Terri

It is not clear to me why you wish to measure the RNA and DNA and if
semi quantitative measurements for comparisons are all that you need.
Are you interested in RNA just in nuclei or also in the cytoplasm?
With sections there is always the problem that you generally do not have
many complete nuclei, and the thinner the section the greater the number
of partial cells and of course nuclei.
You can carry out analysis by dissociation of cells from sections
followed by FACS analysis but this is generally accomplished using thick
sections and is dependent on fixation and processing procedures.

It is relatively simple to stain for nucleic acids in section and there
are numerous methods in the literature that will do this. Can also use
RNAse to eliminate the RNA.  It is difficult to carry out in a
statistically significant manner on sections unless you use multiple
sections and can be certain that sections are uniform in thickness
If you are interested in total nucleic acids in normal compared to
pathological tissue then the total amount of dye using histochemical
reactions for nucleic acids may suffice.
If you would supply us with some more information that would be most
helpful.
Thanks
Barry