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

Duke University, Durham NC

Investigators

Abstract

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.