RNA extraction with smear after electrophoresis - (Nov/01/2005 )
Hi, i am newbie for RNA extraction. I had extracted RNA and run on 2% TBE gel. But it has a very serious smear along the RNA sample lane. I attacted the photo... Please give some guidance for how should i ratify the smear and is it possible to perform q-RT-PCR.
1/ I favoured that one, your RNA is partially degrade, you should toroughlly wash your gel chamber and only use sterile water (some people use DEPC treatment for every thing)
2/ Your RNA is heavilly contaminated by Genomic DNA which of course appears as a smear of nucleic acid on your gel
3/ Your sample is full of salts and they alter the migration running up as a smear !
In any case if you look at the ribosomal RNA bands they don't look too bright and the 16s is as bright as the 23s which is not such a good sign
Here is a link to a RNA gel from Quiagen look at the fluorescence of the 23s and 16s
RNA agarose gel