Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations

John Reif
Duke University
Computer Science

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 {\it 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 tileĀ¹s 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


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