Weixuan Han ◽  
Changjun Zhou
Keyword(s):  
Dna Computing ◽  
Logic Gates ◽  
Logic Circuits ◽  
Calculation Model ◽  
Strand Displacement ◽  
High Concentration ◽  
Low Concentration ◽  
Molecular Logic ◽  
Dna Strand Displacement ◽  
Dna Strand

DNA strand displacement, which plays a fundamental role in DNA computing, has been widely applied to many biological computing problems, including biological logic circuits. However, there are many biological cascade logic circuits with domain labels based on DNA strand displacement that have not yet been designed. Thus, in this paper, cascade 8-bit adder/subtractor with a domain label is designed based on DNA strand displacement; domain t and domain f represent signal 1 and signal 0, respectively, instead of domain t and domain f are applied to representing signal 1 and signal 0 respectively instead of high concentration and low concentration high concentration and low concentration. Basic logic gates, an amplification gate, a fan-out gate and a reporter gate are correspondingly reconstructed as domain label gates. The simulation results of Visual DSD show the feasibility and accuracy of the logic calculation model of the adder/subtractor designed in this paper. It is a useful exploration that may expand the application of the molecular logic circuit.

Research of Molecule Logic Circuit Based on DNA Strand Displacement Reaction

2016 ◽  
Vol 13 (10) ◽  
pp. 7684-7691 ◽  
Author(s):  
Zicheng Wang ◽  
Zijie Cai ◽  
Zhonghua Sun ◽  
Jian Ai ◽  
Yanfeng Wang ◽  
...  
Keyword(s):  
Logic Circuits ◽  
Logic Circuit ◽  
The Other ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Gold Nanoprobe ◽  
Decoder Circuit ◽  
Strand Displacement Reaction

Because of its outstanding advantages, DNA strand displacement (DSD) reaction has been widely used for signals processing and molecular logic circuit constructing. Two digital logic circuits are constructed in this paper. One is the encoder circuit with four inputs and two outputs, and the other is the decoder circuit with two inputs and four outputs. Of particular interest to us is the multicolor fluorescent gold nanoprobe detection part, where a gold nanoparticle is modified with multicolor fluorophores which exploits the ultrahigh quenching ability of gold nanoparticles (AuNPs). Finally, the circuits can be programmed and simulated with the software Visual DSD. The simulated results based on DSD show that the molecular circuits constructed in this paper is reliable and effective, which has wide prospects in logical circuits and nano-electronics study.

scholarly journals Abstractions for DNA circuit design

2011 ◽  
Vol 9 (68) ◽  
pp. 470-486 ◽  
Author(s):  
Matthew R. Lakin ◽  
Simon Youssef ◽  
Luca Cardelli ◽  
Andrew Phillips
Keyword(s):  
Reaction Kinetics ◽  
Computational Cost ◽  
Logic Gates ◽  
Strand Displacement ◽  
Levels Of Detail ◽  
Molecular Detail ◽  
Dna Strand Displacement ◽  
Displacement System ◽  
Dna Strand ◽  
High Level

DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.

Using Threshold DNA Strand Displacement to Construct a Half Adder

2021 ◽  
Vol 13 (8) ◽  
pp. 1565-1573
Author(s):  
Zhen Tang ◽  
Zhi-Xiang Yin ◽  
Jian-Zhong Cui ◽  
Jing Yang ◽  
Xi-Yuan Wang ◽  
...  
Keyword(s):  
Arithmetic Function ◽  
Logic Gates ◽  
Strand Displacement ◽  
Xor Gate ◽  
Logical Operations ◽  
Half Adder ◽  
Dna Strand Displacement ◽  
Design Idea ◽  
Dna Strand ◽  
Logic Operations

DNA strand displacement has the advantages of product predictability, programmability and threshold, and it is often used to build DNA-based logic operation systems. In this paper, we use DNA strand displacement to have different reaction priorities in different length ranges of the toehold domain to form the effect of the threshold and construct the logical AND gate and XOR gate. Logical operations use single-stranded DNA as the input signal, and the brightness of the fluorescence is used to measure the results. Then, the logic AND gate and XOR gate are used as basic logic units to form a half adder in parallel. Finally, we use Visual DSD to simulate and analyze the logic AND gate, XOR gate and half adder. The simulation results show that the logic gates constructed in this paper have good theoretical feasibility and effectiveness. This work provides a potential design idea for DNA-based arithmetic function operations and more advanced logic operations.

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of

Fluorescent Molecular Logic Gates Driven by Temperature and by Protons in Solution and on Solid

2021 ◽  
Author(s):  
Amilra Prasanna de Silva ◽  
Matthew West ◽  
Chao-Yi Yao ◽  
Gavin Melaugh ◽  
Kyoko Kawamoto ◽  
...  
Keyword(s):  
Logic Gates ◽  
Molecular Logic ◽  
Molecular Logic Gates
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