Unusual bands on silver stained AFLP
liz_parks at ncsu.edu
Mon May 14 09:36:36 EST 2001
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?
North Carolina State University
Department of Plant Pathology
Raleigh, NC 27695
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