Two conjugated polyelectrolytes with same electronic structure with/without molecular spacer (or bumper) are compared in functioning as a donor in fluorescence resonance energy transfer (FRET) to a fluorescein-labeled single-stranded DNA (ssDNA-Fl). Fluorescence quenching of the acceptor (M) in the polymer/ssDNA-Fl electrostatic complex is a main concern to improve detection sensitivity. This study can show one important example of structure-property relationships for the FRET-based biosensing assays. Structure modification such as molecular bumper can fine-tune the competition between energy transfer and electron transfer quenching in FRET-based DNA sequence detection.