Hi. I have an isolated small RNA from cancer cells. I want to be sure that there is no contamination with DNA. Does anyone have experienced in agarose gel electrophoresis with small RNA samples? The 1% Agarose Gel that I made did not show nice and clear bands.
Hi Aruzhan,
the easiest way would be to load some of your samples simply on a BET stand agarose gel and see smears, the other one would be to do some PCR on intergenic sequences (with no luck to get transcribed sequences, just check it in UCSC genome browser).
I guess you didn't use DNAase step after isolation?
fred
There is a minimum amount of RNA required before you can see it on an agarose gel with ethidium bromide.
The gDNA would show up as a "smear", not as a single band.
I'd treat with a DNase enzyme. If you want to be more confident that there is no gDNA, then set up some 1-step qPCR using primers that would give a large product from gDNA & small product from RNA. Include a full set of controls (gDNA, cDNA/mRNA, water).
Good luck!