Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs

Abstract

The bottom-up spatial organization of potential nanoelectronic components is a key intermediate step in the development of molecular electronics. We describe robust three-space-spanning DNA motifs that are used to organize nanoparticles in two dimensions. One strand of the motif ends in a gold nanoparticle; only one DNA strand is attached to the particle. By using two of the directions of the motif to produce a two-dimensional crystalline array, one direction is free to bind gold nanoparticles. Identical motifs, tailed in different sticky ends, enable the two-dimensional periodic ordering of 5 and 10 nm diameter gold nanoparticles.

Figure 1. The DNA Motif Used to Build the Arrays

(a) A Schematic of the Motif. In this schematic diagram, double helices are shown as opaque rods around which the individual strands are wrapped. Note the 3-space-spanning character of the three DX domains. (b) A Detailed Molecular Structure. Each nucleotide is shown in a representation that illustrates a color-coded backbone virtual atom connected to its neighbors along the helix. A gray line representing the base is drawn from this atom to the helix axis, which is also drawn. Both diagrams drawn by the program Gideon..

Figure 2. The 2D Arrays Assembled Here

(a) A Schematic Showing the Formation of a Two-Component Array. Four triangles of two species in which each domain has been color coded are shown connected. The view parallel to the three-fold axes shows how only two domains (cyan bonding to magenta and brown bonding to red) are involved in array formation, while the end of the third domain (blue or green) is free to be involved in scaffolding operations. (b) Diagrams Showing the Attachment of Nanoparticles. The color-coding is the same as in (a). This view is perpendicular to the rhombic surfaces of the 2D array. Its three panels show, top to bottom, 5 nm particles attached to only one of the two triangular tiles, 5 nm particles attached to both of the tiles, and 5 nm particles attached to one of the tiles and 10 nm particles attached to the other tile. (c) A Tapping-Mode Atomic Force Micrograph of an Underivatized Array. Note that despite a pseudo-trigonal appearance, the features in the lighter portion of the array are all parallel to each other, and there is no threefold axis at the centers of the triangles, nor at their vertices. There is a prominent high feature in the lower-left-to-upper-right direction that we interpret as the domain not involved in lattice formation.

Figure 3. Transmission Electron Micrographs of 2D Arrays of Organized Gold Nanoparticles

(a) An array where one tile contains 5 nm particles. It is clear that this arrangement results in one short distance and one long distance. Sometimes a particle is missing. (b) An array where both tiles contain 5 nm particles. The distances between particles are seen to be equal here. (c) An array where one tile contains a 5 nm particle and the other tile contains a 10 nm particle. The alternation of 5 nm particles and 10 nm particles is evident from this image. Note that the spacings are precise in both directions, and that the pattern mimics the rhombic pattern of the tile array.