Synthetic Biology - Devices - Pulse Generator

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The Genetic Pulse Generator: A test of rational engineering in synthetic biology

Figure 1. A Genetic Pulse Generator.

A holy grail of a synthetic biology is the goal of rational engineering of genetic circuits from a “parts repository” of DNA elements. This goal is premised on the notion that genetic “parts” (promoters, RBSs, terminators) can be mathematically characterized in isolation and then combined into circuits whose behavior can be predicted from a computational model combining these individual characterizations. In other words, the rational engineering paradigm requires a strong assumption of composability. This assumption is violated if:

   * Genetic devices perform differently when composed in circuits vs. when characterized in isolation.
   * Performance of genetic circuits is strongly influenced by interactions with their host environments.
   * Estimation of kinetic parameters for genetic elements is overly dependent on the specific experimental conditions of the measurement.
   * Noise in genetic devices is compounded in circuits so as to preclude quantitative prediction.

The goal of the pulse generator project is to test the fundamental assumption of composability in the rational engineering of genetic circuits.

We have built a genetic circuit which implements a pulse response (the genetic pulse generator or GPG, depicted in Figure 1). The GPG is encoded on a single medium copy plasmid and transformed into E.coli. The circuit produces a transient pulse in the expression of GFP in response to a step input of inducer. In addition to the pulse generator I build control circuits which report on the activity of each promoter within the GPG. Using data on these control circuits I fit mathematical models of the individual promoters. We then test the hypothesis that these promoter models can be combined to predict the behavior of the GPG at quantitative resolution (Figure 2). A pulse generator is an ideal circuit for this exercise because, unlike previously studied synthetic circuits such as toggle switches and oscillator, GPG dynamics are not robust to variation in parameter values. A pulse generator contains conceivably engineerable characteristics such as pulse height, width, and time to peak which are highly sensitive to the kinetics of its genetic elements. Quantitative prediction/engineering of GPG behavior will therefore rely heavily on the composability of its promoter models.