An efficient synthesis of 2-selenouridine and its phosphoramidite precursor

Article abstract of DOI:10.3987/COM-15-13349

We describe an efficient and scalable synthetic route to the natural occurring 2-selenouridine (Se²U) and its suitably protected derivative for phosphoramidite synthesis. From known fully TBDMS-protected thiouridine, the corresponding selenouri

Full text of DOI:10.3987/COM-15-13349

HETEROCYCLES, Vol. 92, No. 1, 2016, pp. -. © 2016 The Japan Institute of Heterocyclic Chemistry
Received, 24th October, 2015, Accepted, 25th November, 2015, Published online, 8th December, 2015
DOI: 10.3987/COM-15-13349
AN EFFICIENT SYNTHESIS OF 2-SELENOURIDINE AND ITS
PHOSPHORAMIDITE PRECURSOR
Masakazu Kogami,a Darrell R. Davis,b and Mamoru Koketsua*
a Department of Chemistry and Biomolecular Science, Faculty of Engineering,
Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; E-mail:
koketsu@gifu-u.ac.jp
b Department of Medicinal Chemistry, College of Pharmacy, University of Utah,
Salt Lake City, Utah 84112, USA
Abstract – We describe an efficient and scalable synthetic route to the natural
occurring 2-selenouridine (Se2U) and its suitably protected derivative for
phosphoramidite synthesis. From known fully TBDMS-protected thiouridine, the
corresponding selenouridine was synthesized via the reaction of methylthiouridine
with NaHSe, which was then completely deprotected without affecting the
selenocarbonyl moiety to deliver Se2U. Next, Se2U was converted into the
2′-O-TBDMS-5′-O-DMT derivative in 81% yield over four steps including
di-tert-butylsilylene (DTBS) introduction at O3′ and O5′, O2′-silylation, selective
cleavage of DTBS, and DMT introduction. This synthetic route enabled
gram-scale preparation of both Se2U and its phosphoramidite precursor in
excellent yields. Furthermore, the predicted C3′-endo conformational preference
of Se2U was experimentally confirmed by NMR spectroscopy.
INTRODUCTION
Selenium is an essential trace element for humans and animals and used in a wide variety of biological
process.1 It is incorporated into selenoproteins in the form of selenocysteine (Sec) for the reduction of
antioxidant enzymes such as glutathione peroxidases.2 Furthermore, selenium modified nucleosides have
proven to be useful in biochemistry, molecular biology, gene therapy, and drug discovery.3 The covalent
radius of sulfur (1.05 A˚) is larger than that of oxygen (0.66 A˚) and although sulfur is less
electronegative, it is more polarizable.4 The replacement of oxygen at the nucleobase C-2 position with
sulfur stabilizes the sugar C3′-endo conformation primarily through steric repulsion between the

2-thiocarbonyl group and sugar 2′-hydroxy group.5 Moreover, 2-thiouridine (S2U) selectively destabilizes
the S2U/G wobble-pair geometry relative to an unmodified U primarily due to the weaker hydrogen
bonding ability of sulfur relative to oxygen.6 Therefore, the naturally occurring selenium (1.20 A˚)4
modification of nucleobase C-2 position is expected to be even more efficient than sulfur modification in
mediating these effects. Recently, Huang et al. reported that selenium modification at the nucleobase C-2
position confers greater base pairing specificity compared to unmodified uridine.7
Thiouridine and selenouridine nucleoside modifications may be therapeutically relevant since in human
immunodeficiency virus type-1 (HIV-1) a key step in the viral life cycle requires base pairing of the
reverse transcriptase primer, human tRNALys3, to the HIV-1 genomic RNA.8 This interaction of viral
RNA and human tRNALys3 initiates viral reverse transcription and key interactions between
sulfur-modified nucleosides in the tRNA anticodon domain and a conserved region of the HIV genome
are necessary for efficient viral replication. Functional study of nucleobase modification in the initiation
complex of HIV-1 reverse transcription is important since targeting this step could be a target for new
drugs.9 Modification of nucleosides with S2U in tRNALys3 stabilized the RNA-RNA interaction,10 that is
used by the viral reverse transcriptase as a primer.11 Oligonucleotides containing selenium modification
could also mimic the interaction between the native tRNA and the HIV primer binding site, and inhibit
viral replication more effectively than either sulfur or unmodified oligonucleotide therapeutics.
