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

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 angstrom resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 angstrom), 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.

Automated summary

The self-complementary L-d(CGCGCG)(2) hexanucleotide, which contains the enantiomeric 2'-deoxy-L-ribose, forms a right-handed Z-DNA duplex when crystallized in complex with cadaverine and potassium cations. The ultrahigh-resolution crystal structure at 0.69 angstrom resolution confirmed the right-handed structure. Mistakenly assuming the presence of 2'-deoxy-D-ribose, the X-ray diffraction data revealed the wrong hand of the structure due to the weak anomalous signal of P and K atoms. The crystal structure also showed the interaction of the cadaverinium dication and K+ cation with the Z-DNA duplex.