Does this mean that ssRNA or ssDNA can preserve some folded structure or local base pairing, in high denaturating conditions, such as 50% formamide and 8 M urea?
Or is there another mechanism of EtBr intercalation? For instance, within the stacking region of the bases, instead of the base pairing region...
Denatured RNA and ss-DNA can still be detected (but much less efficiently, 10-20x less than ds) since they can loop back into itself to form secondary structures (not efficiently though), even after treatment with denaturing agents and then provides local base pairing which allows EtBr to intercalate.
Ethidium binds between the stacked bases in DNA. Being a large planar molecule it binds by forming close van der Waals contacts between the stacked bases of a single DNA (or RNA) strand as well as between the bases of the complementary strand. The distortion of the intercalated EtBr molecule increases its fluorescence intensity. The distortion is greater when EtBr binds to both strands, but binding to a single strand is sufficient to create an observable increase in fluorescence intensity.
Great! Thank you, Ian. Do you think that the distortion of the EtBr molecule when it is intercalated within the stacking is different from its state when it is intercalated between the base pairs (implying thus differentiable emission spectra)? In other words, is it possible to find a way to correlate the emission of EtBr to the presence of secondary structure in nucleic acids? Thanks in advance.
I also find out that this happens when I run a synthetic primer on an agarose gel and stain with EtBr. As Ian said they bind to ssDNA as well but the flourescence they emit is less.
see this:
https://www.nature.com/articles/emm200368.pdf
"The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures "
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