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

DNA纳米技术的一个中心目标是为纳米制造任务开发组装复杂的非周期结构的方法。在这项工作中解决的关键挑战是稳健的生物分子系统设计，以避免通过控制定向组装复杂的纳米尺度图案形成的错误。算法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，但受到严重的组装错配错误的限制，从而阻碍了进一步的生长。这个项目吗?他的创新方法是利用DNA聚合酶驱动的DNA自激活和再激活协议来避免组装错误（而不是晶体错误纠正）。一种新的保护/去保护策略（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，瓷砖处于非活动状态，输出垫受到保护，不会与其他瓷砖绑定，从而防止晶格向（不需要的）相反方向生长。在其他瓷砖绑定到这个瓷砖之后？S输入衬垫，它进入一个活动状态，它的输出衬垫暴露，允许进一步生长。任务包括各种可激活瓷砖的实验演示和计算机模拟软件工具，用于设计和瓷砖组装过程和协议的动态概率模拟。瓦片组件的定向控制组装消除了DNA晶格应用开发中的主要障碍，为大大增加合成分子模式纳米结构的复杂性提供了一种方法。其他新应用还包括用于分子传感的组件、浓缩（仅当特定目标分子停靠在组件上的特定位点时，通过激活组装组件）和催化。这项工作跨越了许多领域&amp；#64257；领域包括化学、生物化学、物理和计算机科学，应用于生物工程、生物医学工程和纳米工程。它为学生提供令人兴奋和具有挑战性的跨学科培训机会，其多学科跨度的独特程度，影响了国家对多学科培训的关键需求。

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.