DNA Origami Chromophore Scaffold Exploiting HomoFRET Energy Transport to Create Molecular Photonic Wires

DNA-scaffolded molecular photonic wires (MPWs) displaying prearranged donor-acceptor chromophore pairs that engage in extended Forster resonance energy transfer (FRET) cascades represent an emerging nanoscale photonic material with numerous potential applications in data storage, encryption, and communications. For translation to such applications, these devices must first demonstrate robust performance with high transfer efficiencies over extended distances. Here, we report the optimization of FRET in a 6-helix DNA origami architecture supporting a 14-dye site system that contains a central 10-dye homogeneous FRET (HomoFRET) relay span and overall extends over 29 nm in length. Varying the dye density by controlling their presence or absence across all of the individually addressable sites presented an incredibly large optimization space (1024 HomoFRET and 16 384 total permutations). High-throughput experiments, with over 500 measurements of DNA templates assembled in parallel, allowed for the study of HomoFRET transfer as a function of fluorophore density and arrangement. Transfer within solution-phase MPWs initially obtained with steady-state spectroscopy experiments revealed values only reaching -1% efficiency. Extensive photophysical characterization, utilizing six different spectroscopic techniques and 11 total methodologies, determined that the diminished FRET efficiency of each individual component step is the principal cause of the limited transfer in solution. Monte Carlo and machine-learning methods provided additional insights into design optimization. A representative MPW set selected based on the previous findings was subsequently characterized in film deposition and also under cryogenic conditions. Under these improved conditions, selected MPWs demonstrated 59 +/- 6% energy transport efficiency over a length of 29 nm; this is similar to 25% longer and 10-fold more efficient than the previously reported optimized DNA MPWs.