A New Desk! for the week.

So today I performed two different control experiments. In the first one I put quantum dots and DNA on a slide at the same time and waited five minutes before washing it out and adding buffer. I did four trials where in the first two trials I waited five minutes and in the second set of two trials I waited only 2 trials. The intention was to view whether it would be possible to distinguish the DNA from the quantum dots, since we are hoping to use the quantum dots as markers so that our measurements for the distances between proteins and DNA. It was not difficult to identify the quantum dots or to find the proper positioning for the microscope, but I am not positive I saw any DNA at all. The quantum dots are continuously blinking but all at different rates so it is difficult to determine where I see a particle that fades as it photo bleaches and where I just see a quantum dot becoming temporarily dark. I took three videos but the fourth slide (using the second protocol) leaked and had to be thrown out.

My guesses, without talking to Rachid first, for why the DNA was so difficult to spot would be
-The DNA got accidentally photobleached before being viewed by the microscope (it is almost two weeks old)
-The DNA is there but we have to look very closely to notice it next to the bright multitude of quantum dots
-The Quantum dots were put on the slide first so maybe it was more difficult for the DNA to find places on the slide to stick and thus were more likely to be washed out.

Then after lunch, I set up the second experiment. Here, I added Blocking Reagent with Biotin,waited ten minutes, washed it out, added streptavidin, waited ten minutes, washed it out, and viewed it on the microscope. Ideally since neither of these surfaces have fluorescent markers I should have seen nothing. Of course though, dust and dirt also glow some, although they photobleach even faster than DNA. After observing that it was generally dark, I added the protein and focused on the proper surface. This time the objective was to see how good the blocking reagent was. Ideally, the protein would never come too close to the surface because of the Blocking Reagent, or at least never stick there for several seconds. Instead I should have only observed general brownian motion with the proteins coming near the surface and then being "repelled" in the opposite direction. Without analyzing the video closely, it is difficult to measure the time frames in which the protiens appeared but it seemed that they were in general corresponding to theory.