Metal‐mediated base pairs represent an elegant way for the site‐specific functionalisation of nucleic acids. In this type of base pair, the hydrogen bonds between complementary nucleobases are replaced formally by coordinative bonds to one or more transition‐metal ions. This Review presents an overview of metal‐mediated base pairs reported so far. It gives an insight into the characterisation of metal‐mediated base pairs and into the structures of the resulting metal‐modified nucleic acids. In addition, a summary of applications exploiting the formation of metal‐mediated base pairs is presented. The applications include, for example, metal‐ion sensors of various types, a protein sensor, and DNA‐based molecular machines. Initial reports on the potential use of metal‐mediated base pairs in the context of charge transfer through nucleic acid double helices are summarised as well.

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

Excess electron transfer through one set of DNA duplexes comprising either one or two metal-mediated thymine-Hg -thymine base pairs was studied. Towards this end, the metal-mediated base pair(s) were introduced between an artificial nucleoside bearing a N,N,N',N'-tetramethyl-1,5-diaminonaphthalene derivative (dN, acting as a photoinducible electron donor) and 5-bromo-2'-deoxyuridine (dB, acting as an electron acceptor). Upon one-electron reduction, dB loses a bromide ion. The amount of unreacted dB remaining after irradiation-determined by LC/ICP-MS-was used to evaluate the charge-transfer efficiency across the metal-mediated base pair(s). Reference measurements with canonical adenine:thymine base pairs prove the applicability of this approach for the detection of charge transfer in DNA. The data indicate that, for the set of DNA duplexes under investigation, excess electron transfer across a thymine-Hg -thymine base pair proceeds with low efficiency, comparable to the transfer across a thymine:thymine mispair. Two contiguous thymine-Hg -thymine base pairs effectively shut down excess electron transfer.

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.

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DNA‐mediated charge transfer represents a topical area of research. The influence of the site‐specific introduction of a metal ion into the base pair stack is a matter of current debate. In their communication on page 10244 ff., U. Karst, J. Müller et al. contribute to this debate by reporting an experimental study on excess electron transfer across a metal‐mediated base pair within a DNA double helix. To this end, LC/ICP‐MS was applied for the first time to quantify the electron‐transfer efficiency. The data suggest that a thymine–HgII–thymine base pair influences charge transfer in the same way as a thymine:thymine mispair does.

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