EMT/NANO: Polymerase-Based Self-Activating and Reactivating DNA Systems

DNA纳米技术的一个中心目标是开发组装复杂的非周期性结构的方法，用于纳米制造任务。在这项工作中解决的关键挑战是强大的生物分子系统的设计，以避免通过控制定向组装在复杂的纳米级图案形成的错误。DNA自组装利用DNA纳米结构（瓦片），通过杂交组装在一起，理论上形成具有复杂图案的DNA晶格，但受到阻止进一步生长的显著组装错配错误的限制。项目？的创新方法是使用DNA聚合酶驱动的自激活和再激活DNA协议来避免组装错误（而不是晶体错误校正）。一种新的保护/脱保护策略（使用DNA聚合酶置换）强制平铺组装生长的方向，以避免生长错误。最初，拼块处于非活动状态，其中输出焊盘被保护免于与其他拼块结合，从而防止在（不期望的）相反方向上的晶格生长。在其他瓷砖与此瓷砖结合后？的输入焊盘，它进入一个活跃的状态，其输出焊盘是暴露的，允许进一步增长。任务包括可激活瓷砖和计算机模拟软件工具的设计和动力学概率模拟瓷砖组装过程和协议的各种实验演示。平铺组件的受控定向组装消除了图案化DNA晶格的应用开发中的主要障碍，提供了用于极大地增加合成分子图案化纳米结构的复杂性的方法。待证明的另外的新颖应用包括用于分子传感、浓缩（仅当特定靶分子停靠在瓦片上的特定位点时通过激活组装瓦片）和催化的组件。工作跨越许多fi包括化学、生物化学、物理学和计算机科学在内的电子领域，并在生物工程、生物医学工程和纳米工程中应用。它为学生提供了令人兴奋和具有挑战性的跨学科培训机会，独特的多学科跨度的程度，影响在多学科培训的关键国家需求。

A central goal of DNA nanotechnology is to develop methods for assembling complex, aperiodic structures for nanofabrication tasks. The critical challenge addressed in this work is robust biomolecular system design to avoid errors in complex nanoscale pattern formation via controlled directional assembly. Algorithmic DNA self-assembly makes use of DNA nanostructures (tiles), which assemble together via hybridization, theoretically forming DNA lattices with complex patterns, but are limited by significant assembly mismatch errors that prevent further growth. The project?s innovative approach is assembly error avoidance (rather than crystal error correction) using self-activating and reactivating DNA protocols driven by the use of DNA polymerase enzyme. A novel protection/deprotection strategy (using DNA polymerase displacement) enforces the direction of tiling assembly growth to avoid growth errors. Initially, a tile is in an inactive state, with output pads protected from binding with other tiles, preventing lattice growth in (unwanted) reverse direction. After other tiles bind to this tile?s input pads, it enters an active state where its output pads are exposed, allowing further growth. Tasks include various experimental demonstrations of activatable tiles and computer simulation software tools for design and kinetic probabilistic simulation of the tile assembly process and protocols. The controlled directional assembly of tiling assemblies eliminates a major roadblock in the development of applications of patterned DNA lattices, providing a methodology for vastly increasing the complexity of synthetic molecular patterned nanostructures. Additional novel applications to be demonstrated include assemblies for molecular sensing, concentration (via activation of assembling tiles only when a specific target molecule docks at a particular site on the tile), and catalyzation. The work spans many fields including chemistry, biochemistry, physics, and computer science, with applications in bioengineering, biomedical engineering and nano-engineering. It provides students exciting and challenging interdisciplinary training opportunities unique to the degree of its span of multiple disciplines, impacting the critical national need in training in multiple disciplines.