Yu L, Salzberg A A, Dedon P C
Division of Toxicology, Massachusetts Institute of Technology, Cambridge 02139, USA.
Bioorg Med Chem. 1995 Jun;3(6):729-41. doi: 10.1016/0968-0896(95)00054-k.
Using the Xenopus borealis 5S RNA gene, we have identified several new features of the interaction of calicheamicin (CAL), an enediyne antitumor agent, with nucleosomal and naked DNA targets. CAL-mediated DNA damage was generally reduced by incorporation of the DNA into a nucleosome. However, in one instance, the frequency of DNA damage was enhanced in the nucleosome compared to naked DNA. This increase in CAL damage may result from bending-induced changes in the target site, while the association of histone proteins with DNA in the nucleosome may generally reduce the affinity of CAL for its targets by imposing dynamic constraints on the DNA, by altering target structure, or by steric hindrance. One implication of these observations is that new structural features created by incorporation of DNA into chromatin may produce 'hot spots' for CAL-mediated DNA damage not apparent in naked DNA studies. In a second set of experiments, the orientation of CAL at damage sites in naked 5S rDNA was determined. The results suggest that minor groove width per se is not a major determinant of CAL target selection. Our studies support the generality of an oligopurine recognition element, with the additional requirement that the purine tract is interrupted at the 3'-end by a pyrimidine(s). To account for these observations, we propose a model in which CAL recognizes the unique structural and dynamic features associated with the 3'-end of an oligopurine tract. Finally, we conclude that the dyad axis of pseudosymmetry of the 5S rRNA gene nucleosome cannot be determined with any degree of certainty. This places significant limitations on the interpretation of results from the study of drug-DNA interactions with reconstituted nucleosomes.
利用北方爪蟾5S RNA基因，我们已经确定了烯二炔抗肿瘤药物刺孢霉素（CAL）与核小体及裸露DNA靶点相互作用的几个新特征。将DNA整合到核小体中通常会降低CAL介导的DNA损伤。然而，在一个实例中，与裸露DNA相比，核小体中DNA损伤的频率有所增加。CAL损伤的这种增加可能是由于靶点部位弯曲诱导的变化导致的，而组蛋白与核小体中DNA的结合通常可能会通过对DNA施加动态限制、改变靶点结构或产生空间位阻来降低CAL对其靶点的亲和力。这些观察结果的一个含义是，将DNA整合到染色质中产生的新结构特征可能会产生CAL介导的DNA损伤“热点”，而在裸露DNA研究中并不明显。在第二组实验中，确定了CAL在裸露5S rDNA损伤位点的取向。结果表明，小沟宽度本身不是CAL靶点选择的主要决定因素。我们的研究支持寡嘌呤识别元件的普遍性，另外还要求嘌呤序列在3'端被一个或多个嘧啶打断。为了解释这些观察结果，我们提出了一个模型，其中CAL识别与寡嘌呤序列3'端相关的独特结构和动态特征。最后，我们得出结论，5S rRNA基因核小体的假对称二聚体轴无法确定。这对药物与重组核小体DNA相互作用研究结果的解释造成了重大限制。
