Strange problem with agarose gel electrophoresis

Arjun Sivasundar arjun at eden.rutgers.edu
Mon Apr 16 16:02:42 EST 2001


I'm running PCR products on 3.5% Metaphor agarose gels (in 1X TBE) to
separate
small PCR products from microsatellite loci. The gels are the large 96
well type, run in
0.5X TBE buffer, at 400 volts with cooling. This lab has been running
gels this way for
a while now without problems. What I have started seeing is that the
products in the
one set of (48) wells rapidly start disappearing and in about 10 minutes
there is nothing there...no DNA, no loading buffer, no DNA ladder
either. The other 48 samples run just fine. This has happened both to
the top set of wells closer to the red (+) end as well as the set closer
to the black (-) end but not both at once (so far at least). I have
tried changing the running buffer, tried a new batch of agarose, cleaned
the electrodes etc. but it persists. If somebody can help it would save
me a lot of PCR products (and time). Thanks a lot.





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