Thursday, April 20, 2017

Reducing DNA context dependence in bacterial promoters

Swati Carr's work on insulating promoters is now out as an article in PLOS ONE, with me and Doug Densmore. I've talked about this work before, and I'm very happy to have been involved in it as something that I consider a very solid piece of engineering.

Basically, promoters are the "control switches" that determine how much a gene is expressed, and which other chemicals in the cell can regulate that expression. The problem is, at least in bacteria, that the promoters we usually use are extremely sensitive to what you put in front of them---even to the point that the tiny "scars" left in the DNA sequence from stitching genes together can have a radical effect on their operation. With Swati's method, Degenerate Insulation Screening (DIS), we now have a simple "shake and bake" engineering method for insulating these promoters, which works very well to make a promoter behave consistently, despite changes in what is placed in front of it.

Let me illustrate it very simply, with two images that I suspect will be clear to even a non-synthetic-biologist. In these pictures, the green and red bars show the behavior of two genes in a bunch of different variations of a small circuit. The more similar the bars are, the better, because it means the genes are behaving more reliably.

In short, this is your circuit:

This is your circuit without DIS:

Any questions?
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