Oligonucleotide analogues with integrated bases and backbone: Part 21 - Influence of the hydrogen-bonding motif on the gelation of self-complementary A*[s]U(*) dinucleosides

Article abstract of DOI:10.1002/hlca.200900075

Gelation of organic solvents by the A*[s]U(*) dinucleosides 1 and 2 requires the formation of linear associates cross-linked by H-bonding involving either the nucleobase or HOCH₂-C(6/I). This is evidenced by the absence of gel formation of the

Full text of DOI:10.1002/hlca.200900075

Helvetica Chimica Acta – Vol. 92 (2009)
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Oligonucleotide Analogues with Integrated Bases and Backbone
Part 21
Influence of the Hydrogen-Bonding Motif on the Gelation of Self-Complementary
A*[s]U(*) Dinucleosides
by Nicolas Bogliotti and Andrea Vasella*
Laboratorium fꢀr Organische Chemie, ETH Zꢀrich, Wolfgang-Pauli-Strasse 10, CH-8093 Zꢀrich
(e-mail: vasella@org.chem.ethz.ch)
Gelation of organic solvents by the A*[s]U(*) dinucleosides 1 and 2 requires the formation of linear
associates cross-linked by H-bonding involving either the nucleobase or HOCH2ꢀC(6/I). This is
evidenced by the absence of gel formation of the N6-methyladenosine analogue 5 of 1 and the dehydroxy
analogue 4 of 2.
Introduction. – The A*[s]U(*)1) dinucleosides 1 and 2 were synthesised to analyse
the self- and hetero-association of thiomethylene linked oligonucleotide analogues
(ONIBs), and found to form thermoreversible gels in organic solvents [1][2]. The
gelation involves a network of dinucleosides, associated by H-bonds between the
nucleobases, as shown by correlating solvent polarity and properties of the gels, and by
the absence of gel formation of the C(6)-deaminated analogue 3 of 1 [3].
To generate a network, these dinucleosides must preferentially associate to form
linear rather than cyclic duplexes, as only linear duplexes can lead to higher associates
[1][2][4 – 6]. Moreover, the linear associates must be cross-linked to form a three-
dimensional network that cannot result from a mere linear sequence of dinucleosides
A*[s]U(*) ··· (A*[s]U(*) ··· )nA*[s]U(*). We assumed that cross-linking the linear
oligoplexes involves the adenosine moiety that can simultaneously form Watson –
Crick and Hoogsteen-type H-bonds, as in the fundamental motif for triple helixes
[7]. Analysis of the gel formation by the A*[s]U* dimer 2 must also take into account
that substitution at C(6/I) results in a predominant syn-conformation of the nucleobase,
and that this conformation favours the formation of cyclic duplexes (cf. [1]). We thus
wondered if the CH2OH group at C(6/I) has the function of bridging linear oligoplexes,
as it was observed in the crystal structure of a U*[s]A* dinucleoside [1].
1
)
Conventions for abbreviated notation: The substitution at C(6) of pyrimidines and C(8) of purines is
denoted by an asterisk (*); for example, A* and U* for hydroxymethylated adenosine and uridine
derivatives, respectively. U(*) represents both unsubstituted and hydroxymethylated uridine
derivative. The replacement of the amino group at C(6) of adenosine by a methylamino group
and the replacement of the hydroxymethyl group of uridine by an H-atom are denoted by ꢂMeꢃ in
superscript (Me) and ꢂ Hꢃ in superscript (H), resp.; for example, MeA and HU represent N6-
methyladenosine and C(6)-methyluridine derivatives, resp. The moiety x linking C(8)ꢀCH2 of unit
II and C(5’) of unit I is indicated in square brackets, i.e., [s] for a S-atom.
ꢁ 2009 Verlag Helvetica Chimica Acta AG, Zꢀrich

