Synthesis and conformation of a novel bridged nucleic acid having a trans-fused 3,5,8-trioxabicyclo[5.3.0]decane structure

Article abstract of DOI:10.1016/j.tetlet.2004.04.082

A novel bridged nucleic acid analogue, 2′-deoxy-trans-3′, 4′-BNA thymine monomer, was successfully synthesized. An ab initio calculation and X-ray structure analysis revealed that the trans-fused bicyclo[5.3.0]decane structure of the 2′-deoxy-trans-3′,4′-BNA effectively constrained the sugar puckering in C_2′-endo with appropriate γ, δ and χ angles.

Full text of DOI:10.1016/j.tetlet.2004.04.082

Tetrahedron
Letters
Tetrahedron Letters 45 (2004) 4801–4804
Synthesis and conformation of a novel bridged nucleic acid having a
trans-fused 3,5,8-trioxabicyclo[5.3.0]decane structure
Satoshi Obika, Tomohisa Osaki, Mitsuaki Sekiguchi, Roongjang Somjing,
Yasuki Harada and Takeshi Imanishi*
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
Received 18 February2004; revised 30 March 2004; accepted 5 April 2004
Abstract—A novel bridged nucleic acid analogue, 20-deoxy-trans-30,40-BNA thymine monomer, was successfully synthesized. An
ab initio calculation and X-raystructure analysis revealed that the trans-fused bicyclo[5.3.0]decane structure of the 20-deoxy-trans-
30,40-BNA effectivelyconstrained the sugar puckering in C 2 -endo with appropriate c, d and v angles.
0
Ó 2004 Elsevier Ltd. All rights reserved.
The sugar moietyin nucleosides is well known to have
relativelylarge conformational flexibilit.y We have
synthesized the nucleic acid analogue, 20,40-BNA1/
LNA,2 of which sugar puckering is exactlyrestricted to
N-type, and the 20,40-BNA oligonucleotides showed high
OH
HO
H
T
T
O
O
OH
OH
C1'-exo
C2'-endo
(Leumann, C. et al. Ref. 7)
(Leumann, C. et al. Ref. 8)
3
binding affinitytowards ssRNA and dsDNA.4 Thus,
preorganization of a nucleoside sugar moietyin an
appropriate conformation is one promising strategyto
develop nucleic acid analogues with superior binding
ability.
OH
O
HO
T
O
T
O
HO
O
OH
C2'-endo
C3'-exo
OH
(Wengel, J. et al. Ref. 9)
(Nielsen, P. et al. Ref. 10)
Oligonucleotides containing a nucleoside with S-type
sugar conformation are expected to form a stable duplex
of B-DNA and to be applicable to post-genome tech-
nologies, such as DNA microarray5 and decoynucleic
acid.6 Therefore, nucleoside analogues with a restricted
S-type sugar conformation have been designed and
synthesized to date (Fig. 1).7–11 Some of them were
introduced into oligonucleotides and the hybridizing
properties were studied. However, these oligonucleotide
analogues showed onlymoderate increase or consider-
able decrease in the duplex stability, probably due to
insufficient and/or improper restriction of the sugar
conformation. In the B-DNA, the furanose rings are
Figure 1. Selected bicyclic and tricyclic nucleoside analogues with
S-type conformation.
exhibited bytorsion angle d ranged from 79° to 157°,
and the c angle is in the +sc range, 40°–73° (Fig. 2).12 In
addition, the v angle around )100° is one important
characteristic of the B-DNA.12 Thus, besides the S-type
sugar puckering, these torsion angles c, d and v must be
in the appropriate range to prepare an ideal nucleoside
analogue for B-DNA modification.
