Theoretical and Experimental DNA Computation (Natural ...

5.3 Initial Set Construction Within Filtering Models 111
Substrate
Enzyme
(b)
Ligand
Fig. 5.1. (a) Components of enzymatic switch. (b) Enzyme recognizes substrate
and cleaves it. (c) Ligand binds to enzyme, changing its conformation; enzyme no
longer recognizes substrate
initial multi-set. This is achieved as follows: for each pair (piki,pi+1ki+1) we
construct an oligo which is the concatenation of the complement of the second
half of the oligo representing piki and the complement of the first half of the
oligo representing pi+1ki+1. We also construct oligos that are the complement
of the first half of the oligo representing p1k1 and the last half of the oligo
representing pnkn. There is therefore a total of 2nk + 1 oligos in solution.
The effect of adding these new oligos is that double-stranded DNA will be
formed in the tube and one strand in each will be an element of the desired
initial set. The new oligos have, through annealing, acted as “splints” to join
the first oligos in the desired sequences. These splints may then be removed
from solution (assuming that they are biotinylated).
(a)
(c)