Information Technology Reference
In-Depth Information
3
between strands
γψβ
λ
λ
(
αϕγ
)
example, that of type 3
−
c
). Figure 2.40 displays
the possibility of hybridizations in a pool with two target strings and two extremal
primers (boxes includes the equal substrings in the two target molecules). It is easy
to check that the overall effect, in any case, is the amplification of the overlap con-
catenation of the two target molecules. In fact, either the doubling of the two target
molecules plus a seed of overlap concatenation, or two seeds of overlap concatena-
tion plus the initial pair of target molecules is obtained after hybridization.
and
Fig. 2.40
Possible hybridizations of
XPCR
We t e s t e d
XPCR
in several different experimental conditions and every time it
provided correct results [28, 30]. In most cases, the amplification signal is very clear
and a small noise consisting of unspecific products is reported in the electrophoresis
results. Surprisingly enough, on the basis of the simple mechanism of
XPCR
,we
have been able to build more sophisticated procedures, which find two main kinds
of applications in DNA extraction and DNA recombination.
2.5.2
DNA Extraction by
XPCR
DNA extraction is a fundamental procedure where the “good solutions” are discrim-
inated in a space of possible solutions. For example, given a DNA pool consisting
of a family of genes with an indefinite identity (their sequences are not known),
one might be interested in extracting the subfamily of those genes where a given
subsequence
occurs, which, for instance, refers to an important biological prop-
erty. The classic extraction procedure
by affinity
uses a probe
¯
γ
γ
which is “marked”
in such a way that, after denaturation, single strands where
occurs hybridize with
the probe, and so are selected from the original pool. Here we show a different way
of performing extraction, based on
XPCR
, outlined in TTL notation, in Table 2.6
(
P
γ
denotes the pool
P
after removing its strands of length
n
).
The main idea of the algorithm is as follows. Consider all the lengths of strands
in a given pool. For each length
n
, pieces of strands which include the substring
γ
−
separate
(
P
,
n
)
in their types are copied. This is performed by means of usual PCR to amplify
both strands of type
. Strings shorter than
n
are then separated
by length and finally joined by an overlapping concatenation performed by
XPCR
.
<
αγ
>
and
<
γβ
>
