Bernard Murray, PhD spam at
Mon Nov 15 16:30:01 EST 1999

In article <3830525A.A98B327C at>, james stevenson
<pcxjs at> wrote:

> Also, do you autoclave the MOPS before you use it? i think this decomposes
> the MOPS.
> If its gone yellow, then its decomposed.

This is nonsense.  Clear straw-yellow MOPS solutions are just fine
(I consider it a helpful indication that it has been autoclaved
- although MOPS buffer will turn yellow spontaneously on exposure
to air).
   If it is lumpy, opaque, the wrong pH or not the "classic" yellow
color then there may be a problem.

> > If the MOPS buffer for running formaldehyde gels to separate RNA is
> > "bad", will it affect integrity of RNA?  Or else, does it affect the
> > migration of RNA? How about pH?

How did your bromphenol blue look during the run?  If it started
to turn yellow the pH is not stable and you need to recirculate
your buffer and/or run it slower.  A local change in pH is a likely
culprit for apparent degradation.  Did your RNA ladder degrade as well?
It may be worth cleaning your gel comb to get rid of RNase (eg. with
hydrogen peroxide).  Is your formamide suitably deionised?


Bernard P. Murray, PhD
bpmurray at cgl . ucsf . edu
Department of Cellular & Molecular Pharmacology, UCSF

More information about the Methods mailing list