Project Description

WM iGEM 2016 Presents: The Circuit Control Toolbox.

Genetic circuits can be described according to their input-output relation by using a Transfer Function, which plots the concentration of output protein with respect to concentrations of input molecule. Such functions are well-modeled by Hill Functions, and as such have three parameters: the hill coefficient n, the half-max concentration K, and the saturation level V. These mathematical parameters correspond to the physical circuit properties of response steepness, input sensitivity, and maximal response level, respectively, in addition to the emergent properties which arise from their combinatorial modification.

We present a toolbox of BioBrick parts that will allow for the modification of the Transfer Functions of arbitrary circuits via the incorporation of these parts into the final steps of the circuit. These parts include Decoy Binding Arrays, which buffer the sensitivity of the circuit to low levels of input concentration, promoters driven by synthetic enhancers to allow the circuit to reach up to four levels of discrete output levels, and a suite of ribosome binding sites to modulate the circuit's total output level. Our parts are all buffered by the inclusion of characterized ribozymes downstream of the promoter, in order to insulate the specific circuit component's transfer function from the choice of expressed protein, allowing for greater orthogonality and modularity in our toolbox components.

In addition to creating, characterizing, and submitting these Toolbox parts to the Registry, we will also create a Circuit Toolbox Calculator which experimenters can use to navigate the high-dimensional space of possible Transfer Function modifications. Experimenters who have built a genetic circuit will input two transfer functions: their empirical observations of the circuit's response at different input molecule concentrations, and a desired transfer function for their modified circuit. The calculator then finds the optimal match to the target function by iterating through the possible modifications to the empirical transfer function through the parts in our Toolbox, returning to the user a list of Toolbox parts and small-molecule inducer concentrations that will replicate this best-match function in vitro. These calculations will be based on both theoretical and observational insights from mechanistic models and kinetic simulations of the interactions between our Toolbox components and arbitrary genetic circuits.