12 bp per turn of the duplex. Both structures have typical Watson–Crick base pairs, which are displaced
4.4 Å from the helix axis and so form a very deep major groove and a rather shallow minor groove.
These features were confirmed by the analysis of the first single crystal structure of an RNA oligonu-
cleotide, the 14 mer r(UUAUAUAUAUAUAA).^44 This 14-mer can be treated as three segments of A-helix
separated by kinks in the sugar–phosphate backbone, which perturb the major groove dimensions. It is
noteworthy that the 2-hydroxyl groups are prominent at the edges of the relatively open minor groove.^45
They are extensively hydrated and can be recognised by proteins (Figure 2.40). Many more crystal struc-
tures of oligoribonucleotides have now been determined, some to atomic resolution. These structures have
provided a wealth of information regarding canonical RNA duplexes, the effects on conformation by mis-
matched base pairs, hydration and cation co-ordination.
In one of the first NMR studies of a RNA duplex, Gronenborn and Clore combined 2D NOE analysis^46
(Section 11.2) with molecular dynamics to identify an A-RNA solution structure for the hexaribonu-
cleotide, 5-r(GCAUGC) 2.^47 It shows sequence-dependent variations in helix parameters, particularly in
58 Chapter 2
Figure 2.40 Van der Waals representation of the RNA duplex [r(UUAUAUAUAUAUAA)] 2 (PDB code 1RNA). The
view is into the narrow major groove of the central part of the duplex, with the minor groove visible
near the top and bottom. Atoms are coloured grey, red, blue and magenta for carbon, oxygen, nitrogen
and phosphorus, respectively. 2-Oxygen atoms lining the minor groove are highlighted in cyan