Science Buddies: "Ask an Expert"

Hello and thank you, Mr./Ms. Scientist!

While performing the Forensic Science: Building Your Own Tool for Identifying DNA project, my partner and I came up with a few questions.

What exactly is meant when the instructions mention "bands" of color?

Why do some of the colors travel further in the gel than others? Does it deal with electrical charge, the size of the molecules, or perhaps something else?

Also, after hooking the alligator clips to the electrodes and letting the chamber run for a while, some sorts of substances (minerals?) seemed to deposit around the positive electrode. The same electrode gathered some rust. Is this normal?

Thanks again for your time! Since the project is due this Friday, April 19th, I'd really appreciate it if you could respond ASAP! Have a great day!

-- Jessica

Hi Jessica,

I hope this helps - let me know if more questions come up

Tonya

What exactly is meant when the instructions mention "bands" of color? The samples are loaded into those wells, that are shaped like rectangles. When the gel runs, those samples stay the shape of the wells (rectangle), so they look like bands... like this: http://biology.clc.uc.edu/fankhauser/La ... 290110.JPG

Why do some of the colors travel further in the gel than others? Does it deal with electrical charge, the size of the molecules, or perhaps something else? Yes - the size of the molecules. The molecules have to travel through the gel, the gel has holes in it. The big molecules cant move through as fast as the smaller ones, so they dont go as far.

Also, after hooking the alligator clips to the electrodes and letting the chamber run for a while, some sorts of substances (minerals?) seemed to deposit around the positive electrode. The same electrode gathered some rust. Is this normal? I don't think so. Is is touching the buffer?

Thank you very much, Tonya! Your answers helped quite a lot!

Regarding the electrodes: yes, they touched the buffer. Are they not supposed to?

Note: I find it peculiar that only the positive electrode rusted, even though both were touching the buffer...

Thanks, again!
Jessica

Right - they should not touch the buffer. There is a reason why the salts gather to the positive electrode only... what do you know about these salts and why they could attract to the positive??? HINT - they have a charge...

Does that mean the salts/minerals have a negative charge? Since they gather around the positive electrode?

Also, are there macromolecules other than DNA, RNA, and proteins that gel electrophoresis can isolate? Somehow I am under the impression that food coloring doesn't contain those molecules...

Right - negatively charged ions gathering on the positive electrode.

Yes - any molecule that has a charge can be separated by gel electrophoresis. Depending on the size of your molecule, you may have to make gels with bigger or smaller holes.