I'm developing an analytical HILIC-HPLC method, and I am interested in seeing how the oc/ss-pDNA isoforms separate out from other isoforms, and if they do at all. To do this, I need to prepare a "spiking sample" of purely single-stranded plasmid to spike into my plasmid samples and identify where the oc/ss-pDNA peak falls on the chromatogram relative to other peaks.

I know that you can get a lot of single-stranded isoform from allowing the alkaline lysis step of a miniprep to continue for too long, but this doesn't seem like a "clean" method for obtaining the isoform. Does anyone know of a good way to effectively denature a plasmid?