Effect of chromophore-charge distance on the energy transfer properties of water-soluble conjugated oligomers

The synthesis of 1,4-bis(9,9'-bis(3-(NNN-trimethylammonium)-propyl)-2'-fluorenyl)benzene tetrabromide (C-3), 1,4-bis(9,9'-bis(4-(N, N, N-trimethylammonium)-butyl) -2'-fluorenyl)benzene tetrabromide (C-4), 1,4-bis(9,9'-bis(6-(N, N, N-trimethylammonium)-hexyl)-2'-fluorenyl) benzene tetrabromide (C-6), and 1,4bis(9,9'-bis(8-(N,N,N-trimethylammonium)-octyl)-2'-fluorenyl)benzene tetrabromide (C-8) is reported. Fluorescence energy transfer experiments between C-3-C-8 and the acceptors pentasodium 1,4-bis(4'(2,4-bis(butoxysulfonate)-styryl)styryl)-2-(butoxysulfonate)-5-methoxybenzene (3), fluorescein labeled single-stranded DNA and fluorescein labeled double-stranded DNA in water, buffer, and methanol reveal the importance of hydrophobic and electrostatic forces in determining chromophore-chromophore close proximity. In water, the oligomers with longer side chain length show better energy transfer, as well as higher Stern-Volmer quenching constants (K-sv), largely due to a stronger hydrophobic attraction between the optically active components. In methanol, the differences in energy transfer are leveled, and the oligomers with shorter side chain lengths show higher K-sv values. Compounds C-3, C-4, C-6, and C-8 were also used to dissect the different contributors to DNA hybridization assays based on cationic conjugated polymers.