Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.
Physik Department, Walter Schottky Institute, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany.
Nano Lett. 2016 Aug 10;16(8):4871-9. doi: 10.1021/acs.nanolett.6b01338. Epub 2016 Jul 27.
Self-assembled DNA origami nanostructures enable the creation of precisely defined shapes at the molecular scale. Dynamic DNA devices that are capable of switching between defined conformations could afford completely novel functionalities for diagnostic, therapeutic, or engineering applications. Developing such objects benefits strongly from experimental feedback about conformational changes and 3D structures, ideally in solution, free of potential biases from surface attachment or labeling. Here, we demonstrate that small-angle X-ray scattering (SAXS) can quantitatively resolve the conformational changes of a DNA origami two-state switch device as a function of the ionic strength of the solution. In addition, we show how SAXS data allow for refinement of the predicted idealized three-dimensional structure of the DNA object using a normal mode approach based on an elastic network model. The results reveal deviations from the idealized design geometries that are otherwise difficult to resolve. Our results establish SAXS as a powerful tool to investigate conformational changes and solution structures of DNA origami and we anticipate our methodology to be broadly applicable to increasingly complex DNA and RNA devices.
自组装 DNA 折纸纳米结构能够在分子尺度上创建精确定义的形状。能够在定义的构象之间切换的动态 DNA 器件可为诊断、治疗或工程应用提供全新的功能。开发此类对象强烈受益于关于构象变化和 3D 结构的实验反馈，理想情况下是在溶液中，没有来自表面附着或标记的潜在偏差。在这里，我们证明小角 X 射线散射 (SAXS) 可以定量解析 DNA 折纸双稳态开关器件的构象变化，作为溶液离子强度的函数。此外，我们展示了 SAXS 数据如何允许使用基于弹性网络模型的正常模式方法来细化 DNA 物体的预测理想三维结构。结果揭示了与理想设计几何形状的偏差，否则难以解决。我们的结果确立了 SAXS 作为研究 DNA 折纸构象变化和溶液结构的强大工具，我们预计我们的方法将广泛适用于越来越复杂的 DNA 和 RNA 器件。
