Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting

DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, U_bpy- 3 , in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand Ni^II(bpy)₃ complex at the junction core (ΔT_m=+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside U_bpy- 2 , the degree of the Ni^II-mediated stabilization observed with U_bpy- 3 was comparable to that of U_bpy- 2 . Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of Ni^II ions. Furthermore, Ni^II-mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of Ni^II(bpy)₃ complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.