The interaction between pyren-1-ylmethyl tri-n-butylphosphonium bromide (PMTP), a water-soluble cationic pyrene derivative and the double-strand polynucleotides Poly[dA-dT], Poly[dA].Poly[dT], Poly[dG-dC] and Poly[dG].Poly[dC] was studied using UV-Vis absorption and fluorescence spectroscopy. The PMTP probe interacts with polynucleotides through both weak and intercalative binding, evidenced through changes in the absorption spectrum (hypochromicity and red shift). The two binding types were distinguished using time-resolved fluorescence, as the intercalative environment differs from that of the surface. Thymine and cytosine are more efficient quenchers of PMTP situated on the surface because of the higher proton accessibility to this region. In contrast, adenine does not quench PMTP fluorescence, whereas guanine residues are always very efficient quenching sites. Therefore, through the use of spectroscopic techniques, it was possible to obtain information concerning the partition of PMTP in each form of binding. In the heteropolymers, Poly[dA-dT] and Poly[dG-dC], PMTP exhibits a significant preference for intercalation in AT sequences, while with GC, the intercalation is lower. In the homopolymers, Poly[dA].Poly[dT] and Poly[dG].Poly[dC], the main mechanism of interaction is weak binding, but some base preferences are elucidated. Additionally, Poly[dA].Poly[dT] can be distinguished from Poly[dA-dT] through a direct energy-transfer process between several bound PMTP molecules.