Cationic water-soluble poly(fluorene-co-phenylene)s with electron withdrawing or donating substituents the conjugated backbone were designed and synthesized. Fluorescence resonance energy transfer (FRET) experiments between these conjugated polymers and dye-labeled single-stranded DNA (ssDNA-C*) reveal the importance of matching donor and acceptor orbital energy levels to improve the sensitization of C* emission. Quenching of polymer fluorescence with ssDNA-C* and differences in C* emission suggest involvement of photoincluced charge transfer (PCT) as an energy wasting mechanism. The HOMO and LUMO energy levels of the, conjugated polymers and C* serve as a preliminary basis to understand the competition between FRET and PCT. Dilution of C* in polymer/ssDNA-C* complexes by addition of ssDNA yields insight into C*center dot center dot center dot C* self-quenching. Under optimized conditions, where there is no probe self-quenching and minimum PCT, efficient signal amplification is demonstrated despite poor spectral overlap between polymer and C*.