Utilizing guanine-coordinated Zn 2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

Caixia Hou, Oleg V. Tsodikov

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


The experimental phase determination of crystal structures of nucleic acids and nucleic acid–ligand complexes would benefit from a facile method. Even for double-stranded DNA, software-generated models are generally insufficiently accurate to serve as molecular replacement search models, necessitating experimental phasing. Here, it is demonstrated that Zn 2+ ions coordinated to the N7 atom of guanine bases generate sufficient anomalous signal for single-wavelength anomalous diffraction (SAD) phasing of DNA crystal structures. Using zinc SAD, three crystal structures of double-stranded DNA oligomers, 5′-AGGGATCCCT-3′, 5′-GGGATCCC-3′ and 5′-GAGGCCTC-3′, were determined. By determining the crystal structure of one of these oligomers, GAGGCCTC, in the presence of Mg 2+ instead of Zn 2+ , it was demonstrated that Zn 2+ is not structurally perturbing. These structures allowed the analysis of structural changes in the DNA on the binding of analogues of the natural product mithramycin to two of these oligomers, AGGGATCCCT and GAGGCCTC. Zinc SAD may become a routine approach for determining the crystal structures of nucleic acids and their complexes with small molecules.

Original languageEnglish
Pages (from-to)32-40
Number of pages9
JournalActa Crystallographica Section D: Structural Biology
Issue number1
StatePublished - Jan 2019

Bibliographical note

Funding Information:
This study was supported in part by US Department of Defense grant PC150300P1 to OVT.

Publisher Copyright:
© International Union of Crystallography, 2019


  • DNA–drug complexes
  • SAD phasing
  • double-stranded DNA
  • mithramycin
  • nucleic acid crystals
  • zinc coordination

ASJC Scopus subject areas

  • Structural Biology


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