Abstract
Sequence-specific DNA interactions are a powerful means of programming nanoscale locomotion. These systems typically use a DNA track that is tethered to a surface, and molecular interactions enable a signal or cargo to traverse this track. Such low copy number systems are highly amenable to mechanized analyses such as probabilistic model checking, which requires a formal encoding. In this paper we present the first general encoding of tethered DNA species into a formal language, which allows the interactions between tethered species to be derived automatically using standard reaction rules. We apply this encoding to a previously published tethered DNA circuit architecture based on hairpin assembly reactions. This work enables automated analysis of large-scale tethered DNA circuits and, potentially, synthesis of optimized track layouts to implement specific logic functions.
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Lakin, M.R., Petersen, R., Gray, K.E., Phillips, A. (2014). Abstract Modelling of Tethered DNA Circuits. In: Murata, S., Kobayashi, S. (eds) DNA Computing and Molecular Programming. DNA 2014. Lecture Notes in Computer Science, vol 8727. Springer, Cham. https://doi.org/10.1007/978-3-319-11295-4_9
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DOI: https://doi.org/10.1007/978-3-319-11295-4_9
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