Selective recognition of CG interruption by 2′,4′-BNA having 1-isoquinolone as a nucleobase in a pyrimidine motif triplex formation

Article abstract of DOI:10.1016/S0040-4020(03)00728-2

To develop a novel nucleoside analogue for the effective recognition of CG interruption in a homopurine-homopyrimidine tract of double-stranded DNA (dsDNA), we succeeded in the synthesis of a triplex-forming oligonucleotide (TFO) containing a novel 2′,4′-

Full text of DOI:10.1016/S0040-4020(03)00728-2

Tetrahedron 59 (2003) 5123–5128
Selective recognition of CG interruption by 20,40-BNA having
1-isoquinolone as a nucleobase in a pyrimidine motif
triplex formationq
†
Yoshiyuki Hari, Satoshi Obika, Mitsuaki Sekiguchi and Takeshi Imanishi
*
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
Received 11 September 2002; accepted 28 April 2003
Abstract—To develop a novel nucleoside analogue for the effective recognition of CG interruption in a homopurine–homopyrimidine tract
of double-stranded DNA (dsDNA), we succeeded in the synthesis of a triplex-forming oligonucleotide (TFO) containing a novel 20,40-BNA
(QB) bearing 1-isoquinolone as a nucleobase, and the triplex-forming ability and sequence-selectivity of the TFO (TFO-QB) were examined.
On melting temperature (Tm) measurements, it was found that the TFO-QB formed a stable triplex DNA in a highly sequence-selective
manner under near physiological conditions. q 2003 Elsevier Science Ltd. All rights reserved.
1. Introduction
For several years, we have been developing novel nucleic
acid analogues, bridged nucleic acids (BNAs).15 One of
these analogues, 20-O,40-C-methyleneribonucleic acid (20,40-
BNA) has a fixed N-type sugar conformation (Fig. 2) and its
oligonucleotides were found to exhibit extraordinarily high
binding affinity for not only single-stranded RNA or DNA
but also homopurine–homo0pyrimidine dsDNA.16 – 22
Moreover, we demonstrated a 2 ,40-BNA derivative bearing
a 2-pyridone nucleobase (PB), nicely recognized CG
interruption in a homopurine–homopyrimidine tract.23,24
In this triad, the carbonyl oxygen in a 2-pyridone nucleobase
(P) would play an important role in the recognition of CG
interruption through hydrogen bonding with the 4-amino
hydrogen in C (Fig. 3(a)).
Certain homopyrimidine or homopurine oligonucleotides
[triplex-forming oligonucleotides (TFOs)] are well-known
to bind with double-stranded DNA (dsDNA) to form a
triplex DNA in a sequence-specific manner, and they have
attracted widespread attention, due to their potentiality as a
practical tool to control a specific gene-expression in vitro
and in vivo.1–5 In a pyrimidine motif triplex formation, the
sequence-specificity is derived from a Hoogsteen-type
interaction of T and Cþ with AT and GC base pairs,
respectively (Fig. 1(a)). On the other hand, in a purine motif
triplex DNA, the formation of the reverse Hoogsteen-type
base triads, A·AT, T·AT and G·GC, also results in the
sequence-specific interaction (Fig. 1(b)). Thus, the TFOs in
both motifs bind to only the homopurine–homopyrimidine
tract of dsDNA, and pyrimidine–purine interruption in a
homopurine–homopyrimidine region leads to a drastic
decrease in the stability of a triplex. In addition, a triplex
is well known to be much more unstable than a duplex.
Therefore, many attempts to develop nucleoside analogues
to effectively recognize pyrimidine–purine interruption and
to stabilize a triplex have been made to date;6–14 however,
most of the approaches have not reached the practical level.
