What is it you're trying to find out? If you're trying to determine if your compounds are topo II poisons, you can run cleavage assays on a DNA substrate (i.e. supercoiled DNA) with different amounts of drug present (drug titration). You can then separate the products with electrophoresis, allowing you to identify how much single-stranded, double-stranded, or supercoiled DNA you have at the end of each reaction. If your compounds are topo II poisons, you should see an increase in the number of dsDNA breaks as the concentration of drugs increases. Topo poisons stabilize the cleavage complex, so running a cleavage assay and monitoring the amount of DNA with ds breaks allows you to see if you have more cleavage (more stable cleavage complexes) with drug than without drug.
This paper was published by my lab and shows you some examples of assays you can run and what the different effects of drugs look like: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033629/
Of course, your compounds could be topo II catalytic inhibitors and not poisons. I'm not as familiar with inhibitors as I am with poisons, but I presume you'd see the cleavage levels go down with the inhibitor as you increase the concentration, as opposed to rising with the topo poisons.
You can benefit from this research and formulas for effectiveness calculation Article HPLC fractioning to study the synergy and antagonism of rue ...
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