Yesterday, after looking over the data from overnight, Prof. Andresen and I began running more samples. Instead of varying the salt concentration (the amount of K in each sample for dilutions of 1x, 2x, and 4x) we began changing the contents of each sample and diluting that. The samples were separated into the categories of blue and red and each had 6 types of samples. The first three were tetramers and the last three were dodecamers. The first in each series was simply the nucleosomes in solution of TEK10, the second included globular H1 protein, and the last included globular H5 protein. For these samples, we did not use any TEK but instead had a buffer of 1mM Mg. This could change much about how the nucleosomes interact because of the change from a +1 ion to a +2 ion in the solution. Because tetramers and dodecamers are more prone to aggregation, we began cleaning the sample cell after each sample much more thoroughly. We washed the buffer solution through the cell twice after running the sample and then washed the water and alcohol through twice as much than on Saturday. On Sunday, we were able to run all of the Red series, a trimer and a large portion of the Blue series. Our other group finished that series and began to run their own samples of proteins.
Today, we ran the gold samples that were given to us by Prof. Thompson for his experiments. Because the composition of the gold samples was so different than the nucleosome arrays, our sample cell was wrecked and Prof. Andresen had to insert a new cell and reconfigure the alignment. While he was doing this, I attended a thesis defense on the ion interactions with single and double stranded DNA measured using solution x-ray scattering. This talk included several biophysical techniques that we discussed in physics 246 this past spring such as SAXS (obviously), spFRET and molecular dynamics. The presenter also used data obtained from Gettysburg's ICP-AES that Prof. Andresen ran. To finish off the day, we are going to run the R series with a 2x dilution for the different levels of TEK (50, 100 and 200) including double the buffer between samples (the TEK of the previous and the TEK of the next). Hopefully we will get through most of the series before we switch off at midnight.