Science Buddies: "Ask an Expert"

Hi expert! I conducted the science project Forensic Science: Building Your Own Tool For Identifying DNA and had very successful results! I just had a few questions about analyzing the results. In my experiment, I used the food coloring dye colors blue, yellow, and green. Green 'ran' the farthest. I was wondering if there was any really specific reason why green's macromolecules would have a smaller mass? Is that just the way it is or does it have something to maybe do with the fact that green is the only secondary color? I'm looking for an explanation of why green would have smaller macromolecules than yellow or blue.
Secondly, during and after the experiment copper colored bubbles at the positive end of the box appeared. (The same copper bubbles were in the video of this experiment science buddies provided on you tube. Here is the link. https://www.youtube.com/watch?v=QWkfXjGohVk.) The "bubbles" were at the very end where the two girls show the results on a plate. The "bubbles are imprinted in the gel. I was wondering why the bubbles were just on the positive end of the box and not the negative end also.
Also, after leaving the gel in the plastic box, (which was in a plastic bag,) Around 24 hours after the experiment had ended (at room temperature) the gel had drastically changed. The colors have all blended together. The imprinted colors are severely more smeared and darkened than they were during and in the first hours of the experiment. There is no clear gel left in the plastic box. Most of the gel changed to a reddish brown and green color. What caused this? Why is it so different from the experiment? After the 24 hours no other change occurred.
I had one more question about the results. I understand why green separated into blue and yellow, but why did blue separate into blue and red? Also, why did yellow just separate into more yellow while no other color stayed the same?
Thanks in advance for any feedback you can provide! I really appreciate it and sorry for the long questions!

Hi there.

What a fun project idea. I worked in a forensic DNA lab for over 10 years.

You've asked a bunch of questions. Let me see if I can address all of them for you.

1. Why green ran the farthest: more than likely, it has to do with the components of the green food coloring. You hypothesize that maybe it is because green was the only secondary color. That's a great idea. Why not test it? Run some more secondary colors and see if they all run faster than the primary colors. You could also try using different brands of food coloring as well to see if they are all composed of the same dyes.
2. Copper colored bubbles: I don't know for sure, but it looks like something is getting baked into the gel, possibly from the baking soda? Aren't they at the electrode?
3. The colors blending together: the dyes in your gel will diffuse over time. If you want to store it, then keep it in the fridge. That will help the agarose stay hard and reduce the amount of diffusion. The best thing to do is to take a picture of your get once you're finished running it.
4. Color separation: you asked when blue separated into blue and red. The answer is pretty simple. The "blue" food coloring was actually made up of two different dyes. Perhaps they added a bit of red to get a darker blue. As for yellow, apparently it was made of only one type of dye and not a blend of more than one dye.

I think that's answers all your questions. Play with some more colors to see if all these theories are correct.

Good luck!
-Lisa

Lisa~
I can't tell you how thankful I am for your great answers! I think that's about it for my questions. I am going to try my best to run more secondary colors, but if I don't have time for this years science fair a more in depth project on secondary vs. primary colors for next year would be a awesome idea for an update! If it so happens that I accept my hypothesis that secondary colors have smaller macromolecules, would you say that this might be because there are two colors in one so there needs to be more 'room' for more color components? As for the copper bubbles, yes they were surrounding the positive electrode. I read (from a different question on this website) that there are certain salts in the baking soda that are negatively charged, and therefore are attracted to the positive electrode, that would cause the copper colored bubbles. I believe that this is the reason for the bubbles.
Thank you, thank you, thank you, for your answers!
~LoverOfScience1234