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Alu I digestion of mouse genomic DNA

Donald W. Finley pavzaj at basenet.net
Wed Nov 8 01:33:30 EST 1995

In article <47ag3c$3o4 at mozo.cc.purdue.edu>, CK Wen <cwen at aux.btny.purdue.edu> says:
>I have recently digested mouse DNA with a range of restriction
>enzymes which I hope to use in my resaearch. Most seem to digest
>the DNA to smears after 3 hoours, whilst others require longer.
>Alu I however increases the size of the genomic DNA and doesn't
>seem to digest the DNA at all. The uncut genomic DNA runs on agarose
>at about 23 Kbp, the AluI digests, even after only 1 hours digestion
>increase the effective size such that the DNA does not leave the wells?
>Can anybody help to explain this?
>Thanks for your time
>Are you sure your AluI is good?  Did you tried a positive control which
>you use the same AluI to digest a plasmid DNA, for example?
It could be that the Alu I or some contaminant is binding to the DNA. 
Try adding 0.5% SDS to the loading buffer.  If that doesn't work, try
treating the DNA with proteinase K after restriction.

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