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   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.
Source: Acta Crystallographica Section D - Category: Biochemistry Authors: Tags: Z-DNA handedness anomalous signal 2 ′ -deoxy-l-ribose dual-conformation backbone cadaverinium cation biogenic polyamines biological potassium complex research papers Source Type: research