Hi all,
I have run a bacterial PCR on my polyA tailed RNA, to check for DNA contamination. The RNA is from the rumen protozoa. I have 2 bands, indicative of RNA (I think) however the upper band (presumably 28S) is smudged. I'm not sure whether this is RNA degradation or DNA contamination (please see photo)?
Advice is appreciated.
I used a 1Kb DNA ladder (Promega) and ran on a 1% gel in 0.5% TAE buffer.
When you perform a PCR reaction with pure RNA (that is, no DNA contamination) you should see no bands at all. Could it be that you used way too much template in your PCR reaction? Then you'll see the rRNA bands in an EtBr-stained agarose gel. Try to use a small amount of template (i. e., 50 ng). I hope this helps solving your problem.
Cheers, Christian
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