title: Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene.
abstract: Quantitative real-time PCR (qPCR) has become a gold standard for the quantification of nucleic acids and microorganism abundances, in which plasmid DNA carrying the target genes are most commonly used as the standard. A recent study showed that supercoiled circular confirmation of DNA appeared to suppress PCR amplification. However, to what extent to which different structural types of DNA (circular versus linear) used as the standard may affect the quantification accuracy has not been evaluated. In this study, we quantitatively compared qPCR accuracies based on circular plasmid (mostly in supercoiled form) and linear DNA standards (linearized plasmid DNA or PCR amplicons), using proliferating cell nuclear gene (pcna), the ubiquitous eukaryotic gene, in five marine microalgae as a model gene. We observed that PCR using circular plasmids as template gave 2.65-4.38 more of the threshold cycle number than did equimolar linear standards. While the documented genome sequence of the diatom Thalassiosira pseudonana shows a single copy of pcna, qPCR using the circular plasmid as standard yielded an estimate of 7.77 copies of pcna per genome whereas that using the linear standard gave 1.02 copies per genome. We conclude that circular plasmid DNA is unsuitable as a standard, and linear DNA should be used instead, in absolute qPCR. The serious overestimation by the circular plasmid standard is likely due to the undetected lower efficiency of its amplification in the early stage of PCR when the supercoiled plasmid is the dominant template.
authors.affiliation: Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America. yhou@wadsworth.org
authors.forename: Yubo
authors.initials: Y
authors.lastname: Hou
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
authors.forename: Lilibeth
authors.initials: L
authors.lastname: Miranda
authors.forename: Senjie
authors.initials: S
authors.lastname: Lin
mesh_terms: D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000378:metabolism; D015723:Gene Library; D005821:Genetic Techniques; D016678:Genome; D058086:Microalgae / Q000235:genetics*; D010957:Plasmids / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000592:standards; D018809:Proliferating Cell Nuclear Antigen / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D018809:Proliferating Cell Nuclear Antigen