Northern Hyb:

[Ed Rybicki]

> Is there any reason (other than size fractionation) for running RNA on
> a gel containing formaldehyde.

Yes - it is completely (hopefully) denatured in HCHO / formamide or
glyoxal, meaning no denaturation is necessary before blotting.

> Why not run it on plain agarose gel?
> Has anyone tried it.

Yes, many times - works like a bomb, sometimes just a little smeary.  I
have done any number of plant virus RNAs, dsRNAs, etc - and never had any
problem.

> I am working with Rice RNA.  Will running RNA
> in just agarose gel affect hybridization.

Only if you don't denature it first, before blotting - and this is easily
achieved by incubating in 50mM NaOH as you would a DNA blot in 500mM NaOH
(no higher or the RNA is HYDROLYSED!)

> What is the function of
> glyoxal that is used  during electrophoresis of RNA.

Denaturation.  Have protocol for blotting RNA gels with denaturation if
anyone wants.

Hope was useful,

  ____________________________________________________________________
 | Ed Rybicki, PhD             |    "Now you've got the hang of it    |
 | (ed at micro.uct.ac.za)        | There's nothing you can't do with it |
 | Dept Microbiology           |        If you're very into it        |
 | University of Cape Town     |         You can't go wrong...."      |
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