However, PB was found to also interact with an AT base pair
though the binding affinity was weak compared with that for
a CG base pair (Fig. 3(a)). For discrimination between a CG
and AT base pair, we focused on a bulky 5-methyl group of
T. The 5-methyl group is located in the major groove of the
DNA duplex; therefore, an appropriate substitution of PB
nucleobase would decrease the stability for the AT base pair
by a steric hindrance of the methyl group. After due
consideration, we selected 1-isoquinolone (Q)25 as a
nucleobase to recognize the CG base pair in triplex
formation (Fig. 3(b)). We expected that the steric repulsion
between a 4-hydrogen of Q and the 5-methyl group of T
would prevent Q·AT triad formation, while a 2-carbonyl
oxygen of Q would make a hydrogen bond with a 4-amino
hydrogen of C to form a stable Q·CG triad. In this paper, the
synthesis of the TFO containing a novel 20,40-BNA analogue
bearing 1-isoquinolone (QB) and the selective recognition of
CG interruption by QB are described.
q Y. H. and S. O. have contributed equally to this work.
Keywords: nucleic acid analogues; molecular recognition; triplex; antigene.
*
Corresponding author. Tel.: þ81-6-6879-8200; fax: þ81-6-6879-8204;
e-mail: imanishi@phs.osaka-u.ac.jp
Present address: Graduate School of Pharmaceutical Sciences, Nagoya
†
City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603,
Japan.
0040–4020/03/$ - see front matter q 2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0040-4020(03)00728-2

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Y. Hari et al. / Tetrahedron 59 (2003) 5123–5128
Figure 1. Hydrogen bonding styles of base triads. (a) T·AT and Cþ·GC triads in a pyrimidine motif triplex; (b) A·AT, T·AT and G·GC triads in a purine motif
triplex.
orientation of 1-isoquinolone as the nucleobase moiety was
determined to be anti-orientation from the observation of
NOE between a hydrogen at the 30-position in the sugar
moiety and a hydrogen at the 3-position in 1-isoquinolone.
The result showed that the carbonyl group in 1-isoquinolone
Figure 2. The chemical structure of 20,40-BNA.
was placed in a suitable direction for the formation of a
Hoogsteen-type hydrogen bond with a CG base pair.
Figure 3. The proposed hydrogen bonding styles of base triads. (a) P·CG
and P·AT triads; (b) Q·CG and Q·AT triads.
2. Results and discussion
2.1. Synthesis of a TFO containing QB
As shown in Scheme 1, the starting material 1,26 which was
prepared from D-glucose, was treated with 1-isoquinolone,
N,O-bis(trimethylsilyl)acetamide (BSA) and trimethylsilyl
trifluoromethanesulfonate (TMSOTf) to give the b-isomer 2
in 83% yield according to Vorbru¨ggen’s procedure.27 The
bicyclic nucleoside0 analogue 3 was obtained in 95% yield
by removal of the 2 -O-acetyl group and the following ring-
Scheme 1. Reagents and conditions: (a) 1-isoquinolone, N,O-bis(trimethyl-
silyl)acetamide, TMSOTf, 1,2-dichloroethane, reflux, 83%; (b) K2CO3,
closure of 2. Hydrogenolysis of 3 produced the desired
compound 4 in 95% yield. From 1H NMR measurements, all
MeOH, room temperature, 95%; (c) 20% Pd(OH)2–C, cyclohexene,
hydrogens at the 10-, 20- and 30-positions in 4 were observed
EtOH, reflux, 95%; (d) DMTrCl, pyridine, room temperature, quant.;
(e) 2-cyanoethyl N,N,N0,N0-tetraisopropylphosphorodiamidite, diisopropyl-
ammonium tetrazolide, MeCN–THF, room temperature, 97%.
to be singlet signals, indicating that the sugar puckering in 4
was fixed in an N-type conformation.28 Furthermore, the

Y. Hari et al. / Tetrahedron 59 (2003) 5123–5128
5125
Figure 5. The dissociation curves of the triplexes TFO-QB/Duplex-XY.
