Hi,

i disagree with Majie in the first point. linear DNA stretches do behave different and here the linearization by digest do improve your repeatability and precision of the method So you might consider to test it sde by side

Sven

I would recommend to linearize your plasmid.

Non-linearized plasmid will be supercoiled and might be more difficult to access. The efficiency of the reaction might be different in your samples with plasmid and your AAV samples.

As the plasmid might be accessed poorer, Cq values might shift to larger values and in the end you might ending up overestimating your concentration of AAV.