Structure of a DNA intercalation complex as determined by NMR using a paramagnetic probe.

Longitudinal relaxation rates of the protons of the 3,8-dimethyl-N-methyl-phenanthrolinium (DMP) cation in solutions containing DNA are strongly affected by the addition of the paramagnetic manganese (II) ions due to the electron-nuclear dipolar interaction in the ternary Mn-DNA-DMP Complex. Two possible models for the DMP-DNA intercalation complex are examined and one of them is unequivocally discriminated on the basis of the proton relaxation data. It is concluded that in the intercalation complex the long axis of the DMP molecule is almost perpendicular to the hydrogen bonds of the DNA base-pairs.