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Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
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Programming chemistry in DNA-addressable bioreactors.

Harold Fellermann1, Luca Cardelli2

  • 1School of Computing Science, Newcastle University, King's Gate, Newcastle upon Tyne NE1 7RU, UK Center for Fundamental Living Technology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark harold.fellermann@newcastle.ac.uk.

Journal of the Royal Society, Interface
|August 15, 2014
PubMed
Summary
This summary is machine-generated.

We developed a formal system for programmable chemistry using compartmentalized reactions. This allows for complex molecular construction and computation, mimicking biological systems.

Keywords:
DNA computingbiochemical engineeringcompartmentalizationmembrane computingprogrammable chemistrytheoretical computer science

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Area of Science:

  • Biomimetic Chemistry
  • Chemical Systems Engineering
  • Formal Systems Theory

Background:

  • Compartmentalized reaction systems are complex, involving nested vesicular structures.
  • Molecular cargo and DNA surface markers facilitate targeted transport and fusion.
  • Programmable chemistry requires integration of control, computation, and material production.

Purpose of the Study:

  • To present a formal calculus, the chemtainer calculus, for compartmentalized reaction systems.
  • To introduce a sequential programming language for programmable chemistry in automated environments.
  • To analytically derive the computational and constructive power of the proposed framework.

Main Methods:

  • Formal calculus development (chemtainer calculus).
  • Introduction of a sequential programming language inspired by microfluidics.
  • Non-deterministic semantics for analytical derivation of system capabilities.
  • Constructive proofs for inferring control programs.

Main Results:

  • The chemtainer calculus captures complexity of nested vesicular compartments.
  • Programmable chemistry integrates electronic control, chemical computing, and material production.
  • Analytical derivation of constructable chemicals and supermolecular structures.
  • Automated inference of control programs for target structure synthesis.

Conclusions:

  • The chemtainer calculus provides a unified formal framework for programmable chemistry.
  • The system mimics the integrated capabilities of the subcellular matrix.
  • The framework enables automated synthesis of complex molecules, demonstrated with oligosaccharide synthesis.