Toothpick PCR *Madness*

gustilo at pobox.upenn.edu gustilo at pobox.upenn.edu
Thu Feb 16 14:05:47 EST 1995


In article <wblank.1143341938C at news.srv.ualberta.ca>,
wblank at gpu.srv.ualberta.ca (Walter Blank) wrote:

> So -- 
> I tried the famous stick-the-toothpick-in-the-gel-swirl-it-in-the-reaction
> mix to amplify a faint 800bp band, but when I run the 2nd reaction on a gel
> I find only 200 and 400bp products (both of which were in the original gel)
> -- no 800bp band.  This happened in all 3 reactions that I tried.
> 
> I can understand that the smaller products may be "hung up" in the 800bp
> band, but why no trace of the band I want shows up, I don't get.  The
> primers I am using are degenerate, if that means anything.
> 
> If anyone can help me with this, oh, that would be great.

there is an article in Biotechniques 1995 18(2):225 entitled "Improved
Direct PCR Screen for Bacterial Colonies: Wooden Toothpicks Inhibit PCR
Amplification" Lee, A. B., Cooper, T. A.

They had results similar to you and contacted the toothpick manufacturer
to check if the toothpicks were chemically treated. They were informed
that it was not, leading them to conclude that there is something
intrinsic in the wood that inhibits PCR. They also state that "All
toothpicks made in the US are from white birch" so switching wooden
toothpick brands may not help. 

they ended up using yellow tips or plastic toothpicks to pick their colonies.

--

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    I am not responsible for comments that I make after 3:00 A.M. or after 5 cups of double espresso, whichever comes first.

gustilo at pobox.upenn.edu



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