Mechanistic thermodynamic and kinetic studies to enlighten the details of small molecules binding to biosubstrates

Non-covalent interaction between planar molecules and nucleic acids (NA) takes place mainly through two processes denoted as intercalation and groove binding. The interest for these molecules is very high owing to their applications in biochemistry, biology and medicine. Actually, small NA-binding molecules can be used both as staining agents and probes for NA as well as antitumour, antivirus and antibacterial drugs. In this context, a remarkable role is played by metal complexes and metallo-intercalators. The knowledge of the details of the binding mode of the small molecules to NA is crucial to understand the effects that can be exerted on those biological processes where nucleic acids are involved. The analysis of the thermodynamic and kinetic aspects of the interaction can provide important information for a deep understanding (and optimization) of the binding process. This presentation will focus on the strength of a coupled thermodynamic and kinetic study to enlighten the details of the interaction. In particular: 1) repetition of binding experiments under different experimental conditions (reactant concentrations, temperature, added salt concentration) gives information on the exact type of binding; 2) the kinetic technique enables to characterize the steps of the mechanism of binding to the nucleic acid; 4) reaction forward and backward rates, equilibrium constants, ΔG, ΔS and ΔH can be obtained; 5) the site size (n) can be known where n is defined as the number of ligand molecules per site under saturation conditions; 6) the binding mode can be evidenced by viscometric experiments and fluorescence quenching experiments; 7) breaking of the phosphodiester bond can be put into evidence by gel electrophoresis experiments.