BPS2026 - Force-dependent binding of DNA minor-groove binder netropsin measured via optical tweezers

Using optical tweezers, we measured how netropsin, a polyamide with antibacterial properties, binds to and changes the conformation of DNA. Netropsin binds to the minor groove of DNA and this interaction is modulated by applied tension on the DNA molecule. DNA molecules were held at multiple fixed forces while netropsin was first introduced at varying concentrations, then removed from the sample. The binding and dissociation kinetics of the bimolecular interaction were measured in real time. Additionally, DNA elongation was performed slowly to ensure equilibrium was maintained over all applied DNA tensions in the presence of multiple netropsin concentrations. This force-dependent set of equilibrium DNA extensions is fit to the McGhee-von Hippel binding isotherms to extract the binding affinity of netropsin to DNA in the absence of force. These measurements also enable us to determine the structural change of DNA upon each binding event. Experiments such as these are significant because they provide detailed insight into the molecular binding parameters of minor-groove binders, laying the groundwork for the development of more effective analogs for cancer treatment.