DSSR-PyMOL cartoon-block schematics: PDB entry 180d

PDB-id

180d; SNAP-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.5 Å)

Summary

Sequence-dependent microheterogeneity of z-DNA: the crystal and molecular structures of d(cacgcg).d(cgcgtg) and d(cgcacg).d(cgtgcg)

Reference

Sadasivan C, Gautham N (1995): "Sequence-dependent microheterogeneity of Z-DNA: the crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG)." J.Mol.Biol., 248, 918-930. doi: 10.1006/jmbi.1995.9894.

Abstract

We have solved and refined the crystal structures of the first two non-self-complementary hexadeoxyribonucleotide duplexes with Watson-Crick base pairs, namely d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG). Both the hexamers crystallize in the left-handed Z-DNA conformation. The packing of the molecules is similar in the two crystals: the hexamers are stacked on top of each other to form columns of infinite length, which are arranged in a close-packed hexagonal pattern. In spite of the similar packing, crystals of the first duplex belong to the space group P2(1)2(1)2(1), isomorphous to previous Z-DNA hexamers, while crystals of the other duplex belong to the space group P2(1), which has not been observed before in this context. The molecular structures of the two duplexes are also different. The first is very similar in conformation to the other Z-DNA hexamers and to the idealized ZI model. The other duplex shows large differences in the stacking and the relative disposition of its bases, leading to its possible classification as a novel Z-DNA variant. We conclude that the differences in the structure under similar environmental conditions point to a sequence-dependent plasticity in the DNA molecule which is visible even under close-packed conditions.