Universal PCR

Dick Beeman beeman at crunch.usgmrl.ksu.edu
Tue Aug 2 13:50:14 EST 1994

> Doug Rhoads' response to my response to his response to my response:

> "OK.  But if your application of Universal Primer PCR  is part of your 
> work with Triboleum you are working with genomes 10-100x smaller than 
> mammalian and plant genomes.  Could this partly explain getting no other 
> bands.  During my stay there at KSU I did degenerate PCRs on hamster DNA 
> and we usually got 2-4 bands.  Now working in yeasts and fungi we only get 
> one band.  Of course we were also working with genes that had 10s of 
> pseudogenes around."

A couple of points for Doug: True, we used the Tribolium genome, which is
about the same size as that of Drosophila.  However, the method we adapted
(Sarkar) was applied to genomic DNA of several mammalian species (dog, cow,
rat, pig) and worked on all of them.  Sarkar's gene was coagulation factor
IX, which I'm guessing is a single copy gene.  Our retrotransposon is a
mid-repetitive element (20-40 copies), but we are getting a diversity of
insertion junction fragments, and even fantasize about getting most or all
of them.  Conclusion: universal PCR may be worth a try as an alternative to
inverse PCR, even for a single copy gene in a fairy large genome.  
Dick Beeman
beeman at crunch.usgmrl.ksu.edu
"One of the advantages of being disorderly is that one is constantly making
exciting discoveries".  A. A. Milne

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