0
0
puckered C2 -endo or C3 -exo (S-type), which is also
Recently, we synthesized an S-type nucleoside analogue,
trans-30,40-BNA 1,13 of which sugar puckering was re-
0
stricted to C3 -exo (Fig. 3). However, a trans-fused six-
membered ring of 1 causes large d angle (174.6°), and the
Keywords: Nucleic acid analogues; Conformation; X-raycrystal struc-
tures.
steric hindrance of the 20-substituent group results in
0
low reactivityof 3 -OH (data not shown).14 Here, we
would like to describe the synthesis and structure of a
* Corresponding author. Tel.: +81-6-6879-8200; fax: +81-6-6879-8204;
e-mail: imanishi@phs.osaka-u.ac.jp
0040-4039/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2004.04.082

4802
S. Obika et al. / Tetrahedron Letters 45 (2004) 4801–4804
tively, and sufficient flexibility of c and v is also
O
H3C
O
observed. Thus, it is shown that the 20-deoxy-trans-30,40-
BNA 2 fulfills the conformational criteria for an ideal S-
type nucleoside analogue.
O-
O
O
NH
O
P
O
N
torsion angle
range
χ
γ
γ
~
40
73
To successfullyachieve the synthesis of 2 0-deoxy-trans-
30,40-BNA, we chose thymidine as starting material
(Schemes 1 and 2). According to the literature,16 thy-
midine was converted in a three-step sequence to the 30-
deoxy-30-C-methylenethymidine derivative 3 (Scheme 1).
Stereoselective catalytic osmium tetraoxide oxidation of
3 gave the diol 4 in 65% yield.17 Protection of the thy-
mine nucleobase in 4 using benzyl chloromethyl ether
(BOMCl) afforded 5 in 89% yield, which was treated
with chloromethyl methyl ether (MOMCl) to obtain 6 in
54% yield. The 30-hydroxy group of 6 was protected with
benzyl group to give 7 in 84% yield. Continuously, de-
protection of the 50-O-trytyl group gave the primary
alcohol 8 in 90% yield. Dess–Martin oxidation of 8
affording the corresponding aldehyde 9 was followed by
an aldol condensation using formaldehyde and reduc-
tion with sodium borohydride to give the diol 10 (63%,
two steps). It was reported that the reaction of a MOM
group with a neighboring hydroxyl group gave a cyclic
methylene acetal under acidic conditions.18 Therefore,
we attempted to construct the trans-fused bicy-
clo[5.3.0]decane structure via a direct seven-membered
ring formation of 11 under acidic conditions (Scheme 2).
Although the formation of desired compound 11 was
not observed, it was interesting that the spiro-type
compound 13 was obtained in 53% yield along with the
cis-fused compound 12 (28%) after sufficient reaction
time at 80 °C.19 This result implies that the cis-fused
compound 12 migrated to the thermodynamically stable
spiro-type compound 13 under the acidic reaction con-
ditions.20 To prevent the formation of cis- and spiro-
type compounds, the 50-hydroxy group in 10 was benz-
ylated to give 14 in 49% yield. Then, the obtained 14
δ
~
δ
79
157
O
O
P
O
O-
χ
~
-88 -135
Figure 2. The range of torsion angles c, d and v for the B-DNA.12
O
O
H3C
OH
H3C
OH
NH
NH
N
N
4'
3'
4'
O
O
O
O
O
O
OR
O
3'
OH
OH
trans-3',4'-BNA (1)
S-type (C3'-exo)
2'-deoxy-trans-3',4'-BNA (2)
S-type (C2'-endo)
Figure 3. Structure of trans-30,40-BNA and 20-deoxy-trans-30,40-BNA.
novel S-type nucleoside analogue, 20-deoxy-trans-30,40-
BNA 2, which lacks 20-substituents and has a trans-fused
seven-membered ring containing a methylene acetal to
adjust the d angle.
