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

摘要

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