Abstract Modelling of Tethered DNA Circuits

modelling of tethered DNA circuits Matthew R. Lakin1, Rasmus Petersen2, Kathryn E. Gray2,3, and Andrew Phillips2 1 Department of Computer Science, University of New Mexico, Albuquerque, NM, USA 2 Biological Computation Group, Microsoft Research, Cambridge, UK 3 Computer Laboratory, University of Cambridge, Cambridge, UK [email protected] [email protected] 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. 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.