XY¼CG (a solid line), GC (a dash line), TA (a thin dash line) and AT (a
thin solid line).
clarified. As we have previously reported,23 the nucleoside
analogue PB effectively recognized CG interruption in the
homopurine–homopyrimidine region; however, the differ-
ence in Tm values between the triplexes TFO-PB/Duplex-AT
and TFO-HB/Duplex-AT was relatively large (þ78C). It
seems that PB has a tendency to interact not only with a CG
base pair but also with an AT base pair, though the gross Tm
value of TFO-PB/Duplex-AT was not so large. On the other
hand, almost no difference was observed in the Tm values
between the triplexes TFO-QB/Duplex-AT and TFO-HB/
Duplex-AT. Moreover, thermal stability of the triplexes
TFO-QB/Duplex-GC and TFO-QB/Duplex-TA was the
same as or less than that of the triplexes TFO-HB/Duplex-
GC and TFO-HB/Duplex-TA, respectively. These results
clearly demonstrate that the 1-isoquinolone moiety of QB
made stable interaction with a CG base pair, but not with
AT, TA and GC base pairs. Compared with the triplex TFO-
PB/Duplex-CG, slight decrease in Tm value was observed
for the triplex TFO-QB/Duplex-CG probably due to steric
hindrance of 1-isoqinolone. However, the hindered 1-iso-
qinolone of QB efficiently discriminated the CG base pair
from the other three base pairs (Fig. 3(b)).
Figure 4. The sequence of TFOs and targeted DNA duplexes.
Protection of a primary alcohol of 4 with DMTrCl in
pyridine afforded 5 quantitatively. The phosphoramidite 6
was obtained in 97% yield by phosphitylation of 5, then the
phosphoramidite 6 was successfully introduced into an
oligonucleotide (TFO-QB) on an automated DNA synthe-
sizer using standard phosphoramidite chemistry (Fig. 4).
The purity of the TFO-QB was verified using reversed-phase
HPLC, and the composition was determined by MALDI-
TOF-Mass.
2.2. Triplex-forming ability of TFO containing QB
Triplex-forming ability of TFO-QB was evaluated by an
analysis of the melting temperature (Tm) as shown in Table 1
and Figure 5. All Tm measurements were carried out under
7 mM sodium phosphate buffer (pH 7.0) containing
140 mM KCl, 10 mM MgCl2. Since thymine is well
known to form the most stable traid with the CG base pair
in all four natural nulceobases,29,30 the Tm value of the
synthesized oligonucleotide TFO-QB was compared with
that of the natural oligonucleotide TFO-T. Comparing the
Tm values of the triplexes TFO-QB/Duplex-XY with those
3. Conclusion
In this report, we have accomplished the synthesis of 20,40-
BNA (QB) bearing 1-isoquinolone as a nucleobase. Under
near physiological conditions, the QB incorporated into a
TFO efficiently recognized CG interruption rather than the
three others in the homopurine–homopyrimidine tract of
dsDNA. We believe QB to be a promising candidate to
overcome one of the crucial inherent problems in a TFO,
namely, limitation of the sequence of targeted dsDNA.
of the triplexes TFO-PB/Duplex-XY and TFO-HB31
Duplex-XY, the strict sequence-selectivity of QB was also
/
Table 1. Tm values (8C) of DNA triplexes
Duplex-CG
Duplex-TA
Duplex-GC
Duplex-AT
TFO-T
25
17
20
44
TFO-QB
TFO-PBa
TFO-HBa
29(þ5)
33(þ9)
24
16(24)
14(26)
20
20(^0)
19(21)
20
15(21)
23 (þ7)
16
4. Experimental
4.1. General
Conditions: 7 mM sodium phosphate buffer (pH 7.0), 140 mM KCl, 10 mM
MgCl2, the concentration of a triplex¼1.5 mM. The changes in Tm values
between a TFO and TFO-HB were shown in the parentheses.
All melting points were measured on a Yanagimoto micro
melting points apparatus and are uncorrected. Optical
a
Our previous result.23

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Y. Hari et al. / Tetrahedron 59 (2003) 5123–5128
rotations were recorded on a JASCO DIP-370 instrument.
IR spectra were recorded on a JASCO FT/IR-200
4.1.3. 2-(2-O,4-C-Methylene-b-D-ribofuranosyl)-1-iso-
quinolone (4). A solution of compound 3 (533 mg,
1.14 mmol), 20% Pd(OH)2–C (250 mg) and cyclohexene
(5.80 ml, 57.3 mmol) in EtOH (20 ml) was refluxed for 1 h.
