Designed DNA Nanotube Architectures

Designed DNA Nanotube Architectures

Rebecca Schulman and Abdul M. Mohammed

Chemical and Biomolecular Engineering

Johns Hopkins University

The cytoskeleton and extracellular matrix consist of semiflexible biopolymers that are dynamically assembled into precise topologies and continuously reassembled based on inputs from cells and environmental signals.  This assembly process leads to specific interactions of the resulting materials with cells that enable tissue formation and can lead to properties such as the capacity for the polymer matrix to self-heal or to reassemble continuously, producing motion of the structure. Recapitulating the same assembly mechanisms synthetically is a current challenge that would lead to new materials with novel biological interactions and programmable, active reformation.

We report initial steps toward designing mechanisms to synthetically control the topology of DNA nanotube architectures.  DNA nanotubes consist of units called tiles, approximately 14x4 nm structures that self-assemble via DNA hybridization. Tubes have a persistence length that depends on the radius; for the structures we assemble it is estimated to be 10-20 microns.  We show that the nucleation and termination of tubes can be efficiently directed at specific locations, with the result being that we can create nanotube asters or point-to-point nanotube links. Both nucleation and termination are guided by designed DNA complexes, folded structures that emulate the facet of a growing DNA nanotube.  We characterize controlled nanotube growth using both fluorescence light microscopy to track growth and atomic force microscopy to characterize the structure of individual DNA nanotubes.

	Figure 1: Nanotube networks. (a) Fluorescence micrograph (left) and cartoon (right) of a DNA nanotube aster growing from a bead coated with nucleating complexes. (b) Without nucleating complexes, nanotubes do not grow; bead location is shown by an orange circle. (c) A nanotube can link a bead coated with nucleating complexes and a bead coated with end capture complexes.