What _is_ a PCR smear?

Paul N Hengen pnh at fcsparc6.ncifcrf.gov
Mon May 15 16:27:32 EST 1995


Michael J. Lush (mjl11 at le.ac.uk) asks:

| We often see posts begging for help to get rid of smears
| on (I'm haveing problems myself:-(
| 
| However what I want to know is what is actualy going on 
| in the PCR and the gel?  
| 
| Are there any papers on this subject?

The smears are probably partially composed of amplified contaminating DNA,
complexes of primer and enzymes, primer-dimer concatamers or coagulates of
buffer components. Some people think they are caused by bovine serum albumin
(BSA), added by companies to enyme stocks to protect the enzyme activity, or
supplied in concentrated PCR buffers.

The TIBS article which discusses this with respect to LA PCR is available at
my ftp site (get the file pub/methods/TIBS/aug94.txt), or it can be read
directly using a WWW client (get the URL from my .sig). When I asked Wayne
Barnes what he thinks the smear is, he pretty much said `I have no idea',
although he does describe the phenomenon in his LA PCR papers referenced in my
article.[1,2] Also, Michael Frohman refers to it as "ampli-schmutz", which he
thinks is mostly caused by non-specific amplification in the PCR...Whatever THAT
is... >:^{ [3]

[1] Barnes, W. M. (1994) Proc. Natl. Acad. Sci. USA 91,2216-2220

[2] Cheng, et al. (1994) Proc. Natl. Acad. Sci. USA 91,5695-5699

[3] Frohman, M. A. (1994) In: The Polymerase Chain Reaction,
    K. B. Mullis, F. Ferre', and R. A. Gibbs (eds.) p. 16

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