(579a) Self-Assembling DNA Nanotubes From Programmable Seeds

Self-Assembling DNA Nanotubes from Programmable Seeds

One of the fundamental challenges in the
bottom-up assembly of nanoscale devices is the
limited control over the organization of molecular assemblies. For example, it is
not well understood how to assemble a molecular link between two points in 3D
space. To address this problem, we seek to build a system in which DNA
nanotubes could span from a start point to an end point (green and red in
Figure 1a) even though these points may vary in distance and orientation. We
use DNA nanotubes to study this problem; the structure and assembly mechanism
of DNA nanotubes are well understood and their components can be rationally
designed. In this study, we would like to demonstrate how designed nuclei could
serve as starting points for nanotubes to grow, which may guide strategies for
generalized linking in nanoscale systems.

Using our assembly protocol, DNA
nanotubes are formed in a hierarchical self-assembly process, where individual
DNA strands form DNA double-crossover molecules (DNA tiles), which then
self-assemble into nanotubes via interactions of single-stranded DNA on the
tile ends. Homogenous nucleation of DNA nanotubes from tiles under low supersaturation is very rare because there is an energy
barrier to nucleation. Here we design nanotube nuclei and show that nanotubes
grow quickly in their presence. Our nucleus design consists of a cylindrical
DNA origami resembling the facet of a DNA nanotube. This design orients monomers
into an assembled nanotube rather than producing a high local monomer
concentration (Figure 1b). Using fluorescence microscopy, we observed a
significant increase of the nanotube growth rates in the presence of these
nuclei. AFM images confirm that this increase in growth rates is due to the
growth of nanotubes from the nuclei (Figure 1c).

Figure 1: (a) Schematic representation of a system where DNA
nanotubes connect start (green) and end (red) points; (b) Schematic showing
self-assembly of DNA tiles (brown, green) on nuclei (red) to form DNA
nanotubes. (c) AFM image of DNA nanotubes growing from nuclei (marked). Scale
bar: 100 nm