The interaction between three poly(9,9-bis(6-N,N,N-trimethylammonium)hexyl)fluorene phenylene) bromide (HTMA-PFP) samples of different molecular weights (Mn=14.5, 30.1 and 61.3 kg/mol) and both dsDNA and ssDNA secondary structures has been studied using UV-visible absorption and fluorescence spectroscopies (including steady-state, time-resolved, and anisotropy measurements for the latter), viscosity, and electrical conductivity in 4% (v/v) DMSO-water mixtures. At low nucleic acid concentrations, formation of a 1:1 complex in terms of HTMA-PFP repeat units and DNA bases occurs. This interaction results in quenching of polymer emission. For higher molar ratios of DNA to HTMA-PFP, corresponding to charge neutralization, a second process is observed that is attributed to aggregate formation. From the changes in the absorption spectra, the polymer aggregation constant and the aggregate absorption spectra were calculated by applying an iterative method. Polymer aggregation dramatically quenches HTMA-PFP fluorescence in the region of the electroneutrality point. Under these conditions, the ratio of the emission intensity at 412 nm (maximum) to that at 434 nm (I412/I434) reaches a minimum, the electrical conductivity decreases, and the viscosity of the solution remains constant, showing that the DNA concentration can be determined through various HTMA-PFP physicochemical properties. With respect to the photophysical parameters (emission quantum yield, shape and shift of emission spectra), no significant differences were observed between dsDNA and ssDNA or with conjugated polymer or DNA molecular weight. The two short-lived components in the fluorescence decays are attributed to the presence of aggregates. Aggregates are also suggested to be responsible for the decrease in the fluorescence anisotropy through interchain exciton migration.