Exploring the Holliday Junction in a DNA nanostructure for creating excitonic dimers

DNA nanostructures can perform as scaffolds to organize dye molecules into networks for a variety of applications. Such networks rely on having efficient energy-and/or electron-transport processes, and these in turn depend sensitively on the relative distance and orientation of the dye molecules. In using DNA as a scaffold, a crucial question is - to what extent can it control the dye position and orientation? The ability of DNA nanostructures to dictate the position is reasonably well addressed in the literature, but much less is known about the potential for controlling the orientation and its dependences on the local microenvironment of the DNA and on the dye attachment chemistry. Furthermore, can sites within a DNA nanostructure be used to place dyes in close proximity to create strong excitonic coupling, which, ultimately, could be useful in creating networks that use coherent energy transfer? To investigate these issues, we employ a Cy3 probe dye dimer and use both fluorescence measurements and numerical simulations to determine the degree to which a 30-helix DNA origami bundle can provide the desired excitonic coupling. Overall, the results of this work should be useful for creating DNA-scaffolded dye networks that use strong dye coupling.