Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution

Abstract

The X-ray crystal structure of the d(CGCGCG)₂/putrescine(2+)/K⁺ complex has been determined at 0.60 Å resolution. Stereochemical restraints were used only for the putrescinium dication, and 23 bonds and 18 angles of the Z-DNA nucleotides with dual conformation. The N atoms of the putrescine(2+) dication form three direct hydrogen bonds with the N7_G atoms of three different Z-DNA molecules, plus three water-mediated hydrogen bonds with cytosine, guanine and phosphate acceptors. A unique potassium cation was also unambiguously identified in the structure, albeit at a ∼0.5 occupation site shared with a water molecule, providing the first example of such a complex with Z-DNA. The K⁺ cation has coordination number of eight and an irregular coordination sphere, formed by four water molecules and four O atoms from two phosphate groups of the Z-DNA, including ligands present at fractional occupancy. The structural disorder of the Z-DNA duplex is manifested by the presence of alternate conformations along the DNA backbone. Comparison of the position and interactions of putrescine(2+) in the present structure with other ultra-high-resolution structures of Z-DNA in complexes with Mn²⁺ and Zn²⁺ ions shows that the dicationic putrescinium moiety can effectively substitute these metal ions for stabilization of Z-type DNA duplexes. Furthermore, this comparison also suggests that the spermine(4+) tetracation has a higher affinity for Z-DNA than K⁺.

Keywords: Z-DNA; biogenic polyamine; biological potassium complex; dual-conformation backbone; subatomic resolution.

Figure 1

Stereoview of the d(CGCGCG)₂/Put²⁺/K⁺ com­plex with anomalous difference map (gray) peaks for the K⁺ ion (purple sphere) and P atoms. The map is contoured at 3σ. Note the alternative conformations (I is green and II is orange) along the DNA chain.

Figure 2

The putrescinium(2+) dication in the crystal structure of the d(CGCGCG)₂/Put²⁺/K⁺ com­plex. The 2mFo-DFc map is contoured at the 1.6σ level. Some water molecules have been omitted for clarity. Hydrogen bonds are marked by dashed lines, with D⋯A distances in Å.

Figure 3

The coordination sphere of the hydrated com­plex of K⁺ (purple) at G6. The 2mFo–DFc map is contoured at 1.0σ. Coordination bonds are marked as gray dashed lines and hydrogen bonds are marked as orange dashed lines. Bond distances are in Å.

Figure 4

The d(CGCGCG)₂/Spm⁴⁺/Mn²⁺ (red), d(CGCGCG)₂/Spm⁴⁺/Zn²⁺ (blue) and d(CGCGCG)₂/Put²⁺/K⁺(green) com­plexes in their common reference frame (unit cell). The interactions of the Mn²⁺, Zn²⁺(1) and Zn²⁺(2) ions and of the putrescinium(2+) N atoms with N7_G6, N7_G6ⁱⁱ and N7_G10ⁱ are indicated. A different location of G10ⁱ in the com­plex with Zn²⁺ cations is also visible.