Ligand-modified nucleic acid duplexes, metal 3+1 coordination

To put in perspective the binding of metal ions to ligand-modified nucleic acid duplexes, we summarize the conclusions of these reviews on metal binding to DNA duplexes and emphasize those conclusions that are relevant for the influence of metal coordination on the secondary structure of DNA. These studies have been the prologue of today s efforts to use DNA or its synthetic analogues as scaffold for transition metal ions. 

It is conceivable that an interstrand complex can be created by coordination of a metal ion to the 2PA situated on the PNA or LNA strand and to a nucleobase or phosphodiester group from the opposite, non-modified DNA strand in the nucleic acid duplex. Molecular modeling of LNA DNA duplexes showed that a [3 -I-1] 2PA-M -P04R2 coordination mode can be realized by coordination of a 2PA ligand from one strand and a phosphodiester from either the same strand or from the opposite strand of the LNA DNA duplex (121). This model was supported by data obtained for 2PA-modified PNA DNA duplexes showing that (a) the... 

The rich coordination chemistry of transition metal ions has been used not only to create metal-ligand complexes that play the role of alternative nucleo-base pairs within nucleic acid duplexes, but also to influence the secondary structure adopted by the nucleic acid, for example, hairpin, duplex, or triplex, and to create connectors for such nucleic acid structures. In this context, oligonucleotides that contain terminal ligands can lead to structures distinct from those accessible by using centrally-modified oligonucleotides, such as cyclic structures or hairpins (Fig. 3). 

---