Strings and Genomes - Infobiotics: Information in Biotic Systems - page 43

are Test Tubes which contain DNA pools, rather than numbers, and DNA pool oper-
ations apply to them. The symbol : denotes the usual assignment command typical

of imperative languages. In an assignment P :

=

, the operation op is intended
to be applied to the content of the test tube Q and the resulting DNA pool becomes
the content of the test tube P .
The exact “microscopic” effect of operations in Table 2.2 is not defined, because
in many cases it is hard to say exactly what are the multisets before and/or after the
application of these operations. However, despite such a kind of incomplete knowl-
edge at a microscopic level, DNA algorithms can be designed which are based on
these operations. In fact, it is enough to assume that, after performing a given DNA
operation, an input pool P is transformed into a pool P where a specific relationship
holds between the types of P and P (see Table 2.2 and Figs. 2.18, 2.19, 2.20).
The realization of operations in Table 2.2 is performed by means of standard labo-
ratory procedures based on physical and biological phenomena. Operations mix and
split are simply obtained by merging the content of two test tubes, or by splitting the
content of one test tube in two different test tubes. Operations length and separate
are realized by means of gel-electrophoresis, a specific electrochemical tool for dis-
criminating DNA strands according to their length. The operation hybridize is ob-
tained by raising temperature, while renat ure by (slowly) decreasing it. Operations
ext end , ligate ,and in f ix are realized by Polymerase and Ligase enzymes (see Figs.
2.21, 2.22).

= op ( Q )

P1

P

P2

Fig. 2.18 Split operation (Mix is realized in the inverse way)

In Gel-electrophoresis DNA strands are put over a plate with a gel producing
resistance to the movement of DNA molecules. An electrical field is applied be-
tween the two extremal borders of the plate (see Fig. 2.19). In column 1, strands
of different (known) length are located at different levels. In the other columns,
strands of unknown lengths stop at some level after the effect of the electrical field
(DNA is negatively charged). Their positions, compared with the position of refer-
ence strands, provide a precise estimation of their lengths. The strands at a given