Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method

Abstract

The self-complementary L-d(CGCGCG)₂ purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K⁺ cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K⁺ site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder.

Keywords: 2′-deoxy-l-ribose; Z-DNA; anomalous signal; biogenic polyamines; biological potassium complex; cadaverinium cation; dual-conformation backbone; handedness.

Figure 1

Overall structure of l-d(CGCGCG)₂/Cad²⁺/K⁺ highlighting the inter­actions between the cations and the DNA molecules within the asymmetric unit (orange) and two other symmetry-related DNA molecules (light orange): i (−x, y + 1/2, −z + 1/2) and ii (x + 1/2, −y + 1/2, −z). Potential polar interactions with the Cad²⁺ cation (stick model) are marked as red dashed lines and K⁺ is shown as a purple sphere with the coordination bonds marked as black dashed lines.

Figure 2

Details of the binding mode of the cadaverinium dication within the crystal lattice of the l-d(CGCGCG)₂/Cad²⁺/K⁺ complex. The 2mF _o − DF _c map (blue) is contoured at the 1.0σ level. The color code for molecules and ions is the same as in Fig. 1 ▸.

Figure 3

Potassium (purple sphere) coordination site in the crystal structure of the l-d(CGCGCG)₂/Cad²⁺/K⁺ complex. Water molecules (W) are presented as red spheres. The coordination sphere of this intermolecular potassium binding site is completed by partially disordered phosphate groups from two symmetry-related DNA molecules (orange and light orange). The 2mF _o − DF _c map (blue) is contoured at the 1.0σ level.