Summary:How to clean sequencing gel plates

Alan Gerstein 76467.702 at CompuServe.COM
Tue Nov 23 10:55:23 EST 1993

Thanks for your responses. I enclose a summary.

Alan at Pharmacia


alconox works best.

We have been using 10% PCC-54 (in hot water) for years.  Much safer than NaOH.

douglas prasher
dprasher at
A convenient method for "siliconizing" sequencing plates is to use something
called "RainX", a commercially available (Auto supply stores) product
intended to be used on your car windshield to bead up water. It costs
something like $2 per bottle and it goes a long way. This was featured in a
BRL focus a few years ago. It lasts through several cycles of cleaning (up to
7 the focus article stated). It is less toxic than silane or other such
chemicals, and doesn't have to be used in a hood. We routinely clan our
plates with alconox detergent, rinse with water followed by 70% EtOH. 

Jim Sutcliffe
Institute for Molecular Genetics
Baylor College of Medicine

We routinely rinse off any dried on stuff from the previous run with tap
water, them use glass cleaner stocked at the NIH warehouse, followed by
ethanol just before assembly of the gel sandwich.  One of our group
scrubs the plates with dishwashing detergent and plastic scouring pad,
rinsing with hot tap water then deionized water before storing the plates.

The only reason to use strongly basic cleaners is to remove the silane
applied to the plates.  For that, we use warm KOH by dissolving KOH in a
small amount of water and smearing it over the plates for 15 seconds or

Good luck,
Jim Owens


We only silane treat the short plate.  The KOH treatment is only used on
the plate that is not silane treated only when it shows signs of not being
well cleaned by the dishwashing detergent, and that is rare.  In our
experience, the glass plates behave badly when new.  (Badly means the gel
doesn't entirely stick to the non-silanized plate.)  They also behave badly
after the KOH treatment.  But after one or two gels, things are back to

>A fellow from U. of Md. states that after 15 washes/rinses with 1.0 M NaOH, 
>his glass plate is unable to bind a gel after silane treatment.  We don't see

>this problem in our labs. He sees the buildup of some gray material on the 
>plate, not unlike what he sees in a stock bottle of NaOH.

                                      |    O-  |
                                      |    |   |
Glass is mostly silicon ether polymer |-O-Si-O-|
        OH                            |    |   |
        |                             |    O-  |
with -O-Si-OH on the surface.

The surface alcohol groups can form H bonds with the gel components to make
the gel "stick" to the surface.  The silane treatment converts the surface
to a hydrophobic one by converting the OH groups to ethers
|    O-Me 
|    |  
|-O-Si-O-Me   Me= methyl, if you treat with methanol after silane treatment
|    |   
|    O-Me
This makes the surface slippery and discourages the gel from sticking.

The silicon ethers are hydrolysed slowly in the presence of strong base, so
glass bottles containing KOH and NaOH are slowly dissolving.  Since the
reaction is not uniform over the surface of the glass eventually you get a
ground glass appearance.  Also with time CO2 from the air forms Na
carbonate in NaOH solutions, and forms a deposit since it is insoluble in
strong base.

Jim Owens
I use standard detergent (el cheapo) and a nail brush (CVS brand).

Works fine for me, rinse with plenty of distilled water, silanise the
rabbit ear plate, rinse, assemble, pour.

et voila

un sequencing gel.

or should it be une ;)

Martin Leach
Sounds like serious washing to me! After a run I simply give 'em a rinse in 
water to get off any debris, clamp them back together and squirt some ethanol 
between them; they dry overnight.  About every 7-10 runs I siliconize the 
plates.  Works fine, and saves dishpan hands.  Besides, I don't like leaving 
detergent residues on glassware ;-}



NNNN   NN  Martin A Kennedy (E-mail = mkennedy at  ZZZZZZZ  
NN NN  NN       Cytogenetic and Molecular Oncology Unit          ZZZ
NN  NN NN           Christchurch School of Medicine            ZZZ
NN   NNNN              Christchurch, New Zealand              ZZZZZZZ
              Phone (64-3)364-0880  Fax (64-3)364-0750
After use, we soak in decon neutracon or decon 90 (although the latter is 
recomended for R/A decontamination, it precipitates calcium something 
rotten from our water, requiring a good scrubbing to remove, and so we are 
currently favouring the former which doesn't), rinse in tap water, put 
through our washing machine on its plastic cycle (Neodisher detergent), 
rinse in distilled water and air dry. Prior to plate assembly we wipe with 
propanol, repel-silanise (every time!), rinse in distilled water, air dry 
and use a compressed air line to blow dust away.

Laborious but it works.
NaOH will etch glass if left on long enough.
But I have used and removed Bind-Silane (or gel-goo, I call it) from
plates many times and have had no trouble at all.  If you are worried
about the effect of the NaOH, however, 2% KOH works just as well to
remove the gel from the plate, and you don't have to worry about
etching.  (I've also mistakenly used 20% KOH, and have had no ill
Hope this helps.

Joyce Bock
jbock at
Kalamazoo College

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