When performing encapsulation efficiency (EE), the plasmid still forms a complex with the polymer and cannot dissociate so I cannot detect any band on agarose gel.
You can centrifugate your nanoparticles and collect the supernatant and measure by Nanodrop, oligreen kit or using a labeled DNA the amount of DNA in your supernatant. Then you can calculate the amount of DNA loaded into the nanoparticles with the following equation: the DNA-loaded= initial DNA - DNA in the supernatant.
Thanks for answer. Using uv was not successful due to interference from the formulation. But with fluorescence kit from bPromega quantification in the supernatant was ok.