X-ray crystallographic study of the possible binding sites of the monovalent cations in the Z-DNA structure

Determination of the binding positions of light metal ions in the structure of oligonucleotides remains a challenge owing to their irregular coordination geometries, low electron densities and mobility in the crystals. To study the interactions between monovalent cations and DNA, the heavier alkali metal ion Rb+ was used to replace Na+ and K+ in the Z-DNA crystal and the structure was analyzed using X-ray cryocrystallography. The resolution of the Rb-d(CGCGCG)(2) crystal data set is 1.76Angstrom, with an R-merge, of 0.061. The final residual factor (R factor) for the crystal structure is 0.175. The positions of 16 Rb+ ions were tentatively assigned, with most of them having partial occupancies. Three rubidium ions with full occupancies coordinated to two DNA double strands were located in the Z-DNA crystal. The results of this work suggest that there are numerous relatively low-energy sites for binding of monovalent cations to Z-DNA and that these sites are cation-water hybrid positions.