DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 360

(subsequences at which protein enzymes can cut the DNA backbone). The input
sequence was defined by specific sticky-ends that assembled a specific input layer
(Figure 13.6).
Here is the next question of concern:
How can one execute a step of computation using DNA tiles?
To execute steps of computation, the TX tiles were designed to have pads at
one end that encoded the cumulative XOR value. Also, since the reporter strand
segments ran though each tile, the appropriate input bit was also provided within
its structure. These two values implied that the opposing pad on the other side of
the tile be the XOR of these two bits.
This is the final question of concern:
How can one determine and/or display the output values of a DNA tiling
computation?
The output in this case was read by determining which of two possible cut
sites (endonuclease cleavage sites) were present at each position in the tile
assembly. This was executed by first isolating the ligated reporter strand, then
digesting separate aliquots with each endonuclease separately and then two
together; finally, these samples were examined by gel electrophoresis and the
output values were displayed as banding patterns on the gel.
Another method for output (presented below) is the use of AFM observable
patterning. Such patterning can be made by designing the tiles computing a bit 1
to have a stem loop protruding from the top of the tile or by providing a site for
binding of a marker protein. Sequences of such molecular patterning are clearly
viewable under appropriate AFM imaging conditions.
Although they are quite simple computations, the experiments of [9] and [10]
did demonstrate pioneering methods for autonomous execution of a sequence of
finite-state operations via algorithmic self-assembly, as well as for providing
inputs and for outputting the results. Further DNA tile assembly computations
[11, 12] will be presented below in Figure 13.11.
13.5.2. Autonomous Finite-State Computations via Disassembly
of DNA Nanostructures
An alternative method for autonomous execution of a sequence of finite-state
transitions was subsequently developed by [13]. Their technique essentially
operated in the reverse of the assembly methods described above and instead
was based on disassembly. They began with a linear DNA nanostructure whose
sequence encoded the inputs; then they executed series of steps that digested the
DNA nanostructure from one end. On each step, a sticky-end at one end of the
nanostructure encoded the current state, and the finite transition was determined
by hybridization of the current sticky end with a small ''rule'' nanostructure