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Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions.

Yusuke Takezawa1, Shuhei Yoneda1, Jean-Louis H A Duprey1

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

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Artificial DNA strands modified with 2,2'-bipyridine (bpy) ligands transform between duplexes and three-way junctions (3WJs) in response to nickel ions. This metal-templated assembly enables stimuli-responsive DNA materials.

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Area of Science:

  • Biochemistry
  • Materials Science
  • Nanotechnology

Background:

  • DNA three-way junctions (3WJs) are critical building blocks for DNA nanotechnology and materials.
  • Developing controllable and reversible DNA structures is key for advanced applications.

Purpose of the Study:

  • To engineer a metal-responsive structural transformation between DNA duplexes and 3WJs.
  • To utilize artificial oligonucleotides with 2,2'-bipyridine (bpy) ligands for this transformation.

Main Methods:

  • Synthesized DNA oligonucleotides modified with 2,2'-bipyridine (bpy) ligands.
  • Investigated self-assembly in the presence and absence of transition metal ions (NiII).
  • Analyzed structural changes using techniques sensitive to DNA conformation.

Main Results:

  • Bpy-modified DNA and complementary strands formed duplexes without metal ions.
  • In the presence of NiII ions, these components self-assembled into 3WJs.
  • The NiII(bpy)3 complex acted as a template, directing 3WJ formation.
  • Metal ion concentration and type influenced 3WJ induction efficiency.
  • EDTA treatment quantitatively reverted 3WJs back to duplexes.

Conclusions:

  • Demonstrated a novel metal-dependent structural conversion between DNA duplexes and 3WJs.
  • The NiII(bpy)3 complex is crucial for templating 3WJ assembly.
  • This reversible transformation offers potential for creating stimuli-responsive DNA-based materials.