Single-Molecule Assessment of DNA Hybridization Kinetics on Dye-Loaded DNA Nanostructures

DNA nanostructures offer a versatile platform for precise dye assembly, making them promising templates for creating photonic complexes with applications in photonics and bioimaging. However, despite these advancements, the effect of dye loading on the hybridization kinetics of single-stranded DNA protruding from DNA nanostructures remains unexplored. In this study, the DNA points accumulation for imaging in the nanoscale topography (DNA-PAINT) technique is employed to investigate the accessibility of functional binding sites on DNA-templated excitonic wires. The results indicate that positively charged dyes on DNA frameworks can accelerate the hybridization kinetics of protruded ssDNA through long-range electrostatic interactions. Furthermore, the impacts of various charged dyes and binding sites are explored on diverse DNA frameworks with varying cross-sizes. The research underscores the crucial role of electrostatic interactions in DNA hybridization kinetics within DNA-dye complexes, offering valuable insights for the functionalization and assembly of biomimetic photonic systems.