SDS-PAGE problem

Taskan Cuatro taskan4 at
Thu Mar 4 15:02:21 EST 2004

We once had what seems to be a similar problem with sequencing gels
(diffuse and streaky dye front). The problem turned out to be the
poor-quality additive-containing ethanol we were using to clean the
glass plates. Changing to a more-expensive additive-free ethanol
completely solved the problem.

Hope this helps

> Hello All,
> For the last few weeks we have been experiencing a problem with our
> SDS-PAGE gel system (a typical vertical gel system from CBS scientific
> for running 18 cm long gels).  What happens is that for the first part
> of the run all looks well and we see a nice tight bromophenol blue dye
> front and good separation of our pre-stained standards.  Then about
> half-way through the run the dye front becomes more diffuse and
> streaky.  Also we observe the gel slipping down between the plates in
> the direction of the bottom buffer reservoir.  When we detect the
> proteins from such gels the bands appear streaky and diffuse as if
> there was a non-uniform electrical field through the gel.  Generally,
> the plates behave a bit like they have been siliconized (even though
> we have not knowingly treated  them with anything out of the
> ordinary).
> We doubt if the gel reagents are a problem because we use the same
> reagents on our mini SDS-PAGE gel system and we never experience any
> problems.  Almost all of the reagents have been re-made since we began
> experiencing the problem.  In addition,  the problem with our large
> SDS-PAGE system is intermittent.  This made me suspect the plates.  We
> typically wash our plates in warm sudsy water,  rinse with distilled
> water,  drip dry, and wipe down with 95% ethanol with a kim-wipe. We
> tried soaking our gel plates in 2 M NaOH for 2 hr followed by washing
> to get rid of any foreign substances but this didn't solve the
> problem.  Recently we bought all new gel plates and for a while the
> problem seemed solved but just yesterday we had a gel run poorly once
> again.  The problem doesn't seem to correlate with using a particular
> rig or position on the rig (each rig has 2 positions).
> I have been running SDS gels for 20 years (9 years with the CBS
> system) and have never experienced a problem like this.  We are
> desperate.  If you have any ideas please let me know.  Thanks.
> Steve


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