scholarly journals Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions

2016 ◽  
Author(s):  
Mathias Foo ◽  
Rucha Sawlekar ◽  
Vishwesh V. Kulkarni ◽  
Declan G. Bates
Keyword(s):  
Feedback Control ◽  
Control Systems ◽  
Strand Displacement ◽  
Biologically Inspired ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Feedback Control Systems ◽  
Biologically Inspired Design ◽  
Dna Strand

scholarly journals Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations

2019 ◽  
Author(s):  
Nuno M. G. Paulino ◽  
Mathias Foo ◽  
Tom F. A. de Greef ◽  
Jongmin Kim ◽  
Declan G. Bates
Keyword(s):  
Nucleic Acid ◽  
Feedback Control ◽  
Control Systems ◽  
Scale Up ◽  
Building Blocks ◽  
State Feedback Control ◽  
Dna Strand Displacement ◽  
Feedback Control Systems ◽  
Control Circuits ◽  
Dna Strand

AbstractChemical reaction networks based on catalysis, degradation, and annihilation may be used as building blocks to construct a variety of dynamical and feedback control systems in Synthetic Biology. DNA strand-displacement, which is based on DNA hybridisation programmed using Watson-Crick base pairing, is an effective primitive to implement such reactions experimentally. However, experimental construction, validation and scale-up of nucleic acid control systems is still significantly lagging theoretical developments, due to several technical challenges, such as leakage, crosstalk, and toehold sequence design. To help the progress towards experimental implementation, we provide here designs representing two fundamental classes of reference tracking control circuits (integral and state-feedback control), for which the complexity of the chemical reactions required for implementation has been minimised. The supplied ‘minimally complex’ control circuits should be ideal candidates for first experimental validations of nucleic acid controllers.

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 Configuring robust DNA strand displacement reactions for in situ molecular analyses

2011 ◽  
Vol 40 (7) ◽  
pp. 3289-3298 ◽  
Author(s):  
Dzifa Y. Duose ◽  
Ryan M. Schweller ◽  
Jan Zimak ◽  
Arthur R. Rogers ◽  
Walter N. Hittelman ◽  
...  
Keyword(s):  
Strand Displacement ◽  
Molecular Analyses ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand
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