Making Samples, Graphs, and Reading Data

What have we been up to? For starters, the project about measuring Zn2+ binding to DNA has really taken off. We started by doing some samples of DNA in NaCl and MgCl2, which you might remember from our previous blog post. We did those several times to try to get some results that showed a change in the DNA structure. We ran all of our samples in the CD spectroscopy instrument, which measures how long it takes for DNA to unwrap. This time, we measured over the right span (320 nm to 200 nm), which means we can now read our data!

 What we wanted from these graphs was to observe a difference in the magnitude of the peak and trough of the graph, which was proportional to the sodium and magnesium concentration. In these graphs, it is possible to see that the concentration of the sodium and magnesium is directly proportional to the change in the DNA, however, we do have some outliers. Nonetheless, we decided we were ready to move on to the next step of the project, measuring the effects of zinc binding to DNA. We made two sets of similar Zinc and Magnesium samples, with varying concentrations, with the hopes of getting similar (but better) results to the ones above. We are doing both zinc and magnesium samples in order to compare the changes, to see if it’s the +2 charged ions that is causing the change, or the zinc itself. Then, we will do it all over again until we have a significant batch of good data.

We will also be looking to see if this change is reversible, or if the zinc binds so tightly to the DNA that it cannot be washed away. This will be achieved by exposing the DNA to zinc and later washing it with Tris, NaCl, and MgCl2.

Here are our latest results, which look very promising! We also learned a very handy tool to make our graphs look better and more accurate. By normalizing the line of each sample with the experimentally measured concentration of the sample, we are able to get rid of any variation read by the CD that comes with human error when making the samples.

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