Retroviral integration into topologically-interlocked DNAs to probe the role of DNA structure and screen viral inhibitors

拓扑特异性DNA结构，如小环、超螺旋、结和链状小环和大环，在体内的许多情况下发生。除了它们在体内的存在，具有互锁单元的合成分子在几十年前在大分子化学中实现，并且是结构DNA纳米技术中当前感兴趣的主题。由于这些微环和互锁DNA的环状性质，它们的结构和拓扑结构类似于核小体DNA。因此，具有和不具有互锁结构的DNA微环是探测DNA和DNA-蛋白质相互作用的拓扑特征的有吸引力的靶标。在这项研究中，我们的目的是设计和制备自由和拓扑连锁形式的DNA微环。这些微环在大小和结构上模仿核小体DNA。此外，我们设计了一个框架状的DNA折纸纳米结构，并纳入拓扑联锁轮烷和索烃。在我们的研究中，我们注意到这些微环/互锁结构以及DNA折纸框架在特定应用条件下相对不稳定。因此，在研究DNA-蛋白质相互作用和药物筛选之前，有必要稳定这些结构。我们花了相当长的时间来开发这些DNA结构的稳定化方法，并最终获得了用于DNA-蛋白质相互作用和药物筛选的稳定底物。

Topology-specific DNA structures, such as small loops, supercoils, knots, and catenated mini and maxicircles, occur in numerous instances in vivo. Besides their presence in vivo, synthetic molecules with interlocked units were achieved in macromolecular chemistry decades ago and are the current topic of interest in structural DNA nanotechnology. Due to the circular nature of these minicircles and interlocked DNAs, their structure and topology resemble nucleosomal DNA. Therefore, DNA minicircles with and without interlocked structures are attractive targets to probe the topological features of DNA and DNA-protein interactions. In this study, we aimed to design and prepare the DNA minicircles in free and topologically interlocked forms. These minicircles mimic nucleosomal DNA in terms of size and structure. Also, we have designed a frame-shaped DNA origami nanostructure and incorporated the topologically interlocked rotaxanes and catenanes. During our study, we noticed that these minicircles/interlocked structures and also the DNA origami frame are relatively unstable under application-specific conditions. Thus, before the investigation of the DNA-protein interactions and drug screening, it was necessary to stabilize these structures. We spent a reasonable amount of time in developing the stabilization methods for these DNA structures, and finally achieved stable substrates for the DNA-protein interactions and drug screening.