Synthesis and characterization of linear and cyclic ... - EleA@UniSA

HO
HO
O
NHCbz
89
Scheme 2.2. Synthesis of the PNA monomer 51. Reagents and conditions: a) t-Butanol, DMAP, DCC, CH2Cl2,
overnight, 58%; b) H2, Pd/C (10 % w/w), acetic acid, methanol, 1h and 30 min., quant.; c) Cbz-Cl, CH2Cl2, 0°C,
overnight, quant.; d) I2, imidazole, PPh3, CH2Cl2, 3h, 77%; e) K2CO3, CH3CN, reflux, overnight, 67%, f)
fluorenylmethoxycarbonyl chloride (Fmoc-Cl), NaHCO3, 1,4-dioxane/H2O, overnight, 97%; g) H2, Pd/C (10 %
w/w), acetic acid, methanol; 1h, quant.; h) ethyl glyoxalate, NaHB(AcO)3, triethylamine in CH2Cl2, overnight,
25%; i) thymine-1-acetic acid, Et3N, PyBOP in DMF; overnight, 70% l) LiOH, 1,4-dioxane/H2O, 30 min., 30%.
The oligomers 52-55 were manually assembled in a stepwise fashion on a Rink-amide NOVA-PEG
resin solid support. The unmodified PNA monomers were coupled using 2-(1H-benzotriazole-1-yl)-
1,1,3,3-tetramethyluronium hexafluoro-phosphate (HBTU). HATU was used for the coupling reactions
involving the less reactive secondary amino groups of the modified monomers 50 and 51. The decamers
were detached from the solid support and quantitatively deprotected from the t-butyl protecting groups,
using a 9:1 mixture of trifluoroacetic acid and m-cresol. The water-soluble oligomers were purified by
RP-HPLC, yielding the desired 52-55 as pure compounds. Their identity was confirmed by MALDI-
TOF mass spectrometry.
2.2.2 Hybridization studies
5
a
t-BuO
NHCbz
5
b
O
90
c d
NH2 HO
NHCbz
In order to verify the ability of decamers 49-52 to bind complementary DNA, UV-monitored melting
experiments were performed mixing the water-soluble oligomers with the complementary antiparallel
37
t-BuO
I
O
91
92 93 94
91 + 94
Fmoc
t-BuO
O
N
5
H
N
98
e
O
f
g
O
t-BuO
R
O
N
5
NHR'
95, R = H, R' = Cbz
96, R = Fmoc, R' = Cbz
97, R = Fmoc, R' = H
i
Fmoc
t-BuO
O
l
N
5
N
NH 2
5
NHCbz
O
O N
h
NH
O
O
R
O
99, R = CH 2CH 3
51, R = H