DNA Gels and Poor Digestion

As Travis mentioned in an earlier post, today we finished running our gel. With the help of the Steve James lab, we imaged our DNA. The results were not promising.

What you see on the left is just the DNA ladder. Those numbers correspond to the number of base pairs (bp). On the right, in the lane labeled 1, you see our DNA ladder with red lines tracing the corresponding markers. As you can see, we can clearly see the 330bp and 100bp markers. What we can't see are all of those nice little lines in between. This could be a problem in the future, but is small beans compared to the mess further to the right.

In lanes 2-12, we had placed DNA samples that had gone through various times of digestion. What we were trying to do was take DNA that was all kinds of different lengths and snip most of it down to 146bp. Each lane corresponds to 5 minutes later than the one before it. So lane 2 is time zero, lane 3 is 5 minutes of digestion, lane 4 is 10 minutes of digestion, and so on. Now, you don't have to be an expert to realize that lane 2 looks identical to lane 12! This is a bad sign. But what does it mean?

There could be many issues: The gel could have been run incorrectly, the samples could be contaminated, or we could have so much DNA (gels aren't normally this bright) that it somehow makes us unable to see what is actually happening. But I'm pretty sure none of these are the cause.

The procedure for digestion I used was a modification to the procedure I had used the first time I did a nucleosome preparation. The modification required a few more measurements, but it was claimed in the paper I pulled it from that this procedure gave better results (i.e. more nucleosomes at the end). We did these extra measurements (I believe correctly) and added the amount of nuclease (the digestors or eaters of the DNA) that the new procedure called for. However, as both Travis and I found out in later calculations (that perhaps should have been done before the trial digestion) this new procedure called for 100 times less nuclease than the former procedure called for. The final result: No digestion.

Luckily enough a) We were doing a trial digestion, not the real thing, so we didn't lose any real amount of samples and b) It is quite easy to repeat the trial digestion with the old method and then rerun our gel. And that's exactly what we are going to do tomorrow.

Wish us luck.