Smith C K, Brannigan J A, Moore M H
Department of Chemistry, University of York, Heslington, England.
J Mol Biol. 1996 Oct 25;263(2):237-58. doi: 10.1006/jmbi.1996.0572.
As part of an investigation into the sequence selectivity of the nogalamycin-DNA interaction, the 1.58 A structure of nogalamycin complexed with d5'(TGTACA)2 has been determined by single-crystal X-ray analysis. The complex crystallised in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions a = 26.3 A, b = 52.0 A and c = 67.1 A, incorporating two B-DNA duplexes and four nogalamycin molecules in the asymmetric unit. The final refined structure included 97 water molecules, one spermine molecule, two acetate ions and one sodium ion, yielding an overall R factor of 19.2% (calculated using all 12,358 reflections in the resolution range 10.7 to 1.6 A) and an Rtree of 23.7% (using 1229 test reflections). The d5'(TGTACA)2 sequence was designed to include the d5'(TpG) pyrimidine-purine base step that has been ascertained as a preferential intercalation site. The complexes in the asymmetric unit are globally similar; one nogalamycin molecule intercalates between each d5'(TpG) step in each duplex. The DNA of each complex exists as a distorted B-DNA duplex displaying some Z-DNA character in the form of C3' endo sugars at some residues. Structural comparisons between the d5'(TGTACA)2-nogalamycin2 complex and the complexes of this drug with the sequences d5'(TGATCA)2 and d5'(5MeCGT(pS)A5MeCG)2 highlight differences in binding interactions between nogalamycin and these various triplet DNA binding sites, with regards to the stability of drug intercalation, which in turn is correlated to effective levels of cytotoxicity towards tumour cells. The number of both direct and water-mediated hydrogen bonds and van der Waal's interactions between substituents of nogalamycin and the d5'(TGTACA)2 and d5'(5MeCGT(pS)A5MeCG)2 sequences are significantly greater than those made with the d5'(TGATCA)2 sequence, suggesting that the central d5'(TpA) in the former confers additional stability to the complex once the drug has bound.
作为对诺加霉素与DNA相互作用序列选择性研究的一部分，通过单晶X射线分析确定了诺加霉素与d5'(TGTACA)2复合的1.58 Å结构。该复合物在正交空间群P2(1)2(1)2(1)中结晶，晶胞尺寸a = 26.3 Å，b = 52.0 Å，c = 67.1 Å，不对称单元中包含两条B-DNA双链和四个诺加霉素分子。最终精修结构包括97个水分子、一个精胺分子、两个乙酸根离子和一个钠离子，总体R因子为19.2%（使用分辨率范围为10.7至1.6 Å的所有12358个反射计算），Rtree为23.7%（使用1229个测试反射）。d5'(TGTACA)2序列设计为包含已确定为优先嵌入位点的d5'(TpG)嘧啶-嘌呤碱基步。不对称单元中的复合物在整体上相似；每个双链中的每个d5'(TpG)步之间插入一个诺加霉素分子。每个复合物的DNA以扭曲的B-DNA双链形式存在，在某些残基处以C3'内型糖的形式显示出一些Z-DNA特征。d5'(TGTACA)2-诺加霉素2复合物与该药物与序列d5'(TGATCA)2和d5'(5MeCGT(pS)A5MeCG)2的复合物之间的结构比较突出了诺加霉素与这些不同三联体DNA结合位点之间结合相互作用的差异，涉及药物嵌入的稳定性，这反过来又与对肿瘤细胞的细胞毒性有效水平相关。诺加霉素取代基与d5'(TGTACA)2和d5'(5MeCGT(pS)A5MeCG)2序列之间直接和水介导的氢键以及范德华相互作用的数量明显多于与d5'(TGATCA)2序列的相互作用，这表明一旦药物结合，前者中的中心d5'(TpA)赋予复合物额外的稳定性。
