Cleaning seq. plates with "Bon Ami"??

Shiao Y. Wang sywang at
Fri Apr 1 12:35:35 EST 1994

Dan Diaz (bl275 at cleveland.Freenet.Edu) wrote:

: In a previous article, balt at spieden.Stanford.EDU (Steven Balt) says:

: >
: >Hello, all!  Our sequencing gels have been pouring rather poorly 
: >lately (no pun intended :) ) and we think we have narrowed down the
: >source of the problem to our new glass plates.
: >
: >The glass plates have been scrubbed with "Bon Ami" brand cleanser
: >instead of the normal ICN "7X" cleaning solution or Windex.  Has anyone
: >else experienced any weird phenomena after cleaning with Bon Ami??
: >(In our case, the acrylamide solution accumulates in the _center_ of the
: >glass plates instead of sliding down the sides, like it should.)

: here is the procedure we use in our lab.  we use the BRL S2 apparatus with
: BRL plates and the IBI sharkstooth combs and spacers, since we dont like
: the IBI apparatus or the BRL combs and spacers.

: - soak brand new plates in 2M NaOH for 1-2 h and rinse thoroughly with
: deionized water.  place a sliver of tape on one side of each plate to
: ensure consistent use of the same side of each plate for inside/outside.

: - clean both plates with glass plus followed by isopropanol

: - coat the small plate with Rain-X, a water repellent for windshields
: available at many auto parts stores.  none of that yucky disgusting silane
: chloroform shit.  put two coats of Rain-X on the small plate, let it
: dry, then wash again with glass plus and isopropanol

: - assemble the plate-spacer sandwich and clamp (tape is for sissies).  we
: use three small clips on either side.  the plate sandwich is laid
: horizontally on an empty pipet tip box or similar rectangular flat surface
: a few inches from the benchtop

: - prepare your gel mix and pour the gel horizontally, allowing the acryl
: mix to enter by capillary action.  we put the mix in a plastic cylinder
: with lip, start on one corner of the gel, move to the other corner and then
: back to the middle, allowing the gel mix to move as a single front down the
: gel - its quick, easy and never fails.  put some lab matting down to soak
: up possible spills.

: - put the comb in and clamp (we use two large clips placed so that they hold
: the comb in place, but dont let the clips extend beyond the bottom of the
: comb, i.e. clamp only where the clip is over comb or spacer, and never
: where there is only glass)

: - read a journal (a cool one) for 30-40 min and prepare your running buffer
: (or just prepare several litres of Tris-Taurine (glycerol-tolerant) buffer
: at once and store at RT)

: - use a thin spatula to separate the comb from the gel plate, then ease
: gently up.  clean the surface of the gel plate which will contact the
: aluminum plate to ensure even heat distribution.  make sure its dry.

: - set the gel in the apparatus and clamp tightly enough to avoid leaks, but
: not to maximum tightness.  pour in running buffer and wash out the top of
: the gel with a pasteur pipet.  start your prerun (we do 15-30 min at 40-60
: W when using Tris-Taurine)

: - get your sequenase reactions ready and wash yucky acrylamide from the
: comb with water.  rinse the top of the gel and insert the comb slowly until
: the teeth just barely kiss the surface of the gel.  tighten the gel until
: finger-tight.

: - rinse the wells once again and load.  run the gel.

: - after the run, the plate treated with RainX will come off with minimal
: effort.  we then rinse with water and set the plate to dry for next time. 
: the larger plate goes into the fixing bath with the gel.  once done, it
: also gets rinsed.

: - for the next run, simply clean with glass plus and isopropanol and youre
: ready to go.  the RainX treatment will last for 20 gels or more.  fun fun.

: diz

Thanks for the tip. One question: what is the purpose of soaking the new
glass plates in 2M NaOH? Won't the glass be etched or is that the intended
purpose so that acrylamide will stick better? 

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