Millie, there are a variety of symptoms that seem to go together
and which all arise from contamination on the glass plate, as far
as anyone can tell. We have seen blank sections, band-broadened
regions, "smeared" lanes and many variations and combinations of
these. In our hands, when we've seen blank regions at the start of
the gel, it's been followed by smeared lanes rather than "good"
data. We have, however, seen blank regions in the middle of the gel
followed by apparently fine bands. My best guess is that you are
seeing a new variation of our old enemy.
In our case, as with yours, plate contamination started after
*years* of trouble-free sequencing, and with absolutely no warning
or reason. Something changed - whether water, acrylamide production,
or "something else" - and we've been fighting it ever since.
Those who see these problems have found various procedures that
cure it, including:
- MultiTerge (works best for band-broadening, useless against
other symptoms).
- HOT water wash, especially in a dishwasher. We don't have hot
water in our building, only tepid, so I bought industrial-
size coffee pots to heat up wash water.
- Cerium oxide polishing. This is one type of "jeweler's rouge",
an abrasive that can polish your rings, remove scrathes from
CD's and remove surface deposits from sequencing plates.
The last option was the one that made a huge difference for us. For
a while, using other wash procedures, we lost up to 10% of our gels
to "smearing". Once we started using cerium oxide scrubs, it went
to just a couple lanes out of every few thousand samples. As a side-
benefit, I was able to remove some scratches from the face of one of
my favorite radios. :)
Cerium oxide is sold by The Gel Company (1-800-256-8596) under
the trade name "Plate Doctor" (cat# MJK-360, $89). I'm sure it's
also available from numerous other sources like jewelry stores or
lapidary suppliers. I'm now looking for a battery-powered polisher
such as might be used on cars ... or sequencing plates.
Good luck with your artifacts.
Bob Lyons
University of Michigan
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Robert Lyons, Ph.D.
Director, DNA Sequencing Core
University of Michigan
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