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The Δ G° of B- to Z-DNA transitions are estimated to be −0.5 kcal/mol for d(m 5CG), 0.69–1.30 kcal/mol for unmethylated d(CG), 1.32–1.48 kcal/mol for d(CA)-d(TG), and 2.3–2.4 kcal/mol for d(TA). In addition to the intrinsic sequence dependence, the Z-form is stabilized by a variety of environmental factors such as a high degree of hydration, high ionic strengths, transition-metal complexes, spermine, cytosine methylation, and/or negative supercoiling ( 49, 51, 52). The major groove of B-DNA is replaced in Z-DNA by a convex surface on which purine N-7 and C-8 and the pyrimidine C-5 positions are exposed.Īlternating Pu–Py tracts such as the hexanucleotide d(CGCGCG) or poly have the propensity to adopt the Z-helix ( 48, 50).

There is one deep groove that corresponds to the minor groove in B-DNA. The interphosphate distances also differ from those of B-DNA. The deoxyribose–phosphate backbone follows a zigzag left-handed course rather than the smoothly spiraling right-handed path found in B-DNA. Z-DNA is thus characterized by a dinucleotide repeat in which anti and syn conformations of the bases alternate in succession along the chain. The pyrimidine bases maintain an anti conformation. The purine bases of Z-DNA, formed for example with d(CG) 3, are rotated into the syn ( C3′-endo) conformation. Z-DNA is thinner (by ∼10%), more extended (by 29%), and has more base pairs per turn than B-DNA (see Fig. Z-DNA is a Watson–Crick base-paired, left-handed helix that is distinct from the Watson–Crick right-handed B-DNA ( 48, 49). Hyone-Myong Eun, in Enzymology Primer for Recombinant DNA Technology, 1996 c. In general nonalternating sequences can form Z-DNA structures in the crystalline state when the nonalternating pyrimidines are able to adopt a syn conformation ( Basham, Eichman, and Ho, 1999). This has been borne out by subsequent structural studies on uracil-containing Z sequences ( Schneider et al., 1992). It is likely that replacement of thymine by uracil would increase Z-form stability, since the methyl group of the former presents a significance hydrophobic hindrance to solvent-ordering around the Z helix. Nonetheless, its existence suggests that the requirement for the formation of a Z-DNA structure is not so much that the sequence should be an alternating C/G-rich one, but that it retains the key feature of alternating syn and anti nucleosides. This energetically unfavorable Z structure was only stabilized by having the cytosine bases methylated or brominated at the 5 position of the base. so that it is no longer purely alternating) in the structure of d(CGATCG), still retains a Z-DNA type structure ( Wang et al., 1985), albeit with the thymidines and adenines adopting syn and anti glycosidic conformations respectively. It is then surprising that reversal of the central pyrimidine-3′,5′-purine sequence (i.e. 2) is also a factor in the GC preference of Z-DNA. The slight preference of guanosine nucleosides (unlike adenosine) to adopt the syn rather than the anti glycosidic conformation (see Chap.

T base pairs cannot by themselves form a Z-DNA structure.

T base pairs are not able to take part in the ordered Z-DNA groove hydration, which plays an important role in maintaining the integrity of the Z-DNA structure ( Egli et al., 1991), by contrast with G.

It has been suggested ( Wang et al., 1984) that A The cytosines are required to be 5-methylated in order for stabilization of the d(CGTACG) sequence, and in general modified cytosines are necessary if a Z-DNA structure contains A

T base pairs, although they do tend to destabilize the structure.

This shows that Z-DNA can tolerate some A The central CpG can be replaced by TpA whilst maintaining the left-handed structure ( Wang et al., 1984). All show the resilience of the Z-DNA structural entity. Z-DNA oligonucleotides have been crystallized with a range of related sequences, including pure analogues such as d(CGCGCGCG) ( Fujii et al., 1985) and d(CGCGCGCGCG) ( Ban, Ramakrishnan, and Sundaralingam, 1996), as well as variants where changes have been made to base and sequence type.

Stephen Neidle, in Principles of Nucleic Acid Structure, 2008 3.5.4 Other Z-DNA Structures