(7.6 to 8.3 with C5–H close to 5.9). The anomeric hydrogen is a doublet for ribonucleosides and a
double-doublet for 2-deoxynucleosides at 5.8–6.4. The pentoses provide a multi-spin system that gen-
erally moves from low to high field in the series: H-2, H-3, H-4, H-5and H-5in the region 4.3 to 3.7.
Lastly, 2-deoxynucleosides have H-2and H-2as an ABMX system near 2.5. The 400 MHz spectrum
of a simple nucleoside, cytidine (Figure 2.10), shows why two-dimensional (2D) spin techniques are
required for the complete analysis of the spectrum in a large oligomer, which may be equivalent to a dozen
such monomer spectra superimposed.
2.1.4 Shapes of Nucleotides
Nucleotides have rather compact shapes with several interactions between non-bonded atoms. Their molecu-
lar geometry is so closely related to that of the corresponding nucleotide units in oligomers and nucleic
acid helices that it was once argued that helix structure is a consequence of the conformational preferences
of individual nucleotides. However, the current view is that sugar–phosphate backbone appears to act as
no more than a constraint on the range of conformational space accessible to the base pairs and that –
interactionsbetween the base pairs provide the driving force for the different conformations of DNA
(Section 2.3.1).
The details of conformational structure are accurately defined by the torsion angles , , , , , and in
the phosphate backbone, 0 – 4 in the furanose ring, and for the glycosylic bond (Figure 2.11). Because
many of these torsional angles are inter-dependent, we can more simply describe the shapes of nucleotides
in terms of four parameters: the sugar pucker, the syn–anticonformation of the glycosylic bond, the orien-
tation of C4–C5and the shape of the phosphate ester bonds.
2.1.4.1 Sugar Pucker. The furanose rings are twisted out of plane to minimise non-bonded inter-
actions between their substituents. This ‘puckering’ is described by identifying the major displacement of
carbons-2and -3from the median plane of C1–O4–C4. Thus, if the endodisplacement of C-2is
greater than the exodisplacement of C-3, the conformation is called C2-endoand so on (Figure 2.11).
The endoface of the furanose is on the same side as C-5and the base; the exoface is on the opposite face
to the base. These sugar puckers are located in the north (N) and south (S) domains of the pseudorotation
cycleof the furanose ring and so spectroscopists frequently use Nand Sdesignations, which also fortuitously
reflect the relative shapes of the CCCC bonds in the C2-endoand -exoforms, respectively.^1
In solution, the N andSconformations are in rapid equilibrium and are separated by an energy barrier
of less than 20 kJ mol^1. The average position of the equilibrium can be estimated from the magnitudes of
the^3 J NMR coupling constants linking H1H2and H3H4. This is influenced by (1) the preference
of electronegative substituents at C-2and C-3for axial orientation, (2) the orientation of the base (syngoes
20 Chapter 2
Figure 2.10 Proton NMR spectrum for cytidine (run in D 2 O at 400 MHz)