The structure of 2-selenouridine (Se2U) and its derivatives discovered from tRNAGlu, tRNAGln, and
tRNALys in Escherichia coli or in Methanococcus vannielii are shown in Figure 1.12 The YbbB enzyme
Figure 1. The structures of natural occurring selenium-containing
pyrimidine nucleosides present in tRNAs
necessary for forming Se2U from U has been shown to present in all kingdoms of life, underscoring the
importance of this ubiquitous, yet minimally studied nucleoside modification.13
Despite the biological importance, understanding the functional role of selenium modified nucleosides is
limited by the availability of these nucleosides.14 Few reports are available in the literature for the
synthesis of 2-selenouridine due to difficulties involved in their preparation. Thus, it is useful to have a

scalable route to prepare these nucleosides for both structural and biological study.
To the best of our knowledge, Se2U has been synthesized by five research groups. The first method15a
required difficult to obtain 2-selenouracil16 that was synthesized from expensive and unstable
N,N-unsubstituted selenourea and sodium ethylformyl acetate. Furthermore, glycosylation of silylated
2-selenouracil with glycosyl donors in the presence of tin(IV) chloride provided only a 30% yield. The
second synthesis of Se2U was accomplished by ipso-substitution of isocytidine with gaseous H2Se.15b
This route seems to be the shortest. However, this method requires the use of a difficult to obtain starting
material isocytidine that was synthesized from 2-thiouracil in 5 steps,17 and then required highly toxic
gaseous H2Se, and long reaction times (3 days). In these initial reports, the full characterization and
experimental details for preparing Se2U was not provided. Recently, the synthesis of Se2U has been
reported independently by Huang′s group,15c Moderna Therapeutics,15d and Nawrot′s group.15e Huang′s
method provided the critically useful Se2U-phosphoramidite, which could be synthesized from
2-thiouracil in 8 steps. However, this method gave a nearly 1:1 mixture of undesired but separable 2′- and
3′-O-silyl ether derivatives prior to selenium protection as the Se-cyanoethyl, thus the desired 2′-O-silyl
ether derivative was obtained in 41% yield. The Moderna Therapeutics method provided Se2U from
2-thiouracil in 7 steps. Therefore, their route seems to need improvement for synthetic production on a
large scale. Herein, we describe an efficient and scalable synthetic route that allows gram scale synthesis,
avoidance of tedious isomer purification through regioselective 2′-O-silylation, and finally the mild
deprotection of a triol protecting group on Se2U.
RESULTS AND DISCUSSION
In our route outlined in Scheme 1, we focused on increasing efficiency based on diverse view point.18
First, 2′,3′,5′-O-tris(tert-butyldimethylsilyl) (TBDMS)-2-thiouridine (2) was obtained from commercially
available and inexpensive uridine (1) (ca. $3.3/gram, Tokyo Chemical Industry Co., Ltd., October 2015)
on the 10.4 g scale in 55% overall yield according to the literature method.19 Sekine′s method provides
several advantages over the glycosylation method, involving avoidance of the moisture-sensitive reaction,
inseparable emulsion during the extraction due to insoluble tin(IV) chloride and easy access to the
highly-soluble per-silylated intermediate.
Next, we carried out the S-alkylation of 2 with methyl iodide in the presence of an aqueous sodium
hydroxide in THF to afford the corresponding 2′,3′,5′-O-TBDMS-2-methylthiouridine (3) in excellent
yield. This biphasic condition produced almost a single product, thereby eliminating the requirement for
silica gel chromatography. The resulting 3 was subsequently treated with NaHSe, which was generated by
reduction of selenium with sodium borohydride in EtOH at 60 °C, to afford 6.5 g of
2′,3′,5′-O-TBDMS-2-selenouridine (4) in 90% yield from 2.

O
N
O
N
O
N
NH
N
NH
Ref. [19]
MeI, 10% NaOH aq.
