If your nanoparticle is able to bind the DNA through electrostatic interactions try gel retardation studies, EtBr intercalation, DCF adsorption, nuclease protection etc. These can give you an indication of the association of your DNA with your NP 

Depending on nanoparticle characteristics, magnetic and fluorescent nanoparticles can be easily localized by microscopy. You could try first to corroborate the NPs localization into samples. That will help you to better select the correct technique to study DNA-NPs interaction.

You may use different mixtures of both and evaluate settling behaviour in centrifugal field.