Synthesis and conformation of a novel bridged nucleoside with S-type sugar puckering, trans-3′,4′-BNA monomer

Article abstract of DOI:10.1016/S0040-4039(02)00784-0

A novel bridged nucleoside bearing a 4,7-dioxabicyclo[4.3.0]nonane skeleton, trans-3′,4′-BNA monomer, was successfully synthesized. A ¹H NMR experiment and an X-ray crystallographic analysis revealed that the sugar puckering of the 3′,4′-BNA monomer was restricted to an S-type (C_3′-exo) conformation.

Full text of DOI:10.1016/S0040-4039(02)00784-0

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 43 (2002) 4365–4368
Synthesis and conformation of a novel bridged nucleoside with
S-type sugar puckering, trans-3%,4%-BNA monomer
Satoshi Obika, Mitsuaki Sekiguchi, Tomohisa Osaki, Nao Shibata, Miyuki Masaki, Yoshiyuki Hari
and Takeshi Imanishi*
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
Received 29 March 2002; revised 17 April 2002; accepted 19 April 2002
Abstract—A novel bridged nucleoside bearing a 4,7-dioxabicyclo[4.3.0]nonane skeleton, trans-3%,4%-BNA monomer, was success-
fully synthesized. A 1H NMR experiment and an X-ray crystallographic analysis revealed that the sugar puckering of the
3%,4%-BNA monomer was restricted to an S-type (C3%-exo) conformation. © 2002 Elsevier Science Ltd. All rights reserved.
The importance of the synthesis of novel nucleoside
analogues is increasing more and more in the post-
genome-sequencing era. The nucleic acid analogues
which strongly bind with their RNA complements are
very useful as antisense molecules to regulate the
targeted gene expression.1 On the other hand, the ana-
logues acquiring both strong and sequence selective
binding ability towards the DNA complements are
expected to be applicable to some other beneficial tech-
nologies such as DNA microarray2 and a decoy nucleic
acid.3
Nowadays, some nucleoside analogues with a bicyclic
or tricyclic sugar moiety, of which the conformation
was restricted in S-type (DNA-type), were synthesized
(Fig. 2), and the hybridization property of the oligonu-
cleotides containing these conformationally restrained
nucleoside analogues was evaluated.10–13 However, only
moderate enhancement of the duplex stability by these
nucleoside modifications was observed, probably due to
insufficient and/or improper restriction of the sugar
conformation, or steric repulsion between the addi-
tional ring structure and neighboring nucleotide
residues.
Double-stranded RNA and DNA are well-known to
prefer forming A-type and B-type helical structures,
respectively. In each structure, ribonucleosides predom-
inantly exist in N-type sugar conformation, while
deoxyribonucleosides have S-type puckering.4 Preorga-
nization of nucleic acids into the proper shape would be
a most promising strategy to prepare novel nucleic acid
analogues having strong binding affinity towards their
DNA and/or RNA complements.5 In fact, we have
achieved the synthesis of a novel class of nucleic acid
analogue, 2%-O,4%-C-methylene bridged nucleic acid
(2%,4%-BNA6/LNA7), in which the sugar moiety was
strictly locked in N-type (C3%-endo) conformation, and
we successfully demonstrated that the introduction of
2%,4%-BNA monomers into oligonucleotides significantly
enhanced their binding affinity towards RNA
complements.8,9
To solve these problems, we designed trans-3%,4%-BNA
monomer 1, a novel nucleoside analogue having a
4,7-dioxabicyclo[4.3.0]nonane skeleton as a sugar moi-
ety (Fig. 1). From preliminary molecular modeling
experiments, it was presumed that the ribofuranose ring
of 1 was strictly restrained in S-type (C3%-exo) confor-
mation and that the trans-fused six-membered ring of 1
was located outside of the helix structure when it was
HO
B
T
HO
4'
HO
4'
O
O
O
3'
2'
OR
O
OH
trans-3',4'-BNA
1a: R = H
2',4'-BNA (LNA)
1b: R = Me
N-type conformation
S-type conformation
Keywords: nucleic acid analogues; nucleosides; conformation; X-ray
crystal structures.
(C3'-endo)
(C3'-exo)
* Corresponding author. Tel.: +81 6-6879-8200; fax: +81 6-6879-8204;
e-mail: imanishi@phs.osaka-u.ac.jp
Figure 1. Structures of 2%,4%-BNA and trans-3%,4%-BNA.
0040-4039/02/$ - see front matter © 2002 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(02)00784-0

