Analysis of mixed DNA-bisnaphthalimide interactions involving groove association and intercalation with surface-based and solution methodologies

The bisnaphthalimide cytotoxic agent elinafide exhibits a mixed DNA binding mode including groove-association and intercalation. We have compared the interaction of elinafide and two bisnaphthalimide analogues with various natural and modified DNA sequences using solution NMR and UV-melting methods and surface plasmon resonance (SPR) experiments at different pH conditions. The combined data obtained with these techniques established a high-affinity binding mode comprising intercalation and strong electrostatic contacts with guanine bases in the major groove, and a weaker interaction with A·T pairs likely involving groove association. However, the SPR binding constants and the NMR and UV-melting binding parameters responded differently to variations in DNA bases and ligand intercalating moieties. The rates and equilibrium constants determined by SPR clearly responded to changes in pH and DNA groove composition, but were rather insensitive to alterations in drug rings and DNA bases affecting the intercalation process. Conversely, the intermolecular stacking interactions detected by NMR and the ligand-induced thermal stabilizations measured by UV depended on both sets of factors and were controlled by the sequence-dependent properties of the DNA helices, indicating that these data were modulated by naphthalimide stacking in addition to groove association. A two-step binding process where a groove-bound state is required prior to intercalation is proposed as an explanation for these observations. These findings may be useful for studying other classes of DNA- and RNA-binding drugs, which frequently combine groove-binding and stacking moieties.