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Triple-Stranded DNA As a Structural Element in DNA Origami.

Ken Sachenbacher1, Ali Khoshouei1, Maximilian Nicolas Honemann1

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Researchers developed novel pH-dependent DNA origami building blocks using hybrid duplex-triplex DNA motifs. These new motifs enable enhanced structural control and pH-induced self-assembly for advanced nanostructures.

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Cryo EMDNA origamiDNA triplexnanodevicespH switching

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Area of Science:

  • Nanotechnology
  • Molecular Biology
  • Structural DNA Nanotechnology

Background:

  • DNA origami utilizes double-helical DNA (dsDNA) and phosphodiester strand crossovers for fabricating 3D nanostructures.
  • Expanding the repertoire of DNA origami structural motifs is crucial for advancing nanodevice design.

Purpose of the Study:

  • To introduce and investigate hybrid duplex-triplex DNA motifs as pH-dependent building blocks in DNA origami.
  • To establish design rules for integrating triplex-forming oligonucleotides and duplex-triplex crossovers into multilayer DNA origami.

Main Methods:

  • Design and incorporation of triplex-forming oligonucleotides and noncanonical duplex-triplex crossovers.
  • Utilized single-particle cryo-electron microscopy for structural elucidation of triplex domains and crossovers.
  • Investigated pH-induced self-assembly and structural characteristics of DNA origami objects.

Main Results:

  • Demonstrated that duplex-triplex crossovers can effectively complement or replace canonical duplex-duplex crossovers.
  • Showcased increased crossover density, reduced interhelical spacing, and novel connection possibilities using duplex-triplex crossovers.
  • Achieved pH-induced formation of a DNA origami object solely stabilized by triplex-mediated strand crossovers.

Conclusions:

  • Hybrid duplex-triplex DNA motifs offer versatile, pH-dependent building blocks for DNA origami.
  • These motifs provide enhanced structural control, rigidity, and novel assembly strategies for complex 3D nanostructures.
  • The findings pave the way for new designs in DNA-based nanotechnology and responsive nanomaterials.