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S. Obika et al. / Tetrahedron Letters 43 (2002) 4365–4368
H2SO4 afforded the triacetate 7 in 98% yield as an
OH
T
HO
anomeric mixture. Coupling reaction of 7 with silylated
thymine effectively proceeded to give the desired b-
anomer of 8 in 87% yield. After several attempts to
distinguish the two acetoxy groups in 8, it was found
that the 2%-O-acetyl group in 8 was selectively removed
by treatment with aqueous MeNH2. The 2%-hydroxy
group of the resulting 9 was protected with 2-methoxy-
2-propyl (MOP) group to give 10 in 74% overall yield.
After deacetylation of 10, ring-closure reaction success-
fully proceeded on treatment with NaHMDS to give 12
in 64% overall yield. Deprotection of the 2%-hydroxy
group in 12 with p-toluensulfonic acid followed by
Pd-mediated hydrogenolysis afforded the desired
ribonucleoside analogue 1a, which has a trans-fused
4,7-dioxabicyclo[4.3.0]nonane structure.15
H
B
T
O
OH
OH
C3'-exo (ref. 11)
C1'-exo (ref. 10)
OH
HO
O
T
O
O
HO
O
OH
OH
C3'-exo (ref. 13)
C2'-endo (ref. 12)
Figure 2. Selected bicyclic and tricyclic nucleoside analogues
with S-type conformation.
Next, the 2%-O-methyl congener 1b was also synthesized
as shown in Scheme 2. The thymine nucleobase of 13
was protected with a benzyloxymethyl (BOM) group,
and the resulting 14 was treated with NaH and MeI to
give the 2%-O-methyl derivative 15 in 77% overall yield.
Deprotection of both 3%-O- and 5%-O-benzyl groups and
the BOM group at the nucleobase afforded 1b in 39%
yield.16
introduced into a B-type DNA duplex. Here, we
describe the synthesis and conformation of the trans-
3%,4%-BNA 1.
The synthesis of 1a was successfully achieved by using
the known
D
-allofuranose derivative 214 as the starting
material (Scheme 1). Introduction of a hydroxymethyl
group at the C4 position of 2 proceeded by the conven-
tional aldol-Canizzaro reaction to give 3 in 65% yield
(three steps). The diol 3 was selectively benzylated at
the 5-hydroxy group to afford 4 in 56% yield, which
was treated with p-toluenesulfonyl chloride to give 5 in
80% yield. Reaction of 5 with OsO4 and NaIO4 in
THF/H2O followed by reduction with NaBH4 gave
primary alcohol 6 in 63% overall yield. Treatment of 6
with Ac2O, AcOH and a catalytic amount of conc.
On 1H NMR measurements of 1a and 1b, relatively
large J1%2% values (6.7 Hz for 1a and 7.1 Hz for 1b) were
observed, which means that the trans-3%,4%-BNA
monomers 1 were conformationally restricted in S-type
(S%=83% for 1a and 89% for 1b).17 In addition, an
X-ray structure investigation (Fig. 3 and Table 1)
clearly shows that 1b existed in a typical S-type confor-
O
OH
O
R1O
R2O
BnO
O
O
O
a-c
f
O
O
O
TsO
O
O
O
OBn
OBn
OBn
3: R1 = R2 = H
4: R1 = Bn, R2 = H
5: R1 = Bn, R2 = Ts
2
6
d
e
g
OH
O
OAc
OAc
O
h
k
BnO
TsO
BnO
TsO
BnO
TsO
T
T
O
OAc
OBn
OBn
OBn
OMOP
OR
OAc
11
8: R = Ac
9: R = H
10: R = MOP
7
i
j
l
BnO
BnO
HO
m
n
T
T
T
4'
O
O
O
O
O
O
3'
OMOP
OH
OH
OBn
OBn
OH
12
13
1a
Scheme 1. Reagents and conditions: (a) 80% AcOH aq., 60°C. (b) NaIO4, THF/H2O, 0°C. (c) 37% HCHO aq., 1N NaOH aq.,
THF/H2O, rt, 65% (three steps). (d) NaH, BnBr, DMF, 0°C, 56%. (e) TsCl, Et3N, DMAP, CH2Cl2, rt, 80%. (f) (1) OsO4, NaIO4,
THF/H2O, rt, (2) NaBH4, THF/H2O, 0°C, 63% (two steps). (g) Ac2O, AcOH, H2SO4, rt, 98%. (h) thymine, BSA, TMSOTf,
ClCH2CH2Cl, reflux, 87%. (i) 40% MeNH2 aq., THF, 0°C, 87%. (j) 2-Methoxypropene, TsOH/H2O, CH2Cl2, 0°C, 85%. (k) 2N
NaOH aq. MeOH/THF, rt, 87%. (l) 1 M NaHMDS, THF, reflux, 73%. (m) TsOH/H2O, THF/MeOH, 0°C, 85%. (n) 20%
Pd(OH)2/C, cyclohexene, EtOH, reflux, 69%.

