title: Site exclusion and sequence specificity in binding of 9-aminoacridine to the deoxytetranucleotide dpApGpCpT.
abstract: The interaction of the mutagenic dye 9-aminoacridine (9AA) with the self-complementary tetranucleotide dpApGpCpT has been studied by a combination of proton NMR titrations and thermal denaturation experiments. A minimum of three complexes of well-defined stoichiometry can be demonstrated in this system. Complex I is a 1:2 9AA/tetranucleotide structure occurring in the presence of excess tetranucleotide. The dye appears to intercalate within the GpC/GpC site of a tetranucleotide duplex. Complex II is a 2:2 9AA/tetranucleotide structure, with two dyes intercalated at the ApG/CpT sites of the duplex. Complex III is a low-temperature 4:2 9AA/tetranucleotide structure containing two dye molecules stacked over the terminal A-T residues of the duplex in addition to those present in complex II. These results show that both sequence selectivity and site exclusion can occur in this model system.
mesh_terms: D000609:Aminoacridines / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D007364:Intercalating Agents; D009682:Magnetic Resonance Spectroscopy; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*; D009841:Oligonucleotides / Q000378:metabolism*; D010710:Phosphates
chemical_list: D000609:Aminoacridines; D007364:Intercalating Agents; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D010710:Phosphates