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

Area of Science:

• Synthetic biology
• Nanotechnology
• Materials science

Background:

• DNA three-way junctions (3WJs) are crucial for constructing DNA nanoarchitectures.
• Previous modifications exist for DNA 3WJs, but new methods are needed for enhanced stability and control.

Purpose of the Study:

• To synthesize and characterize a novel bipyridine (bpy)-modified DNA 3WJ using a new nucleoside, U_bpy -3.
• To investigate the impact of this modification on thermal stability and metal-ion responsiveness.
• To explore Ni^II -mediated structural induction and self-sorting of these modified DNA 3WJs.

Main Methods:

• Synthesis of a bipyridine-modified nucleoside (U_bpy -3) with an amide linker.
• Formation of interstrand Ni^II (bpy)₃ complexes at the 3WJ core.
• Thermal denaturation studies (T_m) to assess stability.
• Ni^II ion addition/removal experiments for structural control.
• Self-sorting experiments using modified and unmodified DNA strands.

Main Results:

• The bpy-modified 3WJ exhibited significantly enhanced thermal stability (ΔT_m =+17.7°C) due to Ni^II (bpy)₃ complex formation.
• The stabilization effect of U_bpy -3 was comparable to previous modifications, despite stereochemical differences.
• Ni^II ions effectively controlled the structure induction and self-sorting of the bpy-modified 3WJs.
• Both structural induction and self-sorting were driven by the formation of Ni^II (bpy)₃ complexes.

Conclusions:

• A novel bpy-modified DNA 3WJ (U_bpy -3) enhances thermal stability and allows for metal-ion-controlled structural transformations.
• Ni^II -mediated self-sorting of these DNA nanostructures was successfully demonstrated.
• These findings open avenues for developing responsive DNA materials with potential applications in nanotechnology and beyond.