homo-pyrimidines and one homo-purine (Figure 2.33c). However, despite the backbone distortion that
must result from the hetero-morphism of other base triplet combinations, oligonucleotides containing G
and T, G and A, or G, T and C have been shown to form helices.
Intermolecular triple helices are now well characterised for short oligonucleotides binding in the groove
of a longer DNA duplex,37,38H-DNA provides an example of an intramolecular triple helix because it has
a mirror-repeat sequence relating homo-purine and homo-pyrimidine tracts in a circular double-stranded
DNA molecule, and triplex formation is driven by supercoiling (Figure 2.33d).
DNA and RNA Structure 51
Figure 2.34 The triple helical structure formed in the crystal structure of the 1:1 complex between the DNA 12 mer
d(CTCCTCCGCGCC) and the 9 mer d(CGCGCGGAG) (PDB: 1D3R; available at: http://www.
rcsb.org).^39 The triplex segment consists of two 5-halves of the 12 mer (underlined, top and bottom left)
and two 3-terminal trimers GAG (underlined; top and bottom right) from two 9 mers that are stacked
tail-to-tail in the crystal: 5-...-GAG-3\3-GAG-...-5(visible near the centre, left of drawing). DNA
bases are coloured red, grey, pink and black for G, A, C and T, respectively, and the directions of the
sugar–phosphate backbones are traced by ribbons