Chandran Anandhakumar, Syed Junetha, Taylor Rhys D, Kashiwazaki Gengo, Sato Shinsuke, Hashiya Kaori, Bando Toshikazu, Sugiyama Hiroshi
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Nucleic Acids Res. 2016 May 19;44(9):4014-24. doi: 10.1093/nar/gkw283. Epub 2016 Apr 20.
Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.
化学工程改造的靶向特定基因组序列的小分子在药物研发研究中发挥着重要作用。吡咯-咪唑聚酰胺（PIPs）是一类能够与DNA小沟结合的分子，并且可以经过工程改造以靶向特定序列。它们的生物学效应主要依赖于其对DNA的选择性结合。然而，在染色质化基因组水平上PIPs的结合机制尚不清楚。在此，我们报告一种使用高通量测序来鉴定PIP-吲哚-seco-CBI缀合物的DNA烷基化位点的方法。对缀合物2的高通量测序分析表明，在合成寡核苷酸（无组蛋白DNA）和人类基因组（染色质化DNA环境）上具有高度相似的DNA烷基化位点。据我们所知，这是第一份通过使用高通量测序对PIP缀合物进行烷基化来鉴定全基因组DNA烷基化位点的报告。
