Synthesis and structures of deoxyribonucleoside analogues for triazole-linked DNA (TLDNA)

Article abstract of DOI:10.1016/j.tetlet.2010.02.046

Deoxyribonucleoside analogues bearing acetylene group at the pseudo-5′-position and azido group at the pseudo-3′-position have been synthesized by transglycosylation reaction of deoxythymidine analogue with adenine, cytosine, and guanine nucleobases as nu

Full text of DOI:10.1016/j.tetlet.2010.02.046

Tetrahedron Letters 51 (2010) 2036–2038
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Synthesis and structures of deoxyribonucleoside analogues
for triazole-linked DNA (TLDNA)
Tomoko Fujino a, Nobuhide Tsunaka a, Marine Guillot-Nieckowski b, Waka Nakanishi a, Takeaki Iwamoto a,
Eiichi Nakamura b, Hiroyuki Isobe a,
*
a Department of Chemistry, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
b Department of Chemistry, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
a r t i c l e i n f o
a b s t r a c t
Deoxyribonucleoside analogues bearing acetylene group at the pseudo-50-position and azido group at the
pseudo-30-position have been synthesized by transglycosylation reaction of deoxythymidine analogue
with adenine, cytosine, and guanine nucleobases as nucleophiles. The structures of analogues were stud-
ied in crystalline state by X-ray crystallography as well as in solution phase by NMR spectroscopy and
showed the puckering conformations similar to the natural congeners.
Article history:
Received 20 January 2010
Revised 5 February 2010
Accepted 8 February 2010
Available online 11 February 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Transglycosylation
Artificial deoxyribonucleoside
Puckering conformation
Artificial oligonucleotides with non-natural backbones are an
important class of compounds that cannot be biologically degraded
but can be used as biological tools upon binding to the natural tar-
get strand of DNA. The oligonucleotide needs a sequence of four
different nucleobases to target the natural strand where four
deoxyribonucleosides, that is, deoxythymidine (dT), deoxyadeno-
sine (dA), deoxycytidine (dC), and deoxyguanosine (dG), are coding
genes in the complementary sequence.1 Recently, we have devel-
oped a triazole-linked analogue of DNA (TLDNA, Fig. 1) as a new
artificial oligonucleotide and demonstrated that the oligonucleo-
tide of 10-mer forms a stable double helix with a natural DNA
strand.2 However, the oligomer was synthesized only with dT
analogue and therefore targeted a poly-dA strand. In this Letter,
we report on the synthesis of analogues of the other deoxyribonu-
cleosides, dA, dC, and dG via transglycosylation reaction. Structural
analysis shows that the analogues have conformational flexibility
similar to the natural congeners.
(3A-b) in 26% yield after the separation by middle pressure liquid
chromatography (MPLC; Scheme 1). Transglycosylation of 1 with
the other nucleobases (2C and 2G) also proceeded under similar
conditions, and the desired analogues 3C and 3G were obtained
in moderate yield, respectively.5 Although the anomers of dC ana-
logue 3C could not be chromatographically separated, benzoyla-
tion of amine residue of the base moiety led to the successful
MPLC separation (Eq. 1). Protecting groups of all the nucleosides
were removed under basic conditions to give the corresponding
nucleosides 5 in moderate to good yield (Scheme 2 and Supple-
mentary data). The structures of each anomer were first estab-
lished spectroscopically and later confirmed by X-ray analysis of
the single crystals (vide infra).
O
O
NH
O
O
As we have previously validated a method for the large-scale
synthesis of dT analogue 1,2 transglycosylation reaction3 seems a
straightforward route to the nucleobase diversity. Thus, the trans-
glycosylation of 1 with protected adenine 2A proceeded with cat-
alytic amount of Me3SiOTf in refluxing 1,2-dichloroethane to
afford the desired analogues 3A in moderate yield.4 The stereose-
lectivity of the glycosylation was similar to that of natural congen-
N
SiMe3
Base
Base
O
N
N
N
O
P
O
NH
O
O
O
N
O
O
O
NH
O
O
N
N3
1
O
ers,3 and we obtained
a-anomer (3A-a) in 29% yield and b-anomer
N
O
TLDNA
Natural DNA
* Corresponding author. Tel.: +81 22 795 6585; fax: +81 22 795 6589.
E-mail address: isobe@m.tains.tohoku.ac.jp (H. Isobe).
Figure 1. Structures of natural DNA, TLDNA, and dT analogue 1.
0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2010.02.046

