Unusual bands on silver stained AFLP

[Liz Parks]

Hello all,
I am baffled by the banding pattern on my silver stained AFLP gel.
Normally I run radioactive AFLP, and when I find some interesting bands,
I run a non-radioactive reaction and silver stain it so that I can cut
out the bands and reamplify them for sequencing or cloning.  I've
sequenced 100  bands this way, and it works really well.  However, there
is a polymorphic band that I am interested in, that has been confirmed
in two separate radioactive AFLP reactions, that appears to be
monomorphic on the silver stained gel.  I repeated the PCR, and ran it a
second time, with the same result.  There are other polymorphic bands
that appear on the gel, so I don't think contamination is the answer.
There is a monomorphic band below the band of interest, and the bands
are well resolved, but I wonder if one of the denatured strands migrates
slower with the larger band, and this was not detected with radioactive
AFLP.  Any thoughts on what's going on, and how I can isolate my band?
Thanks,
Liz

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Liz Parks
North Carolina State University
Department of Plant Pathology
Raleigh, NC  27695
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