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known software packages. The melting temperature of a DNA helix is the
temperature at which half of all the molecules are fully hybridized as double
helix, while the other half are single stranded. The kinetics of the DNA
hybridization process is quite well understood; it occurs in a (random) zipper-
like manner, similar to a biased one-dimensional random walk.
Whereas ssDNA is a relatively flexible molecule, dsDNA is quite stiff (over
lengths of less than 150 or so bases) and has the well characterized, double helix
structure. There are about 10.5 bases per full rotation on this helical axis. The
exact geometry of the double helix depends slightly on the base sequence in a way
readily computed by existing software. A DNA nanostructure is a multimolecular
(supramolecular) complex consisting of a number of ssDNA that have partially
hybridized, as designed, along their subsegments.
13.2.2. Manipulation of DNA
In addition to the hybridization reaction, there are a wide variety of known
enzymes and other proteins used for manipulation of DNA nanostructures and
have predictable effects. (Interestingly, these proteins were discovered in natural
bacterial cells and tailored for laboratory use.) These Include:
Restriction enzymes can cut (double-strand break) or nick (single-strand
break) a DNA backbone at specific locations determined by short base
sequences.
Ligase enzymes can heal or repair DNA nicks by forming covalent bonds in
the sugar-phosphate backbone.
Polymerase can extend an ssDNA by covalently coupling further comple-
mentary bases, as dictated by a template ssDNA, thus forming a longer
sequence of dsDNA.
Besides their extensive use in other biotechnology procedures, the above
reactions, together with hybridization, are often used to execute and control DNA
computations and DNA molecular robotic operations. The restriction enzyme
reactions are programmable in the sense that they are site specific, only executed
as determined by the appropriate DNA base sequence. The latter two reactions,
using ligase and polymerase, require the expenditure of energy via consumption of
ATP molecules and can thus be controlled by ATP concentration.
13.2.3. Why Use DNA to Assemble Molecular-Scale Devices?
There are many advantages of DNA as a material for building things at the
molecular scale.
(a) The advantages from a design perspective are:
The basic geometric and thermodynamic properties of dsDNA are well
understood and can be modeled by available software systems. The
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