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

Author:

Bru D.1,Martin-Laurent F.1,Philippot L.1

Affiliation:

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

Abstract

ABSTRACT 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.

Publisher

American Society for Microbiology

Subject

Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology

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