Monday 22 Jan 2018Dynamics Seminar: Programming DNA circuits

Neil Dalchau - Microsoft Research

LSI Seminar Room A 14:30-15:30

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. In this talk, I will describe an approach based on DNA hybridization and strand displacement to implement the computational core of such control circuits. We use domain-specific programming languages to specify the sequence-level circuit design, which compile to chemical reaction networks, a well-established formalism for describing and simulating chemistry. Furthermore, we have integrated parameter inference techniques into this design platform, which facilitates design-build-test cycles via model-based characterization and circuit prediction. A first example will introduce how we designed and constructed a DNA implementation of the approximate majority algorithm, which seeks to establish consensus in a population of agents (molecules). A second example will illustrate how DNA circuits can be considerably accelerated by tethering DNA hairpin molecules to a fixed template, overcoming molecular diffusion as a rate-limiting step.

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