I was planning to run a qPCR assay on amoA genes (bacterial and archaeal) from my marine sediment DNA extracts. After going through literature I observed that many people were using the Arch-amoAF and Arch-amoAR to amplify archaeal amoA (Francis et al 2005) and amoAF1 and amoA2R for the bacteria (Rotthauwe et al 1997). However these are the same primers used for preparing standards for their assays. I have a pure culture N.maritimus to be used as a standard for the archaeal assay. I was wondering if I could use the above mentioned primer to amplify the amoA gene from the cell culture, purify the product and directly use it as a standard without cloning it ? My main concern was if it was fine to run the qPCR assay with primers that were used to prepare the standard itself.