Formaldehyde vs. Formamide for Northern

Nick Theodorakis nicholas_theodorakis at
Mon Apr 24 12:09:54 EST 2000

In article <390460F1.29632C1E at>,
  Vellanoweth's Lab <jwheele at> wrote:
> We've been having a lot of trouble degrading our plant RNA with
> formaldehyde.  We've tried pHing the formaldehyde with NaOH to 5.3, and
> eliminating the formaldehyde from the incubation step.  However we are
> still getting degradation in the gel.  I looked in the Ambion catalog to
> check if our formaldehyde was bio-reagent quality and found they don't
> sell formaldehyde, only formamide.  This leads me to wonder whether
> formamide can be used in a denaturing gel rather than formaldehyde, or
> if you can run it without the denaturant since the sample is already in
> formamide.  Any northern experts out there?

You can make a denaturing acrylamide gel, but urea is more commonly used.
I don't believe you would be able to get an agarose gel to "set" in the
presence of chaotropic denaturants like formamide, though.

I'm wondering about your formaldehyde, though. I have never had a problem
even with ordinary reagent-grade 37% formalin in Northerns. Could some
other component be the problem?


Nick Theodorakis
nicholas_theodorakis at

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