Structure-specific binding and photosensitized cleavage of branched DNA three-way junction complexes by cationic...

The interactions of cationic porphyrins with DNA oligonucleotides that form branched, three-way junction complexes (TWJ) were investigated using native gel electrophoresis, absorption spectroscopy and photochemical probing using DNA sequencing techniques. Meso-tetra(para-N- trimethylaniliniumyl)porphine (TMAP), meso-tetra(4-N-methylpyridiniumyl)porphine (T4MPyP) and meso-tetra(3-N-methylpyridiniumyl)porphine(T3MPyP) were found to bind more tightly to DNA TWJ than to DNA duplexes. The binding to the junction DNA persists at high ionic strength, conditions that greatly decrease porphyrin binding affinity to duplex DNA. THe TWJ DNA binding sites of TMAP and T4MPyP were localized to the junction region based on the observation of site- and structure-specific, porphyrin-sensitized photodamage to guanosine residues flanking the junction region.