XhoI Southern

Malte Buchholz mbuchho at med.uni-goettingen.de
Tue Mar 30 08:09:11 EST 1999

Alan wrote:
> Hi netters,
>     I have a query concerning the digestion of mouse genomic DNA with
> XhoI. I found a pretty strong "undigested" band of >13 kb and a rather
> weak smear (all the way down to 2 kb). I was wondering if XhoI sites are
> really so rare in the mouse genome that most of the resulting fragment
> are bigger than 13 kb, or my genomic DNA is so dirty that it is only
> partially digested (I did try digesting it with EcoRI, and it gives a
> smear...complete digestion!). Anybody came across similar experience
> please kindly drop me a line. Thank you very much.
> Alan Lee

Hi Alan,

according to the New England Biolabs catalogue the average fragment size
of XhoI-digested mouse genomic DNA would be predicted to be 7 kb.
However, bands of greater size (seemingly undigested) like the one you
describe are something I see quite often in restriction digested mouse
DNA prior to blotting; so far this has never proven to pose serious
problems for fragment detection.

Hope this helps,


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