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 1a – 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 .