Metal-Dependent Base Pair Switching of N,N-Dicarboxymethyl-5-Aminouracil Nucleosides

The base pair switching of UOH has had limited application because it requires the consecutive introduction of multiple UOH bases into DNA strands. In this chapter, I aimed to develop metal-responsive base pair switching by a singly incorporated ligand-type nucleobase. To this end, I designed N,N-dicarboxymethyl-5-aminouracil (dcaU) containing an iminodiacetate ligand. The dcaU base was expected to show higher coordination ability than UOH due to its negative charges and chelate effects. After obtaining dcaU phosphoramidite, dcaU-containing DNA strands were synthesized by an automated DNA synthesizer. In the presence of GdIII ions, a DNA duplex with a dcaU–dcaU pair was significantly stabilized due to the formation of dcaU–GdIII–dcaU pairs. As a result, the addition of GdIII ions reversed the relative stability of two duplexes containing dcaU–A or dcaU–dcaU pairs, indicating base pair switching between dcaU–A and dcaU–GdIII–dcaU. The base pair switching of dcaU was further applicable for GdIII-responsive DNA strand exchange. These results showed that the efficiency of the base pair switching can be rationally controlled by careful design of ligand-type nucleobases.