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Figure 9.4 (a) The thymine-Hg(II) (T-Hg(II)-T) base pair and (b) the cytosine-Ag(I) (C-Ag(I)-C)
base pair.
9.3 Design and Synthesis of Metal Base Pairs
9.3.1 Rational Design of Metal Base Pairs
Although both the T-Hg(II)-T and the C-Ag(I)-C base pairs have proven to be very useful
and have the advantage that no artificial ligands have to be introduced into the DNA, the
latter circumstance also means that mixed sequences with Watson-Crick base pairs have
to be carefully designed in order to prevent undesired interactions between the metal ions
and parts of the sequence that were not supposed to be metallated.
Another approach to introduce metal ions into specific positions of a DNA double helix
was therefore developed by Shionoya and others using artificial ligand-type nucleobases
that are specifically designed to coordinate metal ions without undergoing any interac-
tions with the natural base pairs [20].
The basic design principles that have to be considered for the development of these
so-called metal base pairing systems are summarized in Figure 9.5. In brief, one has to
consider mainly geometric and electronic features. The former ones include the dimen-
sions of the metal complex in terms of the distance between the connection points to
the sugar moieties (Figure 9.5a), the steric bulk when viewed along the base stack
(Figure 9.5b) and the angle between the metal base pairs' long axis and the bonds to the
C1 0 position of the sugars (Figure 9.5c). Furthermore, the coordination number and geom-
etry favored by the used metal ion (Figure 9.5d) and provided by the donor atom(s) of the
ligands (Figure 9.5e) and the net charge of the resulting metal base pairs must be carefully
adjusted. The electronic interactions between the metal ion and the ligand's donor atoms
must be chosen to enable tight binding of the metal ion to the ligands alone (and not to the
Figure 9.5 (a-e) Features to be considered in the design of metal base pairs. Ligands consist-
ing of (f) an N -glycosidic base (hydroxypyridone) and (g) a C -glycosidic base (salicylaldimine).
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