Theoretical and Experimental DNA Computation (Natural ...

120 5 Physical Implementations
3. To test the error-resistance of a sequence of removal operations that would
occur during an actual algorithmic implementation.
Encoding colorings in DNA
We construct an initial library of (not necessarily legal) colorings in the following
manner. For each vertex vi ∈ V we synthesize a single oligonucleotide (or
oligo) to represent each of vi =red,vi = green, and vi = blue. The structure
of these strands is depicted in Fig. 5.8.
Binding site (20 b.p.)
Restriction site (4 b.p.) Colour site (6 b.p.)
Fig. 5.8. Oligonucleotide structure
With reference to Fig. 5.8, each oligo (apart from those representing v1 and
v8) is composed of the following:
1. a unique 20-base binding site, within which is embedded a 4-base restriction
site, GAT C
2. a 6-base color identification site. The sequences chosen to represent “red”,
“green”, and “blue” are AAAAAA, GGGGGG, andCCCCCC respectively
3. a unique 20-base binding site
Oligos representing v1 and v8 are 34 bases long (8-base binding section, 6base
color section and 20-base binding section). The initial sequences chosen
to represent each vertex coloring are listed in Table 5.1. Note that restriction
sites are underlined (e.g., GAT C) and color sequences are depicted in bold.
The melting temperature (Tm) of each strand is specified in the final column.
All sequences described here were originally designed by hand. This process
is laborious and prone to error, and several researchers have described
subsequent attempts to automate the sequence design process. The sequences
were then checked with the Microgenie [127] package to check for common
subsequences and hairpin loops.
We now describe how the initial library is constructed from these oligos.
In order to reduce to a minimum the number of oligos to be synthesized, we
reject the splinting method described in [3, 98] in favor of an overlapping
approach.