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. 2007 Dec 1;63(Pt 12):1008-13.
doi: 10.1107/S1744309107047781. Epub 2007 Nov 21.

Hexammineruthenium(III) ion interactions with Z-DNA

D Bharanidharan  1 , S Thiyagarajan, N Gautham
Affiliations

Hexammineruthenium(III) ion interactions with Z-DNA

D Bharanidharan et al. Acta Crystallogr Sect F Struct Biol Cryst Commun. .

Abstract

The hexamer duplex d(CGCGCA).d(TGCGCG) was crystallized with hexammineruthenium(III) ions in an orthorhombic space group; the crystals diffracted to 1.54 A resolution. Strong ion interactions with the adenine base induce a tautomeric shift from the amino to the imino form. Consequently, the A.T base pairing is disrupted. This structural study may be relevant to metal toxicity.

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Figures

Figure 1
Figure 1
Least-squares superposition of the hexamer in the ruthenium complex (black) with the respective hexamer in the cobalt complex (grey).
Figure 2
Figure 2
The conformation of the phosphate groups at residues C3 (a), C5 (b), C9 (c) and C11 (d); the respective 2F obs − F calc electron-density maps are contoured at the 1.0σ level. The dotted lines represent hydrogen bonds.
Figure 3
Figure 3
Stereoview of two base pairs from each of the three symmetry-related helices (A, x, y, z; B, −x + ½, −y, z + ½; C, x + ½, −y + ½, −z) interacting with the ion. The electron density shown for the ruthenium ion corresponds to the anomalous difference map.
Figure 4
Figure 4
Ruthenium-ion interactions with helix A and its symmetry-related helix C. The electron-density map was calculated with (2F obs − F calc) as coefficients and contoured at the 1.0σ level.
Figure 5
Figure 5
Schematic sketch of three possible explanations of ruthenium-ion interactions with the A6·T7 base pair. (a) Adenine is modified to hypoxanthine (H). (b) The amine groups of the ruthenium ion are exchanged with water. (c) The N3 imino proton of thymine is transferred to the environment.
Figure 6
Figure 6
Geometry of the interaction of the ruthenium ion with helix B and helix C. The dotted lines represent hydrogen bonds.
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