Problems with sequencing gels

john wolff wolffie at u.washington.edu
Mon Jun 10 12:38:32 EST 1996


In article <31B736D1.31C1 at rrzn-user.uni-hannover.de>, Juergen Serth
<ndxdurjs at rrzn-user.uni-hannover.de> wrote:

> During prerunning, some of our sequencing gels (0.2 mm) are swelling up, 
> thereby pushing out the wells of the gel into the upper chamber. 
> We use the "base - runner" equipment (Europe: Integra Biosciences), both 
> glass plates siliconized with Dichlordimethylsilan in order to facilitate 
> subsequent transfer on filter sheets.
> Any ideas or suggestions would be very appreciated.

Been there, done that.  I'm almost certain your problem is too much
silanization on the plates.  I've heard of others having the same pain.

Maniatis describes how to de-siliconize them:  some horrendous amount of
KOH in methanol, I think, but scrubbing them with strong NaOH seems to
work.  We use some kind of product like "Rain-X" or "Gel-Slick" (AT
Biochem) to coat  one plate.  Not sure if it's silicone, or silane, or
whether there's a difference.  Too much IS too much.

Nowadays, I re-coat the plate as seldom as possible, and always strip it
first (NaOH in methanol, I think, is my current fashion).  Coat it as
thinly as possible.



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