Sequencing gels -bubbles

weazel at weazel at
Tue Mar 17 19:30:49 EST 1998

I never "clean" my plates - after the gel run, I rinse off any acrylamide bits
with water and dry the plates completely with a paper towel. No scrubbing with
any soap stuff. Using sigmacote usually prevents bubble formation for me. I
also use a "wonder wedge" to separate the plates a bit whilst pouring. If
you've got a residue on the plates that prevents bubbleless gels even with
sigmacote, you're going to have to strip that stuff off with something like
Chromerge (a nasty, acidic conconction). You should only have to do this once
in a long while. Otherwise, it may be time to invest in some new plates.

DNA Hacker's Resource

> Hi,
> I do quite a bit of manual sequencing, and am getting very tired of
> cleaning glass plates, -have tried lots of different chemicals/reagents,
> -and from time to time, think I've found womething that work for
> everything, only to find some dirt resistant to all I have in the
> cupboard.
> Anyway, I had this silly idea, that as opposed to cleaning the glass
> plates carefully, if you could reduce the surface tension of the
> polymerising mix (I assume that completely without it, -there would be
> very little tendency to form bubbles- though this is something I know
> very little about,just guessing) - then the tendency to form bubbles
> would be smaller. -- So I tried dumping in a bit of SDS (0.02-0.1%) in
> the mix, and then pouring onto some fairly dirty plates. -- This didnt
> seem to make much difference, but I still have the feeling that there
> should be something one could add to the mix to change its properties
> such that one could get away with far dirtier plates.
> Question is, -am I barking up the wrong tree, -and is there maybe
> someone out there with a better understanding of bubble formation,
> chemistry and so on, who might have a better idea as to what to chuck
> in?
> I am hoping that there will be a brilliant reply with some ingenious
> suggestion, casue I am getting very tired of cleaning.
> cheers,
> Martin Jakt
> dept. of Biochemistry
> University of HK
> ps, if someone should have an idea, please also email me this,, -- at
> mjakt at

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