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markers for Rnase protection assay

Winoto lab lab_winoto at maillink.berkeley.edu.
Sun Jul 3 15:53:47 EST 1994

In article <2v61e5INN8na at s-crim1.dl.ac.uk>
mbgmg at s-crim1.dl.ac.uk (G. Majdic) writes:

> Hi!
> I am starting to use rnase protection assay method and I would like to hear
> what, if any molecular weight markers could be used for estimating lenght of
> protected fragments in the gel. I would appreciate information how fast (in
> comparison to BB and xylene cianol) single and double stranded RNAs travel
> in polyacrilamide gels (I didn't find that data in Maniatis or Current 
> protocols). Thanks!
>                  Gregor


I'm not sure why you would need to know about dsRNA.  The RPA is
generally used to detect ssRNA (your denatured, protected probe).  I
use an end-labeled HaeIII digest of pUC19 as a marker (denatured before
loading).  You could also use end-labeled 123 bp ladder available from
BRL.  There is info in Maniatis describing the positions of BB and
Xylene cyanol relative to DNA in native and denaturing (urea) gels at
various polyacrylamide concentrations.  ssDNA gernerally runs about 10%
faster than ssRNA.


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