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Chapter 3
+
i
ii
iii
Scheme 3-2: i) 1 eq. Gly-OMe·HCl, 1 eq. NaBH 3 CN, 1.1 eq. CH 3 COOH, CH 3 OH, η: 50%; ii)
2eq. carboxymethyl-(Z)-cytosine, 2 eq EDC·HCl, 2 eq DhBTOH, 3 eq DIPEA, DMF η: 83%.iii)
2eq. BaOH THF: H 2 O = 1:1, η: 75%
activating the carboxylic group with N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide
(EDC)/ 3-Hydroxy-1,2,3-benzotriazin-4(3H)-one (DhbtOH). Finally the methyl ester was
hydrolyzed, obtaining the desired monomer (Scheme 3-2). All the above compounds were
characterized by 1 H and 13 C NMR and ESI mass spectrometry.
According to previously reported procedures 15 , the chiral submonomers units were inserted by
manual coupling with the HATU/DIEA protocol and, after Fmoc deprotection, the nucleobase
residues were introduced by a double coupling with DIC/DhBTOH. All the PNA oligomers
were purified by RP-HPLC and characterized by ESI-mass spectrometry (Figure 3-3).
The analysis of HPLC-MS data in figure 3-3 shows that PNA 1 was obtained with good purity
(>90%), whereas PNA 2, even after HPLC purification, showed ~28% of a byproduct
identified by MS as the PNA2 without a carboxymethyladenine moiety. This byproduct was
originated because of the low coupling efficiency between the carboxymethyladenine and the
PNA in the last 2D chiral monomer, probably due to the steric hindrance exerted by the
previous monomers. The iteration of the same coupling many times, as well as the use of
other coupling agents or different reaction conditions, did not allow to obtain a quantitative
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