THF, rt
Se, NaBH4
O
SMe
S
HO
TBDMSO
TBDMSO
O
O
55% overall yield
4 steps
EtOH, 60 °C
90% (2 steps)
[gram scale]
O
HO
OH
TBDMSO
OTBDMS
TBDMSO
OTBDMS
[decagram scale]
[gram scale]
[chromatography-free]
3
2
uridine (1)
(ca. $3.3/gram)
O
N
O
1) DTBS(OTf)2, imidazole,
DMF, 0 °C
2) TBDMSCl, imidazole,
0 °C to 60 °C
O
NH
Se
NH
NH
Se
TFA-H2O (3 : 2)
N
Se
N
HO
O
rt
TBDMSO
O
O
t-Bu
O
94%
93% overall from 5
Si
HO
Se2U (5)
OH
t-Bu
O
N
OTBDMS
[gram scale]
[chromatography-free]
[gram scale]
[one-pot]
TBDMSO
OTBDMS
6
4
O
O
NH
Se
formal synthesis
Ref. [15c]
CN
1) HF-Py, pyridine, CH2Cl2, 0 °C
N
Se
N
2) DMT-Cl, pyridine, rt
DMTO
O
DMTO
O
O
O
OTBDMS
87% overall from 6
NC
HO
OTBDMS
P
N(i-Pr)2
[gram scale]
7
8
Scheme 1. Synthesis of Se2U and its phosphoramidite precursor
After extensive optimization, mild desilylation of 4 was accomplished by using aqueous trifluoroacetic
acid (TFA) to yield 2.3 g (94% yield) of 5. When tetra-n-butylammonium fluoride (TBAF) was used as a
deprotection reagent, the yield dropped dramatically to 31%.15d The treatment with TBAF caused
deselenation to give the mixture of uridine and selenium as byproducts, which required a multi-step,
tedious silica gel column chromatography procedure to separate these products from 5. In contrast to the
previously reported synthesis, the mild deprotection using aqueous TFA offers the following advantages:
(i) complete absence of depyrimidination and deselenation from acidic hydrolysis of the nucleobase; (ii) a
facile purification process including only simple precipitation of 5 with diethyl ether. The structure of 5
1
was confirmed by H, 13C NMR and 77Se NMR spectra compared to the previous report.15e The
production of a newly formed 2-selenocarbonyl group of 5 provided a 77Se NMR peak at 353.8 ppm.
With a scalable (>2 g) route to Se2U secured, our attention turned to the Se2U-phosphoramidite precursor.
Widely-used solid-phase RNA chemical synthesis offers advantages for the preparation of
oligoribonucleotides, however, facile and relatively inexpensive access to the phosphoramidite is required.
A major drawback in the previously reported method is non-regio-selective protection for the secondary
hydroxyls of Se2U with TBDMS groups. Due to this non-selectivity, there is generally an arduous
purification step to separate the desired 2′-O-silyl derivative from its 3′ regio-isomer.

To solve this problem, we tried 5′-O-dimethoxytritylation, followed by selective 2′-O-silylation using
silver nitrate.20 However, the desired 2′-O-silyl compound was not obtained due to decomposition from
oxidization of the selenocarbonyl group. Next, we employed the di-tert-butylsilylene (DTBS) group21 for
simultaneous protection of 3′- and 5′-hydroxyl functions of 5. The reaction of 5 (1.2 g) with 1.1 equiv. of
di-tert-butylsilyl bis(trifluoromethanesulfonate) (DTBS(OTf)2) in DMF at 0 °C proceeded smoothly to
afford the 3′,5′-O-protected intermediate, which was subsequently silylated at O-2′ in one pot, producing
2.0 g of isolated product (93% yield from 5). Then, selective removal of DTBS group using hydrogen
fluoride–pyridine in dichloromethane at 0 °C furnished the 2′-O-TBDMS Se2U, which was then subjected
to next reaction without chromatographic purification. Reaction with 4,4′-dimethoxytrityl chloride
(DMT-Cl) in pyridine gave 2.3 g of compound 7 in 87% yield from 6, which can be converted to the
Se2U-phosphoramidite 8 in 2 steps.15c As a result, we succeeded in the synthesis of phosphoramidite
precursor 7 in 38% over 11 steps, from the inexpensive, commercially available uridine 1.
1
In order to investigate the structural characteristics of the 2-selenocarbonyl group of Se2U, the H NMR
spectra of 5 was acquired. As mentioned above, sulfur modification in S2U has been shown to generally
stabilize the sugar C3′-endo conformation because of steric repulsion between 2-thiocarbonyl group and
2′-hydroxyl group.
