Structural variations in Z-DNA

Abstract

The first crystal structure of Z-DNA, i.e. of the sequence d(CGCGCG)2 established many sequence-dependent micro- structural features. Nevertheless, a regular model of Z-DNA could be built for alternating pyrimidine-purine sequences, with a dinucleotide duplex as the repeating unit, rather than the mononucleotide used in regular models of A and B type helices. In our laboratory, we have made systematic crystallographic studies to explore the precise influence of sequence on the microstructure of Z-DNA, especially the effect of the introduction of A.T base pairs in sequences that otherwise consisted of C.G base pairs. Using chiefly the technique of X-ray crystallography, we studied the following sequences: d(CACGCG).d(CGCGTG), d(CGCACG).d(CGTGCG), d(CACGCG).d(CGCGTG), d(CCCGGG)2, d(CGCGCA).d(TGCGCG), d(CGCGTACGCG)2, and d(CGCGCGTACGCGCG)2. These sequences were studied under various conditions of salt, pH, temperature, etc. Some of the results we obtained from these studies may be summarized as follows. Firstly, we observe sequence-dependent structural micro-heterogeneities in Z-DNA, which are correlated with the extent of the stretch of G.C base pairs, as well as with the degree and nature of the pyrimidine-purine alternation in the sequence. Secondly, the Z-DNA helices, which may be approximated to solid cylinders, achieve the closest packing in the crystals in the following manner. The cylinders are stacked on top of each other to form long infinite, pseudo-continuous columns, which are then bundled together in a hexagonal close packing arrangement. This packing motif is common to almost all the Z type structures that have been studied, both in our laboratory as well as elsewhere. Despite this common packing principle, it is possible to index the crystals in several different crystals systems and space groups, sometimes in a degenerate manner. The differences arise due to the alignment between adjacent columns. Also if the sequences are non-self complementary, like many of those above, the helical columns can point ‘up’ or ‘down’ and this allows an extra degree of freedom in choice of crystal system and space group. The third set of results obtained from these studies pertains to the interactions of various metal ions with the helices. We find, in particular, that cobalt and ruthenium hexammine ions perturb the tautomeric state of the adenine and thymine bases, leading to changes in the base pairing schemes.