Specific binding ofo-phenanthroline at a DNA structural lesion

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Abstract
DNA intercalators are found to recognize a DNA lesion as a high affinity receptor site. This lesion-specific binding is observed with one strand of a DNA double helix contains an extra, unpaired nucleotide. Our assay for binding controls for the effects of sequence with a series of oligodeoxynucleotide duplexes which are identical except for the location of the lesion, an extra cytidine. Scission of the series of oligodeoxynucleotides by the cuprous complex of ortho-phenanthroline (OP-Cu) indicates that OP-Cu binds at the lesion-specific stable intercalation site, suggesting that OP-Cu intercalates into DNA. The dispersion of OP-Cu scission sites over three residues is consistent with scission via a diffusible intermediate. The location of the scission sites, directly on the 3'' side of the lesion, is consistent with minor groove binding in B DNA.