Theoretical and Experimental DNA Computation (Natural ...

5.8 Experimental Investigations 119
to cut any double-stranded DNA containing the appropriate restriction site,
whereas hybridization separation is never 100% efficient. Instead of extracting
most strands containing a certain subsequence we simply destroy them
with high probability, without harming those strands that do not contain the
subsequence. In reality, even if restriction enzymes have a small nonzero error
rate associated with them, we believe that it is far lower than that of hybridization
separation. Another advantage of our model is that it minimizes
physical manipulation of tubes during a computation. Biological operations
such as pipetting, filtering, and extraction lose a certain amount of material
along the way. As the number of operations increases, the material loss
rises and the probability of successful computation decays. Our implementation
uses relatively benign physical manipulation, and avoids certain “lossy”
operations.
5.8 Experimental Investigations
In this section we describe the results of an experimental implementation of
the parallel filtering model. In particular, we concentrate on testing the efficiency
of the implementation of the remove operation, which is central to our
model. Although we have not yet advanced to the stage of fully implementing
an entire algorithm, the results obtained are promising. However, it is important
to note that the implementation of the remove operation is completely
separate in conceptual terms to the actual nature of the model. The success
or failure of any particular implementation does not detract in any way from
the power of the model.
Experimental objectives
The primary objectives of the experiments detailed in this section are as
follows:
1. To first ascertain optimal experimental conditions.
2. To test the implementation of the remove operation. We do this by performing
a sequence of removal experiments, comprised of primer annealing,
primer extension, and restriction.
Experimental overview
The primary objectives of the experiments detailed in this section are as
follows:
1. To first ascertain optimal experimental conditions.
2. To test the implementation of the remove operation. We do this by performing
a sequence of removal experiments, comprised of primer annealing,
primer extension, and restriction.