Unusual bands on silver stained AFLP

'Toby' H D Bradshaw toby at u.washington.edu
Mon May 14 13:51:08 EST 2001


Consider the possibility that your silver stain recognizes all AFLP bands
(Eco/Eco, Eco/Mse, Mse/Mse), while your radioactive bands are labeled on
the Eco primer only [if you are running conventional AFLPs as described by
Vos et al.].  The 'monomorphic' band may be an Mse/Mse fragment that you
have never seen with radioactivity, sitting on top of the polymorphic
Eco/Mse (usually) band.

Of course I have no idea what sort of AFLP protocol you are using so this 
advice may be off base.

Toby Bradshaw               | (206)616-1796 (voice)
College of Forest Resources | (206)685-2692 (FAX)
University of Washington    | http://poplar2.cfr.washington.edu/toby


In article <3AFFED74.4471ED9C at ncsu.edu>, Liz Parks  <liz_parks at ncsu.edu> wrote:
>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
>
>--
>
>~~~~~~~~~~~~~~~~~~~~~
>Liz Parks
>North Carolina State University
>Department of Plant Pathology
>Raleigh, NC  27695
>~~~~~~~~~~~~~~~~~~~~~
>
>





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