Chemistry Reference
In-Depth Information
O
1. hexamethyldisila-
zane, (NH
4
)
2
SO
4
2.
1. DMT-Cl, pyridine
2. pivalic anhydride
iPr
2
EtN, THF
3.
OPiv
O
O
OH
OBn
AcO
O
N
DMTO
OAc
Cl
O
O
P
N
CN
N
HO
H
O
OAc
TMSOTf, MeCN
3. H
2
/Pd, AcOEt
4. NH
4
OH, MeOH
O
O
P
CN
OH
iPr
2
EtN, CH
2
Cl
2
N(iPr)
2
Figure 9.11 Synthesis of the
N
-glycosidic hydroxypyridone base and its phosphoramidite.
9.5.2 The Hydroxypyridone Base Pair
One of the most widely used metal base pairing systems is the hydroxypyridone metal
base pair (Figure 9.10g) which can be employed for the coordination of Cu(II) (and also
Fe(III), see Section 9.6.1) inside DNA [47]. The synthesis of the
N
-glycosidic ligand is
briefly shown in Figure 9.11, the incorporation into artificial DNA strands according to
Section 9.3.4 is followed by a cleavage and deprotection step using aqueous ammonium
hydroxide in order to cleave the pivaloyl protecting group alongside all other protecting
groups of the synthesized oligonucleotide.
Using this ligand, it was shown for the first time that not only one but up to five directly
stacked Cu(II)-mediated base pairs could be incorporated into a DNA duplex without
compromising the integrity of the double helical structure [48]. Most interestingly, EPR
measurements showed a ferromagnetic coupling between the stacked paramagnetic cop-
per complexes (Figure 9.12 and Section 9.6.3). Like the salen metal base pair discussed in
the following section, the hydroxypyridone base pair was successfully used in the pro-
grammed assembly of heterobimetallic stacks inside DNA (see Figure 9.15) [49].
9.5.3 The Salen Base Pair
Whereas all metal base pairing systems discussed so far are composed of two individual
mono- or bidentate ligands reacting with the metal ion in a 2 : 1 fashion, the following
example effectively forms one tetradentate ligand inside the DNA that covalently
cross-links a strand and its counterstrand and thereby leads to a tremendous thermal
stabilization of the double helical structure. This system is based on the well known
N
,
N
0
-
ethylene-bis-salicylimine (“salen”) ligand which is widely used in catalysis and binds a
Figure 9.12 (a) Assembly and (b) stacking of the Cu(II)-mediated hydroxypyridone base pair.
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