In recent years a number of triple helix-specific ligandshave been characterized (Figure 9.20). The func-
tion of such ligands is to overcome the inherent instability of triplex DNA and effect triplex stabilization.
The addition of a third strand into the major groove of a DNA duplex leads to the creation of two new
grooves on either side of the third strand in what was previously the major groove, and the minor groove
is left largely unchanged. One of the new grooves on either side of the third strand is essentially feature-
less. However, the other groove resembles the minor groove, except that its walls have hydrophobic
residues from pyrimidine C-5 methyl groups while the polar C-4 carbonyl/amino groups are buried.
This unique groove in triplex DNA with its bifurcated hydrogen-bonded centres on the floor, as well as the
hydrophobic nature of the groove walls, has led to the development of a new group of ligands designed to tar-
get this previously unexploited binding site in triplex DNA.^55 Thus, Terry Jenkins has synthesized a series of
para- and meta-carbonyl substituted 1,3-diaryltriazenes(Figure 9.20) intended to target one of the two new
grooves created during triplex formation. The concave inner surface of the ligand formed by triazene and
phenyl rings has no protrusions and so in principle the ligand can penetrate deeply into the narrow triplex
groove. The ligand possesses hydrogen bond acceptor groups, which can interact with hydrogen bond donors
on the groove floor. In addition, the -conjugated core residues make close van der Waals contacts with the
hydrophobic groove walls by alignment of phenyl rings in both ligand and DNA. Solution studies confirm
that these ligands bind preferentially to triplex DNA and stabilize this structure more than they stabilize a cor-
responding duplex. For example, sub-saturating amounts of the ligand produce a Tmof 2°C in duplex
DNA compared to triplex melting, where the presence of ligand shifts Tm20–25°C higher relative to ligand-
free DNA triplex. Binding of the triazene compounds is enthalpically driven, which is consistent with hydro-
gen bonding in the groove. It appears that these ligands bind through good surface matching, and the complex
is stabilized by favourable groove wall–ligand and hydrogen bond base–ligand interactions.
374 Chapter 9
Figure 9.20 The structures of a range of triplex-selective ligands