The complementarity of Watson-Crick base pairing makes DNA a versatile, programmable material for constructing precise nanostructures. Single-stranded DNA tiles (SSTs) enable the self-assembly of a variety of nanopatterns, with potential applications in biosensing and nanologic circuits. However, existing SST design tools are limited by their complexity, lack of flexibility, and incompatibility with modern simulation platforms, which restrict their broader use. To overcome these limitations, we developed a design approach for SST structures based on caDNAno. This method simplifies the design process through a user-friendly graphical interface and integrates with the oxDNA simulation platform, allowing for accurate design validation. The proposed strategy significantly improves the efficiency of SST design and broadens the available tools for DNA nanostructure engineering.

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Simulation and Design of DNA Nanostructures with Single-Stranded DNA Tiles Based on caDNAno

  • Shichen Wang,
  • Kuiting Chen

摘要

The complementarity of Watson-Crick base pairing makes DNA a versatile, programmable material for constructing precise nanostructures. Single-stranded DNA tiles (SSTs) enable the self-assembly of a variety of nanopatterns, with potential applications in biosensing and nanologic circuits. However, existing SST design tools are limited by their complexity, lack of flexibility, and incompatibility with modern simulation platforms, which restrict their broader use. To overcome these limitations, we developed a design approach for SST structures based on caDNAno. This method simplifies the design process through a user-friendly graphical interface and integrates with the oxDNA simulation platform, allowing for accurate design validation. The proposed strategy significantly improves the efficiency of SST design and broadens the available tools for DNA nanostructure engineering.