Download MendeleyRight-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.
Drozdzal, P., Manszewski, T., Gilski, M., Brzezinski, K., Jaskolski, M.(2023) Acta Crystallogr D Struct Biol 79: 133-139
- PubMed: 36762859
- DOI: https://doi.org/10.1107/S2059798322011937
- Primary Citation of Related Structures:
8A71 - PubMed 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.
Organizational Affiliation:
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
