Well, we certainly had a productive day today.
To start things off, Travis started a new sub-project for the nucleosome experiments. He is looking at how the nucleosomes I made respond to an increasing amount of magnesium (a +2 ion). Theory says that as we add more magnesium the nucleosomes clump up and fall out of solution. This is an indication that they are attracting each other so strongly that they would rather be next to each other than dissolved in solution. The crazy thing about nucleosomes (and as it turns out naked DNA does this as well in different solution conditions) is that if you keep adding more magnesium, the nucleosomes go back into solution (in other words they no longer attract each other). This is pretty crazy if you think about it: You make the nucleosomes attractive by adding +2 ions and then get them to then be repulsive by adding more +2 ions. This is one of the reasons this system is so interesting to look at.
Travis started this process, slowly adding more and more +2 ions. And low and behold, we saw some aggregation happening (in the form of white wisps of material in our solution). Unfortunately, they redissolved after a bit of time. Tomorrow we'll try to get up to higher concentrations of Mg and hopefully see the full transition.
John, meanwhile, has extended yesterday's experiments to look at a lot of samples (11 or so, I think). The reason for all of this is that we have some samples from our collaborator that we need to run. Unfortunately, when we run them, we destroy them, so we need to do it right on the first shot. To ensure that we are taking the measurements under the correct conditions, we are going to look at a lot of samples that are very similar to the ones we want to look at. Once we get the correct conditions for those samples and are really happy with how they are running, we can think about looking at the real samples. Not the most exciting thing in the world, but that's science folks: There's always a lot more build up to the experiments than there is time spent doing the experiment itself.
Finally, Xiangyun Qiu and Chongli Yuan are joining me in a collaboration to look further into the mechanisms behind nucleosome folding. We are hoping to do and x-ray run later in the year to look at what happens to nucleosomes when you remove or modify the tails or put them in different types of solution. Our preferred tool, SAXS, should give us some idea of what's going on.