Table 1. Calculated the %[C3′-endo] value of the nucleosides from the Coupling Constants (Hz)
Nucleosides
J1′2′ (Hz)
4.6
J3′4′ (Hz)
%[C3′-endo]
U
5.2
6.0
c
53a
71a
80d
S2U
Se2U
2.5
2.0
b
a These values of %[C3′-endo] were reported in ref. 22. Measured by 600 MHz NMR in D2O. c overlap
d
C3′ and C4′ proton peak. This value was calculated according to the equation: %[C3′-endo] = (10 -
J1′2′)/10 x 100.
Therefore, selenium with a covalent radius of 1.20 A˚ when replacing oxygen at the nucleobase C-2
position is expected to stabilize the sugar conformation even more. As shown in Table 1, the %
[C3′-endo] value of the Se2U 5 was calculated to be 80%, whereas for U and S2U it were 53% and 71%,22
respectively. This result indicated that 2-selenium modification does indeed stabilize the sugar C3′-endo
conformation at the nucleoside level.
In conclusion, each of the synthetic steps in our optimized procedure has been successfully conducted on
a gram scale, attesting to the scalability and efficacy of this route. In addition, we have applied this
methodology to the synthesis of the Se2U phosphoramidite precursor, demonstrating the feasibility of this
route for obtaining Se2U containing RNA oligonucleotides. The presented synthesis of Se2U will

contribute to further functional studies on Se2U regarding to the initiation complex of HIV-1 reverse
transcription. Se2U will also be useful as a tractable key intermediate that is applicable to the synthesis of
other natural occurring selenium-containing pyrimidine nucleosides in tRNAs. The synthesis of these
nucleosides is ongoing in our laboratory.
EXPERIMENTAL
Commercially available reagents were used without further purification. All reactions were performed in
a dry solvent under an argon atmosphere. Transfer of air- and moisture-sensitive reagents was performed
via cannula under a positive pressure of argon atmosphere. DMF was degassed by argon bubbling prior to
use. Analytical thin-layer chromatography (TLC) analysis was performed on Merck TLC (silica gel
60F254 on glass plate). The developed chromatography was analyzed by UV lamp (254 nm) or by
spraying 10% H2SO4 solution in EtOH, followed by heating. Silica gel 60N (spherical, neutral)
manufactured by Kanto Chemical Co., Inc. was used for flash column chromatography. NMR spectra
were recorded on JEOL JNM-ECA600 (1H NMR: 600 MHz, 13C NMR: 150 MHz, 77Se NMR: 113 MHz)
1
spectrometer. Chemical shifts of H NMR are reported in δ values referenced to CHCl3 (G 7.26 ppm) or
D2O (G 4.79 ppm) as an internal standard and the following abbreviation were used as follows: s: singlet,
d: doublet, t: triplet, m: multiplet. Chemical shifts of 13C NMR are reported in δ values referenced to
CHCl3 (G 77.1 ppm) as an internal standard. The 77Se NMR chemical shifts are reported in ppm (G)
relative to the external standard. High-resolution mass spectra (HRMS) was measured with a Waters
UPLC system (Aquity UPLC XevoQTof). Melting points were measured by a Yanagimoto micromelting
point apparatus. IR spectra were measured on JASCO FT/IR-410 Fourier Transform Infrared
Spectrometer in CHCl3 or MeOH. Optical rotations were measured with Union PM-201 Automatic
Digital Polarimeter.
2′,3′,5′-O-Tris(tert-butyldimethylsilyl)-2-methylthiouridine (3)
To a solution of 2 (6.70 g, 11.12 mmol) in a mixture of THF (20 mL) and 10% NaOH aq. (20 mL) was
added methyl iodide (0.83 mL, 13.34 mmol) at rt. The mixture was stirred for 4 h at rt (TLC monitoring;
EtOAc:n-hexane = 1:2). The reaction mixture was extracted with CH2Cl2 (80 mL), and the organic layer
was washed with water (40 mL), dried over Na2SO4, and concentrated in vacuo to afford 3 as a white
foam. Compound 3 was then used in the next step without further purification.
