Sorry I did not include more detail. DNA is the molecule found in a cell nucleus that can vary in size and always has a negative charge. The traditional method to separate DNA fragments is by agarose gel electrophoresis. The gel module you are using was designed for this application.http://en.wikipedia.org/wiki/Gel_electr ... leic_acids
However, electrophoresis is a general technique that can be used to separate any type of charged molecule. http://en.wikipedia.org/wiki/Electrophoresis
You are purifying anthocyanins. Look at the structure of the anthocyanins in the link below. The ring structures are composed of carbon and hydrogen, the R groups are usually sugar molecules, which are composed of carbon, hydrogen, and oxygen and have a neutral charge. Notice that there is an oxygen with a positive charge in the molecule. The molecular weight is about 450 Daltons. http://en.wikipedia.org/wiki/Anthocyanin
Here is the structure of DNA. Notice all of the phosphorus atoms on the molecule; these all have a negative charge and the molecule is much larger, up to several million Daltons. http://en.wikipedia.org/wiki/DNA
As I recall, you did not want to do the DNA project because DNA is colorless and you would have to stain the DNA molecules with a DNA specific stain. Since you wanted to separate molecules that were already colored, you chose flower pigments. So you are using the same technique that is used for DNA separations, however, your basic application is different.
I see that your project deadline is coming soon, so you will need to revise whatever background information you have written and make sure your project board refers to plant pigments/anthocyanins and not to DNA. With your extraction protocol, I would not expect there would be any DNA at all in the samples. Since the anthocyanins are positively charged, not negatively charged like the DNA and food coloring, you will need to run the gel in the opposite direction compared to the food colors.
Does this help? If not, then post more questions. I want to make sure you understand all of the details before you put your project board together. You need to be able to explain the science behind your project to the science fair judges.