Nucleic Acids Research, 2001, Vol. 29, No. 5 1208-1215
© 2001 Oxford University Press
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA, 1Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, IL 60611, USA, 2Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA, 3IMCA-CAT, Sector 17 and 4DND-CAT Synchrotron Research Center, Sector 5, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA and 5Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., Carlsbad, CA 92008, USA
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 strong hydrogen bonds between well-ordered water molecules. We demonstrate here that replacement of Na+ by K+, Rb+ or Cs+ and precise measurements of anomalous differences in intensities provide a particularly sensitive method for detecting alkali metal ion-binding sites in nucleic acid crystals. Not only can alkali metal ions be readily located in such structures, but the presence of Rb+ or Cs+ also allows structure determination by the single wavelength anomalous diffraction technique. Besides allowing identification of high occupancy binding sites, the combination of high resolution and anomalous diffraction data established here can also pinpoint binding sites that feature only partial occupancy. Conversely, high resolution of the data alone does not necessarily allow differentiation between water and partially ordered metal ions, as demonstrated with the crystal structure of a DNA duplex determined to a resolution of 0.6 Å.
* To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 6707; Email: martin.egli{at}vanderbilt.edu Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 760 603 2381; Fax: +1 760 929 0036; Email: mmanohar@isisph.com
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