Wednesday, November 18, 2009

Saturation and Chaser

EDITED: Used bad mol per cell calculation earlier.

How much DNA does an average cell in a competent culture take up? I did two experiments today, which were aimed at trying to decide how much degeneracy we can tolerate in our degenerate USS experiment. There's several issues, but one simple one is just to know how much of an "optimal" USS is taken up in the presence of competing "suboptimal" USS...

In the first experiment, I added different amounts of hot USS-1 DNA (the new-fangled ones designed for Illumina sequencing... ~200 bp) to a fixed amount of competent cells to find out how much DNA was enough to saturate the cells with DNA. Here's the results for several amounts of USS-1 incubated with 200 ul of competent cells for 20 minutes:
Looks like less than 8 ng (or ~200 molecule per cell) is sub-saturating and greater than 8 ng is near saturation.

In the second experiment, I looked at how well USS-1 is taken up in the presence of a competitor mutant USS (USS-V6, which is taken up 10X worse than USS-1). Based on the results of the first experiment, I used two different amounts of hot USS-1, either sub-saturating (4ng) or saturating (16ng). For each of these, I had four samples in which different amounts of cold USS-V6 were added. Here's the results for subsaturating USS-1:

And now for saturating USS-1:

Though adding the competitor did reduce uptake, uptake decreased only by ~1/4, even when there was several-fold more competitor. Also, it appears that using saturating amounts of USS-1 yields a different decline in uptake with excess inhibitor than when USS-1 is sub-saturating.

So what's this all mean? I think it means that even when "optimal" USS are only 1/10 as common as "suboptimal" USS, uptake proceeds quite nicely. What does this mean practically for making our fancy oligo purchase? Not too much, except that I think we can err on the side of more degeneracy without too many problems. (This will be good for several reasons, probably the most important of which is that our preliminary data collection plans will work best with more degeneracy.)


  1. One molecule per cell is a surprisingly low amount of uptake. Our previous experiments found much higher uptake (~50-100 molecules per cell) for molecules of about the same length.

    Is such low uptake likely to be a big problem for the sensitivity of our sequencing experiments?

  2. Oops! It's not the data; it's my calculations. Off by a factor of 200!