I was recently confused about why the average base pair MW is ~660Da (information needed for rationalisation of qPCR results).
Whilst calculating how much difference this generalization made to the scale used to present data (my fragment is 65% GC), I worked out the average base pair MW to be 616Da (see attached file).
After a bit of reading, I think the difference is accounted for by nucleophilic addition (eg. Na+ interacting with phosphate group O- and incorporation of zinc between bases), but now I wonder whether ion association makes any difference to the spectrophotometric properties of DNA?
Because if it doesn't, surely we should use the deionised MW to work out the number of moles in a solution, for example in standards used for qPCR, to increase accuracy?
(I'm aware that the differential expression ratio remains constant, so the significance of results does not change; this purely affects the scale used)
Turns out the association of ions does make a difference, as explained by structural changes here: http://www-f1.ijs.si/~rudi/sola/Seminar_Lucija_Coga.pdf
I'm guessing the average MW of a base pair has therefore been worked out experimentally (if you know a paper showing this, please post it).
So now I suppose the question is; how does a spectrophotometer know whether ions are incorporated, and to what extent? Or is the ionised state of DNA constant once double strands are formed?
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