A Programming Language for Composable DNA Circuits

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Executive Summary

In recent times, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors are some of the evident examples. This paper presents a programming language and compiler for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language was developed to take into account recent experimental and theoretical results on the design of large-scale, efficient, modular DNA circuits. It includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. A case study was also used to illustrate how to translate a set of chemical reactions to DNA molecules. As a proof of concept, a prototype compiler for the DNA strand displacement language was implemented. This new language is a first step towards the design of modeling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.

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