Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms

The binding of a macrocyclic bisacridine and an antitumor intercalator amet antrone to DNA has been studied. We carried out X-ray diffraction analyses of the complexes between both intercalators and CGTACG. We have determined the crystal structure, by the multiple wavelength anomalous diffraction (MA D) method, of bisacridine complexed with CCTA[br(5)C]G at 1.8 Angstrom reso lution. The refined native crystal structure at 1.1 Angstrom resolution (sp ace group C222, a = 29.58 Angstrom, b = 59.04 Angstrom, c = 40.22 Angstrom, and R-factor = 0.163) revealed that only one acridine of the bisacridine d rug binds at the C5pG6 step of the DNA, with the other acridine plus both l inkers completely disordered. Surprisingly, both terminal G.C base pairs ar e unraveled. The C1 nucleotide is disordered, and the G2 base is bridged to its own phosphate P2 through a hydrated Co2+ ion. G12 is swung toward the minor groove with its base stacked over the backbone. The C7 nucleotide is flipped away from the duplex part and base paired to a 2-fold symmetry-rela ted G6*. The central four base pairs adopt the B-DNA conformation. An unusu al intercalator platform is formed by bringing four complexes together (inv olving the 222 symmetry) such that the intercalator cavity is flanked by tw o sets of G.C base pairs (i.e., C5.G8 and G6.C7*) on each side, joined toge ther by G6.G8* tertiary base pairing interactions. In the bisacridine-CGTAC G complex, the intercalation platform is intercalated with two acridines, w hereas in the ametantrone-CGTACG complex, only one ametantrone is bound. NM R titration of the bisacridine to AACGATCGTT suggests that the bisacridine prefers to bridge more than one DNA duplex by intercalating each acridine t o different duplexes. The results may be relevant in understanding binding of certain intercalators to DNA structure associated with the quadruplet he lix and Holliday junction.