At first, an ab initio calculation using 3-21G(*) basis
set15 for the 20-deoxy-trans-30,40-BNA 2 was carried out
to evaluate the conformation of the furanose ring and
flexibilityof the torsion angles c and v. The results show
0
that the C2 -endo sugar puckering is the most favorable
with the d angle of 159.4°. The torsion angles c and v in
the optimized structure are 50.0° and )129.3°, respec-
O
O
O
N
H3C
H3C
H3C
NR1
NH
NH
N
O
N
O
O
R4O
R2O
HO
TrO
O
O
Ref. 16
3 steps
O
i)
OR3
OH
thymidine
3
4 R1 = H, R2 =H, R3 = H, R4 = Tr
ii)
5 R1 = BOM, R2 =H, R3 = H, R4 = Tr
6 R1 = BOM, R2 =MOM, R3 = H, R4 = Tr
7 R1 = BOM, R2 =MOM, R3 = Bn, R4 = Tr
8 R1 = BOM, R2 =MOM, R3 = Bn, R4 = H
iii)
iv)
v)
O
O
BOM
BOM
O
H3C
H3C
N
N
vi)
N
O
N
vii)
MOMO
HO
O
O
O
HO
OBn
OBn
MOMO
10
9
Scheme 1. Reagents and conditions: (i) OsO4, N-methylmorpholine-N-oxide, pyridine–H2O–tert-BuOH, 75 °C (65%); (ii) BOMCl, DBU, DMF, 0 °C
(89%); (iii) MOMCl, i-Pr2NEt, pyridine–ClCH2CH2Cl, rt (54%); (iv) NaH, BnBr, n-Bu4NI, DMF, rt (84%); (v) (+)-10-camphorsulfonic acid,
CH2Cl2–MeOH, rt (90%); (vi) Dess–Martin periodinane, CH2Cl2, rt; (vii) 37% H2CO aq, 1 M NaOH aq, THF, 15 °C, then NaBH4, THF, 0 °C (63%
from 8).

S. Obika et al. / Tetrahedron Letters 45 (2004) 4801–4804
4803
O
N
O
N
O
BOM
O
BOM
O
H3C
H3C
H3C
OH
N
N
BOM
N
O
N
O
O
i)
O
O
O
O
O
O
10
O
HO
OBn
OBn
OBn
HO
12
13
11
HO
HO
HO
O
13
12
HO
HO
OBn
OBn
OBn
O
O
HO
O
H3C O
H
O
N
BOM
O
H3C
H3C
OBn
N
BOM
N
N
BnO
O
O
O
iv)
ii)
iii)
O
O
2
10
HO
OBn
14
OBn
MOMO
15
Scheme 2. Reagents and conditions: (i) p-TsOHÆH2O, benzene, reflux (28% for 12, 53% for 13); (ii) NaH, BnBr, DMF, 0 °C (49%); (iii) p-TsOHÆH2O,
(CH2O)n, ClCH2CH2Cl, reflux (47%); (iv) HCOONH4, 20%Pd(OH)2/C, EtOH, reflux (60%).
Table 1. Selected torsion angles, maximum torsion angle (mmax) and
pseudorotation phase angle (P) in the X-raystructure of 2
was allowed to react under acidic conditions; however,
this reaction caused partial deprotection of the MOM
group and the desired trans-fused compound 15 was not
obtained. After some trials it was found that an addition
of excess amount of paraformaldehyde under acidic
conditions afforded the trans-fused compound 15 in 47%
yield.21 A Pd-mediated hydrogenolysis successfully gave
the fullydeprotected compound 2 in 60% yield.22
m0 (C40–O40–C10–C20)
m1 (O40–C10–C20–C30)
m2 (C10–C20–C30–C40)
m3 (C20–C30–C40–O40)
m4 (C30–C40–O40–C10)
d (O30–C30–C40–C50)
c (C30–C40–C50–O50)
v (O40–C10–N1–C2)
mmax
)19.0°
40.1°
)44.5°
34.9°
)10.2°
164.0°
)178.8°
)126.1°
44.7°
The trans-fused structure of 2 was confirmed byan X-ray
crystallographic analysis (Fig. 4 and Table 1),23 which
also indicates that the furanose ring of 2 has a typical S-
P
174.2°
0
type conformation, C2 -endo puckering (pseudorotation
phase angle P ¼ 174:2°). The maximum torsion angle
mmax and d angle of 2 are 44.7° and 164.0°, respectively.
