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。这项工作解决的关键挑战是稳健的生物分子系统设计，以避免通过受控定向组装形成复杂纳米级图案的错误。算法DNA自组装利用了DNA纳米结构(Tiles)，它们通过杂交组装在一起，理论上形成了具有复杂图案的DNA晶格，但受到严重的组装失配错误的限制，这些错误阻止了进一步的生长。这个项目？S的创新方法是利用DNA聚合酶驱动的自激活和重新激活DNA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)加强了瓷砖组件生长的方向，以避免生长错误。最初，瓷砖处于非活动状态，输出焊盘受到保护，不会与其他瓷砖结合，从而防止晶格在(不需要的)相反方向上生长。在其他瓷砖绑定到该瓷砖-S输入垫后，它进入活动状态，其中其输出垫暴露，允许进一步增长。任务包括各种可激活瓷砖的实验演示，以及用于瓷砖组装过程和协议的设计和动力学概率模拟的计算机模拟软件工具。瓦片组件的受控定向组装消除了图案化DNA晶格应用发展的主要障碍，为极大地增加合成分子图案化纳米结构的复杂性提供了一种方法。待演示的其他新应用包括用于分子传感、浓缩(仅当特定的目标分子停靠在瓷砖上的特定位置时才通过激活组装瓷砖)和催化的组件。这项工作横跨许多领域，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，其跨度是多学科所独有的，影响到国家在多学科培训方面的关键需求。

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.