Metal-Responsive DNA Strand Displacement Reactions Driven by Base Pair Switching of 5-Hydroxyuracil Nucleobases

Toehold-mediated DNA strand displacement reactions (SDRs) are an essential tool for the construction of DNA-based molecular machines. In this chapter, I demonstrated “base pair switching” of 5-hydroxyuracil (UOH) bases and applied it for metal-responsive SDRs. The UOH bases were known to form both hydrogen-bonded UOH–A pairs and metal-mediated UOH–GdIII–UOH pairs. Therefore, it was expected that the base-pairing partner of UOH can be switched from A to UOH by the addition of GdIII ions, resulting in metal-responsive base pair switching. UV melting analysis revealed that the order of thermal stability was inverted among two UOH-containing duplexes, one with UOH–A pairs and the other with UOH–UOH mismatches, by the addition of GdIII ions. This result supported GdIII-responsive base pair switching from UOH–A to UOH–GdIII–UOH, which was utilized for metal-responsive SDRs. According to time-course fluorescence measurement, the addition of GdIII ions triggered the SDR from the duplex containing UOH–A pairs to that with UOH–GdIII–UOH pairs. The SDR driven by the base pair switching of UOH will be a powerful tool for developing metal-responsive DNA nanodevices.