How Ethidium Bromide intercalates between RNA? - (Feb/02/2006 )
We use ethidium bromide to view DNA in agarose gels. Ethidium Bromide is said to intercalate between the double strands of DNA and exhibit florescence under UV light.. However, Ethidium Bromide is also used to view RNA in Agarose gel. I would be very glad if anyone explains me how the molecule attaches itself to the single stranded molecule..
Regards...
Regards...
l think that ethidium bromide react with bases .it doest free interaction with DNA or RNA . so ethidium bromide exits affinity DNA or RNA with hidrofobic or covalent bonds or another chemical interaction . RNA have base . so ethidium bromide exits affinity its bases.
It intercalates between the bases, rather than between the base-pairs
can't be 
If it was true, in a standard SSCP technique we could use ethidium bromide staining instead of this time-consuming, dirty silver staining... 
I guess that RNA makes double - stranded secondary structures in some parts, that's why...
I've always thought this was the reason as well...
I've always thought this was the reason as well...
I always thought that it would interact with both single stranded and double stranded but the flourescent intensity was increased significanty more when intercalated into double stranded...
This is why it is possible to stain RNA in a formaldehyde gel with EtBr --but you have to use more EtBr and some people suggest adding to the RNA loading dye in the sample to increase the visibility of the bands etc. b/c of the decreased fluorescence... also your sensitivity is decreased-- that is why you have to load more RNA to see it in formaldehyde gels by EtBr...
I used to think that RNA would form a funky secondary structure, and that would create enough dsRNA for the EtBr to interact with. Now that I think about it, however, it seems like EtBr must interact with both single-stranded and double-stranded RNA/DNA. Why? I run a glyoxal reaction prior to running RNA gels to denature secondary structures, thus ensuring smooth electrophoresis. I then stain with EtBr and see results.
It would be interesting to stain ss/dsRNA and ss/dsDNA samples of the same length with EtBr and note any differences in fluoresence between the single and double-stranded forms.
If anyone cares, here is EtBr (orange) bound to a dsRNA:
Ugh, I can't stand being out of the research loop... I can't wait until I'm back to work!
-Hank
EtBr can bind bases It has got affinity to bind them even more than bases themself that couses to enter between two strand of DNA . is it wrong? 
EtBr is an intercalator, therefore it inserts itself between DNA bases, i believe john buckels is right and thus ssDNA and dsDNA can both be visualised for this reason.
why it doesnt work in SSCP i cant tell you having never done that, but I would imagine that SSCP, needing a quite high resolution to see single polymorphisms, that EtBR staining might not be sensitive enough for this procedure
Ethedium Bromide is a flat molecule and intercalates between the two bases of a strand by hydrophobic interaction.