The Final Countdown

As I enter my final week of research, I am almost rushing to tie up a couple of projects so that they do not dangle the two weeks before I come back to school.

The past week I have been spending a lot of quality time with Florence (or Flo) our fluorimeter. We are finally starting to become better friends. If you recall what my main project is, I am inserting an unnatural amino acid called fluorotyrosine (FY) into green fluorescent protein. The change in the pKa (due to the additional fluorines) results in a shift in fluorescence which can be detected using the fluorimeter. As we have different amount of fluorines attached to the tyrosine and in the GFP, there should be a number of different shifts. And there are! While we are not quite sure yet what the exact pattern is at this point, it is promising to simply see a difference.

Other projects are progressing exceptionally well. The Glaser-Hay reactions (a chemical joining of two alkynes) have been progressively successful. We have now determined that the fluorophore (our detection of a successful reaction) is actually attached to the protein. However, if we let the reaction go for too long the catalysts degrade the protein. Our current efforts have, for the past week, been directed at determining the optimum conditions for the reaction. Too long of a time and the protein degrades, but too short and the reaction does not produce much product. It is a delicate balance. Once we finish this we will work on some of the applications of this reaction, which should quickly lead to a publishable paper! This is definitely a project that we are hoping to wrap up before I leave.

In other projects, excitement can easily be found in a mailbox. After multiple weeks of waiting, we finally received a number of needed materials. One of these was a new set of reagents for PCR. This new set makes a huge amount of product when used for thermal PCR. Hopeful, we used this in the microwave, thinking that it might work. It didn’t.  But not going to give up that easily, we tried using the coolmate system that keeps it much cooler. That also didn’t work. But we will still keep attempting this (if a published paper was able to do this, we should be able to too…right?).

But now the final week is here, sadly. And as ever, much work remains to be done.


  1. Hi Jordan, I hope your research is doing well. I was wondering if you ever found the exact balance of the reaction? I find it very interesting that the catalyst that produces the reaction also degrades the amino acid it produces. Is the amino acid considered an intermediate in this case? Thanks and have a great semester.