Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides

Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (Im(OC)) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (Im(OA)) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The Im(OC) nucleobases were found to form stable Im(OC)–Cu(II)–Im(OC) and Im(OC)–Hg(II)–Im(OC) base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The Im(OC) bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The Im(OC)–Cu(II)–Im(OC) base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of Cu(II). Furthermore, we demonstrated the quantitative assembly of three Cu(II) ions inside a DNA duplex with three consecutive Im(OC)–Im(OC) pairs, showing great potential of DNA-template based Cu(II) nanoarray construction. The study of easily-prepared Im(OC) base pairs will provide a new design strategy for metal-responsive DNA materials.