Building Connections Between Terminals with Location Uncertainty Using DNA Nanotubes

Abstract

While DNA nanostructures designed with 2- and 3-dimensional nanoscale attributes can now be routinely synthesized, we cannot yet assemble structures whose dimensions depend on the particularities of its environment. For example, an important assembly problem of this type is the construction of a wire or tether that connects two terminals when the location of (or distance between) the terminals is unknown or uncertain. Fabricating such assembly by top down methods is challenging as it is not a parallel process and nanometer scale positioning accuracy is required. We propose to develop a bottom-up method for interconnect assembly where chemical tags located at terminals guide interconnect self-assembly.DNA nanotubes, which are 20 nm in diameter and self-assembled from small DNA tiles, are used as connection filaments. We design and construct DNA origami seeds that serve as nanotube nucleation templates to control DNA nanotube assembly. The idea is that by placing DNA origami seeds at the two terminals, two DNA nanotubes would nucleate from the respective seeds, grow longer (by addition of DNA tiles to their growing ends), diffuse until the two growing ends find each other and join to form a continuous single DNA nanotube.We successfully demonstrate that when these seeds are randomly deposited and affixed to passivized glass surfaces, DNA nanotubes grown from these points join together to create point-to-point interconnects with lengths varying from 100 nm up to 10 microns. This autonomous assembly process could potentially be used to connect nanodevices that are either randomly arrayed on a surface or are positioned using low-resolution lithography, and techniques to functionalize DNA could conceivably allow us to construct optical or electronic links between these devices using the DNA nanotube filaments as a scaffold.