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To test this hypothesis, we planned to synthesise the N6-methyladenosine analogue
4, and the deoxy analogue 5, and to evaluate their ability to gelate solvents.
Results and Discussion. – Synthesis of the MeA*[s]U Dinucleoside 4. To synthesize
the dinucleoside 4, we substituted the chloromethylated N6-methyladenosine derivative
13 by the thiolate resulting from deacetylation of the known thioacetate 14 [1]
(Scheme 1). In view of obtaining 13, we treated the protected adenosine 6 [1] with MeI
in a biphasic CH2Cl2/1m aq. NaOH mixture under phase-transfer conditions [8], and
obtained the desired N6-methyladenosine 7 in 68% and the 1-methyladenosine 8 in
21% yield. Attempts at introducing a CH2OH group at C(8) of N6-methyladenosine 7
by deprotonation with lithium diisopropylamide (LDA) [9], formylation with DMF,
hydrolysis, and reduction of the resulting aldehyde with NaBH4 [10] failed. We,
therefore, started from the hydroxymethylated adenosine derivative 9 [1]. Methylation
under phase-transfer conditions afforded the regioisomeric monomethyl adenosines 10
(73%) and 11 (21%). Detritylation of 10 gave the alcohol 12 that was transformed into
the chloro derivative 13 by mesylation, followed by in-situ substitution with LiCl.
Treating a mixture of 13 and 14 with MeONa in dry, O2-free MeOH yielded 96% of the
dinucleoside 15 that was desilylated with (HF)3 · Et3N to provide 4 in 98% yield.
Synthesis of the A*[s]HU* Dinucleoside 5. Similarly to 15, the protected dinucleo-
side 23 was obtained by thioether formation between the chloromethylated adenosine
derivative 17 and the thiolate generated from the uridine derived thioacetate 22
(Scheme 2). Mesylation of the known C(8)-(hydroxymethyl)-adenosine 16 [1] gave

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1169
Scheme 1
a) MeI, Bu4NBr, CH2Cl2/1m aq. NaOH; 68% of 7 and 21% of 8; 73% of 10 and 21% of 11. b) Et3SiH,
Cl2CHCO2H, CH2Cl2; 79%. c) MsCl, EtNiPr2, CH2Cl2, then LiCl; 94%. d) MeONa, MeOH; 96%. e)
(HF)3 · Et3N, THF; 98%. MMTr¼ (monomethoxy)trityl (¼(4-methoxyphenyl)diphenylmethyl). TDS ¼
dimethyl(thexyl)silyl (thexyl ¼ 1,1,2-trimethylpropyl).
chloride 17; the intermediated methanesulfonate was not isolated. The uridine
thioacetate 22 was synthesized from the known C(6)-(hydroxymethyl)-uridine 18 [1].
Mesylation afforded the chloro compound 19 that was reductively dechlorinated in the
presence of Pd/C and MgO to yield 89% of the corresponding C(6)-methyl derivative
20. Desilylation afforded the alcohol 21 (96%). Tosylation of 21 and treatment of the
resulting crude product with AcSK in DMF yielded 78% of the thioacetate 22. The
A*[s]HU* dinucleoside 23 was initially prepared in 46% yield by exposing 17 and 22 to

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MeONa in dry, O2-free MeOH. Formation of several by-products suggested that
deprotonation of the methyl group at C(6) of 22 could compete with S-deacetylation.
Thus, we treated 22 first with K2CO3 in degassed MeOH to obtain the corresponding
thiolate, and then added chloro derivative 17. This indeed resulted in a yield of 78% of
23 that was desilylated to give 92% of the alcohol 5.
Scheme 2
a) MsCl, EtNiPr2, CH2Cl2; 81% of 17; 81% of 19. b) H2, 10% Pd/C, MgO, AcOEt; 89%. c) Bu4NF ·
3 H2O, THF; 96%. d) 1. TsCl, pyridine; 2. AcSK, DMF, 708; 78%. e) K2CO3, MeOH, then 17; 78%.
f) (HF)3 · Et3N, THF; 92%. TDS ¼ dimethyl(thexyl)silyl (thexyl ¼ 1,1,2-trimethylpropyl).
Conformation of the Adenosine-Derived Monomers. The N6-methyladenosine
derivative 7 adopts an anti-conformation, as revealed by d(HꢀC(2’)) of 5.23 ppm
(Table 3 in the Exper. Part). HꢀC(2’) of the 1-methyladenosine derivative 8 resonates
at 5.07 ppm. This upfield shift (Dd ¼ 0.16 ppm) could reflect a different syn-
conformation, a larger proportion of the anti-conformer, as previously reported for
inosine derivatives [3], or differences in the electronic structure of the nucleobase. A
weak predominance of the (S)-conformation of 7 and 8 is evidenced by J(1’/2’)/J(3’/4’)
ratios of 1.2 and 1.1, respectively. A large population of the gg-conformer (gg/gt/tg
60 :22 :18 of 7 and 49 :24 :27 of 8)2) is revealed by J(4’/5’a) and J(4’/5’b) of 3.7 –
4.4 Hz.
2
)
See [1] for the calculation of the rotamer distribution.