[D]D24 -60.5 (c 0.2, CHCl3).
IR (film): 2929, 2897, 2858, 1658, 1476, 1445, 1349, 1257, 1221, 1157, 1108, 1071, 1036, 1004, 963,
938, 891, 833, 778 cm-1.
1H NMR (600 MHz, CDCl3): Gꢀ ꢀ7.92 (d, 1H, J = 7.6 Hz, H-6), 6.05 (d, 1H, J = 7.6 Hz, H-5), 5.92 (d, 1H,

J = 6.9 Hz, H-1′), 4.13 (dd, 1H, J = 6.8, 4.8 Hz, H-2′), 4.05-4.04 (m, 2H, H-3′, H-4′), 3.87 (dd, 1H, J =
t
11.7, 2.8 Hz, H-5′b), 3.72 (dd, 1H, J = 11.7, 1.4 Hz, H-5′a), 2.56 (s, 3H, SMe), 0.93 (s, 9H, Bu), 0.92 (s,
9H, tBu), 0.84 (s, 9H, tBu), 0.12 (s, 6H, Si(CH3)2), 0.10 (s, 3H, Si(CH3)2), 0.07 (s, 3H, Si(CH3)2), -0.02 (s,
3H, Si(CH3)2), -0.16 (s, 3H, Si(CH3)2).
13C NMR (150 MHz, CDCl3): G = 168.6, 163.7, 138.5, 109.9, 90.6, 87.2, 73.2, 63.4, 26.1, 25.91, 25.88,
18.5, 18.2, 18.0, 14.8, -4.4, -4.9, -5.41, -5.45.
HRMS (ESI): calcd for C28H56N2O5SSi3Na [M+Na]+: 639.3116; found: 639.3115.
2′,3′,5′-O-Tris(tert-butyldimethylsilyl)-2-selenouridine (4)
Sodium borohydride (1.77 g, 46.70 mmol) was added to a suspension of Se (3.06 g, 38.92 mmol) in
degassed EtOH (30 mL) at 0 °C under an argon atmosphere, and the mixture was stirred for 30 min. After
this time, compound 3 was added at 0 °C. The resulting solution was stirred for 4 h at 60 °C (TLC
monitoring; EtOAc:n-hexane = 1:2), then cooled to rt, the reaction mixture was extracted with EtOAc
(100 mL), and the organic layer was washed twice with water (40 mL) and brine (40 mL), dried over
Na2SO4, and then solvent removed by evaporation. The residue was purified by column chromatography
on silica gel (EtOAc:n-hexane = 1:20 to 1:5) to afford 4 as a yellow foam; yield: 6.52 g (90%, 2 steps);
[D]D24 +20.0 (c 0.2, CHCl3).
IR (film): 3087, 2929, 2858, 1686, 1618, 1471, 1441, 1389, 1362, 1256, 1216, 1166, 1134, 1109, 1074,
1053, 1037, 996, 964, 939, 836 cm-1.
1H NMR (600 MHz, CDCl3): Gꢀ ꢀ10.84 (br s, 1H, NH), 8.38 (d, 1H, J = 7.6 Hz, H-6), 6.56 (d, 1H, J = 2.8
Hz, H-1′), 6.08 (d, 1H, J = 8.2 Hz, H-5), 4.27-4.26 (m, 1H, H-2′), 4.15 (d, 1H, J = 6.2 Hz, H-4′),
t
t
4.06-4.02 (m, 2H, H-3′, H-5′b), 3.79 (d, 1H, J = 12.4 Hz, H-5′a), 0.94 (s, 9H, Bu), 0.904 (s, 9H, Bu),
t
0.897 (s, 9H, Bu), 0.17 (s, 3H, Si(CH3)2), 0.13 (s, 3H, Si(CH3)2), 0.12 (s, 3H, Si(CH3)2), 0.11 (s, 3H,
Si(CH3)2), 0.09 (s, 3H, Si(CH3)2), 0.07 (s, 3H, Si(CH3)2).
13C NMR (150 MHz, CDCl3): G = 176.8, 159.2, 141.4, 107.8, 95.7, 84.5, 70.5, 61.4, 26.18, 26.16, 26.08,
18.7, 18.34, 18.31, -3.5, -3.9, -4.4, -4.7, -5.1, -5.5.