T. Fujino et al. / Tetrahedron Letters 51 (2010) 2036–2038
SiMe3 SiMe3
2037
H
HN(SiMe3)2
(22 equiv.)
Me3SiCl
1
Me3SiOTf
(0.5 equiv.)
O
O
O
aq. NH4OH/MeOH
60 ºC
(22 equiv.)
Base
PG-Base
Base
nucleobase 2
reflux
ClCH2CH2Cl
reflux
(2.4 equiv.)
N3
N3
N3
3
5A: 87% from 3A-β
5C: 56% from 4C-β
5G: 95% from 3G-β
2 = Base-H
3A-α, 3A-β = 29%, 26% (Base = A)
3C-α+3C-β = 80% (66:34 mixture; Base = C)
3G-α, 3G-β = 31%, 31% (Base = G)
(2A, 2C, 2G)
PG-Base =
N
N
N
N
N
O
NHBz
Base =
N
N
N
N
N
O
NH2
N
N
N
NH
N
O
N
NH
N
O
N
O
NH
O
N
O
NH
O
G
C
n-C7H15
HN
n-C7H15
HN
A
i-Pr
i-Pr
Base =
N
N
N
N
N
NH2
Scheme 1. Synthesis of deoxyribonucleoside analogues.
N
N
NH2
N
N
O
O
NH
C
H2N
A
G
SiMe3
SiMe3
Scheme 2. Deprotection of deoxyribonucleoside analogues.
BzCl
NHBz
NHBz
O
O
(2.0 equiv.)
N
N
+
N
N
3C
ð1Þ
tries in the South of pseudorotational cycle (S-type, 20-endo).3,8 On
the other hand, the puckering of purine analogues (dA 5A and dG
3G-b) was in the North (N-type, 30-endo).9
pyridine
rt, 8 h
O
O
N3
N3
4C-α
38%
4C-β
27%
In solution, puckering conformations of b-anomers equilibrate
between S-type and N-type, as such observed with natural congen-
ers. Proton NMR spectra of b-analogues were recorded in DMSO at
room temperature (25 °C),10 and the puckering population was esti-
mated by Altona–Sundaralingam approximation using the vicinal
coupling constants (3J) of H10, H20 and H30, H40 (Table 1).1,11 Thus,
in all the analogues, the population of S-type conformer was slightly
higher than that of N-type and estimated as 56% for dT (1), 56% for dA
(3A-b), 53% for dC (4C-b), and 53% for dG (3G-b), respectively.
In summary, we have developed a method for the synthesis of
deoxyribonucleoside analogues bearing adenine, cytosine and
guanine nucleobases. All the analogues showed the puckering flex-
ibility similar to the natural congeners, which may help the duplex
Yield based on 1 (2-step transformation)
With single crystals of dT 1, dA 5A, dC 5C, and dG 3G-b, the
structural analysis by X-ray crystallography unequivocally estab-
lished the structures and revealed the preferred conformations in
solid state. Representative molecular structures and the puckering
parameters are shown in Figure 2 (see Supplementary data for the
a
-anomers). In all the analogues, the glycosidic linkage to the
nucleobase adopts anti conformations favorable for the base pair-
ing. The azido group preferred the geometry trans to the C20–C30
bond,6 which may help to free the group from steric hindrance
for the subsequent click coupling.2,7 Pyrimidine analogues (dT 1
and dC 5C) adopt two puckering conformations both with geome-
(a)
(b)
North
(C3'-endo)
C3'
C5'
Base
O
C2'
dG
0º
dA
C5'
C5'
C3'
C3'
O
90º
270º
dT-1 1
(P = 142.9º, νmax = 32.5º)
dA 5A
(P = 23.3º, νmax = 36.8º)
Base
O
Base
C2'
West
C2'
East
dT-1
180º
dC-1
dT-2
dC-2
Base
C2'
C5'
O
C3'
South
(C2'-endo)
dC-1 5C
(P = 156.6º, νmax = 26.1º)
dG 3G-β
(P = 10.6º, νmax = 37.0º)
Figure 2. (a) Representative molecular structures and the structural parameters of analogues obtained by X-ray diffraction analysis of the single crystals. The structures are
viewed along the plane of C10–O40–C40. One of the two conformers found for dT and dC is shown, respectively. The phase angle (P) and the puckering amplitude (
max) are
m
shown. Solvent molecules were omitted for clarity. Carbon: gray, hydrogen: white, nitrogen: blue, oxygen: red, and silicon: yellow. (b) Locations of puckering conformations
of analogues in the pseudorotational cycle where twist and envelope forms appear alternatively every 18°.

