Can a DNA Origami Structure Constrain the Position and Orientation of an Attached Dye Molecule?

There has been significant interest in using DNA origami nanostructures 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 rigidity of the DNA, on the dye attachment chemistry, and on other aspects of the local microenvironments of the dye. To investigate these issues, we here employ a Cy3 probe dye and use its measured fluorescence properties and numerical simulations to compare the degree to which a DNA duplex and a 30-helix DNA origami bundle can provide the desired control over the dye. Experimentally, we find that the excited state lifetimes and rotational anisotropy decays are longer for the bundle than for the duplex indicating that the Cy3 is more constrained in the former. Atomistic molecular dynamics (MD) simulations are found to be in good agreement, and they further provide insight into how the microenvironment of the bundle is limiting the dye motion. Moreover, Forster resonance energy transfer simulations based on the MD data indicate that the constraints imposed by the DNA bundle can be sufficient to substantially raise the transfer efficiency (over the duplex) if the siting of the donor and acceptor is well chosen. Overall, the results of this work should be useful for improving the performance of DNA-scaffolded dye networks.

Automated summary

DNA origami nanostructures show potential for organizing dye molecules into networks, but the ability to control the orientation of the dye, as well as the factors influencing it, are still not well understood.