Low-Concentration Initiator Primers Improve the Amplification of Gene Targets with High Sequence Variability

  • Kenneth E. PierceEmail author
  • Lawrence J. Wangh
Part of the Methods in Molecular Biology book series (MIMB, volume 1275)


The amplification and detection of diverse strains of an infectious virus or bacteria, or variants within a gene family is important for both clinical and basic research but can be difficult using conventional PCR. This report describes and illustrates a novel closed-tube method for amplifying and characterizing heterogeneous target sequences using members of the CTX-M beta-lactamase gene family. Different subgroups of CTX-M genes exhibit low sequence identity, but accurate and efficient detection of these variants is critical because they all confer resistance to penicillin, cefotaxime, and other antibiotics of the beta-lactam class. The method combines a single pair of “thermodynamic consensus primers” (tcPrimers) with one or more “initiator primers” (iPrimers), added at low concentration (5–10 nM). Each iPrimer improves the initial amplification of one or more variants because it has fewer mismatches to its intended target than the more abundant tcPrimers. As a result of initial amplification, each heterogeneous sequence is shifted stepwise toward a better match with the tcPrimers. As soon as the tcPrimer hybridization takes place, amplification proceeds with high efficiency. The tcPrimer pairs can be designed for symmetric PCR or for Linear-After-The-Exponential (LATE)-PCR. LATE-PCR offers the advantage of generating single-stranded DNA that can be characterized for different gene variants in the same closed tube, using low-temperature mismatch-tolerant fluorescent probes.

Key words

Asymmetric PCR Consensus primers CTX-M beta-lactamase Degenerate primers Hybridization probes Initiator primers LATE-PCR Molecular diagnostics Nucleic acid sequence diversity 



This work was supported by Brandeis University and Smiths Detection Diagnostics. The authors thank Dr. Harald Peter and Dr. Till Bachmann for providing alignments of the CTX-M genes.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Biology MS-008Brandeis UniversityWalthamUSA

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