Hi there,

Intercalant agents are interacting through stacking forces with nucleic acid polymers. The stacking effect is the same in dsDNA and dsRNA so intercalant will interact both with DNA and RNA (as RNA contains naturally less double stranded structures than dsDNA, the intensity of fluorescence wil be less). 

I think so that dyes is not intercalated but interact with DNA and RNA through electrostatic, H-bond and hydrophobic interactions. The difference may be possible only if interaction occured due to specific part of one molecule that absent in another one.

For an intercalating dye, possibility of intercalation between base pairs will be logically similar for both dsDNA and dsRNA. If a dye shows large differences in fluorescence enhancements on interacting with dsDNA and dsRNA, there could be involvement of other interactions like electrostatic binding, grove binding, etc.

Hello,

My answer is that:

In accordance with the chemistry of both the dye and the two nucleic acids (DNA and RNA) the dye can interact with both of them and the bonding type depends mainly upon the available moieties in each of the dye and the acid, this bonding may be physical bond of chemical bond s in a critical cases. In addition, the force of this interaction may be easier with the less double stranded structure RNA than the more compact double strand DNA.