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Area of Science:

  • Biomolecular Engineering
  • Nanotechnology
  • Molecular Biophysics

Background:

  • DNA-templated dye aggregation is crucial for engineering molecular excitons.
  • Holliday Junctions (HJs) are used for templating, but their dynamic nature causes structural heterogeneity.
  • Minimizing this heterogeneity is key for precise control over dye aggregates.

Purpose of the Study:

  • To selectively tune the global conformation of Holliday Junctions (HJs).
  • To restrict the position and orientation of HJs using DNA origami constructs (DOCs).
  • To investigate the impact of conformation on dye-DNA interactions and aggregate structure.

Main Methods:

  • Utilized sheet-like DNA origami constructs (DOCs) to physisorb HJs onto glass surfaces.
  • Fixed HJ arms with four different designed interduplex angles (IDAs).
  • Employed atomic force microscopy, dipole imaging, and super-resolution microscopy for characterization.

Main Results:

  • Confirmed successful binding of HJs to DOCs with tuned IDAs via AFM.
  • Observed dispersed dye orientation distributions, suggesting dye-base stacking.
  • Found that the narrowest IDA minimized heterogeneity, indicating dye intercalation.
  • Established a strong correlation between IDA and dye orientation along the HJ plane.

Conclusions:

  • The HJ conformation significantly restricts dye orientation and influences dye-DNA interactions.
  • Dye-base stacking is a consistent interaction, regardless of HJ global conformation.
  • This methodology enables solid-supported single-molecule characterization of biomolecule-templated assemblies with controlled conformations.
  • Provides a pathway for scalable dye aggregate engineering for applications in light-harvesting and catalysis.