DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 364

projecting from every DNA tile on an odd column. This limited sort of patterning
needed to be extended to large classes of patterns.
In particular, the key capability needed is a programmable method for
forming distinct patterns on 2D DNA lattices, without having to completely
redesign the lattice to achieve any given pattern. There are at least three methods
[16] for assembling patterned 2D DNA lattices that now have been experimentally
demonstrated, as described in the next sections.
13.6.3. Use of Scaffold Strands for Programmable Assembly
of Patterned 2D DNA Lattices
The first published use of a scaffold strand, a long ssDNA around which shorter
ssDNA assemble to form structures larger than individual tiles, is given in [1].
Scaffold strands were used to demonstrate programmable patterning of 2D DNA
lattices in [17] by propagating 1D information from the scaffold into a second
dimension to create AFM observable patterns. The scaffold strand weaves though
the resulting DNA lattice to form a desired and distinct sequence of 2D barcode
patterns (Figure 13.9).
In this demonstration, identical scaffold strands ran through each row of the
2D lattices, using short stem loops extending above the lattice to form pixels. This
determined a bar code sequence of stripes over the 2D lattice that was viewed by
AFM. In principle, this method may be extended to allow for each row's
Figure 13.9. Use of scaffold strands for programmable assembly of barcode
patterned 2D DNA lattices.