LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

Transducers with Programmable Input by DNA Self-assembly 235
sticky ends at a time hybridize, and those with less than three don’t, or (2) by
including competitive imperfect hairpins that will extend to proper sticky ends
only when all three sites are paired properly.
An iterated computation of the machine can be obtained by allowing third,
fourth etc. rows of assembly and hence primitive recursive functions can be
obtained. The input for this task is a combination of DX and TX molecules as
presented in Figure 10. The top TX duplex (not connected to the neighboring
DX) will have the right end sticky part encoding one of the input symbols and
the left sticky end will be used as connector. The left (right) boundary of the
assembly is obtained with TX molecules that have the left (right) sides of their
duplexes ending with hairpins instead of sticky ends. The top boundary contains
different motifs (such as the half hexagon in Figure 11 (b)) for different symbols.
For a two symbol alphabet, the output tile for one symbol may contain a motif
that acts as a topographic marker, and the other not. In this way the output
can be detectable by atomic force microscopy.
Fig. 10. Input for the computational assembly.
5.2 Programable Computations with DNA Devices
Recent developments in DNA nanotechnology enable us to produce FSM’s with
variable and potentially programmable inputs. The first of these developments is
the sequence-dependent PX-JX2 2-state nanomechanical device [26]. This robust
device, whose machine cycle is shown in Figure 11 to the left, is directed by the
addition of set strands to the solution that forms its environment.
The set strands, drawn thick and thin, establish which of the two states the
device will assume. They differ by rotation of a half-turn in the bottom parts
of their structures. The sequence-driven nature of the device means that many
different devices can be constructed, each of which is individually addressable;
this is done by changing the sequences of the strands connecting the DX portion
AB with the DX portion CD where the thick or thin strands pair with them.
The thick and thin strands have short, unpaired extensions on them. The state
of the device is changed by binding the full biotin-tailed complements of thick
or thin strands, removing them from solution by magnetic streptavidin beads,
and then adding the other strands. Figure 11 to the right shows that the device
can change the orientation of large DNA trapezoids, as revealed by atomic force
microscopy. The PX (thick strand) state leads to parallel trapezoids and the JX2
(thin strand) state leads to a zig-zag pattern.
Linear arrays of a series of PX-JX2 devices can be adapted to set the input
of a FSM. This is presented in Figure 12 where we have replaced the trapezoids