Transport Properties of Self-Assembled DNA Systems

实用的纳米技术需要精确和廉价地将纳米尺寸的组件放置到操作单元中。DNA纳米技术正是利用DNA的自组装特性来实现这一目标的。本项目将探索利用自组装DNA材料来控制分子在流体环境中的运动。计算机模拟将阐明自组装DNA结构的导电性机制。纳米级物体将被设计成电线、管道和晶体管的类似物。模仿自然，跨膜DNA系统将被开发来调节生物分子跨越细胞边界的通道。这些研究活动将与教育和推广紧密结合，并将为DNA纳米技术的快速发展领域提供计算方法和工具，用于自组装DNA结构的理论探索。本项目旨在表征自组装DNA纳米结构在生物传感、纳米流体和仿生系统中的潜在应用的传输特性。全原子分子动力学模拟将表征各种DNA折纸设计的离子电导率，并探测其在外电场下的结构完整性。模拟将探索DNA网格和DNA砖结构的行为，并评估它们在纳米孔传感应用中的有用性。带电和中空的DNA折纸结构将被设计成流体环境中离子和小生物分子的管道，类似于宏观的电线和管道。利用DNA折纸对电场的结构响应来设计和演示DNA折纸晶体管。门控和选择性生物离子通道的物理原理将在跨膜DNA构建中实现。理论工作将与实验人员密切合作，通过自组装DNA结构表征运输。该项目有望为流体环境中带电溶质运移的物理机制提供新的见解，并在生物分子的纳米孔检测、非常规计算和合成组织工程中找到实际应用。这个研究项目将通过为研究界提供方法和工具来构建、可视化和模拟自组装DNA系统，对功能性DNA纳米技术的发展产生直接影响。通过该计划获得的技术知识和专业知识将通过循序渐进的教程、流行的计算机程序VMD的模块以及nanoHUB的研究和教育工具提供。在这个项目中产生的材料将用于准备生物物理学本科和研究生课程的一系列讲座和演示。该项目将开发教育DNA折纸拼图和DNA乐高构造器套件，并将利用3D打印技术将它们提供给每个人。

Nontechnical SummaryPractical nanotechnology requires precise and inexpensive placement of nanometer-size components into an operational unit. The DNA nanotechnology achieves exactly that by utilizing the self-assembly property of DNA. This project will explore the use of self-assembled DNA materials for controlling the motion of molecules through fluid environment. Computer simulations will elucidate the mechanism of electrical conductivity of self-assembled DNA structures. Nanoscale objects will be designed to function as analogs of electrical wires, pipes and transistors. Mimicking nature, membrane-spanning DNA systems will be developed to regulate the passage of biomolecules across a cell boundary. These research activities will be closely integrated with education and outreach and will provide the rapidly expanding field of DNA nanotechnology with computational methods and tools for theoretical exploration of self-assembled DNA structures. Technical Summary This project aims to characterize the transport properties of self-assembled DNA nanostructures for possible applications in biosensing, nanofluidics, and biomimetic systems. All-atom molecular dynamics simulations will characterize the ionic conductivity of various DNA origami designs and probe their structural integrity in an external electric field. The simulations will explore the behavior of DNA gridirons and DNA bricks structures, and evaluate their usefulness for nanopore sensing applications. Charged and hollow DNA origami constructs will be designed to serve as conduits for ions and small biomolecules in fluid environment, analogous to macroscopic wires and pipes. The structural response of the DNA origami to electric field will be exploited to design and demonstrate a DNA origami transistor. The physical principles of gated and selective biological ion channels will be implemented in membrane-spanning DNA constructs. The theoretical work will be carried out in close collaboration with experimentalists characterizing the transport through self-assembled DNA structures. This project is expected to provide new insights into the physical mechanisms of charged solutes transport in fluid environment, finding practical application in nanopore detection of biomolecules, unconventional computing and synthetic tissue engineering. This research program will have a direct impact on the development of functional DNA nanotechnology by providing the research community with methods and tools to build, visualize and simulate self-assembled DNA systems. The technological knowledge and expertise acquired through this program will be made available through step-by-step tutorials, modules of the popular computer program VMD and as research and educational tools at nanoHUB. Material generated within this project will be used to prepare a set of lectures and demos for the biophysics undergraduate and graduate courses. The project will develop educational DNA origami puzzles and a DNA LEGO constructor kit and will make them available to everyone by taking advantage of the 3D printing technology.