DNA and RNA Structure 31
whereas B-DNA has little roll and small positive slide. These and other movements of base pairs are illus-
trated in Figure 2.19(a) and values of the parameters given in Table 2.4. This results in a greater hydropho-
bic surface area of the bases being exposed in A-DNA per base pair. From this, it has been argued that
B-DNA will have the lesser energy of solvation, explaining its greater stability at high humidity (95%) and
that this hydrophobic effect may well tip the balance between the A- and B-form helices.
Other B-DNA structures have much lower significance. C-DNA is obtained from the lithium salt of nat-
ural DNA at rather low humidity.^2 It has 28 bases and three full turns of the helix. D-DNA is observed for
alternating AT regions of DNA and has an overwound helix compared to B-DNA with 8 bp per turn. In
phage T2 DNA, where cytosine bases have been replaced by glucosylated 5-hydroxymethylcytosines, the
B-conformation observed at high humidity changes into a T-DNA form at low humidity (60% RH),
which also has eightfold symmetry around the helix (see Table 2.3).
2.2.5 Z-DNA
Two of the earliest crystalline oligodeoxyribonucleotides, d(CGCGCG) and d(CGCG), provided structures
of a new type of DNA conformer, the left-handed Z-DNA, which has also been found for d(CGCATGCG).
Initially it was thought that left-handed DNA had a strict requirement for alternating purine–pyrimidine
sequences. We now know that this condition is neither necessary nor sufficient since left-handed structures
have been found for crystals of d(CGATCG) in which cytosines have been modified by C-5 bromination
or methylation and have been identified for GTTTG and GACTG sequences by supercoil relaxation stud-
ies (Section 2.3.4).
The Z-helix is also an anti-parallel duplex but is a radical departure from the A- and B-forms of DNA.
It is best typified by an alternating (dG–dC)npolymer. Its two backbone strands run downwards at the left
of the minor groove and upwards at the right (↓↑), and this is the opposite from those of A- and B-DNA
(↑↓) (NB: the forward direction is defined as the sequence O3→P→O5). In an idealised left-handed
duplex, such reversed chain directions would require all the nucleosides to have the synconformation for
their glycosylic bonds. However, this is not possible for the pyrimidines because of the clash between O-2
of the pyrimidine and the sugar furanose ring (Section 2.1.4). So the cytosines take the anticonformation
and the guanines the synconformation. The name Z-DNA results from this anti–synfeature of the glyco-
sylic bonds that alternates regularly along the backbone(Figure 2.20). It causes a local chain reversal that
generates a zig-zag backbonepath and produces a helical repeat consisting of two successive bases
(purine-plus-pyrimidine) and with an overall chain sense that is the opposite of that of A- and B-DNA. The
synconformation of Z-DNA guanines is represented by glycosylic angles close to 60° while the sugar
pucker is C2-endoat dC and C3-endoat dG residues (Table 2.3).^13
The switch from B- to Z-DNA conformation appears to be driven by the energetics of – base-stacking.
In Z-DNA the GpC step is characterised by helical twist of –50.6° and a base pair slide of –1.1 Å. However,
for the CpG steps the twist is –9° and the slide is 5.4 Å (Table 2.4; see Figure 2.19 for an explanation of
these terms). These preferences occupy the two extremes of the slide axis and thus appear to be incompatible
Table 2.5 Average torsion angles (°) for DNA helices
Structure type
A-DNAa
50 172 41 79
146
78
154
GGCCGGCC
75 185 5 691
166
75
149
B-DNAa
41 13 638 139
133
157
102
CGCGAATTCGCG
63 171 54 123
169
108
117
Z-DNA (C residues)
137
139 5 6138
95 80
159
Z-DNA (G residues) 47 179
169 99
104
6968
DNA–RNA decamer
69 175 55 82
151
75
162
A-RNA
68 178 54 82
153
71
158
aFibres.