with C2-endo), and (3) the formation of an intra-strand hydrogen bond from O-2in one RNA residue to
O-4in the next which favours C3-endopucker. However, in RNA helical regions, this latter hydrogen
bond is not often observed and an axial CHO interaction between the C2H2(n) group and the
O-4(n1) atom appears to make a more important contribution to the stability of RNA helices.
2.1.4.2 Syn–Anti Conformation. The plane of the bases is almost perpendicular to that of the sugars
and approximately bisects the O4C1C2angle. This allows the bases to occupy either of two principal
orientations. The anti conformer has the smaller H-6 (pyrimidine) or H-8 (purine) atom above the sugar ring,
whereas the synconformer has the larger O-2 (pyrimidine) or N-3 (purine) in that position. Pyrimidines
occupy a narrow range of anticonformations (Figure 2.12) whereas purines are found in a wider range of anti
conformations that can even extend into the high-antirange for 8-azapurine nucleosides such as formycin.
One inevitable consequence of this anticonformation for the glycosylic bonds is that the backbone
chains for A- and B-forms DNA run downwards on the right of the minor groove and run upwards on the
left of the minor groove, depicted as (↑↓).
There is one important exception to the general preference for antiforms. Nuclear magnetic resonance,
CD and X-ray analyses all show that guanine prefers the synglycoside in mono-nucleotides, in alternating
DNA and RNA Structure 21
Figure 2.11 (a) Torsion angle notation (IUPAC) for poly-nucleotide chains and structures for the C2-endo(S)and
C3-endo(N)preferred sugar puckers. (b) Schematic of the pseudorotation phase angle (P) cycle with
the angle ranges of selected pucker types indicated