This is from the Nanodrop people..”After RNase treatment I would purify the DNA by passing through a column. The free nucleotides themselves will pass through the column (e.g by Qiagen or Sigma), leaving only intact DNA bound, which can then be eluted. I cannot find a definitive answer in the literature, but I would expect the degraded RNA to still absorb at 260nm, therefore I would recommend the additional purification step.”
I don’t know fully if digested RNA fragments are co-precipitated with DNA and hence a column/gel cutting is the only way of separating these 260nm absorbing fragments from the DNA. Anyone got any evidence?
Also- in general be careful with preps from columns- there is definitely something ‘weird’ with absorbance profiles samples from the silica plate method (and possibly from other columns). If in doubt use the ‘safer’ quant. method (presuming that Hoeschst dye binds only to DNA).
Anyway…I hope you get the picture!!