A new approach utilizing high‐resolution proton NMR in structural analysis of intercalation complexes of natural DNA

Protons on the antimalarial intercalator quinacrine and a substituted phenanthrene intercalator were monitored on titration with sonicated DNA. The titrations were carried out below the DNA Tm but at a temperature, ionic strength, and intercalator concentration sufficient to give fast exchange conditions and a minimum of dimerization of the planar aromatic intercalators. Line widths were kept within reasonable limits by using sonicated DNA, high temperature, fast exchange conditions and an excess of intercalator over DNA binding sites. Proton assignments were made using analysis of chemical shifts, coupling patterns, NOE and 2D methods. 2D COSY experiments on DNA-intercalator complexes were performed to assist in assigning protons for the bound intercalator. Line broadening with quinacrine is more severe than with the phenanthrene, and the acridine essentially represents the limit of the NMR titration method. The phenanthrene intercalator, on the other hand, illustrates the power of the method, particularly when analyzing a series of compounds. Using chemical shift changes of the phenanthrene on titration with DNA and space filling molecular modeling studies, we have been able to propose a general structure for the phenanthrene intercalation complex.