SELECTIVE BINDING OF A MACROCYCLIC BISACRIDINE TO DNA HAIRPINS

The reversible hairpin to coil transition of d(GCGAAACGC), named sA(3), was investigated by melting experiments. This oligomer also adopts a bulged duplex structure whose formation from the hairpin is a slow process. The binding of the compound 1, a macrocycle containing two acridine subunits linked by two diethylenetriamine arms, to the hairpin form was studied using absorption and fluorescence spectroscopy as well as gel filtration. 1 forms two complexes with sA(3) hairpin. The first complex presents a 1/1 1/sA(3) stoichiometry, and the binding site of 1 was attributed to the hairpin loop by fluorescence spectroscopy. A similar binding site can be confirmed by the comparison of sA(3) and related hairpins, sA(5), sT(5) and sTAR. The binding constant of 1 for this site is high: K= (4.5 +/- 0.5) x 107 M(-1). The second complex presents a 2/1 stoichiometry. The comparison of the hairpin melting temperature in the absence and in the presence of 1 shows a 25 degrees C stabilization of the hairpin structure by the macrocyclic molecule 1. In contrast, the reference compound 2, a monomeric acridine substituted by two propylaminomethyl groups, does not stabilize the hairpin. The results emphasize the selectivity of 1 for the hairpin compared to both double helices and single stranded oligomers arising from its macrocyclic structure. They agree with the initial hypothesis that cage compounds of bicyclointercaland type would bind preferentially to single-stranded than to double-helical nucleic acids domains.