77Se NMR (113 MHz, CDCl3): Gꢀ ꢀ423.4.
HRMS (ESI): calcd for C27H54N2O5SeSi3Na [M+Na]+: 673.2403; found: 673.2405.
2-Selenouridine (5)
Compound 4 (5.27 g, 8.12 mmol) was added to a mixture of TFA (21 mL) and water (14 mL). The
resulting solution was stirred for 6 h at rt (TLC monitoring; CHCl3:acetone = 1:1). The reaction mixture
was co-evaporated with toluene in vacuo, the resulting precipitate was filtered, then washed with Et2O (60
24
mL) to afford 5 as a white solid; yield: 2.35 g (94%); Mp 186.5-188.5 °C (H2O); [D]D -20.0 (c 0.1,

DMSO).
IR (film): 2917, 2834, 2605, 1778, 1712, 1622, 1472, 1433, 1396, 1257, 1030, 840, 745 cm-1.
1H NMR (600 MHz, D2O): G = 8.11 (d, 1H, J = 8.3 Hz, H-6), 6.61 (d, 1H, J = 2.0 Hz, H-1′), 6.21 (d, 1H,
J = 8.3 Hz, H-5), 4.35 (d, 1H, J = 2.0 Hz, H-2′), 4.12 (m, 2H, H-3′, H-4′), 3.94 (d, 1H, J = 11.7 Hz, H-5′b),
3.79 (d, 1H, J = 13.1 Hz, H-5′a).
13C NMR (150 MHz, D2O): G = 175.7, 161.7, 141.6, 108.1, 95.9, 84.0, 74.9, 68.3, 59.7.
77Se NMR (113 MHz, D2O): G = 353.8.
HRMS (ESI): calcd for C9H12N2O5SeNa [M+Na]+: 330.9809; found: 330.9820.
2′-O-tert-Butyldimethylsilyl-3′,5′-O-(di-tert-butylsilanediyl)-2-selenouridine (6)
Compound 5 (1.20 g, 3.92 mmol) was suspended in DMF (10 mL) and di-tert-butylsilyl
bis(trifluoromethanesulfonate) (1.40 mL, 4.31 mmol) was added dropwise over 5 min while the solution
was stirred at 0 °C. The resulting solution was stirred for 40 min at 0 °C (TLC monitoring;
EtOAc:n-hexane = 1:1) and then imidazole (1.33 g, 19.6 mmol) added to the solution at 0 °C. The
mixture was stirred for 5 min at 0 °C and further stirred for 25 min at rt. tert-Butyldimethylchlorosilane
(0.89 g, 5.88 mmol) was added to the solution at rt and the reaction allowed to proceed at 60 °C for 2 h
(TLC monitoring; EtOAc:n-hexane = 1:1). The reaction mixture was extracted with EtOAc (60 mL), and
the organic layer was washed with sat. NaHCO3 aq. (30 mL) and brine (30 mL), dried over Na2SO4, and
then evaporated. The reaction mixture was co-evaporated with toluene under reduced pressure. The
resulting residue was purified by column chromatography on silica gel (EtOAc:n-hexane = 1:15 to 1:4) to
afford 6 as a yellow foam; yield: 2.04 g (93%); [D]D24 +22.0 (c 0.2, CHCl3).
IR (film): 3098, 2934, 2895, 2860, 1689, 1625, 1471, 1438, 1387, 1260, 1167, 1126, 1064, 896, 828, 757
cm-1.
1H NMR (600 MHz, CDCl3): Gꢀ ꢀ7.33 (d, 1H, J = 8.3 Hz, H-6), 6.66 (s, 1H, H-1′), 6.14 (d, 1H, J = 8.2 Hz,
H-5), 4.55 (dd, 1H, J = 9.6, 4.8 Hz, H-5′b), 4.36 (d, 1H, J = 4.8 Hz, H-2′), 4.25 (ddd, 1H, J = 9.6, 9.6, 5.5
t
Hz, H-4′), 4.03-4.00 (m, 1H, H-5′a), 3.80 (dd, 1H, J = 9.6, 4.8 Hz, H-3′), 1.05 (s, 9H, Bu), 1.03 (s, 9H,
tBu), 0.95 (s, 9H, tBu), 0.25 (s, 3H, Si(CH3)2), 0.16 (s, 3H, Si(CH3)2).