2038
T. Fujino et al. / Tetrahedron Letters 51 (2010) 2036–2038
Table 1
spectral data and X-ray crystallographic data) associated with this
article can be found, in the online version, at doi:10.1016/
j.tetlet.2010.02.046.
Vicinal coupling constants and puckering population in DMSO
3
3
0
0
0
0
Analogue
JH1 ,H2 (Hz)
JH3 ,H4 (Hz)
%South
1 (dT)
6.8
7.2
6.2
6.4
5.2
5.6
5.6
5.6
57
56
53
53
References and notes
3A-b (dA)
4C-b (dC)
3G-b (dG)
1. Saenger, W. Principle of Nucleic Acid Structure; Springer: New York, 1984.
2. Isobe, H.; Fujino, T.; Yamazaki, N.; Guillot-Nieckowski, M.; Nakamura, E. Org.
Lett. 2008, 10, 3729–3732; Fujino, T.; Yamazaki, N.; Isobe, H. Tetrahedron Lett.
2009, 50, 4101–4103.
3. Imazawa, M.; Eckstein, F. J. Org. Chem. 1978, 43, 3044–3048; Vorbrüggen, H.;
Bennua, B. Chem. Ber. 1981, 114, 1279–1286.
4. Although the transglycosylation also proceeded with SnCl4 as a Lewis acid, the
yield was much lower than that with Me3SiOTf. Vorbrüggen, H.; Krolikiewicz,
K.; Bennua, B. Chem. Ber. 1981, 114, 1234–1255.
5. The reaction with guanine nucleophile gave two other transglycosylated
products (ca. 4% yield, respectively) which are tentatively assigned as 7-
glycosylated byproducts (Ref. 3). We did not observe similar isomeric
byproducts with adenine nucleophile.
6. Van Roey, P.; Salerno, J. M.; Duax, W. L.; Chu, C. K.; Ahn, M. K.; Schinazi, R. F. J.
Am. Chem. Soc. 1988, 110, 2277–2282.
7. Bock, V. D.; Hiemstra, H.; van Maarseveen, J. H. Eur. J. Org. Chem. 2006, 51–68.
8. The puckering of furanose rings can be described by the pseudorotational cycle
which correlates all possible twist and envelope conformations to the
pseudorotional phase angle P. The puckering amplitude mmax shows the
degree of distortion of the ring from the planar form.
formation of the oligonucleotides. The puckering preference of the
new analogues may also be informative for the 30-azidonucleosides
of biological importance.12 With the library of four nucleoside ana-
logues, we can now design and synthesize functional TLDNA that
targets a specific natural complementary strand. In addition, the
transglycosylation reaction should be applicable to artificial nucle-
obases, and we will explore the scope in future.
Acknowledgments
This work was partly supported by KAKENHI (20655026/
20108015, H.I.). M.G.-N. thanks JSPS for a postdoctoral fellowship.
9. Observed phase angles of the analogues were in the range similar to the natural
congeners (Ref. 1). See also: Altona, C.; Sundaralingam, M. J. Am. Chem. Soc.
1972, 94, 8205–8212; Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1973, 94,
8205–8212.
Supplementary data
10. Coupling analysis in aqueous solution was not successful due to low solubility
of the analogues.
Crystallographic data (excluding structure factors) for the struc-
tures in this paper have been deposited with the Cambridge Crys-
tallographic Data Centre as supplementary publication (CCDC
761746–761752). These data can be obtained free of charge from
The Cambridge Crystallographic Data Centre via www.ccdc.cam.
ac.uk/data_request/cif. Supplementary data (experimental details,
11. The population of S-type conformer was estimated by the following equation:
3
3
%South = 100 ꢀ (3JH1 ,H2 /( JH1 ,H2
+
JH3 ,H4 )).
0
0
0
0
0
0
12. Mathé, C.; Périgaud, C. Eur. J. Org. Chem. 2008, 1489–1505; Sørensen, M. H.;
Nielsen, C.; Nielsen, P. J. Org. Chem. 2001, 66, 4878–4886.