The mixture was filtered and the filtrate was concentrated
under reduced pressure. The residue was purified by flash
silica gel column chromatography [CHCl3/MeOH (23:1,
v/v)] to give compound 4 (37 mg, 95%) as a white powder.
Mp 91–948C. [a]D22¼þ139.3 (c 0.84, CH3OH). IR nmax
(KBr): 3388, 1650, 1270, 1060 cm21. 1H NMR (CD3OD) d:
3.85, 4.01 (2H, AB, J¼8 Hz), 3.97 (2H, s), 4.14 (1H, s), 4.36
(1H, s), 5.92 (1H, s), 6.75 (1H, d, J¼8 Hz), 7.63–7.75 (2H,
m), 7.79 (1H, d, J¼8 Hz), 8.29 (1H, d, J¼8 Hz). 13C NMR
(CD3OD) d: 57.9, 70.4, 72.6, 80.9, 89.0, 90.2, 107.5, 126.3,
126.7, 127.3, 127.8, 128.0, 133.9, 138.4, 163.1. Mass (EI):
m/z 289 (Mþ, 32.3), 145 (100). Anal. calcd for
C15H15NO5·H2O: C, 58.63; H, 5.58; N, 4.56. Found: C,
58.90; H, 5.43; N, 4.56.
1
spectrometer. H and 13C NMR spectra were recorded on
a JEOL EX-270 (1H, 270 MHz; 13C, 67.8 MHz) and 31P
NMR spectrum was recorded on a Varian VXR-200 (31P,
81.0 MHz). Mass spectra of nucleoside analogues were
recorded on a JEOL JMS-D300 or JMS-600 mass
spectrometer. For flash column, Fuji Silysia BW-300
(200–400 mesh) was used. MALDI-TOF-Mass spectra
were recorded on a Perceptive Inc. Voeygerw-DE.
4.1.1. 2-[2-O-Acetyl-3,5-di-O-benzyl-4-(p-toluenesul-
fonyloxymethyl)-b-D-ribofuranosyl]-1-isoquinolone (2).
Under a nitrogen atmosphere 1-isoquinolone (308 mg,
2.12 mmol)
and
N,O-bis(trimethylsilyl)acetamide
(0.61 ml, 2.48 mmol) were added to a solution of compound
126 (1.06 g, 1.77 mmol) in anhydrous 1,2-dichloroethane
(20 ml) at room temperature and the mixture was refluxed
for 1 h. TMSOTf (0.19 ml, 1.06 mmol) was added to the
reaction mixture at room temperature and the mixture was
refluxed for 2 h. The reaction was quenched by addition of a
saturated aqueous solution of NaHCO3. The mixture was
extracted with AcOEt. The organic phase was washed with
water and brine and dried over Na2SO4 and concentrated
under reduced pressure. The residue was purified by flash
silica gel column chromatography [CH2Cl2/AcOEt (50:1,
v/v)] to give compound 2 (1.00 g, 83%) as a colorless oil.
[a]2D7¼þ26.3 (c 0.58, CHCl3). IR nmax (KBr): 1747, 1661,
1364, 1230, 1181, 1101 cm21. 1H NMR (CDCl3) d: 2.02 (3H,
s), 2.40 (3H, s), 3.59, 3.81 (2H, AB, J¼10 Hz), 4.21, 4.27 (2H,
AB, J¼11 Hz), 4.37–4.56 (5H, m), 5.43 (1H, dd, J¼5, 5 Hz),
6.20–6.23 (2H, m), 7.20–7.48 (12H, m), 7.62 (1H, dd, J¼8,
8 Hz), 7.75 (2H, d, J¼8 Hz), 8.34 (1H, d, J¼8 Hz). 13C NMR
(CDCl3) d: 20.8, 21.7, 69.3, 70.3, 73.7, 74.4, 75.1, 77.4, 85.2,
87.9, 106.2, 125.7, 125.8, 126.8, 127.0, 127.7, 127.8, 127.8,
127.9, 128.0, 128.3, 128.4, 129.7, 132.3, 132.5, 136.7, 137.1,
137.2, 144.9, 161.6, 169.5. Mass (EI): m/z 683 (Mþ, 3.5), 91
(100). Anal. calcdforC38H37NO9S:C, 66.75;H, 5.45; N, 2.05;
S, 4.69. Found: C, 66.46; H, 5.47; N, 1.93; S, 4.62.
