Difference between revisions of "Team:BostonU/Model"

Currently, there is not yet a defined relationship between the concentration of DNA added to the cell-free system and protein expression as well as the maximum amount of DNA that the system can handle. Part of this is due to the variety in capabilities of a particular ‘batch’ of cell-free, even if the same protocol is used. Modeling this relationship allows us to maximize expression when performing experiments that use many different pieces of interacting DNA; such as in later tests where a plasmid containing a toehold switch driving a recombinase interacts with a reporter plasmid.

We collected data on the fluorescence from a plasmid containing constitutive deGFP. The plasmid was added to the cell free reaction at 10 nM, 20 nM, 30 nM, and 40 nM. There was also a reaction with no DNA. The resulting data can be seen in Figure 1.

FIGURE

Initially we planned on modeling this capacity with a single logistic curve. The results of this initial model are shown in figure 2.

FIGURE

After looking at the data more closely, we determined that a more complex curve was required and fit a bell shaped dose response curve. A bell shaped dose response curve is the sum of two dose response curves. Here, low concentrations of DNA stimulate gene expression while high concentrations inhibit gene expression.

FIGURE