By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

中文翻译：

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超螺旋DNA的结构多样性。

通过调节对遗传密码的访问，DNA超螺旋强烈影响DNA代谢。尽管它很重要，但是关于超螺旋DNA（尤其是正超螺旋DNA）的许多知识仍然未知。在这里，我们将电子冷冻断层扫描与生化分析一起使用，以研究具有一定超螺旋度的单个纯化的DNA小环拓扑异构体的结构。我们的结果表明，每个拓扑异构体，无论是阴性的还是阳性的，都采用独特且令人惊讶的三维构象分布。此外，我们发现拓扑异构体在处理扭转应力方面的显着差异。随着负超卷的增加，基础越来越暴露。除了尖锐的超螺旋阈值外，我们还可以检测正超螺旋DNA中暴露的碱基。分子动力学模拟独立地确认构象异质性，并提供超螺旋DNA灵活性的原子学见解。我们的综合方法揭示了DNA的三维结构对其功能至关重要。