DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 362

13.5.3. Applications of Autonomous Finite-State Computations
at the Molecular Scale
Even very simple operations, such as the above Boolean or finite-state transitions,
operating at the molecular-scale could have important potential applications, for
example, for drug mediation [13]. The idea is for the DNA nanostructures to take
as input a set of RNA sequences, whose level of expression (or lack of expression)
within a cell indicates a particular disease state. Then the execution of simple
Boolean operations executable by finite-state transitions can determine that a
disease exists, and execute a response (e.g., the release of RNA sequences which
provide a remediation of the disease by altering the expression of proteins
expressed by the cell). While such a scheme was demonstrated by [13] in the test
tube, it remains to be demonstrated in the much more challenging environment of
a cell. Another class of applications is for control of molecular robotic devices,
described in Section 13.7.
13.6. ASSEMBLING PAT TERNED AND ADDRESSABLE
2D DNA LAT TICES
One of the most appealing applications of tiling computations is their use to form
patterned nanostructures to which other, perhaps functional, materials can be
selectively bound.
An addressable 2D DNA lattice is one that has a number of sites with distinct
ssDNA. This provides a superstructure for selectively attaching other molecules at
addressable locations. The input layer for the computational assembly described in
Figure 13.6 is an example of an addressable system, since unique ssDNA pads
defined the tile locations. Other examples will be presented in the following text
discussion. As Many types of molecules exist for which we can attach DNA.
Known attachment chemistry allows them to be tagged with a given sequence of
ssDNA. Each of these DNA-tagged molecules can then be assembled by hybridi-
zation of their DNA tags to a complementary sequence of ssDNA located within
an addressable 2D DNA lattice. In this way, we can program the assembly of each
DNA-tagged molecule onto a particular site of the addressable 2D DNA lattice.
13.6.1. Attaching Materials to DNA
Many materials can be made to directly or indirectly bind to specific segments of
DNA using a variety of known attachment chemistries. Materials that can directly
bind to specific segments of DNA include other (complementary) DNA, RNA,
proteins, peptides, and various other materials. Materials that can be made to
indirectly bind to DNA include a variety of metals (e.g., gold) that bind to sulfur-
labeled compounds, carbon nanotubes (via various attachment chemistries), etc.
These attachment strategies provide molecular-scale ''Velcro'' for attaching hetero-
geneous materials to DNA nanostructures. For example, they can potentially be