Yonsei University, University College, Incheon 21983, South Korea.
Department of Mathematics, University of Iowa, Iowa City 52242, USA
Biol Open. 2020 Apr 3;9(4):bio048603. doi: 10.1242/bio.048603.
An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the knotted product(s). We develop the mathematics needed to analyze the results and apply these results to model the topology of DNA bound by 13S condensin and by the condensin MukB.
一种名为差异拓扑学的实验技术与纠结分析的数学方法相结合，已被用于揭示 Mu 转座子结合的 DNA 的结构。然而，差异拓扑学实验可能会比较困难和耗时。我们讨论了一种大大简化该实验技术的改进方法。这个简单的实验涉及使用拓扑异构酶来捕获由蛋白质复合物结合的 DNA 交叉，并运行凝胶电泳来确定扭结产物的交叉数。我们开发了分析结果所需的数学方法，并将这些结果应用于分析由 13S 凝聚素和凝聚素 MukB 结合的 DNA 的拓扑结构。
