Recognition of UV-clamaged DNA by antinoglycoside antibiotics

预期与168 rRNA的A位点结合的氨基糖苷类抗生素也将与含有（6-4）光产物的DNA结合，因为这两种核酸的结构彼此相似。利用表面等离子体共振技术分析了11种氨基糖苷类化合物与DNA的结合特性。新霉素，巴龙霉素，安普霉素获得相对较小的解离常数，但损坏和未损坏的双链体之间的差异没有观察到。在该项目开始时，kanarmydn A显示出对含有光产物的双链体的选择性，但详细分析表明，这是由于当时用于SPR测量的14-碱基对双链体的解离。这种药物对单链DNA的亲和力略高于双链DNA。由于DNA和RNA之间的结构差异可能导致阴性结果，我们测试了识别并切割凸起DNA的新卡拉司他丁，其具有与含有（6-4）光产物的DNA几乎相同的结构，但未观察到损伤特异性切割。然后，我们测试了三种胺，它们预计会与（6-4）光产物中线性排列的三个氢键受体相互作用，以寻找直接识别这种病变的化学结构的分子，但它们都没有显示出结合。在另一项研究中，我们发现（6-4）光产物中存在分子内氢键，这种氢键干扰配体结合。我们还详细分析了偏端霉素A与受损DNA的结合，这在以前已经发现，并揭示了这种化合物识别病变部位碱基对的化学结构，而不是受损DNA的结构特性，并且（6-4）光产物意外地满足了偏端霉素A结合所需的条件。

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.