Förster Resonance Energy Transfer in Linear DNA Multifluorophore Photonic Wires: Comparing Dual versus Split Rail Building Block Designs

Abstract DNA scaffolds provide a means to precisely organize chromophores into large biomimetic exciton networks and direct energy transport for nanoscale sensing and light‐harvesting applications. Here, a functional building block of minimal complexity that maximizes the Förster resonance energy transfer (FRET) efficiency is sought. Using a model system consisting of three FRET steps in a 4‐dye cascade: Cy3→Cy3.5→Cy5→Cy5.5, we evaluate how this building block employs multiple interacting versus redundant FRET pathways. Variants of a dual rail design, where one or two copies of each dye are aligned in rigid linear parallel rows, are compared to a split rail format, where varying degrees of spacing are introduced between the rows. The FRET processes are assessed via steady‐state, time‐resolved, and single‐molecule spectroscopy. Experiments and simulation reveal the dual rail design as more efficient than the split rail and suggest the design principle that efficient FRET networks must balance the increase in FRET rate from multiple interacting pathways with undesirable fluorescence quenching between dyes in close proximity. Hybrid fluorophore combinations are identified as a strategy to mitigate this quenching, leading to optimized dual rails capable of 50% end‐to‐end efficiency. These insights can help guide the design of functional photonic wires based on DNA scaffolds.