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

Abstract

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 IImediated 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.

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

“…Metal-mediated control of the structure and function of DNA assemblies is generally based on the stabilization of metalcontaining states. [56][57][58][59] In contrast, metal-dependent hybridization demonstrated in this study stands on the switching between two different states involving hydrogen-bonded base pairs (dcaU-A) and metal-mediated base pairs (dcaU-Gd III -dcaU). We believe that metal-dependent switching of the base pairing properties of the 5-modified nucleobases will be a versatile tool for efficient switching of DNA nanostructures.…”

Phenanthroline-modified DNA three-way junction structures stabilized by interstrand 3 : 1 metal complexation

“…Previous studies have reported that DNA 3WJs modified with three bipyridine (bpy) ligands at the junction core were thermally stabilized by the formation of an interstrand Ni II (bpy) 3 complex. 11–14 Furthermore, structural conversion between duplexes and 3WJs and self-sorting of modified and unmodified 3WJs were demonstrated in a metal-dependent manner. 12,13…”

“…11–14 Furthermore, structural conversion between duplexes and 3WJs and self-sorting of modified and unmodified 3WJs were demonstrated in a metal-dependent manner. 12,13…”

“…However, even in the presence of Ni II ions, no significant structure induction of the 3WJs were observed, while the 3WJs were formed in 59% yield when bpy-modified strands were used instead of the phen-modified ones. 13…”

“…Melting experiments showed that the duplex L1S4 melted at 68.0 °C, which is higher than the T m of the duplex containing a bpy ligand (63.9 °C). 13 The high stability of the phen-containing duplexes may be attributed to the intercalation of the large aromatic moiety of the phen ligand to base pairs within DNA duplexes. The thermal stability of the duplex is unchanged by the addition of Ni II ions ( T m = 66.2 °C), and is comparable to that of the metal-bridged 3WJ L1L2L3 ·Ni II (69.7 °C).…”