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 (Delta T-m=+17.7 degrees 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.

Automated summary

DNA three-way junction (3WJ) structures serve as essential building blocks for constructing DNA nanoarchitectures. By inducing structure through the addition or removal of Ni-II ions, as well as performing Ni-II-mediated self-sorting using bpy-modified strands and their unmodified counterparts, potential applications for metal-responsive DNA materials can be further developed.