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The O(5’)-silylated and 8-substituted adenosines 10, 13, and 17 adopt a syn-
conformation in CDCl3, as revealed by d(HꢀC(2’)) of 5.71 – 5.82 ppm (Table 3 in the
Exper. Part). HꢀC(2’) of the 1-methyladenosine 11 resonates at a higher field
(5.50 ppm). A similar upfield shift (Dd ꢁ 0.25 ppm) as found above for 8 evidences a
strong influence of the nature of the nucleobase on d(HꢀC(2’)). The upfield shift for
HꢀC(2’) of the alcohol 12 (5.53 ppm), however, reflects a ca. 4 :1 syn/anti equilibrium,
presumably due to the stabilization of the anti-conformer by an intramolecular H-bond
between HOCH2ꢀC(8) (dd at 3.52 ppm with 3J(H,OH) ¼ 6.4 and 5.9 Hz) and
OꢀC(5’) (see [1] and [3]). The (N)-conformation of 10 – 13 and 17 is indicated by
J(1’/2’)/J(3’/4’) ratios of 0.7 – 0.8. J(4’,5’a) and J(4’,5’b) values of 5.6 – 6.4 Hz of 10, 11,
13, and 17 evidence a similar rotameric distribution (gg/gt/tg 12 :42 :46, 10 :39 :51,
23 :36 :41, and 19 :36 :45, resp.). In agreement with the above mentioned intra-
molecular H-bond in the syn-conformer of 12, the J(4’,5’a) and J(4’,5’b) values of
4.8 Hz evidence a distinctly larger population of the gg-conformation (gg/gt/tg
40 :28 :32).
Conformation of the Uridine-Derived Monomers. The C(6)-substituted uridine
derivatives 19 – 22 adopt a syn-conformation in solution, as revealed by the downfield
shift of HꢀC(2’) (5.21 – 5.25 ppm; Table 7 in the Exper. Part). The silyl ethers 19 and
20, and the thioacetate 22 prefer the (N)-conformation, as revealed by a J(1’,2’)/J(3’,4’)
value of 0.25. They adopt preferentially the gt- and tg-conformation (gg/gt/tg 8 :54 :38
of 19 and 5 :53 :42 of 20, gt/tg ca. 1:1 of 22). The alcohol 21 forms an intramolecular
H-bond from HOꢀC(5’) to O¼C(2). This is evidenced by the larger population of the
gg-rotamer (gg/gt/tg 56 :32 :12), as deduced from the distinctly smaller J(4’,5’a) and
J(4’,5’b) values (3.1 and 4.6 Hz, resp.). A partial persistence of the H-bond is also
suggested by the downfield shift of HOꢀC(5’) resonating at 3.25 ppm.
Crystals of 22 suitable for X-ray analysis were obtained from MeCN3). In the
crystalline state, 22 adopts a classic syn-conformation (O(4’)ꢀC(1’)ꢀN(1)ꢀC(2) ¼
66.88), with a planar furanose ring (torsion angles < 28; Fig. 1,a). It adopts the gt-
conformation (O(4’)ꢀC(4’)ꢀC(5’)ꢀS(5’) ¼ 58.38), as previously observed for other S-
linked dinucleosides [1]. The molecules are assembled head-to-tail, forming intermo-
lecular N(3)H ··· O(2’) H-bonds (Fig. 1,b).
Association of the MeA*[s]U and A*[s]HU* Dinucleosides in CHCl3. The self-
association of 4, 5, 15, and 23 was investigated by analysing the concentration
dependence of the chemical shift for HꢀN(3/I) and by temperature-dependent circular
dichroism, as discussed in detail in [1].
The MeA*[s]U dimers 15 and 4 associate weakly (Kass ¼ 76 and 95 mꢀ1, resp.;
Table 1) and form linear associates, as shown by the weak curvature of the shift/
concentration curves (SCCs; Fig. 2), the absence of a plateau at concentrations
between 20 and 50 mm, and the numerical analysis of the SCCs according to Gutowski
and Saika [1][11]. The extrapolated chemical-shift values for the duplexes of 15 and 4
(11.44 and 11.42 ppm, resp.; Table 1) support the dominant or exclusive formation of
3
)
The crystallographic data have been deposited with the Cambridge Crystallographic Data Centre as
deposition No. CCDC-717721. Copies of the data can be obtained free of charge via http://
www.ccdc.cam.ac.uk/data_request/cif (or from the Cambridge Crystallographic Data Centre, 12
Union Road, Cambridge CB21EZ (fax: þ 44(1223)336033; e-mail: deposit@ccdc.cam.ac.uk).

