NMR study of the drug-base overlap geometry in the dark complex of 8-methoxypsoralen and d(pApT)4

The dark binding of 8-methoxypsoralen (MOP) to d(pApT)4 was investigated by 270-MHz 1H nuclear magnetic resonance (NMR) spectra. The continuous high-field shifts of the MOP resonances by d(pApT)4 at low temperatures indicate fast exchange between free and bound drug. The limiting complexation shifts of the various MOP protons between 0.36 (CH3) and 1.20 ppm (H5) are in the range expected for an intercalation complex. The NMR line widths of the MOP ring protons vary with the square of the observed complexation shifts (maximum at H5), indicating a dominant effect of the fast exchange between free and bound drug. The corresponding kinetic parameters agree with the values previously reported for a variety of other intercalators. The observed exchange broadenings were also used as a criterion to limit the uncertainty connected with fast averaging of the signals of the drug in potential multiple binding modes: A qualitatively different pattern of broadenings (minimum at H5) is expected from fast exchange between the two binding modes related by the short 2-fold quasi-symmetry axis of MOP. The measured complexation shifts were compared to theoretical values calculated on the basis of coplanar intercalation with base pair arrangements derived from typical published intercalation site geometries. The standard deviation between observed and calculated shifts was considerably smaller for asymmetrical intercalation between the bases of the same strand (less than or equal to 0.11 ppm) than for symmetrical intercalation between the base pairs (greater than or equal to 0.28 ppm).(ABSTRACT TRUNCATED AT 250 WORDS)