Operation of a DNA robot arm inserted into a 2D DNA crystalline substrate

Abstract

The success of nanorobotics requires the precise placement and subsequent operation of specific nanomechanical devices at particular locations. The structural programmability of DNA makes it a particularly attractive system for nanorobotics. We have developed a cassette that enables the placement of a robust, sequence-dependent DNA robot arm within a two-dimensional (2D) crystalline DNA array. The cassette contains the device, an attachment site, and a reporter of state. We used atomic force microscopy to demonstrate that the rotary device is fully functional after insertion. Thus, a nanomechanical device can operate within a fixed frame of reference.

Figure 1

(A) A view perpendicular to the plane of the cassette in the PX state. The PX state is set by the green strands in the middle of the upper two domains. The reporter hairpin seen end on protruding from the plane. Note the sticky ends on the bottom domain that attach the cassette to the 2D array. (B) The same molecule is shown obliquely, so the reporter hairpin can be seen. (C) A view similar to (A), except that the cassette is in the JX₂ state, which is set by the purple strands. Note that the reporter hairpin is now behind the cassette, a point emphasized in (D). All drawings are in a virtual-bond representation produced by the program GIDEON (13). (E) This is a 5% polyacrylamide gel run in TAEMg buffer (3). The two different states are shown both for a cassette and for a cassette including a reporter hairpin. The single bands seen in each lane indicate that the motifs are stable and monodisperse.

Figure 2

The arrays are shown schematically to demonstrate the two states of the device in the cassette. The eight TX tiles that form the array are shown in differently colored outlined tiles. For clarity the cohesive ends are shown to be the same geometrical shape, although they all contain different sequences. The cassette and reporter helix are shown as red filled components; the marker tile is labeled ‘M’ and is shown with a black filled rectangle representing the domain of the tile that protrudes from the rest of the array. Both the cassette and the marker tile are rotated about 103° from the other components of the array (three nucleotides rotation). The PX arrangement is shown at the left and the JX₂ arrangement is on the right. Note that the reporter hairpin points towards the marker tile in the PX state, but points away from it in the JX₂ state.

Figure 3

Panel (A) shows the conversion of the array in the PX state to the array in the JX₂ state. Panel (B) illustrates the reverse motion, JX₂ to PX. The scales of the AFM images are indicated by a 100 nm scale bar in the upper right of each image. In both states, the cassette and the marker tile are visible as a doubly lobed blob-like region. In the PX state, the reporter hairpin is visible as a bright spot at the center of the blob. In the JX₂ state, the reporter arm is visible as a bright spot on one edge of the blob. We have emphasized these features on the four images: In each image, we have put a black box around the unit cell repeat in two cases, and a blue rounded figure within it around the blob-like region. In one of the two boxes we have emphasized the reporter arm by enclosing it in a red circle. Expanded, upright double scale copies of these boxes are shown adjoining the upper left edge of each image. In addition, in the lower left corner of each image, we have taken a 50 × 50 nm portion of the image and have circled the marker in a black ellipse and have enclosed the cassette with a red curve that has a protrusion corresponding to the reporter hairpin. The right side of each pair of images is from an aliquot taken from a solution of the material on the left and then converted to the other state.