I'm treating a cell culture with 5-aza-2'-deoxycytidine to evaluate the effect of demethylation in gene expression. I've extracted the RNA and DNA and when measuring the quantity and the quality of the sample at Nanodrop, I observe a shift in the peak of maximal absorption and discordant ratio 260/280 and 260/230.
This results aren't present in the controls group.
Anyone had the same problems?
I am not sure that this is a problem really. 5 aza cytidine has a maximum absorbance at 241 compared to the max absorbance of ctp at 271 so the incorporation of the analogue will reduce the average OD260 so if the OD280 is unchanged then the 260/280 ratio of dna containing aza cytidine will be lower than that of normal dna which will make it look impure compared to the 1.8 expected of dna but really it is the lower od260 not a raised OD280 that is causing the low ratio
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