Wooden Toothpicks (Taq Inhibitor)

Paul N Hengen pnh at fcsparc6.ncifcrf.gov
Thu Mar 9 18:39:29 EST 1995

The following is my correspondence with Tom Cooper who is
one of the authors of the toothpick paper in BioTechniques:

: To: tcooper at bcm.tmc.edu
: Subject: toothpick inhibitor
: Dear Dr. Cooper:
: I write a monthly column called `Methods and reagents' within the Elsevier
: journal Trends in Biochemical Sciences (TIBS) consisting of highlights of
: discussions and bits of reviews originally posted to the newsgroup
: bionet.molbio.methds-reagnts, available on the Internet. In the April 1995
: issue, I'm including a segment about discussions related to your paper
: published in the February 1995 issue of BioTechniques:
: @article{Lee1995,
: author = "A. B. Lee
:      and T. A. Cooper",
: title = "Improved direct {PCR} screen for bacterial
: colonies: wooden toothpicks inhibit {PCR} amplification",
: journal = "BioTechniques",
: volume = "18",
: number = "2",
: pages = "225-226",
: year = "1995"}
: In the article, you wrote that the inhibitor of Taq polymerase is not known.
: I would like to know if you have found out any more information regarding the
: source of the inhibitor since the article was submitted. Also, I'm including
: the portion of my column which will be published shortly. If you have any
: comments or suggestions, I would appreciate hearing them. Thank You.
: -Paul.

| Picky, Picky!
| *************
| In last month's Methods and reagents column (TIBS 20, 124-125), the
| reamplification of a PCR product was discussed in detail. One of the methods
| for recovering a DNA band for a secondary amplification is the use of a
| toothpick for stabbing the band.  Although it was not spelled out in the
| article, it was assumed that the toothpick would be wooden.   
| A recent study [3] revealed that wooden toothpicks contain a water-soluble
| inhibitor of amplification of DNA by Taq polymerase.  Interestingly, the
| inhibitor is probably intrinsic to the wood, not introduced by the
| manufacturing process.
| Although it was not discussed in the paper [3], and it is unknown how it could
| survive the milling and packaging processes, the contaminant could be a toxin
| of sorts or, oddly enough, genomic DNA from the white birch trees used for
| making the picks.  Whatever the substance is, it could account for many, many
| failed PCR experiments.  Based on this new information, netters are now
| recommending the use of plastic toothpicks or pipette tips for band stabbings.
| [3] Lee, A. B. and Cooper, T. A. (1995) BioTechniques 18, 225-226

> Dear Paul:
> We have not learned anything more about what in wooden toothpicks inhibits
> PCR. Toothpicks are made by stripping the wood, cutting out the picks,
> steaming for several hours, and the toothpicks are heated and tumbled dry
> for polishing. It is possible that heating modifies a component that
> inhibits the polymerase.  With regard to the possibility that genomic DNA
> inhibits PCR, I think it unlikely that sufficient DNA would be released in
> 2 seconds of swirling.
> Thanks for your interest. I think that you are correct in saying that many
> PCR reactions are likely to have been inhibited by use of wooden
> toothpicks. Unfortunately, plastic toothpicks are not easy to come by. We
> have to go to a party supply store to find them. The joke in my lab is that
> we should use the plastic swords.
> Tom

*note added by pnh:

...and while you're out at the party store, pick up a bottle of
Captain Morgan and some of those paper umbrella thingys too ;-)

* Paul N. Hengen, Ph.D.                           /--------------------------/*
* National Cancer Institute                       |Internet: pnh at ncifcrf.gov |*
* Laboratory of Mathematical Biology              |   Phone: (301) 846-5581  |*
* Frederick Cancer Research and Development Center|     FAX: (301) 846-5598  |*
* Frederick, Maryland 21702-1201 USA              /--------------------------/*
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