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Fig. 1. Crystal structure of 22. a) ORTEP Representation. b) Molecular packing showing intermolecular
N(3)ꢀH ··· O(2’) H-bonds (hashed bonds).
Hoogsteen-type H-bonds. The association constants of 15 and 4 are higher than those of
their 6-deamino analogues (23 and 20 mꢀ1, resp. [3]), but lower than those of the
corresponding A*[s]U dimers (225 and 221mꢀ1, resp. [1]). These observations are
consistent with the crystal structure of N6-methyladenine derivatives, which revealed a
s-cis-conformation of the N6-Me group, preventing Watson – Crick pairing [12][13]. Ab
initio calculations revealed that the s-trans-rotamer is less stable by 1.83 kcal/mol than
the s-cis-isomer [14][15]. An almost exclusive Hoogsteen-type H-bonding was also
found by association studies of other N6-methyladenine derivatives in solution,
resulting in a lowering of Kass by ca. 50%, as compared to adenine [16 – 18].
The A*[s]HU* dimers 23 and 5 in CDCl3 (Kass ¼ 806 and 720 mꢀ1; Table 1) associate
more weakly than the C(6/I)-hydroxymethyl analogue of 23 (Kass ¼ 3373 mꢀ1; the
analogue of 5 forms a gel; see [1]). The SCCs show a flattening above 30 mm, without
reaching a plateau, reflecting an equilibrium between monoplex, linear associates, and
cyclic duplexes (Fig. 2). The chemical shift for HꢀN(3/I) of 23 at a concentration of
30 mm (12.0 ppm) and similarly of 5 (11.4 ppm) suggests a large proportion of Watson –
Crick-type base-paired cyclic duplexes of 23, and a large proportion of Hoogsteen-type

Helvetica Chimica Acta – Vol. 92 (2009)
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Fig. 2. Shift/concentration curves (SCCs) for the A*[s]U(*) dimers 4, 5, 15, and 23 in CDCl3 solution
(including a value of 7.70 ppm for a 0.0001-mm soln.)
Table 1. Association Constants Kass from the Concentration Dependence of d(HN(3)) in CDCl3 at 295 K
for the A*[s]U(*) Dimers 4, 5, 15, and 23 (including a value of 7.70 ppm for a 0.0001 mm soln.), DG295
Value, Extrapolated Chemical Shifts of the Monoplexes and Duplexes, and Determination of the
Thermodynamic Parameters by vanꢃt Hoff Analysis of the Temperature Dependence of d(HN(3)) of 5 and
23 for 6 mm Solutions in CDCl3 at 7 – 508
a
b
c
Dimer
Kass
[mꢀ1
dmonoplex
)
dduplex
)
ꢀ DG295
)
ꢀ DH
ꢀ DS
]
[ppm]
[ppm]
[kcal/mol]
[kcal/mol]
[cal/(mol K)]
d
d
15
4
23
5
76
95
806
720
7.78
7.71
7.69
7.70
11.44
11.42
12.63
12.01
2.5
2.7
3.9
3.9
)
)
)
)
d
d
14.2
10.0
34.8
21.0
a) Extrapolated for 0 mm. b) Extrapolated for infinite concentration. c) Calculated from Kass d) Not
.
determined.
base-paired cyclic duplexes of 5 (see [1]), in agreement with the ꢀ DH values of 14.2
and 10.0 kcal/mol, as determined by vanꢀt Hoff analysis of the association of 23 and 5,
respectively.
The temperature-dependent CD spectra recorded for 1 mm solutions of 15 and 4
show a weak variation of the ellipticity, in agreement with the poor stacking expected
for linear associates (Fig. 3). For 15, a positive Cotton effect was observed with extrema
at 265 – 275 nm (positive) and at 230 nm (negative), whereas the curve of 4 shows a
negative Cotton effect, with extrema at 230 and 285 nm. This difference may be traced
back to the intramolecular H-bond between C(5’)ꢀOH and N(3) of the adenosine
moiety of 4, and the concomitant change of the conformation of the ribofuranosyl ring
from N (15) to S (4). The CD spectra of the related pair of dinucleosides 23 and 5 show
a stronger temperature dependence of the ellipticity that decreases with increasing

