DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 367

Figure 13.13. 2D patterns by hierarchical assembly. (Figure adapted with permis-
sion from [19].)
13.6.5. Use of Hierarchical Assembly for Programming
of Patterned 2D DNA Lattices
A further approach is to assemble DNA lattices in a hierarchical fashion [19]. Figure
13.13 gives three examples of preprogrammed patterns displayed on addressable
DNA tile lattices. Tiles are assembled prior to mixing with other preformed tiles.
Unique ssDNA pads direct tiles to designed locations. White pixels are ''turned on''
by binding a protein (streptavidin) at programmed sites as determined in the tile
assembly step by the presence or absence of a small molecule (biotin) appended to a
DNA strand within the tile. Addressable, hierarchical assembly has been demon-
strated for only modest size lattices to date, but has considerable potential
particularly in conjunction with the above methods for patterned assembly.
13.7. ERROR CORRECTION AND SELF-REPAIR
AT THE MOLECULAR SCALE
In many of the self-assembled devices described here, there can be significant levels
of error. These errors occur both in the synthesis of the component DNA and in
the basic molecular processes that are use to assemble and modify the DNA
nanostructures, such as hybridization and the application of enzymes. There are
various purification and optimization procedures developed in biochemistry for
minimization of many of these types of errors. However, there remains a need for
development of methods for decreasing the errors of assembly and for self-repair
of DNA tiling lattices comprised of a large number of tiles. A number of
techniques have been proposed for decreasing the errors of a DNA tiling assembly
by providing increased redundancy.
Winfree [20] developed a ''proofreading'' method of replaced each tile with a
subarray of tiles that provide sufficient redundancy to quadratically reduce errors,
but increase the size of the assembly. This scheme is given in Figure 13.14 (top),
with the original tiles in Figure 13.15 (top) and the modified tiles in Figure 13.14
(bottom).