Nano Drop measurements and RNa Gels incompatible? - (Dec/12/2007 )
Hi!!
I am encountering a strange phenomenon.. I measured the concentrations of RNA extracted from Sea Water samples, disolved in water, extracted with Acid-guanidium phenol Chloroform method. the nanoDrop measurement says I between 335-500 ng/µl of RNA in the samples with a A 260/280 of around 1.8-1.9. then I loaded these samples on a 2% agarose gel, stained it with SYBR Green II... and I do not see anything! Before this, even if i had genomic DNA contamination I would see it on the gel. Then I did a Bioanalyzer run, and I still do not see anything at all... I do not even see a possible DNA contamination, which you normally should see especially if the concentration is detectably high. now I am quite confused, I cannot decide whether I have RNA or not... I repeated the measurements and the gel with positive and negative controls, everything seems to be in order.
anybody have an idea?
maybe your sample became contaminated with rnases after you read it?
I am encountering a strange phenomenon.. I measured the concentrations of RNA extracted from Sea Water samples, disolved in water, extracted with Acid-guanidium phenol Chloroform method. the nanoDrop measurement says I between 335-500 ng/µl of RNA in the samples with a A 260/280 of around 1.8-1.9. then I loaded these samples on a 2% agarose gel, stained it with SYBR Green II... and I do not see anything! Before this, even if i had genomic DNA contamination I would see it on the gel. Then I did a Bioanalyzer run, and I still do not see anything at all... I do not even see a possible DNA contamination, which you normally should see especially if the concentration is detectably high. now I am quite confused, I cannot decide whether I have RNA or not... I repeated the measurements and the gel with positive and negative controls, everything seems to be in order.
anybody have an idea?
seems that the water you used to resuspend your pellets might have been contaminated with RNases. if you plan to run a gel, you might resusped the pellet in formamide, but then no nanodrop measurment is possible.