Counterion effects on fluorescence energy transfer in conjugated polyelectrolyte-based DNA detection

Cationic poly[9,9'-bis[6"-(Af,Af,Af-)hexyl]fluorene-co-a/f-phenylene]s with five different counterions (CIs) were synthesized and studied as fluorescence resonance energy transfer (FRET) donors (D) to dye-labeled DNA (FRET acceptor, A). The polymers with different CIs show same π-conjugated electronic structure with similar absorption (λ_abs = ∼380 nm) and photoluminescence (λ_PL = ∼420 nm) emission spectra in water. The CIs accompanying the polymer chain are expected to affect the D/A complexation and modify the D-A intermseparation by acting as a spacer. Polymers with different CIs function differently as FRET excitation donors to fluorescein (Fl)-labeled single-stranded DNA (ssDNA-Fl). The FRET-induced Fl emission was enhanced significantly by the larger Cl-exchapolymers. The polymers with the CIs of tetrakis(l-imidazolyl)borate (FPQ-IB) and tetraphenylborate (FPQ-PB) showed a 2-4-fold enhancement in the FRET-induced signal compared with the polymer with bromide (FPQ-BR). The delayed FRET signal saturation an low association constants (K_a) with ssDNA-Fl (3.53 × 10⁶ M^-1 for FPQ-BR and 1.80 × 10⁶ M^-1 for FPQ-PB) were measured for the polymers with larger CIs. The delayed acceptor saturation strengthens the antenna effect and reduces self-quenching of F by increasing the polymer concentration near Fl. The weak polymer/ssDNA-Fl association reduces the amount of energy-wasting charge transfer by increasing D-A intermolecular separation. The combined effects lead to increase the overall FRET-induced signal.