Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex

Abstract

Crystal structures of the hexanucleotide d(CACGCG)·d(CGCGTG) were determined in two crystal lattices when different concentrations of the counterion Mn2+ were used in crystallization. The availability of Mn2+ during the crystallization process appears to play an important role in inducing different crystal packings that lead to crystals belonging to the two space groups P2(1) and P6(5). Analysis of the molecular interactions of Mn2+ with the Z-form duplexes shows direct coordination to the purine residues G and A.

Figure 1

(a) Helix 1 (blue), helix 2 (cyan) and two Mn²⁺ ions in Mn_P2₁. (b) Helix 1 (blue), an arbitrary helix 2 (cyan) comprising dinucleotide steps (x, y, z), (y, −x + y, z + 1/6) and (−x + y, −x, z + 1/3) and a disordered Mn²⁺ ion in Mn_P6₅. The anomalous difference Fourier map (blue) and 2F _o − F _c map (orange; for the helices only) are contoured at 3σ and 1σ levels, respectively. The A₂·T₁₁ base pairs are coloured red. The Mn²⁺ ions are shown as spheres. The water molecules are omitted for clarity.

Figure 2

Packing of the helical columns in Mn_P2₁ (a, b) and Mn_P6₅ (c, d). (a) and (c) are views down the helical axis, while (b) and (d) are views perpendicular to the helical axis. Helix 1 and helix 2 [except in (a)] are coloured blue and cyan, respectively. The A·T base pairs in the ordered hexamer helices are coloured red. Spheres represent Mn²⁺ bound to helices. The column with the 6₅ screw symbol indicates the disordered column built from the dinucleotide step. No direction for these columns could be assigned since the position of the A·T base pair is disordered. The unit cell is shown as thin lines.

Figure 3

Interactions of ions: (a) MnA and (b) MnB in Mn_P2₁ and (c) the disordered Mn²⁺ ion in Mn_P6₅ (viewed down the helical axis). The Mn²⁺ ions are shown as spheres, water molecules are shown as crosses, ion-mediated and water-mediated interactions are shown as red dashed lines and hydrogen bonds of base pairs are shown as black dashed lines. The ion induces distortion of the hydrogen-bond base-pair schemes in (b) and (c).