Theoretical and Experimental DNA Computation (Natural ...

154 6 Cellular Computing
x
y
z
x
(a) (b) (c)
Fig. 6.6. Excision
y
z
x z
made (Fig. 6.6b). The pointers connecting the MDSs then join them together,
while the IES self-anneals to yield a circular molecule (Fig. 6.6c).
The second operation is known as hairpin, inverted repeat excision, and
is used in the situation where a pointer has two occurrences, one of which
is inverted. The molecule folds into a hairpin structure (Fig. 6.7a) with the
pointer and its inversion aligned, cuts are made (Fig. 6.7b) and the inverted
sequence is reinserted (Fig. 6.7c), yielding a single molecule.
(a)
(c)
Fig. 6.7. Inversion
The third and final operation is double-loop, alternating direct repeat excision/reinsertion.
This operation is applicable in situations where two repeats
of two pointers have interleaving occurrences on the same strand. The double
loop folding is made such that the two pairs of identical pointer occurrences
are aligned (Fig. 6.8a), cuts are made (Fig. 6.8b) and the recombination takes
place, yielding the molecule from Fig. 6.8c.
The process by which gene assembly takes place using these operations
and the computational properties of the system are discussed in detail in [56].
However, the important difference between this model and that of Landweber
and Kari is that it is more concerned with the mechanics of the gene assembly
process than the computational power of an abstraction of the natural system.
y
(b)