Utilizing guanine-coordinated Zn2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

Hou, Caixia; Tsodikov, Oleg V.

doi:10.1107/S205979831801553X

Utilizing guanine-coordinated Zn²⁺ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

Journal Article · 01 January 2019 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S205979831801553X· OSTI ID:1506507

Hou, Caixia; Tsodikov, Oleg V.

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 Zn²⁺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 Mg²⁺instead of Zn²⁺, it was demonstrated that Zn²⁺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.

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOD

OSTI ID:: 1506507

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Vol. 75, Issue 1; ISSN 2059-7983

Publisher:: IUCr

Country of Publication:: United States

Language:: ENGLISH

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Related Subjects

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

Utilizing guanine-coordinated Zn2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

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Utilizing guanine-coordinated Zn²⁺ ions to determine DNA crystal structures by single-wavelength anomalous diffraction