Dynamic Control of Aptamer–Ligand Activity Using Strand Displacement Reactions

2017 ◽  
Vol 7 (1) ◽  
pp. 30-37 ◽  
Author(s):  
Jonathan Lloyd ◽  
Claire H. Tran ◽  
Krishen Wadhwani ◽  
Christian Cuba Samaniego ◽  
Hari K. K. Subramanian ◽  
...  
Keyword(s):  
Dynamic Control ◽  
Strand Displacement ◽  
Displacement Reactions ◽  
Ligand Activity

Biocomputing based on DNA strand displacement reactions

ChemPhysChem ◽  
2021 ◽  
Author(s):  
Hui Lv ◽  
Qian Li ◽  
Jiye Shi ◽  
Fei Wang ◽  
Chunhai Fan
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

Connecting localized DNA strand displacement reactions

Nanoscale ◽  
2015 ◽  
Vol 7 (30) ◽  
pp. 12970-12978 ◽  
Author(s):  
Ismael Mullor Ruiz ◽  
Jean-Michel Arbona ◽  
Amitkumar Lad ◽  
Oscar Mendoza ◽  
Jean-Pierre Aimé ◽  
...  
Keyword(s):  
Dna Origami ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

Design and characterization of a DNA-based localized amplification circuit which, upon tethering on a DNA origami platform, greatly accelerates the catalytic response.

The fast detection of streptavidin based on the initial reaction rate of the binding-induced DNA strand-displacement reaction

2016 ◽  
Vol 8 (37) ◽  
pp. 6701-6704 ◽  
Author(s):  
Chenxi Li ◽  
Ruoyun Lin ◽  
Tian Li ◽  
Feng Liu ◽  
Na Li
Keyword(s):  
Small Molecules ◽  
Reaction Rate ◽  
Initial Reaction Rate ◽  
Initial Reaction ◽  
Strand Displacement ◽  
Fast Detection ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand ◽  
Strand Displacement Reaction

Binding-induced DNA strand-displacement reactions diversify the applications beyond nucleic acids and small molecules.

scholarly journals A simple DNA gate motif for synthesizing large-scale circuits

2011 ◽  
Vol 8 (62) ◽  
pp. 1281-1297 ◽  
Author(s):  
Lulu Qian ◽  
Erik Winfree
Keyword(s):  
Nucleic Acid ◽  
Large Scale ◽  
Strand Displacement ◽  
Molecular Systems ◽  
Displacement Reactions ◽  
Analogue Circuits ◽  
Practical Synthesis

The prospects of programming molecular systems to perform complex autonomous tasks have motivated research into the design of synthetic biochemical circuits. Of particular interest to us are cell-free nucleic acid systems that exploit non-covalent hybridization and strand displacement reactions to create cascades that implement digital and analogue circuits. To date, circuits involving at most tens of gates have been demonstrated experimentally. Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.

scholarly journals Co-transcriptional RNA strand displacement circuits

2021 ◽  
Author(s):  
Samuel W Schaffter ◽  
Elizabeth Strychalski
Keyword(s):  
Simple Model ◽  
Rational Design ◽  
Biological Systems ◽  
Living Cells ◽  
Signaling Cascades ◽  
Strand Displacement ◽  
Model Driven ◽  
Displacement Reactions ◽  
Circuit Components

Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions have demonstrated the largest and most computationally powerful molecular circuits to date but are limited in biological systems due to the difficulty in genetically encoding components. Here, we develop scalable co-transcriptional RNA strand displacement (ctRSD) circuits that are rationally programmed via base pairing interactions. ctRSD addresses the limitations of DNA-based strand displacement circuits by isothermally producing circuit components via transcription. We demonstrate the programmability of ctRSD in vitro by implementing logic and amplification elements, and multi-layer signaling cascades. Further, we show ctRSD kinetics are accurately predicted by a simple model of coupled transcription and strand displacement, enabling model-driven design. We envision ctRSD will enable rational design of powerful molecular circuits that operate in biological systems, including living cells.

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