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

Toehold strand displacement-driven assembly of G-quadruplex DNA for enzyme-free and non-label sensitive fluorescent detection of thrombin

2015 ◽  
Vol 64 ◽  
pp. 306-310 ◽  
Author(s):  
Yunying Xu ◽  
Wenjiao Zhou ◽  
Ming Zhou ◽  
Yun Xiang ◽  
Ruo Yuan ◽  
...  
Keyword(s):  
Fluorescent Detection ◽  
Strand Displacement ◽  
Quadruplex Dna ◽  
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.

scholarly journals G-Quadruplex formation using fluorescent oligonucleotides as a detection method for discriminating AGG trinucleotide repeats

2016 ◽  
Vol 52 (86) ◽  
pp. 12757-12760 ◽  
Author(s):  
Yoojin Park ◽  
Ki Tae Kim ◽  
Byeang Hyean Kim
Keyword(s):  
Detection Method ◽  
Oligonucleotide Probe ◽  
Trinucleotide Repeats ◽  
Enhanced Fluorescence ◽  
Background Signal ◽  
Low Background ◽  
G Quadruplex ◽  
Quadruplex Formation

A fluorescent oligonucleotide probe induces the formation of intermolecular G-quadruplexes with AGG trinucleotide repeats. The probe also exhibits 35.0- and 44.7-fold enhanced fluorescence signals for DNA AGG and RNA agg repeat oligonucleotides with respect to the low background signal.

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.

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