13C NMR (150 MHz, CDCl3): Gꢀ ꢀ176.8, 158.3, 139.4, 108.4, 99.2, 76.4, 76.0, 75.2, 67.7, 27.6, 27.1, 26.1,
23.0, 20.5, 18.4, -3.2, -4.2.
77Se NMR (113 MHz, CDCl3): Gꢀ ꢀ448.4.
HRMS (ESI): calcd for C23H42N2O5SeSi2Na [M+Na]+: 585.1695; found: 585.1707.
5′-O-(4,4′-Dimetoxytrityl)-2′-O-tert-butyldimethylsilyl-2-selenouridine (7)
Hydrogen fluoride–pyridine (0.54 mL, 21.70 mmol) was carefully diluted with pyridine (2.34 mL, 28.96

mmol) at 0 °C. The resulting solution was added slowly to a stirred suspension of 6 (2.03 g, 3.62 mmol)
in CH2Cl2 (20 mL) at 0 °C and the reaction was allowed to proceed for 3 h at 0 °C (TLC monitoring;
EtOAc:n-hexane = 1:1). The reaction mixture was diluted with CH2Cl2 (20 mL), and washed with water
(20 mL) and sat. NaHCO3 aq. (20 mL). The organic layer was dried over Na2SO4 and concentrated in
vacuo to afford 2′-O-tert-butyldimethylsilyl-2-selenouridine. To
a
stirred solution of
2′-O-tert-butyldimethylsilyl-2-selenouridine in pyridine (10 mL) at 0 °C was added 4,4′-dimethoxytrityl
chloride (2.45 g, 7.24 mmol). The reaction mixture was stirred for 2 h at rt (TLC monitoring;
EtOAc:n-hexane = 1:1), quenched with anhydrous EtOH (2.0 mL) and concentrated under reduced
pressure. The reaction mixture was extracted with CH2Cl2 (40 mL) and the organic layer was washed with
sat. NaHCO3 aq. (20 mL) and brine (20 mL), then dried over Na2SO4, and concentrated under reduced
pressure. The residue was purified by column chromatography on silica gel (EtOAc:n-hexane = 1:10 to
1:2) to afford 7 as a yellow foam; 2.29 g (87%, 2 steps); [D]D24 +4.50 (c 0.2 , CHCl3).
IR (film): 3087, 3016, 2952, 2930, 2857, 2838, 1691, 1608, 1582, 1509, 1465, 1442, 1254, 1177, 1122,
1036, 836, 756 cm-1.
1H NMR (600 MHz, CDCl3): G = 11.18 (br s, 1H, NH), 8.25 (d, 1H, J = 7.6 Hz, H-6), 7.35-7.23 (m, 9H,
Ph), 6.87 (d, 1H, J = 3.5 Hz, H-1′), 6.85-6.83 (m, 4H, Ph), 5.51 (d, 1H, J = 8.3 Hz, H-5), 4.50-4.49 (m,
1H, H-2′), 4.43-4.41 (m, 1H, H-3′), 4.20-4.19 (m, 1H, H-4′), 3.79 (s, 6H, OMe), 3.56-3.51 (m, 2H, H-5′a,
H-5′b), 2.67 (d, 1H, J = 5.5 Hz, OH), 0.94 (s, 9H, tBu), 0.24 (s, 3H, Si(CH3)2), 0.17 (s, 3H, Si(CH3)2).
13C NMR (150 MHz, CDCl3): G = 177.3, 159.1, 158.9, 158.8, 144.2, 141.4, 134.9, 134.7, 130.3, 130.1,
128.2, 128.1, 127.4, 113.4, 108.2, 95.5, 87.5, 84.2, 70.9, 62.3, 55.4, 25.9, 18.3, -3.9, -4.8.
77Se NMR (113 MHz, CDCl3): Gꢀ ꢀ413.4.
HRMS (ESI): calcd for C36H44N2O7SeSiNa [M+Na]+: 747.1981; found: 747.1996.
ACKNOWLEDGEMENTS
This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education,
Culture, Sports, Science and Technology of Japan (No. 15K07856) to which we are grateful.
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