Fluorescence Detection and Discrimination of ss- and ds-DNA with a Water Soluble Oligopyrene Derivative

Abstract: A novel water-soluble cationic conjugated oligopyrene derivative, oligo(N¹,N¹,N¹,N⁴,N⁴,N⁴-hexamethyl-2-(4-(pyren-1-yl) butane-1,4-diaminium bromide) (OHPBDB), was synthesized by a combination of chemical and electrochemical synthesis techniques. Each oligomer chain has five pyrene derivative repeating units and brings 10 positive charges. OHPBDB showed high and rapid fluorescence quenching in aqueous media upon addition of trace amounts of single-stranded (ss) and double-stranded (ds) DNA. The Stern-Volmer constants for ss- and ds-DNA were measured to be as high as 1.3 × 10⁸ mol^-1·L and 1.2 × 10⁸ mol^-1·L, respectively. On the other hand, distinct fluorescence enhancement of OHPBDB upon addition of large amount of ss-DNA or ds-DNA was observed. Furthermore, ss-DNA showed much stronger fluorescence enhancement than that of ds-DNA, thus yielding a clear and simple signal useful for the discrimination between ss- and ds-DNA in aqueous media.