Rather than answer your questions directly, I will describe our
I use Long Ranger - 5% for 36 cm plates and 4.75% with 48 cm plates
(the recommended dilutions). I have never experienced a gel
extrusion, although I have only been sequencing since February...
My colleagues use 40:1 acrylamide from BioRad for VNTR analysis, and
recently had major problems with gel extrusion. Their experience
confirms that APS should not be kept in solution for more than 14
days, but new APS did not solve the problem. I mention this because
our APS is three years old, and I have heard the plausible suggestion
that it is to blame.
My colleagues then left the plates _to soak_ in 3 molar HCl overnight,
and hey presto! the extrusion problem dissapeared. I know that this
is a contradiction to your own experiences, but I thought I would let
you know what we do anyway.
I stopped using Alconex because of background fluorescence some time
ago, and no longer rinse the plates with EtOH after washing (to avoid
getting drying marks, I was told) for the same reason.
After a run, I lift the gel off the plate by placing a dry paper towel
onto the gel then rolling it off, then wash the plates in running hot
water only. I then rinse them in very hot water before placing them
in a rack to air dry. Wahing only takes a couple of minutes, and they
are perfectly clean therafter.
I'm sure you know about all this - but I tell you because if I were
you, I would place my plates in 3M HCl overnight, then use water only
to clean them, and not the dishwasher - just to give it a go.
Good luck - I hope it works (and that you haven't been told to do the
same thing by too many others!).