S. Obika et al. / Tetrahedron Letters 43 (2002) 4365–4368
4367
Scheme 2. Reagents and conditions: (a) BOMCl, DBU, DMF, 0°C, 90%. (b) MeI, NaH, DMF, rt, 86%. (c) 20% Pd(OH)2/C,
cyclohexene, EtOH, reflux, 39%.
and their oligonucleotide derivatives are now in
progress.
Acknowledgements
We thank A. Yamano (Rigaku Corp.) for his help with
X-ray crystallographic analysis. Part of this work was
supported by a Grant for Research on Health Sciences
focusing on Drug Innovation from The Japan Health
Sciences Foundation, Industrial Technology Research
Grant Program in ‘00 from New Energy and Industrial
Technology Development Organization (NEDO) of
Japan, a Grant-in-Aid from Japan Society for the
Promotion of Science, and a Grant-in-Aid from the
Figure 3. ORTEP drawing of 1b.
Ministry of Education, Science, and Culture, Japan.
Table 1. Selected torsion angles, pseudorotation phase
angle (P) and maximum torsion angle (wmax) of 1b deter-
mined from X-ray structure
References
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w0 (C4%ꢀO4%ꢀC1%ꢀC2%)
w1 (O4%ꢀC1%ꢀC2%ꢀC3%)
w2 (C1%ꢀC2%ꢀC3%ꢀC4%)
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0.35×0.20 mm, monoclinic, P21(c4), a=6.034(3), b=10.040(5), c=
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trans-fused six-membered ring. Further studies on 1

4368
S. Obika et al. / Tetrahedron Letters 43 (2002) 4365–4368
7. The 2%,4%-BNA was also called ‘LNA’ by Wengel et al.
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1
(CD3OD): l 1.76 (1H, dd, J=4, 13 Hz), 1.88 (3H, d,
J=1 Hz), 1.91 (1H, ddd, J=6, 13, 14 Hz), 3.58, 4.06 (2H,
ABq, J=10 Hz), 3.77 (1H, dd, J=5, 11 Hz), 3.86, 3.98
(2H, ABq, J=12 Hz), 4.00 (1H, dt, J=11, 4 Hz), 4.73
(1H, d, J=7 Hz), 5.98 (1H, d, J=7 Hz), 8.06 (1H, d,
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1
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(1H, d, J=9 Hz), 3.75 (1H, dd, J=5, 11 Hz), 3.95–4.08
(4H, m), 4.63 (1H, d, J=7 Hz), 6.17 (1H, d, J=7 Hz),
8.10 (1H, d, J=1 Hz). Anal. calcd for C14H20N2O7: C,
51.22; H, 6.14; N, 8.53. Found: C, 51.25; H, 6.12; N,
8.31%.
9. In addition to the unprecedented duplex-forming ability
of the BNA modified oligonucleotides, we also reported
their strong and sequence-selective triplex-forming ability.
See: (a) Obika, S.; Hari, Y.; Morio, K.; Imanishi, T.
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1
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18. Crystallographic data (excluding structure factors) for the
structures in this paper have been deposited with the
Cambridge Crystallographic Data Centre as supplemen-
tary publication numbers CCDC182207. 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 e-mail: deposit@ccdc.cam.
ac.uk].
19. In the X-ray structure of 1b, the torsion angle k
(C3%ꢀC4%ꢀC5%ꢀO5%) was 169.7°, which differs from the k
angle in a canonical B-type DNA (k=ca. 60°). However,
we found that the latter conformer (k=ca. 60°) of 1b is
more stable than the former conformer (k=ca. 180°)
(DE=ca. 3 kcal/mol) from molecular orbital calculations
(HF/6-31G*//HF/3-21G(*)).
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