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Chapter 3
with those of the analogous PNA bearing in the middle a chiral monomer 2D,5L based on
lysine.
Moreover, since the introduction of several adjacent positively charged monomers in the
sequence was demonstrated to improve the binding selectivity, another PNA was designed
combining the features of the “chiral box” PNA and those of 2D,5L PNA. This new PNA was
designed with a 2D,5L arginine-based monomer in the middle, which should determine an
enhanced affinity for the complementary DNA sequence, flanked by 2D-modified and a 5Lmodified
arginine-based monomers, which should improve the PNA selectivity in mismatch
PNA 1 PNA 2
Figure 3-2: Chemical structure of PNA 1: 2D,5L-Arg PNA and of PNA 2: 2D-Arg_2D,5L-Arg_5L-
Arg PNA (right)
recognition (PNA 2, Figure 3-2). The sequence chosen for both probes was a standard
decameric sequence used as model for the development of other modified PNAs, in order to
compare the performances of the new probes with those given by other modifications 10 .
3.2.2 PNA synthesis
PNAs were synthesized by using the common SPPS protocol based on the Boc strategy for
the standard monomers and for the monomer bearing the modification on the carbon atom in
position 5, whereas the Boc submonomer strategy was used for the monomers bearing the
substituents in position 2 or 2 and 5, in order to preserve the optical purity at the 2 position 15 .
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