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Preface
In Chapter 2 a particular type of modified PNA probe will be presented, PNA molecular
beacons. This type of molecule can recognize DNA without the need to label it in a pre-assay
step, because of their ability to selectively recognize complementary sequences and to emit a
fluorescence signal when hybridization takes place. PNA beacons will be applied in AE-
HPLC to develop a system able to detect with good selectivity a single nucleotide
polymorphism diagnostic of an olive cultivar.
In Chapter 3 the synthesis of chiral PNAs based on the structure of arginine will be described.
These PNAs are designed in analogy to those based on lysine, which already demonstrated
enhanced recognition performances compared to standard PNAs, especially in point mutation
recognition. The replacement of lysine with arginine is necessary to develop chiral PNAs to
be used on surfaces, for example for the fabrication of PNA-microarrays. In the chapter, the
synthesis of the modified monomers will be reported and different designs will be tested.
Finally the recognition properties of these probes will be compared with those of lysine-
PNAs.
Chapter 4 will show their application for the fabrication of microarrays to be used for the
recognition of two SNPs into the ApoE gene, which are involved in Alzheimer disease early
onset. The design and synthesis of these PNA probes will be described together with the
optimization of the method for the realization of the microarray system. Finally, the use of the
device for the recognition of the different genotypes which can be given by the combination
of possible SNPs will be reported.
The possibility to upgrade the fabrication of the devices presented in Chapter 4 will be
discussed in Chapter 5. Here, the use of microcontact printing for the derivatization of
surfaces with chiral PNAs will be demonstrated. In the first part the optimization of the
method will be described, since this is the first reported study on the use of microcontact
printing involving PNAs. The potential applications of these simple devices will be
demonstrated, studying the probe performances when linked to the surface, and testing the
selectivity of the devices. The fabrication of microarrays performed by coupling a commercial
array spotter with microcontact printing will be demonstrated, showing the improvements in
terms of time required, reproducibility and cost of the device.
Chapter 6 will explore a new potentiality of chiral PNAs, i.e. the ability to behave as a protein
analogue, rather than as an oligonucleotide analogue. The design and synthesis of a model
chiral PNA mimicking a Nuclear Localization Signal, a peptide able to be actively
internalized in the nucleus by a receptor-mediated system, will be shown. The potential
interaction between the modified PNA and the receptor will be shown through nuclear uptake
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