287705 Self-Assembling DNA Nanotubes From Programmable Seeds

Wednesday, October 31, 2012: 3:15 PM
310 (Convention Center )
Abdul M. Mohammed and Rebecca Schulman, chemical and biomolecular engineering, Johns Hopkins University, Baltimore, MD

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

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