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Figure 10.5 PNA monomers used for the labeling of PNA-containing duplexes with transi-
tion metal complexes [30,31]. These complexes do not function as alternative nucleobase
pairs.
C3
0
-endo conformations [34]. We note that it is common to refer to DNA that contains
only several LNA (or GNA, see p. 341) residues as LNA (or GNA).
The nucleobases of LNA are preorganized for good stacking interactions, which causes
very high thermal stability of LNA-modified duplexes [33b]. For example, the introduc-
tion of LNA into the DNA strand of a DNA
RNA duplex has been shown to increase the
T
m
by 1-8
C per LNA monomer relative to the unmodified duplex. In contrast, the high
flexibility of UNA causes a destabilization of UNA-containing duplexes when compared
to the ones lacking UNA. For example, the
T
m
of a UNA
RNA duplex decreased by up to
10
C per UNA monomer incorporated in the DNA strand.
Glycol nucleic acid GNA has an acyclic three-carbon, propylene glycol-phosphodiester
backbone that includes a stereocenter (Figure 10.4) [17b,35]. GNA oligomers form anti-
parallel, helical duplexes based on Watson-Crick base pairing, which are more stable than
the analogous homo DNA or RNA duplexes. Crystallographic studies of ds GNA that
contained a brominated cytidine or uracil, or a complex of copper with hydroxypyridone
ligands showed the existence of two forms of backbone conformations, namely a con-
densed N-type and an elongated M-type, respectively [36]. Molecular dynamics simula-
tions of a non-modified GNA duplex showed an all-gauche conformation characteristic of
M-type GNA but with a higher helical twist common than N-type GNA structures [37].
GNA and LNA oligomers can be synthesized by standard solid phase DNA synthetic
methods because the backbone of both molecules are formed by phosphodiester bonds.
10.3 Metal-Containing, Ligand-Modified Nucleic Acid Duplexes
An interesting approach to incorporate transition metal ions in nucleic acid duplexes is the
formation of artificial metallo-base pairs (Figure 10.2) [38]. This approach was first
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