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Fig. 3. Temperature-dependent CD spectra (solid lines, in 108 steps from 08 to 508) of 1-mm solutions of 4,
5, 15, and 23 in CHCl3
temperature, evidencing p-stacking of the nucleobases as expected of cyclic duplexes.
At 08, the CD spectra of 23 and 5 are characterised by a negative Cotton effect, with
extrema at 275 – 285 nm (both compounds), and at 260 (23) and 245 (5) nm. Upon
increasing the temperature to 508, the negative Cotton effect of 5 decreases, the one of
23 disappears gradually, and only the positive extrema at 260 and 245 nm remain. At
508, the CD curves of 23 and 5 resemble those of 15 and 4, respectively. This suggests
that the linear associates of the silyl ethers 15 and 23 adopt a similar conformation, and
that it differs from that of alcohols 4 and 5. Hence, the different conformation of the
ribofuranosyl ring correlating with the orientation of the C(4’/II) substituent (gt/tg ca.
1:1 for 15 and 23; gg of 4 and 5), as determined by the intramolecular H-bond in 4 and
5, appears to be responsible for the opposite sign of the CD curves at 508. The molar
ellipticity ([q]) of the four dimers ranges from ꢀ 6 · 104 to þ 4 · 104 deg · cm2/dmol,
and compares well to the one of the corresponding A*[s]U dimers, ranging from ca.

