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 pr ocess. The binding of the compound 1, a macrocycle containing two acri dine subunits linked by two diethylenetriamine arms, to the hairpin fo rm 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 r elated 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 pr esents a 2/1 stoichiometry. The comparison of the hairpin melting temp erature in the absence and in the presence of 1 shows a 25 degrees C s tabilization of the hairpin structure by the macrocyclic molecule 1. I n 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 bot h double helices and single stranded oligomers arising from its macroc yclic structure. They agree with the initial hypothesis that cage comp ounds of bicyclointercaland type would bind preferentially to single-s tranded than to double-helical nucleic acids domains.