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

Chemistry

Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Published: December 2021

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 -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 (bpy) complex at the junction core (ΔT =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside U -2, the degree of the Ni -mediated stabilization observed with U -3 was comparable to that of U -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of Ni ions. Furthermore, Ni -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 (bpy) 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.

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http://dx.doi.org/10.1002/chem.202102977DOI Listing

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