Biophysical methods for evaluating Ligands-G4 interactions

In the absence of NMR and crystallographic data it is often difficult to obtain reliable information on the interaction of small molecules with DNA in various conformations including G4 structures. Building on our experience in the study of the binding of naphthalene diimide monomers and dyads to G4 structures we will give an overview on widely used techniques to investigate binding equilibria. We will discuss an approach that we recently used based on the combination of optical time-resolved spectroscopic techniques, circular dichroism, isothermal titration calorimetry and molecular modeling to find evidence of binding in the pocket at the interface of contiguous G4s. Molecular modeling afforded a structural hypothesis for the bound complex. Ligand fluorescence lifetime data as well as induced circular dichroism afforded crucial information on the occupancy of the interface binding site. ITC thermodynamic parameter s further confirmed the hypothesis. Combination of various techniques revealed to be a valid alternative to find information on the ligand DNA complex and the role played by the ligand structure. This seminar will further be completed by a comparison of these techniques with others such as surface plasmon resonance, fluorescence melting and displacement assays highlighting their strengths and limits.