NANO: EMT: A DNA-Based Autonomous Programmable Molecular Transport Network

最近有相当多的进展证明了一类被称为“DNA步行者”的DNA分子效应器，其沿着自组装的线性DNA纳米结构执行各种形式的平移运动。特别是，由赖夫的小组在杜克建造的步行者是？第一个自动执行的DNA步行者，无需外部干预。该项目将扩展DNA步行者的新兴纳米技术，为自组装DNA晶格内的分子运输和通信提供可编程网络系统。我们的系统将执行一组通信和传输操作。这些包括，除其他事项外，能力（一）执行一类？nite国家的行动提供的信息，由speci？艾德网站的二维晶格，（ii）路线？将纳米状态信息和/或纳米颗粒传送到DNA晶格的瓦片对或从DNA晶格的瓦片对传送到其他指定位点。虽然程度的可编程性的建议构造的限制？尽管如此，可编程性仍然远远超过当前分子效应器和分子马达装置的当前实验演示。 我们打算对杜克现有的自主DNA步行器进行重大改进，使它们对纳米科学和纳米技术产生更大的影响，包括将DNA步行器扩展到至少两种意义上的可编程：（a）它们将沿着嵌入2D DNA晶格中的路径路由到目标位点（相比之下，先前的DNA步行器只穿过线性DNA纳米结构）。(b)DNA步行者将能够处理沿着其路径嵌入的信息，并对其遇到的信息序列执行有限状态操作。我们还将首次自组装完全可寻址的二维DNA晶格，在其上将定义步行者的可编程路径。 我们还将把DNA步行者扩展到纳米运输设备：即，（a）运输各种类型的（例如，金属颗粒和蛋白质），（B）在DNA晶格上的特定位点拾取和卸载纳米颗粒，以及（c）协同携带DNA晶格作为负载。这些大大改进的DNA步行器将分为两种类型：（a）一种类型是以前在杜克开发的自主步行器的延伸，基于蛋白酶;（B）另一种类型纯粹由核酸制成，不使用蛋白酶。除了这些改进的DNA步行器的设计和计算机模拟之外，拟议的工作还包括一系列如上所述的DNA步行器的隔离能力的实验演示，以及一般操作的实验演示，例如晶格范围内的信息传输/处理和材料传输。拟议的工作本质上是跨学科的，将影响多个？包括化学、生物化学、物理学、计算机科学和机器人技术在内的电子领域，在纳米工程和可能的生物医学领域具有潜在的长期应用。它将为杜克研究生和本科生提供令人兴奋和具有挑战性的跨学科培训机会。该项目将提供从现有的简单纳米效应器到可编程纳米机器人网络系统的过渡，产生对纳米工程具有广泛影响的能力。我们提出的自主可编程分子传输网络有许多可行的实际应用。例如，这种可编程的纳米粒子传输系统可能在未来用于构建各种纳米电子器件的复杂组件，这些纳米电子器件附着在DNA晶格上的特定位点上，并用于检测/处理/传播分子信号。

There has been considerable recent progress demonstrating a class of DNA molecular-effectors called "DNA walkers" that execute various forms of biped locomotion along self-assembled linear DNA nanostructures. In particular, the walker constructed by Reif's group at Duke is the ?rst DNA walker that executes autonomously, without external intervention. This project will extend the emerging nanotechnology of DNA walkers to provide a programmable network system for molecular transport and communication within self-assembled DNA lattices. Our system will perform a set of communication and transport operations. These include, among other things, the ability to (i) perform a class of ?nite state operations on the information provided by speci?ed sites of the 2D lattice, (ii) route ?nite state information and/or nanoparticles to and from pairs of tiles of the DNA lattice or to other specified sites. Although the degree of programmability of the proposed constructs is restricted to ?nite state transitions, still the programmability far exceeds current experimental demonstrations of current molecular effectors and molecular-motor devices. We intend to make significant improvements to Duke's existing autonomous DNA walkers to allow them to have far more impact to nanoscience and nanotechnology, including extending the DNA walkers to be programmable in at least two senses: (a) They will be made to route to target sites following paths embedded in the 2D DNA lattices (in contrast, prior DNA walkers traversed only linear DNA nanostructures). (b) The DNA walkers will be able process information embedded along its path and perform finite state operations on the sequence of information it encounters. We will also self-assemble for the first time fully addressable two dimensional DNA lattices, on which the programmable paths of the walkers will be defined. We will also extend the DNA walkers to nano-transport devices: that is, (a) to transport a variety of types (e.g., metallic particles and proteins) of nano-particles, (b) to pick up and unload nano-particles at specific sites on the DNA lattice, and (c) to cooperatively carry a DNA lattice as a load. These much improved DNA walkers will be of two types: (a) One type is an extension of previous autonomous walkers developed at Duke and is based on protein enzymes; (b) the other type is made purely of nucleic acids and does not use protein enzymes. In addition to the design and computer simulation of these improved DNA walkers, the proposed work includes a series of experimental demonstrations of isolated capabilities of DNA walkers as listed above, as well as experimental demonstrations of general operations such as lattice-wide transporting/processing of information and transporting of material. The proposed work is inherently cross-disciplinary and will impact multiple ?elds including chemistry, biochemistry, physics, computer science, and robotics, with potential long-term applications in nano-engineering and possibly in areas of biomedical interests. It will provide exciting and challenging interdisciplinary training opportunities for Duke graduate and undergraduate students. This project will provide a transition from the existing simple nano-effectors to programmable nano-robotics network system, yielding capabilities that have broad impact to nano-engineering. There are numerous feasible practical applications of our proposed autonomous programmable molecular transport network. For example, such a programmable nano-particle transport system might be used in the future for constructing complex assemblies of various nano-electronic devices attached to specified sites on the DNA lattice and for detecting/processing/broadcasting molecular signals.