Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
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DOI：
10.1038/s41467-020-20020-7
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发表时间：
2020-12-04
影响因子：
16.6
通讯作者：
Dietz H
中科院分区：
文献类型：
--
作者：
Kube M;Kohler F;Feigl E;Nagel-Yüksel B;Willner EM;Funke JJ;Gerling T;Stömmer P;Honemann MN;Martin TG;Scheres SHW;Dietz H
DNA纳米技术的方法使人们能够合理地设计定制的形状，这些形状可以从DNA分子的集合中自组装在溶液中。DNA折纸，其中一个长模板DNA单链折叠由许多短DNA寡核苷酸，可以用来制造对象包含数百个独特的DNA链和数千个碱基对，因此在原则上提供了许多自由度的建模复杂的物体定义的3D形状和大小。在这里，我们用基于冷冻电镜的方法解决了DNA对象在溶液中精确结构验证的问题。通过考虑结构波动，与以前的工作相比，我们可以更详细地确定结构。为了解释实验低温电镜图，我们提出了基于分子动力学的方法，以半自动化的方式建立伪原子模型。在其他特征中，我们的数据允许识别细节，如螺旋槽，单链与双链交叉，主干磷酸盐位置和单链断裂。获得这种更高层次的细节是向前迈出的一步，现在允许设计师使用碱基对级别的干预来检查和改进他们的设计。DNA折纸的精密设计需要精密验证。在这里，作者开发了冷冻电镜方法来获得高分辨率的结构数据，并以半自动化的方式构建伪原子模型，允许迭代的纳米器件检查和改进。
The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions. Precision design of DNA origami needs precision validation. Here, the authors developed cryo-EM methods for obtaining high resolution structural data and for constructing pseudo-atomic models in a semi-automated fashion, allowing for iterative nanodevice inspection and refinement.
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影响因子：
14.9
作者：
Kim DN;Kilchherr F;Dietz H;Bathe M
通讯作者：
Bathe M
影响因子：
15
作者：
Ke, Yonggang;Douglas, Shawn M.;Liu, Minghui;Sharma, Jaswinder;Cheng, Anchi;Leung, Albert;Liu, Yan;Shih, William M.;Yan, Hao
通讯作者：
Yan, Hao
影响因子：
14.9
作者：
Douglas SM;Marblestone AH;Teerapittayanon S;Vazquez A;Church GM;Shih WM
通讯作者：
Shih WM
影响因子：
56.9
作者：
Acuna, G. P.;Moeller, F. M.;Tinnefeld, P.
通讯作者：
Tinnefeld, P.
影响因子：
64.8
作者：
Benson, Erik;Mohammed, Abdulmelik;Hogberg, Bjorn
通讯作者：
Hogberg, Bjorn