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EtBr acts on single strand? - (Nov/13/2005 )

I think EtBr acts on double-strand DNA. So running electrophoresis and then detecting on UV , we can identify DNA. But.. why RNA is detected?(after mini-prep)
EtBr acts on single strand? Or RNA automatically pairs each?


EtBr binds to nucleic acids.


Single-stranded nucleic acids will fold back upon themselves which essentially creates a double-stranded structure. The EtBr can then intercalate between the bases. I'm sure you're familiar with the clover leaf-shaped mRNA structure... it's much like that.



Haringsh is absolutely right.
In this webpage I found some information about RNA quantitation with Ethidium bromide, here I pasted part of it.

Ethidium bromide is a polycyclic fluorescent dye that binds to double-stranded DNA molecules by intercalating a planar group between the stacked base pairs of the nucleic acid.

Ethidium bromide can also bind to secondary structure in single-stranded RNA molecules: regions of local base pairing offer the stacked base pairs necessary for the dye molecules to intercalate.

When excited by light at or near 546 nm, the dye-nucleic acid complex exhibits an increased (about 20 fold) fluorescent yield at an emission wavelength of 590 nm.

Interesting to check up these things, I am always learning with other people questions.


But the ss RNA will still run differently from ds DNA because of decrease molecular weight, correct?



Yes, it should run differently because RNA has the extra oxygen and the differences between uracil and thymine. I'm not sure how noticeable the difference would be though.



also dna is a more stiff, rode-like structure, where as RNA, even if folded back onto itself, is a more "globular" structure. if denaturing conditions are chosen, you can of course check the exact length