Difference between revisions of "Team:William and Mary/Part Collection"

The overall input/output behavior of any genetic circuit can be represented by a graph known as a transfer function, which relates concentration of input molecule to output protein expression. Likewise, any modifications to the circuit affecting input/output behavior can be visualized by a transformation of the transfer function representing the circuit. The Circuit Control Toolbox consists of three distinct tools which prompt unique behavioral changes to the circuit’s output relative to its input, and therefore generate different transformations of the circuit’s original transfer function.

The RBS library provides a collection of ribosome binding sites of varying strength; replacing the RBS within a circuit alters the translational efficiency of the output. This tool effectively allows for scaled changes in the magnitude of a circuit’s output response, thus adjusting the amplitude of the transfer function.

The Decoy Binding Array tool implements molecular titration to tune the circuit’s sensitivity to input concentrations. This modification is accompanied by a shift in the threshold of the circuit’s transfer function.

The Synthetic Enhancer Suite exploits a synthetically modified enhancer/promoter system engineered to allow genetic circuits to generate multi-state responses. In other words, circuits are prompted to produce distinct levels of output based on the concentration of input molecule.This creates a staircase-like curve in the transfer function for the circuit.

Each of these tools functions orthogonally to the activity of the other tools; furthermore, each tool is independently tunable to a specific degree. By implementing and adjusting multiple tools to the desired degree, a diverse range of circuit output behaviors can be achieved, generating a plethora of unique transfer function responses.

The implementation of this Toolbox relies on its generalizability and consistency over any arbitrary genetic circuit. A circuit’s relative output behavior may be influenced by the coding sequence for the output which it controls. In order to ensure that behavior remains consistent across any range of coding sequences, we offer an additional Ribozyme Insulator tool. This ribozyme part, known as RiboJ, insulates a circuit’s promoter activity from the genetic context of the coding sequence, allowing for consistency in the levels of relative expression across multiple coding sequence insertions. The addition of RiboJ as an insulator justifies the application of Toolbox components to the end of any genetic circuit, irrespective of its choice of final output protein [4].

Our Circuit Control Toolbox can easily be implemented in any project concerned with the behavior of genetic circuitry by working through the following sequence of events:

1. Visualize the original behavior of the circuit in question by constructing a characteristic transfer function.

2. Determine the appropriate Toolbox parts-to-use using our mathematical model. This model has been parameterized such that the model parameters correspond to actual physical variables (e.g. number of tetO arrays, plasmid backbone).

3. Swap out the final protein coding sequence in the original circuit with a Ribo-J insulated repressor sequence that is compatible with the Toolbox.

4. Apply the appropriate Toolbox parts to the end of your circuit, and express your original final output protein at the end of the series of Toolbox components.

In this manner, future iGEM teams and synthetic biologists will be able to easily obtain higher levels of precision and control over the behavior of their genetic networks.