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Applied and Environmental Microbiology, March 2008, p. 1660-1663, Vol. 74, No. 5
0099-2240/08/$08.00+0     doi:10.1128/AEM.02403-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example{triangledown}

D. Bru, F. Martin-Laurent, and L. Philippot*

INRA, University of Burgundy, Soil and Environmental Microbiology, CMSE, 17 Rue Sully, B.P. 86510, 21065 Dijon Cedex, France

Received 25 October 2007/ Accepted 3 January 2008

We investigated the effects of internal primer-template mismatches on the efficiency of PCR amplification using the 16S rRNA gene as the model template DNA. We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch.

* Corresponding author. Mailing address: INRA, University of Burgundy, Soil and Environmental Microbiology, CMSE, 17 Rue Sully, B.P. 86510, 21065 Dijon Cedex, France. Phone: 33 3 80 69 33 46. Fax: 33 3 80 69 32 24. E-mail: philippo{at}dijon.inra.fr

{triangledown} Published ahead of print on 11 January 2008.

Applied and Environmental Microbiology, March 2008, p. 1660-1663, Vol. 74, No. 5
0099-2240/08/$08.00+0     doi:10.1128/AEM.02403-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Nikolausz, M., Chatzinotas, A., Tancsics, A., Imfeld, G., Kastner, M. (2009). Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities. Appl. Environ. Microbiol. 75: 2850-2860 [Abstract] [Full Text]  


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