XbaI diestion of PCR products

Dr. Hiranya S. Roychowdhury hroychow at nmsu.edu
Thu Jul 22 10:10:06 EST 2004

XbaI, in my experience, is not one of the finnicky enzymes.  It is possible 
that you have been just unfortunate enough to have a misincorporation at the 
presumptive XbaI site in the amplicon; isn't it?  

Quoting Raymond Dalgleish <ray at le.ac.uk>:

> We are having problems digesting PCR-amplified DNA with XbaI. It's for RFLP
> testing and the site is well within the amplified fragment, not at the end.
> The digests are always partial, and cleaning the DNA on Qiagen only seems
> to
> give a marginal improvement. The fragment digests correctly with PvuII
> without any clean up.
> Information on the Pall website (http://www.pall.com/924_25460.asp - see
> end
> of article) alludes to the issue.
> Does anybody else have this problem with XbaI, and how do you work around
> it?
> Thanks,
> Raymond

Hiranya S. Roychowdhury, Ph.D.
Coll. Asst. Professor,
Molecular Biology,
Dept. of Chemistry & Biochemistry
Rm# 336, Chemistry Bldg.; MSC 3MLS
New Mexico State University
Las Cruces, NM 88003

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