Molecular insight into drugs binding to ctDNA: the fluorescence fast kinetic analysis of diclofenac and pentamidine

Diclofenac and pentamidine are renowned drugs able to bind DNA by groove-binding mechanisms. Even though the binding mechanism is known, accurate kinetic constants of the binary interaction have never been directly measured. The present work reports the study of the interaction between ctDNA and the two drugs, with very different molecular structure, by steady-state and stopped-flow fluorescence. From the stopped-flow kinetic measurements, we calculated the association and dissociation rate constants (kon and koff). The kinetic constants were then used to calculate the equilibrium dissociation binding constant (KD) and the values have been compared with what obtained from steady-state fluorescence. Graphical abstract: [Figure not available: see fulltext.]