Orientation preferences of hairpin pyrrole-imidazole polyamides toward mCGG site
Orientation preferences of hairpin pyrrole-imidazole polyamides toward mCGG site
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发夹吡咯-咪唑聚酰胺对 mCGG 位点的取向偏好
DOI：
10.1016/j.bmc.2019.04.006
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发表时间：
2019
影响因子：
3.5
通讯作者：
Hiroshi Sugiyama
中科院分区：
文献类型：
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作者：
Shinsuke Sato;Sefan Asamitsu;Toshikazu Bando;Hiroshi Sugiyama
发夹吡咯-咪唑 (Py-Im) 聚酰胺是有前途的中等大小分子，可以序列特异性地结合到 B 型 DNA 的小沟上。在这里，我们合成了一系列发夹 Py-Im 聚酰胺，并探索了它们与 CGG 靶序列甲基化 DNA 的结合亲和力和方向偏好。热变性测定表明，预计能够在正向识别 mCGG 的五种发夹 Py-Im 聚酰胺，在反向方向与非靶标 DNA GGmC 结合。因此，我们设计了五种可以反向识别 mCGG 的 Py-Im 聚酰胺。我们发现两个含有 Im/β 对的 Py-Im 聚酰胺优先以相反方向结合 tomCGG。反向结合的 Py-Im 聚酰胺成功抑制了 TET1 与甲基化 DNA 的结合。总而言之，这项研究说明了为目标序列 mCGG 设计反向结合 Py-Im 聚酰胺的重要性，这为 Py-Im 聚酰胺可用于难以通过 CG 序列获取 DNA 铺平了道路。
Hairpin pyrrole–imidazole (Py-Im) polyamides are promising medium-sized molecules that bind sequence-specifically to the minor groove of B-form DNA. Here, we synthesized a series of hairpin Py-Im polyamides and explored their binding affinities and orientation preferences to methylated DNA with themCGG target sequence. Thermal denaturation assays revealed that the five hairpin Py-Im polyamides, which were anticipated to recognizemCGG in a forward orientation, bind to nontarget DNA, GGmC, in a reverse orientation. Therefore, we designed five Py-Im polyamides that could recognizemCGG in a reverse orientation. We found that the two Py-Im polyamides containing Im/β pairs preferentially bound tomCGG in a reverse orientation. The reverse binding Py-Im polyamide successfully inhibited TET1 binding on the methylated DNA. Taken together, this study illustrated the importance of designing reverse binding Py-Im polyamides for the target sequence,mCGG, which paved the way for Py-Im polyamides that can be used with otherwise difficult to access DNA with CG sequences.