Recently, I bought a plasmid DNA vector (pBR322 plasmid DNA) with a specified concentration. I plan to use it as lab routine control for nanodrop accuracy checks.
The storage buffer of this plasmid DNA is TE buffer. I wonder if different pH of TE buffer (pH 7.6 and 8.0) which is used as a blank buffer would affect the A260 absorbance?
The difference between pH 7.6 and pH 8 buffers will have no effect on the absorbance coefficient of nucleic acids. The only factor that may affect readings would be the presence of UV impurities if using low grade components to prepare the buffer. Normally, the absorbance of TE buffer, whether at pH 7.6 or 8, should be zero, which you can chek by using distilled water as a blank.
For a quick ballpark estimate of DNA, it shouldn't be a problem. But for accurate and sensitive quantitation, it is best to keep both the test and the blank solutions identical in all aspects except for the thing that you are assaying.
It would be better if you can dilute the plasmid in the TE buffer used for preparing the blank and then use it as a standard.
I think there is no difference, but I would rather be sure. I am not sure if it may affect in a completely different way.
As said by Praveesh Valissery and the Thermo techinical note below, pH and ionic strenght are both required to be the same for the samples and the blank.
https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf
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