Recognition of UV-clamaged DNA by antinoglycoside antibiotics

由于氨基糖苷类抗生素与168 rRNA的a位点结合，由于这两种核酸的结构相似，预计氨基糖苷类抗生素也会与含有（6-4）光产物的DNA结合。利用表面等离子体共振（SPR）分析了11种氨基糖苷的DNA结合特性。新霉素、帕罗霉素和阿帕霉素的解离常数相对较小，但未观察到受损和未受损双链之间的差异。在本项目开始时，kanarmydn A对含有光产物的双相具有选择性，但详细分析表明，这是由于当时用于SPR测量的14碱基对双相的解离。该药物对单链DNA的亲和力略高于对双链DNA的亲和力。由于DNA和RNA的结构差异可能导致阴性结果，我们测试了neocaranostatin，它可以识别和切割凸起的DNA，其结构与（6-4）含光产物的DNA几乎相同，但没有观察到病变特异性切割。然后，我们测试了三种胺，它们有望与（6-4）光产物中线性排列的三个氢键受体相互作用，以寻找直接识别该病变化学结构的分子，但它们都没有显示出结合。在另一项研究中，我们在（6-4）光产物中发现了分子内氢键，该氢键干扰配体结合。我们还详细分析了之前发现的distamycin A与受损DNA的结合，发现该化合物识别损伤部位碱基对的化学结构，而不是受损DNA的结构性质，并且（6-4）光产物偶然满足了distamycin 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.