These angles are remarkablyimproved compared with
those of the trans-30,40-BNA 1 (mmax: 51.9° and d:
174.6°)13 and are in good agreement with those of natural
B-DNA. In addition, the v angle of À126.1° is also within
the range of a typical B-type DNA.
In conclusion, we have successfullydemonstrated the
synthesis of a novel S-type nucleoside analogue, 20-
deoxy-trans-30,40-BNA 2. Bymeans of ab initio calcu-
lation and X-ray crystallography, 2 was found to fully
satisfythe conformational requirements of B-DNA.
Further studies on 2 and its oligonucleotide derivative
are now in progress.
Acknowledgements
We thank M. Shiro (Rigaku Corp) for X-raycrystallo-
graphic analysis. Part of this work was supported by the
Figure 4. ORTEP drawing of 20-deoxy-trans-30,40-BNA monomer 2.

4804
S. Obika et al. / Tetrahedron Letters 45 (2004) 4801–4804
12. Saenger, W. Principles of Nucleic Acid Structure; Springer-
Verlag: New York, 1984, and references cited therein.
13. Obika, S.; Sekiguchi, M.; Osaki, T.; Shibata, N.; Masaki,
M.; Hari, Y.; Imanishi, T. Tetrahedron Lett. 2002, 43,
4365–4368; Nielsen, P. et al. independentlyreported the
synthesis of 1 just after our publication. See: Thomasen,
H.; Meldgaard, M.; Freitag, M.; Petersen, M.; Wengel, J.;
Nielsen, P. Chem. Commun. 2002, 1888–1889.
14. The phosphitilation at the 30-hydroxy group of 1 did not
proceed efficiently, probably due to the steric hindrance of
the 20-substituent group (data not shown).
Japan Securities Scholarship Foundation (JSSF) Aca-
demic Research Grant Program, Industrial Technology
Research Grant Program in 2000 from New Energyand
Industrial TechnologyDevelopment Organization
(NEDO) of Japan, a Grant-in-Aid from the Japan
Societyfor the Promotion of Science, Sunbor Grant
from SuntoryInstitution for Bioorganic Research and a
Grant-in Aid from the Ministryof Education, Science,
and Culture, Japan. We thank JSPS Research Fellow-
ships for Young Scientist (M.S.).
15. The Spartane version 5.1 molecular orbital package
(Wavefunction Inc.) utilizing the HF/3-21G(*) model
was used for the ab initio calculations. Numerical calcu-
lations were performed on an Octanee (SGI) workstation.
16. (a) Froehlich, M. L.; Swartling, D. J.; Lind, R. E.; Mott,
A. W.; Bergstrom, D. E. Nucleosides & Nucleotides 1989,
8, 1529–1535; (b) Sharma, M.; Bobek, M. Tetrahedron
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17. Scheuer-Larsen, C.; Pfundheller, H. M.; Wengel, J. J. Org.
Chem. 1995, 60, 7298–7303.
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3111–3114; (b) Powell, N. A.; Roush, W. R. Org. Lett.
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References and notes
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2. The 20,40-BNA is also called ‘LNA’ byWengel, J. et al.
See: (a) Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel,
J. Chem. Commun. 1998, 455–456; (b) Koshkin, A. A.;
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gaard, M.; Rajwanshi, V. K.; Singh, S. K.; Wengel, J.
J. Am. Chem. Soc. 1998, 120, 13252–13253; (d) Wengel, J.
Acc. Chem. Res. 1999, 32, 301–310; (e) Meldgaard, M.;
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19. Compound 12 and 13 were assigned bycomparing with
the analogues, which were synthesized through another
route.
Selected data for 12: 1H NMR (CDCl3) d 1.97 (3H, d,
J ¼ 1 Hz), 2.31 (1H, dd, J ¼ 6, 8 Hz), 2.45 (1H, dd, J ¼ 7,
14 Hz), 2.79 (1H, dd, J ¼ 6, 14 Hz), 3.54 (1H, dd, J ¼ 8,
11 Hz), 3.86 (1H, dd, J ¼ 6, 11 Hz), 3.92 (2H, s), 4.11 (2H,
s), 4.57 (2H, s), 4.66, 5.04 (2H, AB, J ¼ 6 Hz), 4.70 (2H, s),
5.49 (2H, s), 6.28 (1H, t, J ¼ 6 Hz), 7.27–7.41 (10H, m),
7.71 (1H, s). MS (EI): m=z 524 (Mþ, 1.0), 91 (100). HRMS
(EI): Calcd for C28H32N2O8 (Mþ): 524.2153. Found:
524.2158.
