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.