I usually elute RNA in TE Buffer but most of the protocols describe using water as blank and for the dilution of the samples. So, what is the appropriate blank to be used for RNA samples in TE buffer?
It is better to dissolved RNA pellet with 0.1% DEPC treated water. then you can use 0.1% DEPC treated water as a blank for nanodrop.
Whatever buffer you use to re suspend your RNA pellet (TE, ddH2O) should also be used to measure the RNA concentration on Nanodrop. DEPC treated water is sometimes not the best solvent for your RNA, as it sometimes affects downstream RNA analyses (i.e. SHAPE probing).
according to my best knowledge DEPC treated water is used as blank. I also used TE buffer as sample suspending buffer but during quantification our senior suggest me to use only DEPC as blank in Nanodrop.
Joanna's answer is correct. Whatever you resuspend your RNA in should be used as a blank. In your case, TRIS and EDTA will have some amount of absorbance of 230nm, 260nm, and 280nm light, the wavelengths which are used to determine the purity of your RNA sample. You want to distinguish the absorbance by your buffer with that from your RNA sample. Therefore, you set the baseline absorbance as that of the buffer, and when you measure the sample, any absorbance above that baseline is due to RNA, protein, phenol, etc., in your sample.
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