NMR Structural Studies on a DNA Four-Way Junction: Stacking Preference and Localization of the Metal-ion Binding Site

Abstract

The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked conformer. NOESY spectra showed intermolecular NOE contacts between 4H protons and the ammine protons of the cobalt(III)hexammine complex. These contacts define the metal-ion binding site, located in the vicinity of the junction. The position is similar to the observed site in a recent X-ray structure of a RNA/DNA hybrid 4H and consistent with the position deduced from an uranyl ion photoprobing study on 4Hs with different sequences.