Programming DNA origami assembly for shape-resolved nanomechanical imaging labels
Programming DNA origami assembly for shape-resolved nanomechanical imaging labels
复制标题
DOI：
10.1038/s41596-018-0004-y
复制
发表时间：
2018-07-01
期刊：
影响因子：
14.8
通讯作者：
Fan, Chunhai
中科院分区：
文献类型：
--
作者：
Chao, Jie;Zhang, Honglu;Fan, Chunhai
基于原子力显微镜（AFM）的纳米机械成像提供了一种高分辨率的方法，用于成像生物分子与纳米分辨率。然而，缺乏适当的纳米机械标签对生物应用造成了限制。在这里，我们描述了如何通过利用自组装DNA折纸技术生成一组形状分辨的纳米机械标签。通过设计可以与折纸形状和靶DNA两者杂交的“介体”链，这些折纸形状ID可以用于以高效率和高通量位点特异性标记基因组DNA。当DNA折纸形状ID用于标记包含两个单核苷酸多态性（SNP）的靶序列时，这种方法能够在AFM成像下区分仅由30个核碱基（类似于10 nm）分开的相邻标记位点。该分辨率是使用超分辨率成像的基于成像的基因分型可以获得的分辨率的三倍改进。我们进一步展示了如何使用折纸形状ID对患者疾病相关基因中的SNP进行高分辨率基因分型。整个协议需要类似于2D来完成。
Atomic force microscopy (AFM)-based nanomechanical imaging provides a high-resolution approach for imaging biomolecules with nanometer resolution. Nevertheless, the lack of appropriate nanomechanical labels poses a limit to biological applications. Here, we describe how to generate a set of shape-resolved nanomechanical labels by exploiting self-assembled DNA origami technology. By designing 'mediator' strands that can hybridize with both the origami shapes and the target DNA, these origami shape IDs can be used to site-specifically label genomic DNA with high efficiency and high throughput. When DNA origami shape IDs are used to label target sequences containing two single-nucleotide polymorphisms (SNPs), this approach is capable of differentiating adjacent labeling sites separated by only 30 nucleobases (similar to 10 nm) under AFM imaging. This resolution is a threefold improvement of that which can be obtained with imaging-based genotyping using super-resolution imaging. We further demonstrate how to use origami shape IDs for high-resolution genotyping of SNPs in disease-associated genes in patients. The entire protocol takes similar to 2 d to complete.