Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

The observation of light metal ions in nucleic acids crystals is generally a fortuitous event. Sodium ions in particular are notoriously difficult to detect because-their X-ray scattering contributions are virtually identical to those of water and Na+...O distances are only slightly shorter than str ong hydrogen bonds between well-ordered water molecules. We demonstrate her e that replacement of Na+ by K+, Rb+ or Cs+ and precise measurements of ano malous differences in intensities provide a particularly sensitive method f or detecting alkali metal ion-binding sites in nucleic acid crystals. Not o nly can alkali metal ions be readily located in such structures, but the pr esence of Rb+ or Cs+ also allows structure determination by the single wave length anomalous diffraction technique. Besides allowing identification: of high occupancy binding sites, the combination of high resolution and anoma lous diffraction data established here can also pinpoint binding sites that feature only partial occupancy. Conversely, high resolution of the data al one does not necessarily allow differentiation between water and partially ordered metal ions, as demonstrated with the crystal structure of a DNA dup lex determined to a resolution of 0.6 Angstrom.