oligomers such as d(CpGpCpG) and in Z-DNA. Theoretical calculations suggest that this effect comes
from a favourable electrostatic attraction between the phosphate anion and the C2-amino group in guanine
nucleotides. It results from polarisation of one of the nitrogen non-bonding electrons towards the ring.
Most unusually, this synconformation can only be built into left-handed helices.
2.1.4.3 C4C5Orientation. The conformation of the exocyclic C4C5bond determines the pos-
ition of the 5-phosphate relative to the sugar ring. The three favoured conformers for this bond are the classi-
cal synclinal (sc)and antiperiplanar (ap)rotamers. For pyrimidine nucleosides,scis preferred whereas for
purine nucleosidesscand apare equally populated. However, in the nucleotides, the 5-phosphate reduces
the conformational freedom and the dominant conformer for this -bond issc(Figure 2.13). Once again, the
demands of Z-DNA have a major effect and the apconformer is found for the synguanine deoxynucleotides.
2.1.4.4 CO and PO Ester Bonds. Phosphate diesters are tetrahedral at phosphorus and show anti-
periplanar conformations for the C5O5bond. Similarly, the C3O3bond lies in the antiperiplanar
to anticlinalsector. This conformational uniformity has led to the use of the virtual bond concept in
which the chains P5O5C5C4and P3O3C3C4can be analysed as rigid, planar units
linked at phosphorus and at C-4. Such a simplification has been used to speed up initial calculations of
some complex polymeric structures.
Our knowledge of PO bond conformations comes largely from X-ray structures of tRNA and DNA
oligomers. In general, H4C4C5O5P adopts an extended W-conformation in these structures.
A skewed conformation for the COPOC system has been observed in structures of simple phos-
phate diesters such as dimethyl phosphate and also for polynucleotides. This has been described as an
anomericeffect and attributed to the favourable interactions of a non-bonding electron pair on O-5with
the PO3bond, and vice versa for the PO5bond (Figure 2.14). This may arise from interaction of the
22 Chapter 2
Figure 2.12 Anti and syn conformational ranges for glycosylic bonds in pyrimidine (left) and purine (right) nucleo-
sides, and drawings of the anti conformation for deoxycytidine (lower left) and the syn conformation
for deoxyguanosine 5-phosphate (lower right)