DNA Computing and Molecular Programming

Volume 8141 of the series Lecture Notes in Computer Science pp 133-146

Modular Verification of DNA Strand Displacement Networks via Serializability Analysis

  • Matthew R. LakinAffiliated withDepartment of Computer Science, University of New Mexico
  • , Andrew PhillipsAffiliated withBiological Computation Group, Microsoft Research
  • , Darko StefanovicAffiliated withDepartment of Computer Science, University of New MexicoCenter for Biomedical Engineering, University of New Mexico

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DNA strand displacement gates can be used to emulate arbitrary chemical reactions, and a number of different schemes have been proposed to achieve this. Here we develop modular correctness proofs for strand displacement encodings of chemical reaction networks and show how they may be applied to two-domain strand displacement systems. Our notion of correctness is serializability of interleaved reaction encodings, and we infer this global property from the properties of the gates that encode the individual chemical reactions. This allows correctness to be inferred for arbitrary systems constructed using these components, and we illustrate this by applying our results to a two-domain implementation of a well-known approximate majority voting system.