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structures. Such complexes can have a variety of interesting electronic, magnetic and
chemical properties, including the behavior of single molecule magnets, valence
delocalization, directional charge transfer, and catalysis. The formation of polynuclear
clusters within nucleic acid duplexes requires the presence of multiple ligands, which can
lead to the formation of several isomers. Hence, the synthesis and characterization of
duplexes containing multiple metal-based alternative base pairs are more challenging
than those of duplexes containing one metal complex and require use of a combination of
spectroscopic and structural characterization methods.
Table 10.2 shows the melting temperatures of the nucleic acid duplexes that contain
several isolated or adjacent metal binding sites. Examination of the data in the Table 10.2
shows that typically:
1. The melting temperature of the ligand-containing DNA duplexes is higher in the pres-
ence of the transition metal ion that coordinates to the ligands (entries 3,7,8,9,10). This
property, which is similar to that of duplexes containing one metal binding site, is due
to the formation of relatively strong coordination bonds between the ligands and metal
ion.
2. The melting temperature of the DNA duplexes with the same sequence of nucleobases
increases with the increase in the number of metal-based alternative base pairs, irre-
spective of the metal complexes being isolated or adjacent (entries 2,4,5). There are
exceptions from this trend, for example, the DNA duplex that contains
Spy.Py
pairs is
an exception from this trend (entry 1). In another example, a duplex that contained a
single
SPy
SPy
pair was more stable than a duplex with two
SPy
SPy
pairs, but less
stable than a duplex containing three
SPy
SPy
pairs [47].
3. The melting temperature increases with the number of equivalents of metal ion added
to the ligand-modified DNA duplexes (entries 3 and 6).
An interesting observation regarding the thermal stability of DNA duplexes with adja-
cent metal complexes was made by Megger
et al.
, who synthesized two palindromic 18-
bp DNA duplexes that did not contain any natural nucleobase pair (Table 10.2, entry 10).
Each of the 18 pairs consisted of one 1,3-dideaza-2
0
-deoxyadenosine (
Dda
) and one thy-
mine and could coordinate two Ag
þ
ions to form a Hoogsteen-type alternative base pair.
In one of the duplexes, the self-complementary ss DNA contained a stretch of nine thy-
mine ligands followed by a stretch of Dda. In the other duplex, the strand had alternating
thymines and Dda. The melting temperature measured in the presence of two equiv-
alents of Ag
þ
for the former duplex was 20
C lower than that of the latter duplex.
This observation was found in agreement with the fact that Hoogsteen-type double
helices are preferentially formed from alternating AT sequences.
Multiple bidentate bisimine ligands have been introduced in DNA and PNA duplexes.
These studies made possible a comparison of the effect of the chemical nature of the
duplex on incorporation of multiple metal complexes in duplexes, with the caveat that the
nucleobase sequence of the duplexes was not the same. Multiple, adjacent pairs of bipyr-
idine ligands introduced in both DNA or PNA duplexes caused a systematic decrease of
the duplex stability, as did the pairing of
Bpy
against either a natural base or an abasic site
[16c,70]. Switzer
et al.
[13b] and Franzini
et al.
[16c] examined the effect of Ni
2þ
on
Pur
P
-modified DNA and
Bipy
-modified PNA duplexes, respectively, containing three
adjacent pairs of bidentate ligands. The increase in the melting temperature of the DNA
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