Selected data for 13: 1H NMR (CDCl3) d 1.94 (3H, d,
J ¼ 1 Hz), 1.96 (1H, dd, J ¼ 9, 15 Hz), 2.76–2.79 (1H, br),
2.85 (1H, dd, J ¼ 5, 14 Hz), 3.71–3.78 (3H, m), 4.03 (1H,
dd, J ¼ 8, 13 Hz), 4.17 (1H, dd, J ¼ 1, 12 Hz), 4.49 (1H, br
d, J ¼ 12 Hz), 4.57, 4.72 (2H, AB, J ¼ 11 Hz), 4.69 (2H, s),
4.81, 4.95 (2H, AB, J ¼ 6 Hz), 5.47 (2H, s), 6.02 (1H, dd,
J ¼ 5, 9 Hz), 7.25–7.38 (11H, m). MS (EI): m=z 524 (Mþ,
2.3), 418 (100). HRMS (FAB): Calcd for C28H33N2O8
(MþH): 525.2237. Found: 525.2235.
6. For reviews: (a) Cho-Chung, Y. S.; Park, Y. G.; Lee, Y. N.
Curr. Opin. Mol. Ther. 1999, 1, 386–392; (b) Morishita, R.;
Aoki, M.; Kaneda, Y. Curr. Drug Targets 2000, 1, 15–23.
20. Treatment of the spiro-type compound 13 under the acidic
conditions afforded the cis-fused compound 12 (27%)
along with the recoverd 13 (45%).
€
7. (a) Tarkoy, M.; Bolli, M.; Schweizer, B.; Leumann, C.
Helv. Chim. Acta 1993, 76, 481–510; (b) Tarkoy, M.; Bolli,
21. Nouguier, R.; Gras, J.-L.; Mchich, M. Tetrahedron 1988,
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22. Selected data for 2: mp 244–247 °C (CH3CN). H NMR
€
1
M.; Leumann, C. Helv. Chim. Acta 1994, 77, 716–744; (c)
Bolli, M.; Trafelet, H. U.; Leumann, C. Nucleic Acids Res.
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(CD3OD) d 1.89 (3H, d, J ¼ 1 Hz), 2.36 (1H, dd, J ¼ 6,
13 Hz), 2.48 (1H, dd, J ¼ 9, 12 Hz), 3.73, 4.05 (2H, AB,
J ¼ 11 Hz), 3.81, 3.91 (2H, AB, J ¼ 12 Hz), 4.00, 4.15
(2H, AB, J ¼ 12 Hz), 4.85, 5.55 (2H, AB, J ¼ 8 Hz), 6.32
(1H, dd, J ¼ 6, 9 Hz), 8.15 (1H, d, J ¼ 1 Hz). MS (FAB):
m=z 315 (MþH). HRMS (FAB): Calcd for C13H19N2O7
(MþH): 315.1192. Found: 315.1216.
8. (a) Steffens, R.; Leumann, C. J. J. Am. Chem. Soc. 1997,
119, 11548–11549; (b) Steffens, R.; Leumann, C. Helv.
Chim. Acta 1997, 80, 2426–2439; (c) Steffens, R.; Leu-
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Manoharan, M.; Christman, J. K.; Banavali, N. K.;
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Acids 2001, 20, 451–459.
23. Crystallographic data (excluding structure factors) for the
structures in this paper have been deposited with the
Cambridge Crystallographic Data Center as supplemen-
tarypublication numbers CCDC230411. Copies of the
data can be obtained, free of charge, on application to
CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK [fax:
+44(0)-1223-336033 or email: deposit@ccdc.cam.ac.uk].