Application of a degenerate consensus sequence to quantify recognition sites by vertebrate DNA topoisomerase II.
Application of a degenerate consensus sequence to quantify recognition sites by vertebrate DNA topoisomerase II.
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应用简并共有序列来量化脊椎动物 DNA 拓扑异构酶 II 的识别位点。
DOI：
10.1002/jmr.300020204
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发表时间：
1989
期刊：
影响因子：
--
通讯作者：
Muller,MT
中科院分区：
文献类型：
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作者：
Spitzner,JR;Muller,MT
脊椎动物拓扑异构酶 II 切割 DNA 的共有序列已被推导出来（Spitzner, J. R. 和 Muller, M. T. (1988)Nucleic Acid. Res.16, 5533–5556）。对 65 个拓扑异构酶 II 位点的独立样本（在没有拓扑异构酶 II 抑制剂的情况下获得）进行了分析，发现其与共有序列以及抗肿瘤药物 4'-(9-吖啶基氨基)-甲磺酰马尼西德 (m-AMSA) 存在下确定的酶位点相匹配。正如最初所描述的，共有序列的常规应用提供了位置预测的准确性，但不能提供拓扑异构酶 II 切割频率的准确性。在本报告中，我们描述了一种定量区分位点和非位点的新方法，称为“矩阵平均值”方法（位点与原始一致序列推导的碱基比例矩阵的平均匹配）。此外，我们还得出了第二种方法，称为“独特评分”模型，该模型可以预测切割位点拓扑异构酶 II 活性的频率。在独特的评分方法中，检查位点的两条 DNA 链以确定与潜在位点的至少一条链匹配的共有位置的总数。根据 65 个拓扑异构酶 II 位点的新数据库，对切割进行相对切割强度评分。线性回归分析显示独特得分和切割强度之间存在显着相关性（p < 0.01）。该研究的扩展表明，独特的评分模型可以使用相同的共有序列准确且定量地预测 m-AMSA 不存在或存在的情况下的拓扑异构酶 II 位点。
A consensus sequence has been derived for vertebrate topoisomerase II cleavage of DNA (Spitzner, J. R. and Muller, M. T. (1988)Nucleic Acid. Res.16, 5533–5556). An independent sample of 65 topoisomerase II sites (obtained in the absence of topoisomerase II inhibitors) was analyzed and found to match the consensus sequence as well as enzyme sites determined in the presence of the anti‐tumor drug 4′‐(9‐acridinyl‐amino)‐methanesulfon‐manisidide (m‐AMSA). As originally described, conventional application of the consensus sequence afforded accuracy in the prediction of the locations but not the frequencies of topoisomerase II cleavages. In the present report, we describe a new method which quantitatively discriminates sites from nonsites, called the ‘matrix mean’ method (the mean match of a site to the matrix of base proportions from the original consensus sequence derivation). Furthermore, we derived a second method, called the ‘unique score’ model, which predicts frequency of topoisomerase II activity at a cleavage site. In the unique score method both DNA strands of a site are examined to determine the total number of the consensus positions that match on at least one strand of a potential site. From the new data base of 65 topoisomerase II sites, cleavages were scored for relative cleavage strength. Linear regression analysis showed a significant (p< 0.01) correlation between the unique score and cleavage strength. The study was extended to show that the unique score model accurately and quantitatively predicts topoisomerase II sites either in the absence or presence ofm‐AMSA using the same consensus sequence.