Theoretical and Experimental DNA Computation (Natural ...

j
k
4.6 Proposed Physical Implementation 85
Pml I restriction site
Inputs
j
k
x y z
j
k
Output=1
Fig. 4.4. Structure of a gate strand
2. Add ligase to Tk in order to seal any “nicks.”
3. Add the restriction enzyme PmlItoTk. Because of the strand design, the
enzyme cleaves only those strands that have both input strands annealed
to them. This is due to the fact that the first restriction site CACGTG
is only made fully double stranded if both of these strands have annealed
correctly. This process is depicted in Fig. 4.5.
4. Denature the strands and run Tk through a gel, retaining only strands of
length 3l. This may be achieved in a single step by using a denaturing gel
[136].
5. Add tube Sk to tube Tk. The strands in tube Sk anneal to the second
restriction site embedded within each retained gate strand.
6. Add enzyme PmlItotubeTk, which “snips” off the z j
k
section (i.e., the
output section) of each strand representing a retained gate.
7. Denature and run Tk through another gel, this time retaining only strands
of length l. This tube, Tk, of retained strands, forms the input to Tk+1.
We now proceed to the simulation of level k +1.
j
k
j
k
x y z
j
k
j
k
x y z
j
k
j
k
j j j
(a) x y z (b)
k k k
(c)
j
k
j
k
x y z
Fig. 4.5. (a) Both inputs = 0. (b) First input = 1. (c) Second input = 1. (d) Both
inputs = 1
j
k
(d)