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does not necessarily mean that the metal ion achieves coordination number six as the
tridentate ligands can also bind through fewer than three atoms. Hence, the title of this
section “[3
3] Coordination” defines the presence of six donor atoms in the ligand envi-
ronment created in a duplex but does not identify necessarily the coordination number of
the metal in the complex with the ligands.
A pair of tridentate ligands Pur 2,6-py , Pur 6-bpy , Pyr bpy , Tpy ,or Spy was introduced in
complementary positions in the center of DNA duplexes (Table 10.1, entries 11-14) [13c,
d,47,61]. These ligands were originally intended for the purpose of creating a [3
þ
1]
coordination site in which a three-dentate ligand would be positioned in a complementary
position to a monodentate one, e.g. Py (Figure 10.8). Surprisingly it was found that, in the
presence of transition metal ions, the DNA duplexes containing a pair of tridentate ligands
were usually more stable than those containing a [3
þ
1] pair of ligands (compare entries
11 and 17, or 12 and 18, or 13 and 19 in Table 10.1). This finding can be attributed to the
fact that the stability constants of complexes of [3
þ
þ
3] type are typically very high due to
the chelate effect.
Given the high stability constants of metal complexes with polydentate ligands, com-
plexes that had a pair of tridentate ligands have been used also to create interstrand cross-
links in DNA, PNA, LNA, and UNA. Several of these complexes are mentioned in this
section, although they cannot function as alternative base pairs from a structural point of
view because the two ligands cannot be coplanar.
Yang et al. synthesized DNA duplexes with a terminal pair of terpyridine ( Tpy ) ligands
[62]. The thermal stability of the Tpy -modified DNA duplex was higher than that of the
unmodified DNA duplex, an effect similar to that exerted by nucleobase overghangs on
the stability of duplexes. The addition of Fe(II) and Co(II) to the Tpy -modified DNA
duplex further increased the melting temperature of the duplex (D T m >
17 C). In contrast,
Figure 10.8 Alternative base pairs based on metal complexes that contain one tridentate and
one monodentate ligand.
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