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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References

SHOWING 1-10 OF 22 REFERENCES

Control of DNA strand displacement kinetics using toehold exchange.

This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.

DNA hairpins: fuel for autonomous DNA devices.

A study of the hybridization of complementary DNA hairpin loops, with particular reference to their use as fuel for autonomous DNA devices, finds loop opening via an external toehold to be 10-100 times faster than via an internal toehold.

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.

A simple DNA gate motif for synthesizing large-scale circuits

A simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates is proposed.

Using DNA to Power Nanostructures

  • B. YurkeA. Mills
  • Biology, Chemistry
    Genetic Programming and Evolvable Machines
  • 2004
The emphasis will be on the operation of toeholds, single-stranded sections of DNA that facilitate the process of strand removal during certain points in the operationof a DNA-based motor.

A programming language for composable DNA circuits

A programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism and includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure is presented.

Dynamic DNA strand displacement circuits

The works presented in this thesis were designed using only non-covalent changes to nucleic acid complexes and structures via Watson-Crick base pairing--i.e. hybridization, branch migration, and dissociation, which are sufficient to construct an endless variety of circuits and devices.

Cooperative hybridization of oligonucleotides.

  • D. Y. Zhang
  • Biology
    Journal of the American Chemical Society
  • 2011
Cooperative hybridization is introduced as a mechanism in which two oligonucleotides of independent sequence can stoichiometrically, simultaneously, and cooperatively hybridize to a DNA complex, shown to implement digital concentration comparison with amplification, as well as digital Boolean logic.

Design and Analysis of DNA Circuits using Probabilistic Model Checking

This work uses the probabilistic model checker PRISM, in combination with DSD, to detect and fix an error in a simple strand displacement program, and to analyse the kinetics of the system.

Programmable and autonomous computing machine made of biomolecules

A programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously and has a transition fidelity greater than 99.8%.