Hello all,
I ran native agarose gel electrophoresis to check the integrity of my RNA sample. However, I am a little bit confused with the result. I supposed to get only 2 bands, which are 28S and 18S band, but here I can see there are 4 different types of band in lane 2 and 5. Here I can identify that two of my samples were contaminated with genomic DNA (Lane 2 and 5). However, can someone told me what band that were highlighted in the red box below? Here I attach my result. Thank you in advance.
Lane 1: RNA ladder, Lane 2-5: RNA Sample
Hi Nadhirah,
These could perfectly be dimeric configurations of your product. Notice that MW is almost 2x that of your product. In any case these are NOT unspecific products.
Cheers
Hi Nadhirah,
Which species of the the RNA from? Some species have more / less number of ribosomal peaks.
Anna
Dear Nad
to obtain the 2 canonical bands you mention you need to denature your samples. If you are not already doing this secondary structure can occur complicating the picture. Thus:
I think third band is of RNA (28S) because rather than running on denaturing agarose gel you have run the RNA sample on simple agarose and due to secondary in structures/different oonfirmation in RNA ,more than two band appear. hypothetically if you don't use denaturing agarose gel, more than two band of RNA can appear.
Best wishes
Reference denature RNA gel picture (from ThermoFisher Scientific): https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-purification-and-analysis/rna-protocol/agarose-gel-electrophoresis-of-rna.html
Dear Laurence and Naveed,
I repeat running the agarose gel electropheresis and adding the denaturation steps, and I get very nice bands. Thank you so much!
Hi Nad. That's great. RNA has a lot of secondary structure so you should routinely denature as described
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