Remember that electrophoresis actually works on charge, not molecular weight. It just so happens that the difference in charge between the different component bases of DNA or RNA are negligible, so they appear to sort out by size on a gel, but single stranded nucleic acids are less negatively charged than double stranded ones, so RNA tends to run much slower on a gel for the same linear sized molecule. If you have a mixed product of RNA and DNA all of which is the same length, you should be able to distinguish them relatively easily.

If they are at the same concentration there will also be a difference in fluorescence because Ethidium Bromide (the most common stain) stains RNA at much lower efficiency than DNA, so the DNA band will appear much brighter.

Yes it can, but you would need proper controls to distinguish between the two. DNA and RNA are fundamentally different structures at the molecular level. They contain different bases, different modifications to bases, double vs. single strand, different sugars, etc. Because of this, "size" is not the only determinant affecting the mobility in a gel electrophoresis.

The first question to ask is, "Is the DNA linear or circular (plasmid)?" Circular DNA becomes supercoiled, and runs differently than linear DNA... and obviously RNA. If they are both linear, then you would have to run them together with controls of just RNA and just DNA in separate lanes to match up the bands. I believe RNA would run faster due to its single strand nature vs the double strand nature of DNA, but that is just a guess. Remember, RNA's can have very complex secondary structures as well which may hinder their mobility through gels... this is why you would need controls to differentiate the two. The other option would be to purify the nucleic acid bands once you run them, and then perform sequence analysis (after an RT step for the RNA) to identify your nucleic acid.

The best answer of all though would be "why would I ever do that?" This is why DNases and/or RNases are around... to remove the respective nucleic acid you want removed, so you can purify the target nucleic acid. Gotta work smarter, not harder.

Good luck,

~Adam

Remember that electrophoresis actually works on charge, not molecular weight. It just so happens that the difference in charge between the different component bases of DNA or RNA are negligible, so they appear to sort out by size on a gel, but single stranded nucleic acids are less negatively charged than double stranded ones, so RNA tends to run much slower on a gel for the same linear sized molecule. If you have a mixed product of RNA and DNA all of which is the same length, you should be able to distinguish them relatively easily.

If they are at the same concentration there will also be a difference in fluorescence because Ethidium Bromide (the most common stain) stains RNA at much lower efficiency than DNA, so the DNA band will appear much brighter.