Helvetica Chimica Acta – Vol. 92 (2009)
1175
ꢀ 6 · 104 to þ 2 · 104 deg · cm2/dmol [1]4), and of the corresponding HA*[s]U dimers
(deaminated at C(6)), ranging from ca. ꢀ 5 · 104 to þ 104 deg · cm2/dmol [3].
Conformation of the MeA*[s]U and A*[s]HU* Dinucleosides in CHCl3. The
conformation of unit I is similar for the two MeA*[s]U dimers 15 and 4. The chemical
shift for HꢀC(2’/I) of 15 and of 4 (4.88 – 4.89 ppm; Table 5 in the Exper. Part) reflects a
ca. 1:1 syn/anti orientation of the uracil moiety (see [1][3]). The same (S)/(N) ratio of
conformers is indicated by J(1’,2’/I)/J(3’,4’/I) ¼ 0.6, and a gg/gt/tg rotameric distribution
of 26 :36 :38 and 29 :43 :28, respectively, is deduced from J(4’,5’a/I) and J(4’,5’b/I)
ranging from 5.5 to 6.4 Hz. The syn-conformation of the HU* moiety (unit I) of the
A*[s]HU* dinucleosides 23 and 5 is evidenced by d(HꢀC(2’/I)) of 5.19 and 5.18 ppm,
respectively, while J(1’,2’/I)/J(3’,4’/I) ¼ 0.2 reveals the preference for a (N)-conforma-
tion, and J(4’,5’a/I) and J(4’,5’b/I) (5.5 – 6.4 Hz) suggest a gg/tg/gt rotamer distribution
of 6 :58 :36 and 5 :46 :49, respectively.
Unit II of the silyl ethers 15 and 23 adopts a syn-conformation, as revealed by
d(HꢀC(2’/II)) ¼ 5.91 and 5.97 ppm, respectively, and shows a slight preference for the
(N)-conformation (J(1’,2’/II)/J(3’,4’/II) ¼ 0.5 – 0.6). A ca. 1 :1 gt/tg ratio is deduced for
15 and 23 from J(4’,5’a/II) and J(4’,5’b/II) of 6.2 – 6.9 Hz. HOꢀC(5’/II) of the alcohols
4 and 5 forms a persistent intramolecular H-bond to N(3), as evidenced by the
exclusive population of the gg-rotamer (J(4’,5’a/II) ¼ J(4’,5’b/II) < 1.0 Hz), the strongly
preferred (S)-conformation (J(1’,2’/II)/J(3’,4’/II) > 4.6), the downfield shift for
HOꢀC(5’/II) (4: 6.73 ppm, 5: 6.63 ppm), the upfield shift for HꢀC(2’/II) (5.23 –
5.25 ppm), and the typical small and large J(5’,OH) values (ꢂ1.0 and ꢃ 10.0 Hz; cf.
[1][3][19][20]).
Solubility and Gelation Properties of the Dinucleosides 4 and 5. The solubility of 4
and 5, and their ability to form gels was evaluated with a selection of 16 solvents, based
on Chastretteꢃs classification [21], at a concentration of 1% (w/v), according to the
same procedure as reported for 1 and 2 (Table 2) [3]. Under these conditions, 4 and 5
were soluble in most of the solvents tested, except in hexane, toluene, iPr2O, and H2O.
No significant increase of the viscosity of the solution, indicating the formation of
gelating associates, was detected.
It thus appears that such dinucleosides may associate to form linear aggregates that
are cross-linked by H-bonding involving either the nucleobase or HOCH2ꢀC(6/I)
leading to gels, provided that formation of cyclic duplexes is disfavoured. Stacking of
the nucleobases appears to contribute to gelation without being a decisive factor.
We thank Dr. Bruno Bernet for checking the Exper. Part and for helpful suggestions.
Experimental Part
General. See [3]. vanꢀt Hoff analysis: see [1].
Methylation of 6. A biphasic mixture of 6 [1] (4.000 g, 7.22 mmol) and Bu4NBr (2.327 g, 7.22 mmol)
in CH2Cl2 (18 ml) and 1m aq. NaOH soln. (18 ml) was treated with MeI (1.80 ml, 28.88 mmol), and
vigorously stirred for 30 min at 258. The mixture was extracted three times with CH2Cl2. The combined
4
)
For comparison purposes, the ellipticity (q, [mdeg]) values reported in [1] were converted to [q]
[deg cm2/dmol].

