scholarly journals CRISPR-Mediated Strand Displacement Logic Circuits with Toehold-Free DNA

2021 ◽  
Author(s):  
Roser Montagud-Martínez ◽  
María Heras-Hernández ◽  
Lucas Goiriz ◽  
José-Antonio Daròs ◽  
Guillermo Rodrigo
Keyword(s):  
Logic Circuits ◽  
Strand Displacement ◽  
Free Dna

Enzyme-Free Unlabeled DNA Logic Circuits Based on Toehold-Mediated Strand Displacement and Split G-Quadruplex Enhanced Fluorescence

2013 ◽  
Vol 25 (17) ◽  
pp. 2440-2444 ◽  
Author(s):  
Jinbo Zhu ◽  
Libing Zhang ◽  
Tao Li ◽  
Shaojun Dong ◽  
Erkang Wang
Keyword(s):  
Logic Circuits ◽  
Strand Displacement ◽  
Enhanced Fluorescence ◽  
G Quadruplex

scholarly journals Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement

RSC Advances ◽  
2017 ◽  
Vol 7 (45) ◽  
pp. 28130-28144 ◽  
Author(s):  
Xin Song ◽  
Abeer Eshra ◽  
Chris Dwyer ◽  
John Reif
Keyword(s):  
Logic Circuits ◽  
Reaction Networks ◽  
Strand Displacement ◽  
Scalable Design ◽  
Synchronized Control

We propose a scalable design and verifications for photoregulated renewable DNA seesaw logic circuits, which can be repeatedly reset to reliably process new inputs. Synchronized control of complex DNA reaction networks could be achieved efficiently.

Design of Logic Circuits Based on Metallo-Toehold Strand Displacement

2019 ◽  
Vol 14 (2) ◽  
pp. 232-237
Author(s):  
Ying Niu ◽  
Chaonan Shen ◽  
Xuncai Zhang
Keyword(s):  
Logic Circuits ◽  
Strand Displacement

Pattern Recognition of 2 × 2 Matrices Based on DNA Strand Displacement

2019 ◽  
Vol 11 (10) ◽  
pp. 1357-1365
Author(s):  
Yanfeng Wang ◽  
Aolong LV ◽  
Chun Huang ◽  
Junwei Sun
Keyword(s):  
Pattern Recognition ◽  
Large Scale ◽  
Logic Circuits ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Complex Circuits ◽  
Dna Strand ◽  
Simple Logic

Biochemical circuits have been transformed from simple logic circuits to large-scale complex circuits, benefitting from the maturity of DNA strand displacement technology. Pattern recognition is a process of analyzing perceptual signals and identifying and interpreting objects. In this study, pattern recognition of 2 × 2 matrices based on DNA strand displacement was designed, including dual-rail circuits and seesaw circuits. The effective results were obtained by simulation in Visual DSD software, simultaneously, the pattern recognition and DNA strand displacement technology were perfectly combined.

scholarly journals Thermal cycling of DNA devices via associative strand displacement

2019 ◽  
Vol 47 (20) ◽  
pp. 10968-10975 ◽  
Author(s):  
Jaeseung Hahn ◽  
William M Shih
Keyword(s):  
Thermal Cycling ◽  
Low Temperatures ◽  
Logic Circuits ◽  
Design Parameters ◽  
Strand Displacement ◽  
Base Pairs ◽  
Transient Heating ◽  
Displacement Reactions ◽  
Temperature Responses ◽  
Net Release

Abstract DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce ‘recovery’ strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of ‘recovery’ strands is favored at higher temperatures due to the primacy of a net release of strands. The temperature responses of the devices could be modulated by adjustment of design parameters such as the net increase of base pairs and the concentrations of strands. Degradation of function was not observable even after 500 thermal cycles. We experimentally demonstrated simple digital-logic circuits that evaluate at 35°C and reset after transient heating to 65°C. Thus associative strand displacement enables robust thermal cycling of DNA-based devices in a closed system.

scholarly journals Constructing DNA logic circuits based on the toehold preemption mechanism

RSC Advances ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 338-345
Author(s):  
Cuicui Xing ◽  
Xuedong Zheng ◽  
Qiang Zhang
Keyword(s):  
Logic Circuits ◽  
Displacement Reaction ◽  
Strand Displacement ◽  
Dna Complex ◽  
Strand Displacement Reaction

Preemptor blocks the strand displacement reaction by acting on DNA complex, not by directly hybridizing with the worker.

scholarly journals A programming language for composable DNA circuits

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Andrew Phillips ◽  
Luca Cardelli
Keyword(s):  
Programming Language ◽  
Large Scale ◽  
Implementation Strategies ◽  
Logic Circuits ◽  
Arbitrary System ◽  
Strand Displacement ◽  
Dna Computation ◽  
Simulation Tools ◽  
Dna Strand Displacement ◽  
Dna Strand

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.

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 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.

scholarly journals Programmable intracellular DNA biocomputing circuits for reliable cell recognitions

2019 ◽  
Vol 10 (10) ◽  
pp. 2989-2997 ◽  
Author(s):  
Xue Gong ◽  
Jie Wei ◽  
Jing Liu ◽  
Ruomeng Li ◽  
Xiaoqing Liu ◽  
...  
Keyword(s):  
Logic Gates ◽  
Living Cells ◽  
Logic Circuits ◽  
Chain Reaction ◽  
Free Dna

A reconfigurable hybridization-based chain reaction was introduced to assemble enzyme-free DNA logic gates and advanced logic circuits for analyzing multiple endogenous miRNA expressions and discriminating different living cells.

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