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.

-Hank

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

http://www.turnerbiosystems.com/doc/appnotes/998_2675.php

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?

-Matt

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.

-Hank

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