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Chapter 5
Table 5-1. PNA sequences and melting temperatures of the PNA:DNA antiparallel
fullmatch/mismatch duplexes in phospate buffer (pH=7) at a 5µm concentration for each strand
PNA Sequence [a]
Tm (°C)
Tm (°C)
ΔTm
PNA/DNA
PNA/DNA
(°C)
Fullmatch [b]
Mismatch [b]
1 H-(AEEA) 2 TTACTCT (2D-Arg) TTCACC-
Lys(Fluorescein)-NH 2
2
48 (with c1) 37 (with c2) 11
H-(AEEA) 2 TTACTCA (2D-Arg) TTCACC-NH 2
55 (with c2) 35 (with c1) 20
3
4
5
6
H(AEEA) 2 GCCGCA (2D,5L-Arg) CACGT-NH 2
78 (with c3) 61 (with c5) 17
H-(AEEA) 2 CAGGCA (2D,5L-Arg) CTTCT-NH 2
69 (with c4) 50 (with c6) 19
H(AEEA) 2 GCCGCG (2D,5L-Arg) CACGT- NH 2
85 (with c5) 69 (with c3) 16
H-(AEEA) 2 CAGGCG (2D,5L-Arg) CTTCT-NH 2
75 (with c6) 60 (with c4) 15
[a] The chiral monomer corresponding to the SNP position is underlined in bold
[b] [b] Oligonucleotide sequences: c1: 5’-GGTGAAAGAGTAA-3’, c2: 5’-GGTGAATGAGTAA-3’
c3: 5’-ACGTGTGCGGC-3’, c4: 5’-AGAAGTGCCTG-3’, c5: 5’-ACGTGCGCGGC-3’,
c6: 5’-AGAAGCGCCTG-3’
PNA 1 was first used in order to study the patterning on the surface by a fluorescent label. For
this reason, a lysine unit protected on the side chain with a Dde group was introduced at the
C-end of the PNA, and, when the synthesis was complete, it was removed by hydrazine and a
carboxyfluorescein molecule was coupled to the primary amino group of the lysine side chain,
with the PNA still on resin. This was necessary because the N-terminal primary amino group
was to be used for linking the probe to the surface. Then, the PNA was cleaved from the resin;
characterization of PNA 1 is shown in figure 5-3.
Figure 5-3: HPLC profile and mass spectrum of PNA 1
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