I am doing some research on acridine orange (AO).
I've found out that the emission wavelength of AO depends on whether it binds to double-stranded or single-stranded nucleic acids (DNA/RNA), due to that AO aggregates on single-stranded nucleic acids.
However, I've also read that AO emission wavelength (thus, aggregation) depends on pH. So how come there is a difference in emission spectra (aggregation) when binding double-stranded nucleic acids (mostly DNA but can also be rRNA, tRNA) compared to single-stranded nucleic acids (RNA, sometimes DNA)?
Is it because the single-stranded structure is "more acidic" than the double-stranded structure? I know there is an extra hydroxyl group on ribose (RNA), but since AO binds single-stranded RNA as well as DNA I guess I can't blame an extra hydroxyl for making single-stranded nucleic acids (RNA and DNA) "more acidic" as DNA doesn't have that extra hydroxyl. So what is it that makes single-stranded nucleic acids "more acidic" than double-stranded nucleic acids?
Looking for some serious help to make me understand..