Inter-helical excitonic coupling dye assemblies templated with anti-parallel and parallel DNA motifs

DNA nanostructures were used to template dye molecules for constructing strong coupling dye aggregates as excitonic devices that mimic light-harvesting systems in nature. Such strongly coupled dye assemblies are usually restricted to intra-helical aggregates and lack inter-helical strong coupling, thus limiting the potential for constructing long-range strongly coupled systems based on DNA. Here, a DNA construct utilizing the classic antiparallel double crossover, parallel double crossover, and paranemic crossover motifs was used to study the excitonic coupling between inter-helical dye assemblies. Excitonic coupling between inter-helical cyanine dye molecules was achieved in all three kinds of basic DNA motifs, with different H and J features. A tetrameric cyanine dye assembly templated with the paranemic crossover motif shows the potential for constructing long-range excitonic coupling dye assemblies across DNA duplexes laterally, with the ability of dynamic control of dye assemblies benefiting from the strand displacement reaction on the paranemic crossover motif.