why does EtBr stain also single strand RNA?

Michael L. Sullivan mlsulliv at facstaff.wisc.edu
Thu Mar 29 11:25:38 EST 2001

Although this is true, EtBr will stain RNA even under denaturing conditions
(i.e. a formaldehyde gel) where the amount of double stranded structure
would be fairly minimal.

In solution, the bases of ss RNA or DNA will tend to stack.  I think
probably EtBr will try to intercalate between the stacked bases, and that
is at least one reason single stranded molecules will stain.


>Have you ever run secondary structure predictions on (really almost any) RNA
>sequence? Very often there is a lot of potential to fom DS regions.
>David J. Meyer, Ph.D.
>Pioneer Hi-Bred International, Inc.
>7300 NW 62nd Ave
>PO Box 1004
>Johnston, IA   50131-1004
>"Stefi~" <xxxgifalone at tin.it> wrote in message
>news:99dmqs$i5g$1 at fe2.cs.interbusiness.it...
>> How can EtBr stain also single strand? Isn't it an intercalant agent? How
>> can it stain also DNA and RNA single strand? Thx very much 2 every1.
>> Stefano
>> gifalone at tin.it
>> http://web.tiscalinet.it/gifalone
>> ICQ 110419911

Michael L. Sullivan, Ph.D

U.S. Dairy Forage Research Center
1925 Linden Drive West
Madison WI, 53706

(608) 264-5144 Phone
(608) 264-5147 Fax


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