Help--my genomic DNA is migrating unevenly

[Martin Leach]

baum at mendel.berkeley.edu (Paul Baum) wrote:
>I have been doing many Southern blots using C. elegans genomic DNA.  I 
am
>finding that when I use the same enzyme to digest different samples, I 
get
>similar band patterns, but the bands appear to have migrated at 
different
>speeds (i.e. they are not aligned as I would expect, but skewed up or 
down
>in neighboring lanes.)  I thought that this was a problem with excess
>salt, but repeated EtOH precipitations, spooling out of DNA and 70% 
EtOH


What is the od 260/280 ratio of the DNAs like?

Furthermore, try a phenol - phenol/chloroform/isoamyl alcohol - then 
chloroform/isoamyl alcohol extraction.

It may be that you have different protein contamination in each sample. 
Re ppting the DNA without a phenol extraction would still keep the 
protein there..

Martin

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