Biophysical protocols for interaction evaluation of biologically active compounds with DNA (Calf thymus) using molecular fluorescence

The interaction study between DNA and small molecules has been widely explored aiming to understand the molecular action mechanisms of bioactive compounds in physiological conditions. Due to the structural variety of molecules evaluated by our research group, it was verified the main challenge is the elucidation of the preferential binding mode of the compounds with the DNA (intercalation or groove), considering the peculiarities inherent of each evaluated compound classes. Thus, to circumvent such difficulties, protocols based on the spectroscopic characteristics of the molecules were elaborated and applied. Annonalide (diterpene), piperidines and chromones interact with ctDNA preferably via intercalation, whereas pterocarpans, benzimidazole and benzothiazole, have greater affinity with the major and minor grooves of the macromolecule. In addition, when possible, we established the bioanalytical correlation between Kb and IC50 of these derivatives, suggesting that the action mechanism may be associated to DNA as a biological target.