Removing genomic DNA contamination -- Ambion Turbo DNase or Qiagen RNase-free DN - (Jun/09/2008 )

Hi everyone

I am preparing RNA from E coli cells for GeneChip analysis using the RNeasy kit from Qiagen. I have two options of removing genomic contamination: 1) Extract RNA with RNeasy kit --> Treat with Ambion DNase --> Clean RNA with RNeasy kit 2) Extract RNA with RNeasy column and do on-column digestion with RNase-free DNase from Qiagen.

Does anyone have experience using these two DNases and which is better?

Thanks!

hdc02

The less steps you put your RNA into, the better. When you isolate RNA on columns, it's more convinient to use DNAse on the column.
We use both, (Turbo DNAase for our samples isolated from Trizol) and I didn't see any difference, both works fine.

I have to disagree, and perhaps it depends on how stringent you need to be. I have found that if you are looking for a low abundant target, DNAse on the column is not enough to remove the genomic contamination (qiagen). I typically do both the DNAse on the column and the turbo from ambion-I think that in fact the turbo itself is probably sufficient-but I don't want to waste samples testing it. I know though, that the DNase and column alone have genomic contamination turning up at about 30 cycles

I have to agree with Tara123, in our hands Ambion's Turbo is much more efficient at removing gDNA than the on-column treatment from QIAGEN... It involves adding an extra step, though, so I guess it's a matter of what are you going to be using your RNA, if you're doing RT-PCR if your primers span introns, and if your target is abundantly expressed...