Structural diversity of supercoiled DNA.
Structural diversity of supercoiled DNA.
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DOI：
10.1038/ncomms9440
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发表时间：
2015-10-12
影响因子：
16.6
通讯作者：
Zechiedrich L
中科院分区：
文献类型：
--
作者：
Irobalieva RN;Fogg JM;Catanese DJ Jr;Sutthibutpong T;Chen M;Barker AK;Ludtke SJ;Harris SA;Schmid MF;Chiu W;Zechiedrich L
通过调节遗传密码的访问，DNA超螺旋强烈影响DNA代谢。然而，尽管超螺旋DNA很重要，但关于它的许多信息（特别是正超螺旋DNA）仍然是未知的。在这里，我们使用电子冷冻断层扫描与生化分析，以探讨个别纯化的DNA微环拓扑异构体的结构与定义程度的超螺旋。我们的研究结果表明，每个拓扑异构体，负或正，采用了独特的和令人惊讶的广泛分布的三维构象。此外，我们发现惊人的差异，拓扑异构体如何处理扭转应力。随着负超螺旋的增加，碱基的暴露也越来越多。除了一个尖锐的超螺旋阈值，我们还检测到暴露的碱基在正超螺旋DNA。分子动力学模拟独立地证实了构象的异质性，并提供原子洞察超螺旋DNA的灵活性。我们的综合方法揭示了DNA的三维结构，这些结构对其功能至关重要。 DNA超螺旋强烈影响其代谢。通过电子冷冻断层扫描，生化分析和分子动力学模拟，在这里，作者表明，超螺旋DNA微环采用独特的和广泛的三维构象分布，许多与中断的碱基对。
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. DNA supercoiling strongly affects its metabolism. By electron cryo-tomography, biochemical assays and molecular dynamics simulations, here the authors show that supercoiled DNA minicircles adopt unique and wide distributions of three-dimensional conformations, many with disrupted base pairs.