4.1.4. 2-[5-O-(4,40-Dimethoxytrityl)-2-O,4-C-methylene-
b-D-ribofuranosyl]-1-isoquinolone (5). Under a nitrogen
atmosphere DMTrCl (152 mg, 0.45 mmol) was added to a
solution of compound 4 (100 mg, 0.35 mmol) in anhydrous
pyridine (2 ml) at room temperature and the mixture was
stirred at room temperature for 3 h. The reaction was
quenched by addition of a saturated aqueous solution of
NaHCO3. The mixture was extracted with AcOEt. The
organic phase was washed with water and brine and dried
over Na2SO4 and concentrated under reduced pressure. The
residue was purified by flash silica gel column chromato-
graphy [n-hexane/AcOEt (4:3, v/v)] to give compound 5
(205 mg, 100%) as a white powder. Mp 105–1098C.
[a]2D2¼þ57.9 (c 1.34, CHCl3). IR nmax (KBr): 3373, 3007,
1
2952, 1650, 1593, 1508, 1458, 1251, 1178, 1056 cm21. H
NMR (CD3COCD3) d: 3.55, 3.61 (2H, AB, J¼11 Hz), 3.81
(6H, s), 3.84, 3.96 (2H, AB, J¼8 Hz), 4.40 (1H, s), 4.49
(1H, d, J¼4 Hz), 4.77 (1H, d, J¼4 Hz), 5.93 (1H, s), 6.61
(1H, d, J¼8 Hz), 6.93 (4H, d, J¼9 Hz), 7.27–7.71 (12H,
m), 7.95 (1H, d, J¼8 Hz), 8.31 (1H, d, J¼8 Hz). 13C NMR
(CD3COCD3) d: 55.5, 59.6, 70.6, 72.4, 80.2, 87.1, 88.4,
88.6, 105.8, 113.8, 126.6, 126.9, 127.1, 127.3, 127.5, 127.7,
128.5, 128.8, 130.8, 130.8, 133.1, 136.3, 136.5, 137.8,
145.8, 159.5, 161.5. Mass (FAB): m/z 614 (MNaþ). Mass
(FAB): m/z 598 (MLiþ). Anal. calcd for C36H33NO7·1/
2H2O: C, 71.99; H, 5.71; N, 2.33. Found: C, 71.73; H, 5.91;
N, 2.38.
4.1.2. 2-(3,5-Di-O-benzyl-2-O,4-C-methylene-b-D-ribo-
furanosyl)-1-isoquinolone (3). To a solution of compound
2 (1.00 g, 1.46 mmol) in MeOH (15 ml) was added K2CO3
(600 mg, 4.34 mmol) at room temperature and the mixture
was stirred for 9 h. The solvent was concentrated under
reduced pressure. After addition of water, the residue was
extracted with AcOEt. The organic phase was washed with
water and brine and dried over Na2SO4 and concentrated
under reduced pressure. The residue was purified by flash
silica gel column chromatography [n-hexane/AcOEt (4:1,
v/v)] to give compound 3 (562 mg, 95%) as a white powder.
