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In Fig. 2.37, a PCR process is displayed, where the first two steps are completely
represented, while, for easier reading, only two double strands of the third step
are shown. One of them is a blunt double strand that is a seed of exponential
amplification.
We remark that PCR lemma presented here is different from the analogous lemma
given in [45]. Namely, here we do not claim to cover all the possible cases of am-
plification. In fact, some laboratory experiments have shown cases of exponential
amplification with
YY
forms, where primers hybridize with flanking regions (and
produce amplifications having patterns different from those given in Eqs. 2.2, 2.3,
2.4). Here we do not analyze all the cases of PCR with
YY
forms. The example of
Fig. 2.39 shows the complexity of the combinatorial patterns related to PCR amplifi-
cation. In this figure, starting with a
YY
molecule M1 and two primers that hybridize
on two flanking regions, the molecule M2 is realized, which consists of the exten-
sions of the two primers. Molecules M3 and M4 are obtained by hybridization of
molecules of type M2 with the two strands of M1. In these molecules, it easy to
realize that the extensions of the primers stop when polymerase reaches the other
flanking regions. The resulting extensions hybridize and produce the molecule M5,
that, after polymerase extension, becomes the blunt molecule M6, which is seed of
an exponential amplification.
An example where PCR lemma does not apply is displayed in Fig. 2.38.
Fig. 2.38
A case where PCR lemma does not apply
