"Building Your own Tool for Identifying DNA"

[donnybru]

Hello my name is Donald. For my science project I decided to construct a gel electrophoresis chamber as an engineering project. I precisely based my chamber on the "Building your own tool for identifying DNA" project. Upon testing my contraption, however, my results were completely opposite from the results on the "Building your own tool for identifying DNA" page. Whereas it stated the dye would travel towards the positive electrode, the dye in my experiment (which I conducted 4 times to make sure it was not a fluke and received identical results every time) traveled towards the negative electrode, while a thick, cloudy brownish substance formed around the positive electrode. Is there something I am doing wrong? I followed the directions as closely as possible.
Thank you,
Donald

[donnahardy2]

Hi Donald,

Congratulations on getting the gel box constructed! You obviously have a complete circuit with your system.

Your results sound like the polarity of the electrodes has been reversed. Why don't you switch the position of the electrodes and see if the dye will migrate towards the positive electrode? Let us know what happens if that does not solve the problem.

Donna Hardy

[donnybru]

Hello again,
I have conducted my test once more, this time switching the electrodes so that the positive electrode was directly behind the dye. After completing the circuit, the dye surrounded the positive electrode, which once again began creating some sort of brown cloud. It seems that the dye is going towards the electrode behind it no matter what, and the positive electrode continues to create this strange substance.
Thanks,
Donald

[donnahardy2]

Hi Donald,

I'm sorry my suggestion didn't solve the problem. I don't know what is causing the brown cloud at the positive electrode, but I'll ask if one of the other experts can help explain your results and let you know as soon as possible since I see your project is due on February 4.


Donna Hardy

[donnybru]

Dear Donna,
Thank you so much for your help. I hope I can get to the bottom of this.
-Donald

[donnahardy2]

Hi Donald,

Here's an explanation of your results. You may not be able to fix the problem before your project is due, but an explanation of the results will help you complete your project write up.

The brown cloud indicates the gel is overheating and the current is too high. The most common cause of this is due to using a buffer with a concentration that is too high. Try diluting your buffer by 1:2 or 1:4 in deionized water and try again. You could also remove a battery to see if that will eliminate the brown cloud. You should see production of small bubbles, but not the violent chemical reaction you are seeing. There may be extra ions in your water or contaminants in the baking soda that are creating the high current conditions.

Please let us know if you solve the problem with these suggestions.

Donna Hardy