While the topic of Molecular Computation would have appeared even a
half dozen years ago to be purely conjectural, it now is an emerging subfield
of computer science with the development of its theoretical basis and a number
of moderate to large-scale experimental demonstrations. Talk focuses on a
subarea of Molecular Computation known as DNA self-assembly.
Self-assembly is the spontaneous self-ordering of substructures into
superstructures driven by the selective affinity of the substructures. DNA
provides a molecular scale material for effecting this programmable
self-assembly, using the selective affinity of pairs of DNA strands to form DNA
nanostructures. DNA self-assembly is the most advanced and versatile system
known for programmable construction of patterned systems on the molecular
scale. The methodology of DNA self-assembly begins with the synthesis of
single-strand DNA molecules that self-assemble into macromolecular building
blocks called DNA tiles. These tiles have sticky ends that match the sticky
ends of other DNA tiles, facilitating further assembly into large structures
known as DNA tiling lattices. In principal you can make the DNA tiling
assemblies form any computable two- or three-dimensional pattern, however
complex, with the appropriate choice of the tilešs component DNA. This talk
overviews the evolution of DNA self-assembly techniques from pure theory to
experimental practice. We describe how some theoretical developments have
made a major impact on the design of self-assembly experiments, as well as a
number of theoretical challenges remaining in the area of DNA self-assembly.
We descuss algorithms and software for the design, simulation and optimization
of DNA tiling assemblies. We also describe the first experimental
demonstrations of DNA self-assemblies that execute molecular computations and
the assembly of patterned objects at the molecular scale. Recent experimental
results indicate that this technique is scalable. Molecular imaging devices
such as atomic force microscopes and transmission electron microscopes allow
visualization of self-assembled two-dimensional DNA tiling lattices composed of
hundreds of thousands of tiles. These assemblies can be used as scaffolding on
which to position molecular electronics and robotics components with precision
and specificity. The programmability lets this scaffolding have the patterning
required for fabricating complex devices made of these components. For details,
see http://www.cs.duke.edu/~reif/paper/ICALPassemble/ICALPassemble.pdf