Introducing a Pair of Tools for the in silico Design and Dynamic Simulation of Eukaryotic Genetic Circuits

Synthetic biology often relies on the intuitive design of genetic circuits utilizing bioparts (DNA, RNA, and proteins) to accomplish a desired task; however, this field holds the promise of creating biological systems with complex and useful responses to various stimuli. As an alternative to intuitive approaches, we created two in silico tools which broaden the range, efficacy, and predictiveness of potential synthetic biology designs by applying systems biology and optimization mathematics. This systems biology first approach is advantages in that it allows for non-intuitive designs and the quick in silico screening thereof to give implemented designs the greatest chance of success. The first tool, known as EuGeneCiD (Eukaryotic Genetic Circuit Design tool) aids in the design and/or study of genetic circuits and their behavior by reconstructing a bioparts database describing the potential members of genetic circuits included promotors, genes, transcripts, terminators, and enzymes in terms of their activity, regulation, and interactions. This tool is used to design more than ten logic gates for the model plant Arabidopsis thaliana which respond to the divalent metals Cadmium, Zinc, and/or Copper using fluorescent proteins as reporters. The second tool, known as EuGeneCiM (Eukaryotic Genetic Circuit Modeling tool) allow for dynamic simulation of designs proposed by EuGeneCiD to test the accuracy of the design, particularly with respect to time. EuGeneCiM is applied to all EuGeneCiD-designed circuits, as well as to other time-dependent synthetic biology circuits such as repressilators to demonstrate the utility of the tool. Together, these tools can hypothesize optimal genetic circuit designs and simulate their behavior to increase the chances that a plant might have the desired behavior when transformed potentially saving time and resources. For the ease of use, various programs have been developed to make EuGeneCiD/M user-friendly.