Metal-Responsive DNA Tweezers Driven by Base Pair Switching of 5-Hydroxyuracil Nucleobases

Controlling DNA nanomachines in response to metal ions will broadly extend their functions and rate of operation. In this chapter, I operated DNA tweezers by metal-responsive base pair switching of UOH bases. A pair of DNA tweezers was designed to be closed by hybridization of a UOH-containing closing strand through UOH–A pairing. The addition of GdIII ions was expected to destabilize the UOH–A pairs and release the closing strand with the UOH–GdIII–UOH complexes, opening the tweezers. Native polyacrylamide gel electrophoresis revealed that the UOH-modified tweezers were predominantly closed (66%) in the absence of GdIII ions. On the other hand, the addition of GdIII released the UOH-containing closing strand along with UOH–GdIII–UOH complexes, opening 83% of the tweezers. The GdIII-dependent structural conversion was also proven by fluorescence analysis using tweezers with a pair of fluorophore and quencher. Furthermore, the UOH-modified tweezers were reversibly operated by the addition and removal of GdIII ions under isothermal conditions. These results demonstrated that the base pair switching of UOH would be widely applicable to metal-responsive operation of DNA molecular machines.