Chemistry Letters 2001
635
those with pyrimidine-rich sequences.
It is to be noted that the restriction of the side-chain orien-
tation does not suppress the hybridization, if the orientation is
appropriate. The flexible main chain and the restricted side
chain of PPNA are common conformational characteristics to
DNA and RNA.
This work has been supported by a Grant-in-Aid for
Specially Promoted Research from the Ministry of Education,
Science, Sports and Culture (No.11102003).
References and Notes
1
P. E. Nielsen, M. Egholm, R. H. Berg, and O. Buchardt,
Science, 254, 1497 (1991).
2
a) R. Schultz, M. Cantin, C. Roberts, B. Greiner, E.
Uhlmann, and C. Leuman, Angew. Chem. Int. Ed., 39,
1250 (2000). b) T. Vilaivan, C. Khongdeesameor, P.
Harnyuttanakorn, M. S. Westwell, and G. Lowe, Bioorg.
Med. Chem. Lett., 10, 2541 (2000). c) A. Puschl, T.
Tedeschi, and P. E. Nielsen, Org. Lett., 2, 4161 (2000). d)
T. Wada, N. Minamimoto, Y. Inaki, and Y. Inoue, J. Am.
Chem. Soc., 122, 6900 (2000).
points are observed, indicating that only the hybrid and free
DNA are present under [ppA9] < [dT9] and only the hybrid and
free PPNA under [ppA9] > [dT9]. The CD intensity at 249 nm
showed a minimum when [ppA9] = [dT9]. These facts indicate
that the ppA9 hybridizes with dT9 to form a 1:1 hybrid with
very high affinity and no triplex is formed. Note that the CD
spectrum of the 1:1 hybrid is very similar to that of the oA9-dT9
hybrid.3
3
a) M. Kuwahara, M. Arimitsu, and M. Sisido, J. Am.
Chem. Soc., 121, 256 (1999). b) M. Kuwahara, M.
Arimitsu, M. Shigeyasu, N. Saeki, and M. Sisido, J. Am.
Chem. Soc., 123, 4653 (2001).
4
5
6
K.-H. Altmann, D. Hüsken, B. Cuenoud, and C. García-
Echeverría, Bioorg. Med. Chem. Lett., 10, 929 (2000).
M. Kuwahara, M. Arimitsu, and M. Sisido, Tetrahedron,
55, 10067 (1999).
Compound 3 (5.8 g, 16 mmol), tert-butyl bromoacetate
(6.2 g, 32 mmol), tetrabutylammonium sulfate (1.4 g, 4
mmol) were dissolved into benzene/50% NaOH (3/1) mix-
ture (56 mL). The mixture was stirred at 10 °C for 5 h.
The organic layer was washed with 2M HCl, dried over
anhydrous magnesium sulfate and evaporated. The crude
product was purified by a silica gel column to give 4 (8.8
g, 81%).
7
Compound 5 (2.3 g, 6.94 mmol), 6-chloropurine (1.1 g,
6.94 mmol), and triphenyl phosphine (2.7 g, 10.4 mmol)
were dissolved into anhydrous THF (20 mL) under argon
atmosphere. The mixture was cooled to 0 °C and diethyl
azodicarboxylate (1.6 mL, 10.4 mmol) was added drop-
wise. The reaction was continued overnight at room tem-
perature. The product was purified by a silica gel column
to give 6 (2.75 g, 85%). The latter was dissolved in ammo-
nia-saturated ethanol and stored at room temperature for 3
days. The solvent was evaporated and the residue was
purified by a silica gel column to give 7 (403 mg, 50%). 1H
NMR of 7 showed a single peak for each proton, indicating
that the inversion at the 4th carbon was almost 100%; (300
MHz, CDCl3,) δ = 1.52 (9H, s), 1.53 (9H, s), 2.76 (2H, m),
3.62 (1H, m), 3.80 (2H, m), 4.05 (2H, q), 4.21 (1H, br),
4.30 (1H, br), 5.19 (1H, m), 6.05 (2H, s), 8.22 (1H, s), 8.40
(1H, s).
Temperature dependence of the absorption intensity at 260
nm of the ppA9-dT9 1:1 mixture, together with those for the
oA9-dT9 and dA9-dT9 mixtures are shown in Figure 2. The
melting temperatures were 34 °C for the ppA9-dT9, 35 °C for
the oA9-dT9, and about 15 °C for the dA9-dT9 hybrid, respec-
tively. Similar to the oA9-dT9 case, the melting curve of the
ppA9-dT9 hybrid showed a very sharp transition, suggesting
that the ether linkage in the main chain is responsible for the
sharp melting curve. Presumably, the flexible polyetheramide
main chain causes a large entropy loss and a large enthalpy sta-
bilization when it forms duplex with DNA, and results in the
sharp melting curves. The sharp melting curve is very advanta-
geous for the PPNA and OPNA when they were applied as anti-
sense drugs.
8
9
TOF-mass data of 8, found, m/z 514.8 (M+H)+; calcd for
C27H26N6O5, 515.2. 1H NMR of 8 showed unresolved
peaks that could not be assigned to individual protons.
TOF-mass data of ppA9, found, m/z 2613.5 (M+H)+; calcd
for C114H142N57O19, 2613.2.
Since the ppA9-dT9 and oA9-dT9 hybrids showed similar
melting curves and CD spectra, the side-chain orientations of
the two oxy-peptide nucleic acids in the hybridized state may
be similar. The information will be helpful in designing confor-
mationally matched oxy-peptide nucleic acids, especially for