Control of self-assembly of DNA tubules through integration of gold nanoparticles

Abstract

The assembly of nanoparticles into three-dimensional (3D) architectures could allow for greater control of the interactions between these particles or with molecules. DNA tubes are known to form through either self-association of multi-helix DNA bundle structures or closing up of 2D DNA tile lattices. By the attachment of single-stranded DNA to gold nanoparticles, nanotubes of various 3D architectures can form, ranging in shape from stacked rings to single spirals, double spirals, and nested spirals. The nanoparticles are active elements that control the preference for specific tube conformations through size-dependent steric repulsion effects. For example, we can control the tube assembly to favor stacked-ring structures using 10-nanometer gold nanoparticles. Electron tomography revealed a left-handed chirality in the spiral tubes, double-wall tube features, and conformational transitions between tubes.

Fig. 1

The design of a DNA tile system for the formation of a variety of tubular structures carrying 5-nm AuNPs. (A and B) Top and side view of the four DX tiles (A tile, blue; B tile, red; C tile, green; and D tile, brown). The A tile carries a 5-nm AuNP on the top of the tile. The C tile carries a DNA stem loop pointing downward. (C) The four different tiles are designed to self-assemble into a 2D array displaying parallel lines of AuNPs. (D) Possible ways for the corresponding edge tiles on opposite sides of the 2D array to associate and lead to formation of tubes displaying patterns of AuNPs in stacked rings, single spirals, double spirals, and nested spiral tubes. (E) The different tube conformations were observed in a single TEM image.

Fig. 2

Steric effects on the tube architectures. (A) Schematics and TEM images showing the tubes formed from DNA tile arrays with 5-nm AuNP on the A tile and a DNA stem loop on the C tile (same sample but a different imaging area as shown in Fig. 1E). (B) Schematics and TEM images showing the tubes formed from DNA tile arrays with only 5-nm AuNPs on A tiles without stem loops on C tiles. (C) Schematics and TEM images showing the tubes formed from DNA tile arrays with 10-nm AuNPs on A tiles. (D) Schematics and TEM images showing the tubes formed from DNA tile arrays with 15-nm AuNPs on A tiles. These TEM images are 2D projections of flattened tubular structures. (E) Histogram showing the distribution of tube types observed for the four samples from (A) to (D). One hundred tubes were randomly counted and analyzed from nonoverlapping images for each sample. Additional images are shown in (28). Each image contains a magnified representative tube from each sample. The scale bars in the inserts are all 20 nm.

Fig. 3

Representative 3D structures of nanoparticle tubes reconstructed from cryoelectron tomographic imaging. (A) One view of the tomogram of a single-spiral tube of 5-nm AuNPs. The inset shows a top view from the axis of two helical turns of the spiral tube; scale bar, 60 nm. (B) Tomogram of a stacked-ring tube of 5-nm particles. The inset shows a top view from the axis of a single ring from the stacked-ring tube; scale bar, 60 nm. (C) Tomogram of a double-spiral tube of 5-nm AuNPs with a single spiral of 5-nm nanoparticles inside each coded with a different color. The inset shows a top view from the axis of the double-wall spiral tube; scale bar, 60 nm. (D) Tomograph showing the splitting of a wider single-spiral tube into two narrower stacked-ring tubes of 10-nmAuNPs. All of the spiral tubes show a left-handed chirality. A weakly colored depth cue was applied to each view. The elongated appearance of the gold bead in the top views of the tubes is an effect of limited tilts in the tomography data collection. Movies of electron tomographic reconstruction corresponding to these structures are available in (28).

Fig. 4

The tubes formed with 5- and 10-nm AuNPs placed on opposite surfaces of the DNA tile array. (A and B) The top panels are schematic side and top views of the binary particle tube architectures; the bottom panels are corresponding representative electron tomographic images clearly showing the 3D architectures. Movies of electron tomographic images corresponding to these structures are available in (28).