because the bisintercalator imposes a greater amount of rigidity in the DNA helix compared to dauno-
mycin. There is considerable conformational freedom in the unbound WP631 with free rotation about
many of the bonds in the linker. The process of bisintercalation results in restriction in these bonds, thus giv-
ing rise to unfavourableentropic effects.
Subsequent to the initial characterisation of WP631, a 2.2 Å X-ray crystal structure of the WP631-
d(CGATCG) 2 complex was solved (Figure 9.10).^26
This structure confirmed unambiguously that bisintercalation is the binding mode. Many of the structural
features observed in crystals of the 2:1 daunomycin–DNA structures are conserved in the bisintercalator
complex. For example, intercalation of the anthracycline rings at both terminal d(CpG) steps, and hydro-
gen bond interactions between OH-9 of the ligand and N-2 and N-3 of guanine. However, bisintercalation
alters the DNA conformation relative to monointercalation, primarily in the centre of the oligonucleotide.
Helix unwinding and other distortions propagate to the centre of the WP631 complex much more effi-
ciently than in the daunomycin complex.
While the sugar constituents still occupy the minor groove, their exact position and interactions are dif-
ferent in the bisintercalator from daunomycin alone. The presence of the linker results in the amino sugar
groups being lifted away from the floor of the minor groove. The net result is that hydrogen bonds between
the 3 -amino groups of the sugar that are present in the daunomycin complex are absent in WP631. In
daunomycin–DNA complexes, there are two water molecules in the minor groove that each forms two
hydrogen bonds with the floor of the groove and one hydrogen bond to 3 -amino group of the daunomycin
sugar. The linker of WP631 displaces these water molecules resulting in a forced contact between the
hydrophobic linker and polar functional groups occupying the groove floor. The reduced hydrogen bond-
ing, the greater separation of the amino sugars from the groove floor, and the desolvation of the minor
groove may explain why the binding constant for WP631 falls short of being the square of the daunomycin
binding constant.
9.6.6 Nonclassical Intercalation: The Threading Mode
One group of ligands that bind to DNA by intercalation contain substituent groups on opposite edges of
the planar aromatic intercalating ring system. For the planar part of the molecule to intercalate, one of the
358 Chapter 9
Figure 9.10 X-ray crystal structure of the daunomycin bisintercalator WP631-d(CGATCG) 2 complex, (NDB:
DDF072; PDB: 1AGL). Two views are shown: left, looking into the major groove and right, looking
into the minor groove. A solid black line traces the DNA backbone
(Figure prepared and kindly providedby Loren D. Williams)