DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 357

Figure 13.4. DNA tiles.
hybridization of their pads. A number of prototype computer software systems
have been developed for the design of the DNA sequences composing DNA tiles,
and for optimizing their stability.
To program a tiling assembly, the pads of tiles are designed so that tiles
assemble together as intended. Proper designs ensure that only the adjacent pads
of neighboring tiles are complementary so only those pads hybridize together.
Figure 13.4 illustrates some principal DNA tiles.
Winfree and Seeman [7] developed a family of DNA tiles known collectively
as DX tiles (see left tile illustrated in Fig. 13.4a) that consisted of two parallel
DNA helices linked by two immobile Holliday junctions. They demonstrated that
these tiles formed large 2D lattices, as viewed by AFM. Subsequently, other DNA
tiles were developed to provide for more complex strand topology and inter-
connections, including a family of DNA tiles known as TX tiles (see tile illustrated
in Fig. 13.4b) [8] composed of three DNA helices linked by four crossover
junctions. Both the DX tiles and the TX tiles are rectangular in shape, where two
opposing edges of the tile have pads consisting of ssDNA sticky ends. In addition,
TX tiles have topological properties that allow for strands to propagate in useful
ways though tile lattices. (This property is often used for aid in patterning DNA
lattices as described below). Other DNA tiles known as cross tiles (see Fig. 13.4c)
[8] are shaped roughly square and have pads on all four sides, allowing for
binding of the tile directly with neighbors in all four directions in the lattice plane.
Figure 13.5 gives an AFM image of a 2D lattice using cross tiles.
13.5. AUTONOMOUS FINITE-STATE COMPUTATION USING
LINEAR DNA NANOSTRUCTURES
13.5.1. The First Experimental Demonstration of Autonomous
Computations Using Self-Assembly of DNA Nanostructures
The first experimental demonstrations of computation using DNA tile assembly
was [9], which demonstrated two-layer, linear assemblies of TX tiles that executed