Mp 118–1198C. [a]D27¼þ198.5 (c 0.79, CHCl3). IR nmax
4.1.5. 2-[3-O-[2-Cyanoethoxy(diisopropylamino)phos-
phino]-5-O-(4,40-dimethoxytrityl)-2-O-4-C-methylene-b-
D-ribofuranosyl]-1-isoquinolone (6). Under a nitrogen
atmosphere
2-cyanoethyl-N,N,N0,N0-tetraisopropyl-
phosphorodiamidite (43 ml, 0.14 mmol) was added to a
solution of compound 5 (40 mg, 68 mmol), diisopropyl-
ammonium tetrazolide (14 mg, 82 mmol) in anhydrous
MeCN–THF (3:1, 1.2 ml) at room temperature and the
mixture was stirred at room temperature for 5 h. The solvent
was concentrated under reduced pressure. The residue was
purified by flash silica gel column chromatography
[n-hexane/AcOEt/Et3N (75:25:1, v/v/v)] to give compound
6 (52 mg, 97%) as a white powder. Mp 76–798C. 31P NMR
(CDCl3) d: 148.6, 149.5.
1
(KBr): 1654, 1059 cm21. H NMR (CDCl3) d: 3.80, 3.90
(2H, AB, J¼11 Hz), 3.94, 4.08 (2H, AB, J¼8 Hz), 4.07 (1H,
s), 4.43, 4.58 (2H, AB, J¼12 Hz), 4.62–4.73 (3H, m), 6.04
(1H, s), 6.44 (1H, d, J¼8 Hz), 7.22 (4H, m), 7.37 (4H, m),
7.49–7.53 (3H, m), 7.62–7.69 (3H, m), 8.40 (1H, d,
J¼8 Hz). 13C NMR (CDCl3) dC: 64.9, 72.1, 72.3, 73.7, 76.2,
76.7, 87.1, 88.0, 105.9, 125.6, 125.7, 125.8, 126.7, 127.4,
127.5, 127.7, 127.8, 128.2, 128.4, 132.4, 136.7, 137.0,
137.6, 161.4. Mass (EI): m/z 469 (Mþ, 16.1), 91 (100). Anal.
calcd for C29H27NO5: C, 74.18; H, 5.80; N, 2.98. Found: C,
74.15; H, 5.91; N, 2.96.
4.1.6. Synthesis of TFO-QB. The modified oligonucleotide

Y. Hari et al. / Tetrahedron 59 (2003) 5123–5128
5127
TFO-QB was synthesized on a 0.2 mmol scale on Pharmacia
Gene Assemblerw Plus according to the standard phosphor-
amidite protocol. The solid supported oligonucleotide,
which was protected by 50-terminal DMTr group, was
treated with concentrated ammonium hydroxide at 608C for
18 h, and the solvents were concentrated. After simple
purification through NENSORBe PREP, the oligonucleo-
tide was purified by reversed-phase HPLC (ChemcoPakw
CHEMCOSORB 300-5C18, 4.6 mm£250 mm) with a 11%
MeCN in 0.1 M triethylammonium acetate buffer (pH 7.0).
MALDI-TOF-Mass data for TFO-QB [M2H]2: found
4542.59, calcd 4543.11.
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UV melting experiments were carried out on a Beckmann
DV-650 spectrophotometer equipped with Tm analysis
accessary. The profiles were recorded in 7 mM sodium
phosphate buffer (pH 7.0), 140 mM KCl and 10 mM MgCl2
at a scan rate of 0.58C/min at 260 nm. The final
concentration of each oligonucleotide used was 1.5 mM. A
Tm value was designated the maximum of the first derivative
calculated from the UV melting profile.
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Acknowledgements
Part of this work was supported by the Japan Securities
Scholarship Foundation (JSSF) Academic Research Grant
Program, Industrial Technology Research Grant Program in
’00 from New Energy and Industrial Technology Develop-
ment Organization (NEDO) of Japan, a Grant-in-Aid from
Japan Society for the Promotion of Science, and a Grant-in-
Aid from the Ministry of Education, Science, and Culture,
Japan. We thank JSPS Research Fellowships for Young
Scientists (Y. H. and M. S.).
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22. The 20,40-BNA has been also called “LNA”: Singh, S. K.;
Nielsen, P.; Koshkin, A. A.; Wengel, J. Chem. Commun. 1998,
455–456. Koshkin, A. A.; Singh, S. K.; Nielsen, P.;
Rajwanshi, V. K.; Kumar, R.; Meldgaard, M.; Olsen, C. E.;
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