Information Technology Reference
In-Depth Information
Ta b l e 2 . 1
Basic DNA operations
α
[
i
,
j
]
Substring
αβ
Concatenation
c
(
α
)
Complementation
rev
(
α
)
Reversing
mir
(
α
)
Mirroring
α
][
β
Hybridization
α
β
Pairing
<
α
>
Blunt Pairing
2.2.2
DNA Helix
DNA molecules are constituted by nucleotides arranged in a bilinear structure.
Bilinearity
is accompanied by two other features:
complementarity
and
anti-
parallelism
. Both these features are consequences of the template driven dupli-
cation of DNA, which seems to be essential to the nature of this molecule. In fact,
template duplication is performed in two basic steps: removing the bonds which tie
the two paired sequences and then using each of them as a template by restoring the
missing paired sequence with the appropriate nucleotides matching the templates. In
this manner the two templates produce two equal double strands. In this procedure,
it is essential that paired strands could be unpaired. For this reason any nucleotide
has to be paired by a weak chemical bond, which is better realized between different
(complementary) molecules. In biological organisms this kind of duplication is per-
formed by a class of enzymes called Polymerase. Their action is essentially called
extension
, in fact they extend a strand in the verse 5
to 3
by copying the missing
(complementary) nucleotides according to the sequence specified by the template
strand (by using nucleotides floating in the environment). However, their action can
be performed only when an initial part of the missing strand, usually called
primer
is already present (see Fig. 2.3).
A bilinear structure which realizes a template driven duplication is described in
Fig. 2.4.
From an abstract viewpoint, a monomer
M
of a bilinear structure is charac-
terized by a triangle, say a
monomeric triangle
. In fact, let us consider an
internal point
P
of this monomer, for example its barycenter, which we call its
X-point. Then, the monomeric triangle is defined by the three point
P
P
where
P
is the X-point of the monomer
M
concatenated to
M
,and
P
is the
middle point between
P
and the X-point of the monomer
M
paired with
M
(see Fig. 2.4).
P
,
,
