I am isolating DNA from plasma samples of healthy donors but each time after measuring DNA on two different nanodrops, I get different DNA conc. One machine shows around 50ng/ul however other gives around 5ng/ul. As a control, I measure plasmid DNA which gives almost same DNA conc on both machines.
The factor of 10 between the machines is suspicious. Some nanodrops have the ability in the settings to translate the results to either a 1mm (true reading on a nano) or 10mm path length and this may be happening here. Check the path length setting.The plasmid result is a problem unless the amount of plasmid is below the accurate measuring limit. What type of nano are the 2 machines?
Since the control plasmid DNA yields about the same value on both machines, it is likely that the problem arises from the DNA samples and their purity. Nanodrop spectrophotometers usually yield a full UV spectrum of the sample, or at least readings at 230, 260, 280 and 320 nm, which are usuful to check the purity of nucleic acids. Thus, the first thiing would be to check whether your sample display a meaningful spectrum as expected for DNA. If for example the absorbance is due to a small amount of insoluble matter that scatters heavily in the UV, optical density measurements will depend on the geometry of the detector, which may collect a varying fraction of the scattered light. But again, checking the spectrum of your preparation, or at least the A260/A280 ratio is essential.
Seeing this question here, made me to vividly recall same experience I had sometime ago.
I think the reason why two nanodrop machines giving varying concentration value for same sample could be a technical issue. Possibly they have varying calibration sensitivity to absorbance.
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