óan you run an RNA TBE-agarose gel

Sergey V. Orlov Serge at serge.stud.pu.ru
Sat Aug 26 16:12:19 EST 1995

John Watson wrote:

> We are using a labeled RNA probe for the dectection of enteroviruses.  We
> want to make sure that the we have some probe.  Can we just run it on a
> TBE/agarose gel and stain with EtBr to detect the presence of the RNA.
> Keep in mind that we don't care about getting size estimates.

> John Watson
> Wisconsin State Lab of Hygiene

Hi, John,

I don't experience in RNA electroforesis on a TBE/agarose gel ( I always use
phosphate buffer for gel according Maniatis et al.). However, it is my opinion
that buffer is of no significance for electroforesis in a agarose gels.
I heard that that TAE buffer are used for RNA electroforesis too. I don't
have problems with RNA electroforesis in TBE/PAAG, therefore TBE don't
disturb RNA electroforesis. EtBr stain efficiently the double strand nucleic
acids only, but RNA forms the secondary structure in nondenaturing gels
and stain with EtBr (remember that RNA isn't stained by EtBr in denaturing
gels (containing formaldehyde or glyoxal or urea). Another problem is a
quantity of RNA (usually, small quantities of labeled RNA are used,
it is necessary 10 - 100 ng of RNA for visualization it by staining with
EtBr). If your quantities are unsufficiently, try detect your probes by
radioautograph gel.

Hope, this helps.

Serge Orlov
E-mail: serge at serge.stud.pu.ru

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