Synthesis of cationic conjugated polymers for use in label-free DNA microarrays

We describe the synthesis of poly[9,9'- bis(6 ''-N,N,N-trimethylammonium) hexyl) fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] (PFBT), a cationic, water-soluble conjugated polymer used in label-free DNA microarrays. This polymer was designed to have a maximum absorbance of close to 488 nm, which meets the excitation wavelength of most commercial microarray readers, and to have efficient emission in the solid state. Starting from commercially available chemicals, five steps are required to synthesize PFBT. The first step involves treatment of 2,7-dibromofluorene in 50% potassium hydroxide solution with excess 1,6-dibromohexene at 75 degrees C for 25 min to afford 2,7-dibromo-9,9-bis(6'-bromohexyl) fluorene (A). In the second step, a mixture of A, bis(pinacolato) diborane and potassium acetate in dioxane is stirred at 85 degrees C for 12 h to afford bis[9,9'- bis(6 ''-bromohexyl)-fluorenyl]-4,4,5,5-tetramethyl[1.3.2] dioxaborolane (B). The third step involves bromination of 2,1,3-benzothiadiazole using bromine in the presence of hydrogen bromide to afford 4,7- dibromo-2,1,3-benzothiadiazole (C). Suzuki cross-coupling copolymerization of B and C affords the charge-neutral precursor of PFBT. In the final step, quaternization of pendant groups using trimethylamine yields PFBT. Each step takes up to 3 days, including the time required for product purification. The overall protocol requires approximately 3 weeks.