Optimization of interactions between a cationic conjugated polymer and chromophore-labeled DNA for optical amplification of fluorescent sensors

Cationic conjugated polymers (CCPs) have been widely utilized as signal amplifiers in biosensors to improve the detection sensitivity through fluorescence resonance energy transfer (FRET) from CCPs to dye-labeled probes or targets. This paper investigates the effect of sodium dodecyl sulfate (SDS) on energy transfer between a cationic polyfluoreneethynylene copolymer (P1) and Texas Red labeled single-stranded DNA (ssDNA-TR). The presence of SDS in solution affects both the optical properties of PI and TR emission within P1/ssDNA-TR complexes, which provides basic information on the role of SDS in FRET between P1 and ssDNA-TR. Although the quantum yield of P1 decreases in the presence of low concentrations of SDS, the presence of SDS reduces TR fluorescence quenching within P1/ssDNA-TR complexes and increases the number of optically active polymer repeat units within the proximity of TR, which are beneficial to PI-sensitized TR emission. In the absence of SDS, FRET from P1 to ssDNA-TR provides a 2.6-fold enhancement in TR emission intensity as compared to that upon direct excitation of TR at 595 nm. At the optimum SDS concentration (5 mu M), P1-sensitized TR signal output increases to 11.3-fold relative to direct excitation of TR. This study highlights the importance of modulation of the CCP/ssDNA-dye interaction in improving the signal output of dye-labeled DNA by CCP through FRET.