Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions
Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions
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拓扑互锁小环作为 DNA 拓扑和 DNA-蛋白质相互作用的探针
DOI：
10.1002/chem.202200108
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发表时间：
2022
影响因子：
4.3
通讯作者：
Takashi Morii
中科院分区：
文献类型：
--
作者：
Arivazhagan Rajendran;Kirankumar Krishnamurthy;Seojeong Park;Eiji Nakata;Youngjoo Kwon;Takashi Morii
DNA微环存在于生物环境中，如着丝体DNA，是制造功能性纳米器件的有前途的成分。它们已被用于模拟核小体DNA的拓扑特征，并探测DNA -蛋白质相互作用，如HIV - 1和PFV整合酶，以及DNA旋切酶。在这里，我们在一个框架形状的DNA折纸中合成了拓扑互锁的小环轮烷和连环烷。这些小环长度为183 bp，由6个单独的单链dna组成，通过连接实现双联锁，并采用单链的临时碱基配对实现联锁。为了探究DNA -蛋白质的相互作用，在不同拓扑结构的DNA上进行了限制性反应，如自由线性双工或双工约束在折纸内和自由或拓扑互锁的小环。除了自由的线性双链外，所有测试的结构都能抵抗限制性消化，这表明DNA的拓扑特征，如柔韧性、曲率和凹槽方向，在DNA -蛋白质相互作用中起主要作用。
DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA‐protein interactions such as HIV‐1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically‐interlocked minicircle rotaxane and catenane inside a frame‐shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single‐stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA‐protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically‐interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA‐protein interactions.