Centrifuging and Washing DNA

If you remember from my last blog post, we were about to embark on a new journey. After collecting a lot of data on zinc and what it does to DNA, we want to see if this change is reversible or not. Does the zinc bind so tightly that it cannot be washed away? Answering this question is what I’ve been up to this week. In order to do this, we took some samples of DNA in a 300mM zinc solution, and tried to get all the zinc out via centrifuge. We put the samples through a special filter that lets everything but DNA pass through, and then we add NaCl, MgCl2, and Tris buffer five times, running them through the centrifuge each time. After this was all done, I ran the samples through the CD spectroscopy machine, so we could see any changes in the DNA structure.

This is our latest graph, and we can see that DNA that has been washed with salts and a buffer looks very different from DNA in zinc solution that has not been washed. We can interpret this as the zinc unbinding from the DNA, which makes the peak at 275 nm revert back to how it was before zinc was added. However, we can still see some differences between the washed and unwashed DNA. The through at 245 nm is greater for the washed solutions, but is very similar for the DNA in plain water, and the DNA in zinc.

I am currently in the process of redoing this whole experiment. I hope that the new graphs will corroborate the data that I have already acquired, and help me analyze more accurately the differences between washed and unwashed DNA. Until then, I do think that we have some promising data, and I look forward to elaborate more on this experiment.

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