I have been aware of why a Qubit should give more accurate and often lower DNA concentrations over the nanodrop. Today I finally did a direct comparison of the two (Nanodrop one, Qubit 4) and the difference was a little more extreme than I anticipated.
The average multiple difference between the qubit dsDNA (miniprepped bacterial plasmids) and the Nanodrop is ~ 1.8x
Does this mean my plasmids are particularly contaminated or of poor quality?
Is it normal for there to be such a drastic difference?
Why would the nanodrop be able to give dna concentration readouts if they are off by 2x ??
Thanks
Did you measure them in triplicates? That might mitigate the effect. But yes that difference is possible as you are comparing two different methods: photometry (nanodrop) and fluorescence (qubit). Nanodrop is very sensitive to chemical contamination (eg can give a huge peak w phenol).
Péter Gyarmati Is this more common at lower concentrations? I forgot to mention my samples are from low dna yielding minipreps in the 9 - 60 ng/ul range
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