Schaus Thomas E, Woo Sungwook, Xuan Feng, Chen Xi, Yin Peng
Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA, 02115, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
Nat Commun. 2017 Sep 25;8(1):696. doi: 10.1038/s41467-017-00542-3.
Analysis of the spatial arrangement of molecular features enables the engineering of synthetic nanostructures and the understanding of natural ones. The ability to acquire a comprehensive set of pairwise proximities between components would satisfy an increasing interest in investigating individual macromolecules and their interactions, but current biochemical techniques detect only a single proximity partner per probe. Here, we present a biochemical DNA nanoscopy method that records nanostructure features in situ and in detail for later readout. Based on a conceptually novel auto-cycling proximity recording (APR) mechanism, it continuously and repeatedly produces proximity records of any nearby pairs of DNA-barcoded probes, at physiological temperature, without altering the probes themselves. We demonstrate the production of dozens of records per probe, decode the spatial arrangements of 7 unique probes in a homogeneous sample, and repeatedly sample the same probes in different states.The spatial organisation of nanostructures is fundamental to their function. Here, the authors develop a non-destructive, proximity-based method to record extensive spatial organization information in DNA molecules for later readout.
对分子特征空间排列的分析有助于合成纳米结构的工程设计以及对天然纳米结构的理解。获取组件之间全面的成对邻近信息的能力将满足人们对研究单个大分子及其相互作用日益增长的兴趣，但目前的生化技术每个探针仅能检测到一个邻近伙伴。在此，我们提出一种生化DNA纳米显微镜方法，该方法可原位详细记录纳米结构特征以供后续读取。基于一种概念新颖的自动循环邻近记录（APR）机制，它在生理温度下连续且反复地生成任何附近的DNA条形码探针配对的邻近记录，而不会改变探针本身。我们展示了每个探针可产生数十条记录，解码了均匀样品中7种独特探针的空间排列，并在不同状态下对相同探针进行反复采样。纳米结构的空间组织对其功能至关重要。在此，作者开发了一种基于邻近性的非破坏性方法，用于记录DNA分子中广泛的空间组织信息以供后续读取。
