Once the DNA is broken up into pieces, what do you do? Gel Electrophoresis was a method, developed by Arne Tiselius, that helped analyze the segments. It soon became known as the powerhouse method because it not only yielded results fairly quickly, but accurately, as well as being able to compare multiple samples simultaneously.
Gel Electrophoresis is based on the migration of DNA fragments through gel. Wells are put in the gel and the stained DNA fragments are loaded into the gel. After all the wells are loaded, a charge is applied across the gel. The negative end is hooked up to the end containing the wells of DNA, while the positive end is hooked up to the opposite end. The DNA, being negatively charged, is attracted to the positive end and repulsed by the negative end that it is nearer to. The smaller DNA fragments are able to more quickly and easily move from the negative end to the positive end because they can maneuver through the gel better. The larger, heavier molecules move more slowly through the gel.
Based on the distance each DNA fraction sample moves, you can see the relative sizes, charges, or weights of the samples. This method is able to distinguish between nucleotides of 200-500 bases with only one difference in the bases. Since human DNA is roughly 3 billion bases long, 200-500 bases is a substantial piece of that sequence and highly beneficial to be able to work with at one time.
One of the pros of this method is the accuracy and speed of this method. The method can take several hours to do, but you do not have to be staring at it the whole time. Multiple samples can also be run simultaneously in the same gel. Depending on the size of the gel and the number of wells it contains, the number of samples processed at one time varies. The gel tends to be inexpensive, but it is also disposable rather than reusable.
One of the cons is that although you do not need to be focusing entirely on the gel the whole time, you do need to keep your eye on it. If you run the gel for too long, the multiple bands will reach the edge of the gel and it will appear as though they are composed of the same or similar strands. The method is also sensitive to being bumped, so you have to use caution. Sometimes the bands in the gel are not crisp, as well as the size being relative. Running a ladder with the sample is key, but the ladder only has certain sized fragments in it. Sample fragment sizes are therefore estimated rather than known.
The Human Genome Project and Cancer 