What to use as a blank - (Oct/01/2011 )
I recently did a miniprep using a kit (Zyppy Plasmid Miniprep Kit---http://www.zymoresearch.com/zrc/pdf/D4036i.pdf page 5 for the protocol) and when I went to use the nanodrop to measure the concentration of DNA, I got confused as to what to use as a blank...last time I am preettyy sure I used one of the buffers from the kit but seeing as I wasn't sure this time, I asked someone who said it was ok to use water...seeing as the blank should be what you dissolve your sample in, shouldn't I use the "elution buffer"?
In principle, yes. In practice, it will make little difference. The elution buffer is simply buffered water, typically Tris-Cl 10 mM. It will not absorb significantly at 260 or 280 nm.