Chemistry Reference
In-Depth Information
duplex that contains one base pair with a C3 glycol backbone (Figure 10.4). The phenolic
group and the aromatic nitrogen of
Q
are in an optimal 1,4 relationship for coordinating
metal ions and, consequently, the affinity of
Q
for metal ions is very high. Furthermore,
this ligand is particularly amenable for creating alternative base pairs because it forms
square planar [M
L
2
] complexes. The fact that the [M
Q
2
] complexes with divalent metal
ions are neutral bodes well for the incorporation of multiple, adjacent [M
Q
2
] complexes
within a nucleic acid duplex. The extended hydrophobic and aromatic surface of the lig-
and is ideal for p-stacking.
Substitution of an AT base pair with a pair of
Q
ligands in the middle of DNA, PNA, or
GNA duplexes led to a significant loss of stability for the duplex, which indicates that the
two ligands are not hydrogen bonded at pH 7 (Table 10.1, entry 7) [16b,35b]. Addition of
Cu
2þ
increased the thermal stability of
Q
-DNA,
Q
-PNA, and
Q
-GNA duplexes by
>
29
C. This large increase suggests that the strong coordinative bonds in [M
Q
2
] alterna-
tive base pair are the dominant factor for the stability of the duplexes. In the presence of
Cu
2þ
, the thermal stability of DNA or GNA duplexes that contain a natural base across
from
Q
was significantly lower than that of duplexes containing [Cu
Q
2
] [35b]. This
observation indicates that the [Cu
Q
2
] alternative base pair is highly specific irrespective
of the nucleic acid backbone.
The formation of metal complexes with high binding stability within the PNA duplex
can lead to high mismatch tolerance, that is, the thermal stability of metal-containing,
ligand-modified duplexes is not affected by the existence of several mismatches. For
example, in the presence of Cu
2þ
, the partly self-complementary ssPNAs that contained a
Q
ligand H-GTAG
Q
TCACT-Lys-NH
2
or NH
2
-Lys-CATC
Q
AGTGA-H formed duplexes
with melting temperatures close to those of corresponding [Cu
Q
2
]-containing PNA
duplexes formed from fully complementary oligomers [16b]. The high duplex stability is
likely due to the fact that [Cu
Q
2
] complexes bridge the nucleic acid strands at all temper-
atures, reducing the loss of translational entropy associated with the duplex formation.
Indeed, titrations at 25 and 95
C with Cu
2þ
of PNA duplexes that contained a pair of
Q
ligands in complementary positions showed that [Cu
Q
2
] complexes form with the PNA at
aCu
2þ
:
Q
-PNA oligomer ratio in solution of 1 : 2 [16b]. As a result, the gain in enthalpy
from p-stacking of several but not all base pairs is a sufficient driving force for duplex
formation, even in the absence of hydrogen bonding between several base pairs in the
duplex. In the duplexes that contained mismatches, the nucleobases not involved in
Watson-Crick base pairing can bulge out of the duplex and could be used potentially to
construct higher-dimensionality, hybrid inorganic PNA structures.
An interesting observation made when one compares the titrations of
Q
-containing
PNA with Cu
2þ
at 25 and 95
Cisthat[Cu
Q
] complexes can form at high tempera-
ture (at which the PNA strands are not hold together by Watson Crick interactions)
but cannot form at low temperature (at which the PNA exists in duplex form) [16b].
The hypothesis that this difference is due to a supramolecular chelate effect exerted
by the duplex was verified by isothermal calorimetry (ITC) titrations [16e]. The cal-
orimetric studies showed quantitatively that the Watson-Crick hybridization of two
PNA strands into a duplex that contains a pair of ligands in complementary positions
can significantly increase the stability constants of the metal complexes formed by
the ligands within the PNA by a few orders of magnitude when compared to the
corresponding stability constants for the same type of complexes with free ligands.
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