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.

scholarly journals A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots

Nanoscale ◽  
2016 ◽  
Vol 8 (19) ◽  
pp. 10087-10095 ◽  
Author(s):  
H. D. Gliddon ◽  
P. D. Howes ◽  
M. Kaforou ◽  
M. Levin ◽  
M. M. Stevens
Keyword(s):  
Quantum Dots ◽  
Nucleic Acid ◽  
Strand Displacement ◽  
Multiplexed Detection ◽  
Mrna Detection ◽  
Dna Strand Displacement ◽  
Displacement System ◽  
Dna Strand ◽  
Specific Mrna

On the development of a novel multiplexed assay for Tuberculosis-specific mRNA detection using DNA strand displacement and quantum dots.

scholarly journals A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

2020 ◽  
Vol 17 (167) ◽  
pp. 20190866 ◽  
Author(s):  
Stefan Badelt ◽  
Casey Grun ◽  
Karthik V. Sarma ◽  
Brian Wolfe ◽  
Seung Woo Shin ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Biophysical Model ◽  
Kinetic Properties ◽  
Strand Displacement ◽  
Natural Connection ◽  
Dna Strand Displacement ◽  
Wide Range ◽  
Dna Strand ◽  
High Level ◽  
Domain Level

Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.

Modulating the DNA strand-displacement kinetics with the one-sided remote toehold design for differentiation of single-base mismatched DNA

RSC Advances ◽  
2016 ◽  
Vol 6 (78) ◽  
pp. 74913-74916 ◽  
Author(s):  
Chenxi Li ◽  
Yixin Li ◽  
Yang Chen ◽  
Ruoyun Lin ◽  
Tian Li ◽  
...  
Keyword(s):  
Reaction Kinetics ◽  
Displacement Reaction ◽  
Strand Displacement ◽  
Single Base ◽  
Mismatched Dna ◽  
Dna Strand Displacement ◽  
Fine Control ◽  
Dna Strand ◽  
The One ◽  
Strand Displacement Reaction

A one-sided remote toehold design was proposed to provide the fine control over strand-displacement reaction kinetics with simplicity and versatility.

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

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.

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.

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.

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