Design of DNA Origami Machines and Mechanisms

该研究奖为利用DNA折纸纳米技术开发纳米级机器和机械的系统设计框架提供资金。DNA折纸可以通过分子自组装来构建具有前所未有的几何复杂性的二维和三维纳米形状。大多数DNA折纸研究集中在静态2D或3D结构的组装上。这项工作的目标是将具有定向运动的功能动态部件整合到DNA折纸设计工具箱中。为了实现这一目标，将实施运动学方法来设计DNA折纸机器和机构，这些机器和机构由连杆和关节组成，类似于宏观机器。将设计和制造一系列不同的DNA折纸连接和关节，并将通过实验和分子模拟来表征它们的机械性能。这些连杆和关节将在进行原则证明研究的原型机构设计中使用。一种名为投影运动学的新理论将被开发出来，以根据二维电子显微镜快照来评估这些原型机构的三维运动。为了促进DNA折纸机的未来应用，将开发一个计算机辅助设计和模拟程序，以促进概念性机构设计，并自动整合先前开发的部件目录中的DNA折纸链接和关节。如果成功，这项研究将极大地推动DNA纳米技术、纳米设计和纳米机器人领域的发展。在这项工作中开发的机器和机制与纳米致动器和控制器一起，将使未来纳米机器人的设计能够应用于许多领域，如自组装计算机和化合物、纳米制造、生物反应器中的分子传输和药物输送。这项工作也为将运动学设计应用于DNA纳米技术打开了大门。本研究开发的计算机设计自动化软件将极大地促进DNA折纸机构和机器的广泛使用。

This research award provides funding for the development of a systematic design framework for nanoscale machines and mechanisms using DNA origami nanotechnology. DNA origami enables construction of two and three-dimensional nanoscale shapes with unprecedented geometric complexity via molecular self-assembly. The majority of DNA origami research focuses on assembly of static 2D or 3D structures. The goal of this work is to incorporate functional dynamic parts with directed motion into the DNA origami design toolbox. To achieve this goal, a kinematics approach will be implemented to design DNA origami machines and mechanisms that are comprised of links and joints, similar to macroscale machines. A catalogue of various DNA origami links and joints will be designed and fabricated, and their mechanical properties will be characterized experimentally and by molecular simulation. These links and joints will be implemented in the design of prototype mechanisms for proof-of-principle studies. A new theory called projection kinematics will be developed to evaluate the three-dimensional motion of these prototype mechanisms from two-dimensional electron microscopy snapshots. To facilitate future application of DNA origami machines, a computer aided design and simulation program will be developed that facilitates conceptual mechanism design and automates the integration of DNA origami links and joints from the previously developed part catalogues. If successful, this research will greatly advance the fields of DNA nanotechnology, nanoscale design, and nano-robotics. The machines and mechanisms developed in this work together with nanoactuators and controllers will enable design of future nanorobots for applications in numerous fields such as self-assembling computers and chemical compounds, nano-manufacturing, molecular transport in bio-reactors, and drug delivery. This work also opens the door for applying kinematic design to DNA nanotechnology. The computer design automation software developed in this research will greatly facilitate the widespread use of DNA origami mechanisms and machines.