Size-specific interactions between single- and double-stranded oligonucleotides and cationic water-soluble oligofluorenes

An improved synthetic approach Was developed for the synthesis of 1,4-bis[9',9'-bis(6-(N,N,N-trimethylammonium)-hexyl)fluoren-2'-yl]benzene tetrabromide (1a), 1,4-bis[9',9'.;9,9-tetra(6'-(N,N,N-trimethylammonium)-hexyl)-7',2-bisfluoren-2'-yl] benzene octabromide (1b) and 1,4-bis[9',9';9,9;9',9'''-hexakis(6-(N,N,N-trimethylammonium)-hexyl)-7',2,7,2'''-trifluoren-2'-yl] benzene dodecabromide (1c). These molecules provide a size-specific series of water-soluble oligofluorene molecules with increasing numbers of repeat units to model the interactions between cationic conjugated polymers and DNA. Fluorescence quenching and energy-transfer measurements were performed with la-c and single-stranded (ss) DNA and double-stranded (ds) DNA, with and without fluorescein (Fl). These studies show that, on a per-negative-charge basis, ssDNA quenches the emission of 1a-c more effectively than dsDNA. Furthermore, we show that the energy-transfer ratios dsDNA-Fl/ssDNA-Fl are dependent on the number of repeat units in 1a-c.