Energy Transfer from a Cationic Conjugated Polyelectrolyte to a DNA Photonic Wire: Toward Label-Free, Sequence-Specific DNA Sensing

We demonstrate a label-free, sequence specific DNA sensor based on fluorescence resonant energy transfer (FRET) occurring between a cationic conjugated polyelectrolyte and a small intercalating dye, malachite green chloride. The sensor combines (1) conjugated polymer chain conformation changes induced by the binding with DNA, with the conjugated polymer wrapping/twisting around the DNA helical duplex and experiencing a 3-fold increase in its photoluminescence quantum yield and (2) FRET from the conjugated polymer to the intercalated DNA. Owing to its small size, the dye intercalates at maximal, one-to-one dye-to-base pair load, making the intercalated DNA a molecular photonic wire with dyes excitonically coupled and chiroptically active. Any sequence mismatch between probe and target DNA degrades the intercalated DNA photonic wire by decreasing its brightness, excitonic coupling, and chiroptical properties, and this provides a signal transduction method for the DNA sensor. Coupling of intercalated DNA with the conjugated polymer via FRET provides target signal amplification and increased sensitivity toward sequence mismatch, with the FRET efficiency decreasing with added DNA sequence mismatch.