I made a RNA extraction from mammalian cancer cell line and ı wanted to be sure whether there is a DNA contamination so I run my RNA on a gel. However, interestingly, I saw 3 bands. 2 of them are 18S and 28S RNA but one is nearly 600-700 bp. I run it twice but still I have the same result. I think it is not a DNA but I'm not sure. What could it be? Please, I need your assistance and help. You can find the gel result below.
It could be that secondary structure (looping) is causing a mobility shift of one of the rna bands if this is a result on non denaturing gel.If the band disappears when run on a denaturing gel then secondary structure is the likely cause
As Dr. Rutland stated it could be secondary structure and I think denaturing substances like as urea or formamide can be added to eliminate secondary structures.
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