DNA NANOTECHNOLOGY AND ITS BIOLOGICAL APPLICATIONS - Bio-Inspired and Nanoscale Integrated Computing - page 353

structure of a large number of more complex DNA nanostructures can be
predicted by a number of prototype software systems from details like the
sequence composition, temperature, and buffer conditions (which are the
key relevant parameters).
Design of DNA nanostructures can be assisted by software. To design a
DNA nanostructure or device, one needs to design a library of ssDNA
strands with specific segments that hybridize to (and only to) specific
complementary segments on other ssDNA. There are a number of soft-
ware systems for this combinatorial sequence design task and for design of
DNA nanostructures with desired structures.
(b) The advantages from an experiments perspective are:
The chemical synthesis of ssDNA is now routine and inexpensive; a test
tube of ssDNA consisting of any specified short sequence of bases (

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can be obtained from commercial sources for modest cost (at this time,
about half a U.S. dollar per base); it will contain a very large number
(typically at least 10 12 ) of identical ssDNA molecules. The synthesized
ssDNA can have errors (premature termination of the synthesis is the
most frequent error), but can be easily purified by well known techniques
(e.g., electrophoresis, mentioned below).
The assembly of DNA nanostructures is a very simple experimental process;
in many cases, one simply combines the various component ssDNA into a
single test tube with an appropriate buffer solution at an initial temperature
above the expected melting temperature of the most stable base-pairing
structure, and then slowly cools the test tube below the melting temperature.
The assembled DNA nanostructures can be characterized by a variety of
techniques. One such technique is electrophoresis. It provides information
about the relative molecular mass of DNA molecules, as well as some
information regarding their assembled structures, depending on what type
of electrophoresis (denaturing or native, respectively) is used. Other
techniques like atomic force microscopy (AFM) and transmission electron
microscopy (TEM) provide images of the actual assembled DNA nanos-
tructures on 2D surfaces.

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13.3. ADELMAN'S INITIAL DEMONSTRATION
OF A DNA-BASED COMPUTATION

13.3.1. Adleman's Experiment
The field of DNA computing began in 1994 with a laboratory experiment
described in [5, 6]. The goal of the experiment was to find, within a given directed
graph, a Hamiltonian path, which is a path that visits each node exactly once. To
solve this problem, a set of ssDNA was designed based on the set of edges of the
graph. When combined in a test tube and cooled, they self-assembled into dsDNA.