The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.

A molecular beacon has been developed that depends on the formation of a metal-mediated base pair.

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A GNA (glycol nucleic acid) functionalized nucleoside analogue containing the artificial nucleobase 1H-imidazo[4,5-f][1,10]phenanthroline (P) was used to form a copper(I)-mediated base pair within a DNA duplex. The geometrical constraints imposed by the artificial nucleobase play a pivotal role in this unprecedented stabilization of copper(I) in aqueous medium via metal-mediated base pairing. The formation of the copper(I)-mediated base pair was investigated by temperature-dependent UV spectroscopy and CD spectroscopy. The metal-mediated base pair stabilizes the DNA oligonucleotide duplex by 23 °C. A redox chemistry approach confirmed that this base pair formation was due to the incorporation of copper(I) into the duplex. This first report of a copper(I)-mediated base pair adds metal-based diversity to the field and consequently opens up the range of possible applications of metal-modified nucleic acids.

The C-terminus of dipeptido dinucleotides reacts with the 3′-terminus of a primer strand in template directed fashion with a strong dependence on the structures of peptide and template.

A highly stabilizing metal‐mediated base pair formed from the canonical nucleobase cytosine (C), the transition metal ion AgI, and the artificial nucleobase 1H‐imidazo[4,5‐f][1,10]phenanthroline (P) was used in the generation of molecular beacons for the detection of medicinally relevant single nucleotide polymorphisms (SNPs) based on either a C→T or a T→C transition (T: thymine). The beacons exploit the fact that a P–C pair is strongly stabilized in the presence of AgI, whereas a P–T pair is significantly destabilized. A direct correlation of oligonucleotide sequence, duplex stability prior to the addition of AgI, stabilization due to metal‐mediated base pair formation, and performance of the molecular beacon was not observed. Nonetheless, the data show for the first time that metal‐mediated base pairing can be applied in the detection of medicinally relevant SNPs.

An artificial nucleoside surrogate with 1H-imidazo[4,5-f][1,10]phenanthroline (P) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal-mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag(I) -mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B-DNA duplex.