Hi, I am trying to set up a qPCR using genomic DNA and digested genomic DNA. Essentially, I have two identical conditions (concentration, buffer, etc.), except one has enzyme. From the concentration of gDNA, I can figure out how many copies of my gene should be there and how much I am putting into my PCR reaction for the intact genomic. However, I was wondering if the same applied for the digested genomic DNA? Since they both started with the same amount of genomic DNA, there should be the same number of gene copies in both conditions (and the amount of sample I add to my PCR is based on volume, rather than re-measuring the concentration after digesting). Would the PCR conditions be the same for both? Or does the digestion mess with the kinetics of the qPCR, such that I couldn't compare the two samples directly?