Nogalamycin is an anthracycline antibiotic drug with ability to bind to DNA by threading between its base pairs. This results in increased intercalation that is expected to introduce more negative supercoiling of circular plasmid DNA once DNA is exposed to topoisomerase I. As such, the levels of negative supercoiling indicate the degree of relaxation of circular plasmid, which is  influenced by nogalamycin concentration. Once DNA is relaxed, it moves a shorter distance across the agarose gel electrophoresis and can therefore be used to assess the levels of relaxation due to intercalation with nogalamycin as a function of concentration. The aim is to refine and utilize this method to assess how the binding affinity of nogalamycin to various DNA motifs compare. Even though, nogalamycin is not commercially used due to inducing cardiotoxicity, the study of its binding characteristics given its unique low dissociation rate provides valuable information of property of similar potential anti-tumor drugs.

Analysis of binding affinity of nogalamycin to various DNA motifs based on gel electrophoresis assay

ACS Spring 2022

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