RNA gel - interesting bands? some help - (Dec/03/2008 )
I did bacterial RNA extraction followed by the denaturing agarose gel electrophoresis. I am sure that i extracted RNA but in the gel I only see two huge black bands with a space between them and nothing else!?
For sure there is nothing but mistake on this results but i was wondering the only new thing on my procedure was the DEPC water that I prepared 3 liters and autoclaved only once which was pretty smelly. Is it possible that it can be the problem?
The water treated with DEPC and autoclaved usually have a fruity odor, but if the smell is to strong then autoclave for more time. Did you run a RNA molecular ladder?? only that will tell you more or less if you have RNA or DNA. DNA usually is near the wells. Always clean the area, gloves, materials, etc with a rnase cleaner (like Rnase Erase, Zap, etc). Use only filtered tips and if possible have a set of pipets just for RNA working.
actually i run the RNA ladder too, but did not even see the ladder! and the DEPC was really smelling so much so i thought it would be the problem since there was nothing on the gel picture.
Could you attached a picture of the gel??It will be easier to know what do you have in the gel.