Two-domain DNA strand displacement

@article{Cardelli2010TwodomainDS,
  title={Two-domain DNA strand displacement},
  author={Luca Cardelli},
  journal={Mathematical Structures in Computer Science},
  year={2010},
  volume={23},
  pages={247 - 271}
}
  • L. Cardelli
  • Published 7 June 2010
  • Physics
  • Mathematical Structures in Computer Science
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study fork and join signal processing gates based on these structures, and show that these systems are… 
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135 Citations
Highly Influential Citations
13
Background Citations
69
Methods Citations
29
Results Citations
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135 Citations

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Logic Calculation Based on Two-Domain DNA Strand Displacement

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A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems

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Leakless DNA Strand Displacement Systems

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Integrating DNA strand-displacement circuitry with DNA tile self-assembly

This work demonstrates the triggered and catalytic isothermal self-assembly of DNA nanotubes over 10 μm long from precursor DNA double-crossover tiles activated by an upstream DNA catalyst network.

On the biophysics and kinetics of toehold-mediated DNA strand displacement

This work study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects to provide a biophysical explanation of strand displacement kinetics.

A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

This work builds on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis.

Dynamic DNA nanotechnology using strand-displacement reactions.

Here, this work reviews DNA strand-displacement-based devices, and looks at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.

Principles and Applications of Nucleic Acid Strand Displacement Reactions.

The enormous progress of dynamic DNA nanotechnology over the past years seems poised for practical application, with toehold-mediated strand displacement reactions used with ever increasing sophistication.
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