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.

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 Synchronization of Chemical Reaction Networks Based on DNA Strand Displacement Circuits

IEEE Access ◽  
2018 ◽  
Vol 6 ◽  
pp. 20584-20595 ◽  
Author(s):  
Chengye Zou ◽  
Xiaopeng Wei ◽  
Qiang Zhang ◽  
Yuan Liu
Keyword(s):  
Chemical Reaction ◽  
Chemical Reaction Networks ◽  
Reaction Networks ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

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 Visual synchronization of two 3-variable Lotka–Volterra oscillators based on DNA strand displacement

RSC Advances ◽  
2018 ◽  
Vol 8 (37) ◽  
pp. 20941-20951 ◽  
Author(s):  
Chengye Zou ◽  
Xiaopeng Wei ◽  
Qiang Zhang
Keyword(s):  
Reaction Networks ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

DNA strand displacement as a theoretic foundation is helpful in constructing reaction networks and DNA circuits.

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 Reachability bounds for chemical reaction networks and strand displacement systems

2013 ◽  
Vol 13 (4) ◽  
pp. 499-516 ◽  
Author(s):  
Anne Condon ◽  
Bonnie Kirkpatrick ◽  
Ján Maňuch
Keyword(s):  
Chemical Reaction ◽  
Chemical Reaction Networks ◽  
Reaction Networks ◽  
Strand Displacement

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 ◽  
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