Restriction Mapping of Plasmid DNA Lab

Introduction / Purpose:
For this lab, we were asked to create and run an agarose gel through electrophoresis. We were given samples of DNA, which we loaded into the gel. This procedure allowed us to determine the size of the DNA fragments by observing where the segments were cut by restriction enzymes. Electrophoresis causes the fragments of DNA to travel through the gel. Since each fragment is negatively charged, they are drawn towards the positive end of the gel and away from the negative side. The smaller the fragment, he further down the gel it will travel. The purpose of this experiment was to give us a good understanding of restriction enzymes and how they cut DNA fragments. The gel gave us a great visualization of the different fragments and how they are not cut to be the same size.

Procedure:
*** The procedure calls for an Agarose Gel to be cast, but in our class the gels were already made for us. So that part of the procedure will be skipped in this post.

Analysis:

The results of the gel electrophoresis mainly serve to identify which strands of DNA are the longest and shortest and via this method give us a description of which DNA strands come from the same person or organism. However, for this experiment, the position of the bands on the gel electrophoresis allow us to see the cut sites for each of the restriction enzymes used and where these cuts sites are relative to one another.

As seen in the last picture featured in the procedure section of the lab report, the smallest fragments of DNA for each of the dyes was the same size. This is why there are four marks near the bottom of the gel and relatively all closer to another. The dye in the first row only had its DNA cut into two fragments, indicating that the enzyme used on it only had one cut site. However, dyes number 2 and 4 each had four fragments of DNA all relatively close to the same distance on the gel electrophoresis. This serves to indicate that the restriction enzyme for these substances had three cut sites since it was able to cut the DNA into four pieces. However, this is evidence that the restriction enzyme cut in the same cut sites for both dyes since the DNA fragments are very similar or almost identical to each other.

A similar situation occurred with dyes 1 and 3. They each had only two DNA fragments since the restriction enzyme only had 1 cut site. As with dyes 2 and 4, it is important to note that the DNA fragments are in very similar or identical spots on the gel electrophoresis demonstrating that the DNA strands are very similar or almost identical. This means that the restriction enzyme had the same cut sits when dealing with DNA strands from both dyes 1 and 3.

While the gel electrophoresis seems to have been conducted correctly, several steps may be taken to improve accuracy. For improvement in further testing it is suggested that more care be taken when pouring the dye into the gel. This way the only movement of DNA on the gel will be due to the size of the DNA fragment and not any other factor that could lead to an inaccuracy in the data.