DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 350

scale reduction that so restricts lithography or other more conventional top-down
manufacturing techniques. Other surveys of DNA nanotechnology and devices
have been given by LaBean [1], Mao [2], Reif [3], and Seeman [4].
In attempting to understand these modern developments, it is worth recalling
that mechanical methods for computation date back to the very onset of computer
science (for example to the cog-based mechanical computing machine of Babbage).
Lovelace stated in 1843 that Babbage's ''analytical engine weaves algebraic
patterns just as the Jacquard loom weaves flowers and leaves.'' In some of the
recently demonstrated methods for biomolecular computation described here,
computational patterns were essentially woven into molecular fabric (DNA
lattices) via carefully controlled and designed self-assembly processes.
In general, nanoscience research is highly interdisciplinary. In particular,
DNA self-assembly uses techniques from multiple disciplines such as biochem-
istry, physics, chemistry, and material science, as well as computer science and
mathematics. We will observe that many of these self-assembly processes are
computational-based and programmable, and it seems likely that a variety of
interdisciplinary techniques will be essential to the further development of this
emerging field of biomolecular computation.
13.1.2. The Topics Discussed in this Chapter
While a high degree of interdisciplinarity makes the topic quite intellectually
exciting, it also makes it challenging for a typical reader. For this reason, this
article was written with the expectation that the reader has little background
knowledge of chemistry or biochemistry. We define a few relevant technical terms
in Section 13.3.1. In Section 13.3.2 we list some known enzymes used for
manipulation of DNA nanostructures. In Section 13.3.3 we list some reasons
why DNA is uniquely suited for assembly of molecular-scale devices.
In many cases, the self-assembly processes are programmable in ways
analogous to more conventional computational processes. We present an over-
view of theoretical principles and techniques (such as tiling assemblies and
molecular transducers) developed for a number of DNA self-assembly processes
that have their roots in computer science theory (e.g., abstract tiling models and
finite state transducers). Computer-based design and simulation are also essential
to the development of many complex DNA self-assembled nanostructures and
systems. Error-correction techniques for correct assembly and repair of DNA self-
assemblies are also discussed.
The area of DNA self-assembled nanostructures and robotics is by no means
simply a theoretical topic—many dramatic experimental results have already been
demonstrated, and a number of these will be discussed. The complexity of these
demonstrations has been increasing at an impressive rate (even in comparison to
the rate of improvement of silicon-based technologies). This chapter discusses the
accelerating scale of complexity of DNA nanostructures (such as the number of
addressable pixels of 2D patterned DNA nanostructures) and provides some
predictions for the future.