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
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.
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
Re: SDS-PAGE problem
the problem seems to be gel itself may be jellying does not take place and while you run intially it works fine but after some time or so the gel gets heated and you get the result of that sort. Try to standarize the gel concentration in your lab condition.
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