Strings and Genomes - Infobiotics: Information in Biotic Systems - page 46

2.3.1 Writing and Reading DNA

ADNA clone is a multiset of DNA strands constituted by many copies of the same
DNA molecule, or equivalently, a set of DNA strands or double strands having the
same type. Two important aspects of DNA manipulation are the basic operation
of any system of information representation: writing and reading. Writing DNA
consists in generating a clone of DNA molecules having as type a given string over
the alphabet of nucleotides. Reading means the inverse operation, that is, given a
clone of DNA molecules, discovering which is the string of bases corresponding to
their type.
The first operation, which is called DNA synthesis , is now a routine operation
and is based on the following principle. Consider nucleotides where one of the two
extremities is removed, say the 5 of the phosphoric group. Let us group in different
vessels containing a given number of each nucleotide deprived of the P-terminal:
a vessel A containing A OH (instead of P A OH ), a vessel T containing T OH ,aves-
sel C containing C OH , and a vessel G containing G OH . Let us write, for example,
the sequence ATTCG. We start with a nucleotide (or better, a clone of nucleotides)
P G OH bound to a solid support S by means of some affinity mechanism, which an-
chor them to S ,sayit S

+ P G OH in the vessel C. The loss
of P-extremity of nucleotides in this vessel ensures that when S

+ P G OH . Then we put S

+ P G OH is put in

the vessel only S C OH P G OH can be formed, where C nucleotides are without the

P-terminal. Therefore, we add to S

+

+ C OH P G OH the missing P-terminal. by obtaining

molecules S + P C OH P G OH . The same process can start again with sequences CG an-

chored to the support S and having both the extremities, for completing the process,
by adding the remaining TCG part. In general, writing is performed by anchoring to
a solid support S the last nucleotide of the sequence we want to write (3 terminal),
and then, by proceeding in the verse 3 − 5 , by iterating the cycle of: i) introducing

the solid support S in the right vessel for linking molecules inside it to the OH -
terminal of molecules anchored to S , ii) extracting S from the vessel, and iii) adding
the P-terminal to the molecule anchored to S .
Reading DNA is the process usually indicated as DNA sequencing . In fact, it
provides the sequence bases corresponding to the type of a given DNA clone. In the
reading process, it is essential to assume that DNA which has to be read is provided
as a clone. We will explain the main idea of sequencing by using a metaphor. Let us
assume the availability of a sequence of balls of four colors, say A, T, C, and G. Let
us assume also that these balls are so small that we cannot distinguish their colors.
However, let us suppose that we are able to obtain many copies of the given original
sequence of balls. Then, we can distribute these copies in four different vessels. In
each vessel we use some special scissors S A , S G such that S A cuts after A , S T

cuts after T , S C cuts after C ,and S G cuts after G . Moreover, in order to keep the right
analogy with DNA, our balls are asymmetric, with a left part and a right part, in such
a way that scissors can act only once for each strand, by cutting and by keeping in
the vessels only the left parts. In these hypotheses, after using the corresponding
scissors in each vessel, we get some strands which are copies of prefixes of the
original sequence. If scissors perform their task in a completely random way, then

S T , S C ,