Recognition of UV-clamaged DNA by antinoglycoside antibiotics

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It was expected that aminoglycoside antibiotics, which bind to the A-site of 168 rRNA, would also bind to DNA containing the (6-4) photoproduct because the structures of these two nucleic acids are similar to each other. We analyzed DNA binding properties of eleven aminoglycoside by measuring the surface plasmon resonance (SPR). Relatively small dissociation constants were obtained for neomycin, paromomycin, and apramycin, but the difference between damaged and undamaged duplexes was not observed. At the beginning of this project, kanarmydn A showed a selectivity for the photoproduct-containing duplex, but detailed analysis revealed that it was due to the dissociation of the 14-base-pair duplex, which was used for the SPR measurements at that time. This drug had a slightly higher affinity for single-stranded DNA than for the double-stranded one. Since the structural difference between DNA and RNA might cause the negative results, we tested neocaranostatin that recognizes and cleaves bulged DNA, which has a structure almost the same as that of the (6-4) photoproduct-containing DNA, but lesion-specific cleavage was not observed. Then, we tested three amines, which were expected to interact with the three hydrogen-bond acceptors arranged linearly in the (6-4) photoproduct, to search for a molecule that directly recognizes the chemical structure of this lesion, but none of them showed binding. We have discovered an intramolecular hydrogen bond within the (6-4) photoproduct in another study, and this hydrogen bond interferes with the ligand binding. We also analyzed the binding of distamycin A to damaged DNA, which had been found before, in detail, and revealed that this compound recognized the chemical structure of the base pair at the lesion site, not the structural properties of the damaged DNA, and that the (6-4) photoproduct accidentally fulfilled the conditions required for the distamycin A binding.