Northern background

T. J. Murphy medtjm at bimcore.emory.edu
Tue Nov 16 09:26:36 EST 1993


In article B6u at news2.cis.umn.edu, dubear at molbio.cbs.umn.edu (Dubear Kroening) writes:
> 
> Hi all,
> 
> I have been following the discussion on Northerns with great interest.  In
> our case we have Northern blots that sometimes have high background.
> The probes we get the high background are always larger (>2kb), while an
> identical blot with the same prehyb and hyb solns (except for the probe,
> of course) will turn out just fine.  
> 
> Has anyone else noticed something like this?  Any idea why a larger probe 
> will cause high background (this occurs all over the blot, not just in the
> lanes)?  Any comments or insights would be greatly appreciated.
> 
> Dubear Kroening
> dubear at molbio.cbs.umn.edu
> 

Do your probes have repetitive sequence elements in them?  The simplest way to check
is to run a FASTA with your >2kb probe sequence.  If anything comes up like "transposon"
or repetitive element, your only hope for clean blots will be to trim that sequence
from your probe.  It's amazing how many genes have these little runs of sequence inserted
into them.



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