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DNA plasmids are grown in E. coli host cells, and subsequent purification generally results in some degree of contamination of plasmid DNA preparations with bacterial DNA. Quantitative PCR (qPCR) has become the generally accepted method for determination of residual
genomic DNA in plasmid DNA.
Fortunately, repetitive sequences in the E. coli genome make it relatively easy to quantitate the levels of genomic DNA, over at least five logs of concentration (fig. 1, A&B). Testing involves comparison of a standard curve with samples.
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qPCR testing for genomic DNA is an option with each DNA preparation of 100mg or greater. However, it can also be added onto the cost of a small scale preparation ($150).
For guidance, the FDA has recommended a minimum level of 1% genomic DNA for DNA vaccines that are used in humans[1].
 Fig. 1A Standard curve amplification plot:
genomic DNA
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 Fig. 1B. Standard curve (red) with samples (blue):
genomic DNA
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[1] Guidance for Industry: Considerations for plasmid DNA vaccines for infectious disease indications, 2007.
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