Regensburg 2019 – scientific programme

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BP: Fachverband Biologische Physik

BP 12: Poster II

BP 12.28: Poster

Tuesday, April 2, 2019, 14:00–16:00, Poster B2

Optimization of the Ligase Cycling Reaction (LCR) via Rule-Based Modeling — •Lara Becker, Niels Schlichting, Johannes Falk, Johannes Kabisch, and Barbara Drossel — TU Darmstadt, Germany

Synthetic biologists are working to find a way for efficient and robust implementation of complex genetic circuits into living systems. One approach to this is the employment of computer-aided design tools and the exploitation of automatization procedures, e.g. for DNA assembly. The Ligase Cycling Reaction (LCR) is a powerful method for automated and modularized assembly of DNA. Our goal is to further optimize the LCR based on insights from computer simulation models that mimic, in a simplified fashion, the main steps of the LCR.

To this end, we built a rule-based model of the LCR in Kappa (κ) - a language for modeling systems of interacting agents. The dynamics of the LCR is stochastically simulated in κ, and we explore how changing parameters, concentrations, and timing affects the efficiency. This is done in close collaboration with synthetic biologists from our team who perform assays in the wet lab to validate our findings and predictions, which in turn causes the modelers to include additional features that appear to be relevant in the experiments.