Publication Detail

Heteroduplexes in Mixed-template a Amplifications: Formation, Consequence and Elimination by 'Reconditioning PCR'.

Janelle Thompson, Luisa Marcelino, Martin Polz
2002
6 pp.
MITSG 03-28J
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Although it has been recognized that PCR amplification of mixed templates may generate sequence artifacts, the mechanisms of their formation, frequency and potential elimination have not been fully elucidated. Here evidence is presented for heteroduplexes as a major source of artifacts in mixed-template PCR. Nearly equal proportions of homoduplexes and heteroduplexes were observed after co-amplifying 16S rDNA from three bacterial genomes and analyzing products by constant denaturing capillary electrophoresis (CDCE). Heteroduplexes became increasingly prevalent as primers became limiting and/or template diversity was increased. A model exploring the fate of cloned heteroduplexes during MutHLS-mediated mismatch repair in the "Escherichia coli" host demonstrates that the diversity of artifactual sequences increases exponentially with the number of both variable nucleotides and of original sequence variants. The authors model illustrates how minimization of heteroduplex molecules before cloning may reduce artificial genetic diversity detected during sequence analysis by clone screening. Thus, the authors developed a method to eliminate heteroduplexes from mixed- template PCR products by subjecting them to 'reconditioning PCR', a low cycle number re-amplification of a lo-fold diluted mixed-template PCR product. This simple modification to the protocol may ensure that sequence richness encountered in clone libraries more closely reflects genetic diversity in the original sample.

type: Technical reports

Parent Project

Project No.: 2000-RB-52
Title: Environmental Marine Biotechnology: Development of DNA Microarrays as Sensors for Diverse Marine Pathogens in the Environment