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Table 2. Solubility of the Dinucleosides 4 and 5 (1% (w/v)) in Selected Solvents
Class
Solvent
4a)
5a)
Aliphatic, apolarb)
Aromatic, apolar
Electron-pair donor
Aprotic, dipolar
Hexanec)
Toluene
iPr2O
CH2Cl2
Acetone
ClCH2CH2Cl
Butan-2-one
MeCN
AcOEt
DMF
MeOH
EtOH
I
I
Id)
I
Id)
I
S
S
S
S
S
S
S
S
S
S
S
I
S
S
S
S
S
S
S
S
Aprotic, highly dipolar
H-Bonding
S
S
BuOH
Decanolb)
H2O
Id)
I
H-Bonding, strongly associated
Miscellaneous
CHCl3
S
S
a) I: insoluble, S: soluble. b) Missing in Chastretteꢃs original classification [21]. c) Reclassified solvent.
d) Soluble at 708.
org. layers were dried (Na2SO4) and evaporated. FC (AcOEt/cyclohexane 1:2 ! 2 :1) gave 7 (2.794 g,
68%) and 8 (873 mg, 21%).
Data of N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylidene-N6-methyl-
adenosine (7). Colourless glass. Rf (cyclohexane/AcOEt 1:1) 0.73. [a]2D5 ¼ ꢀ51.0 (c ¼ 0.95, CHCl3).
UV (CHCl3): 283 (15100). IR (ATR): 3059w, 2957w, 2867w, 1669m, 1572s, 1457m, 1447m, 1417w, 1374w,
1320s, 1259m, 1207s, 1125m, 1078s, 1039s, 1021s, 968w, 923w, 893w, 871m, 826s. 1H-NMR (300 MHz,
CDCl3): see Table 3; additionally, 7.47 – 7.43 (m, 2 arom. H); 7.33 – 7.16 (m, 3 arom. H); 3.81 (s, MeN);
1.64, 1.41 (2s, Me2C); 1.59 (sept., J ¼ 6.8, Me2CH); 0.85 (d, J ¼ 6.8, Me2CH); 0.80, 0.78 (2s, Me2CSi); 0.07,
0.05 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 4; additionally, 172.06 (s, C¼O); 136.11 (s);
130.54 (d); 128.57 (2d); 127.87 (2d); 114.23 (s, Me2C); 35.99 (q, MeN); 34.11 (d, Me2CH); 27.39, 25.49 (2q,
Me2C); 25.43 (s, Me2CSi); 20.42, 20.38 (2q, Me2CSi); 18.61 (q, Me2CH); ꢀ 3.19, ꢀ 3.35 (2q, Me2Si). HR-
MALDI-MS: 568.2954 ([M þ H]þ, C29H41N5O5Siþ; calc. 568.2955).
Data of N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylidene-1-methylade-
nosine (8). Colourless glass. Rf (cyclohexane/AcOEt 1:1) 0.22. [a]2D5 ¼ ꢀ76.7 (c ¼ 1.2, CHCl3). UV
(CHCl3): 250 (13080), 306 (11800). IR (ATR): 2956w, 2867w, 1666m (sh), 1640s, 1577m, 1541s, 1505w,
1463w, 1447w, 1431w, 1376s, 1309m, 1251s, 1211s, 1170w, 1156m, 1127m, 1076s, 1019m, 1003m, 969w, 925w,
873m, 828s. 1H-NMR (300 MHz, CDCl3): see Table 3; additionally, 8.18 – 8.14 (m, 2 arom. H); 7.51 – 7.36
(m, 3 arom. H); 3.73 (s, MeN); 1.60, 1.37 (2s, Me2C); 1.55 (sept., J ¼ 6.8, Me2CH); 0.81 (d, J ¼ 6.8,
Me2CH); 0.76, 0.75 (2s, Me2CSi); 0.03, ꢀ 0.01 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 4;
additionally, 177.09 (s, C¼O); 135.78 (s); 131.84 (d); 129.68 (2d); 128.00 (2d); 114.32 (s, Me2C); 37.08 (q,
MeN); 34.12 (d, Me2CH); 27.38, 25.55 (2q, Me2C); 25.37 (s, Me2CSi); 20.37 (q, Me2CSi); 18.62, 18.59 (2q,
Me2CH); ꢀ 3.19, ꢀ 3.32 (2q, Me2Si). HR-MALDI-MS: 568.2955 ([M þ H]þ, C29H41N5O5Siþ; calc.
568.2955).
Methylation of 9. A biphasic mixture of 9 [1] (3.246 g, 3.79 mmol) and Bu4NBr (1.224 g, 3.79 mmol)
in CH2Cl2 (19 ml) and 1m aq. NaOH soln. (19 ml) was treated with MeI (944 ml, 15.16 mmol), and
vigorously stirred for 30 min at 258. The mixture was extracted three times with CH2Cl2. The combined
org. layers were dried (Na2SO4) and evaporated. FC (AcOEt/cyclohexane 1:4 ! 1:1) gave 10 (2.420 g,
73%) and 11 (676 mg, 21%).

Helvetica Chimica Acta – Vol. 92 (2009)
1177
Table 3. Selected 1H-NMR Chemical Shifts [ppm] and Coupling Constants [Hz] of the Adenosine
Monomers 7, 8, 10 – 13, and 17 in CDCl3
7
8
10
8.48
11
7.89
12
8.53
13
8.52
17
8.79
HꢀC(2)
HꢀC(8)
CHaꢀC(8)
CHbꢀC(8)
HꢀC(1’)
HꢀC(2’)
HꢀC(3’)
HꢀC(4’)
HaꢀC(5’)
HbꢀC(5’)
J(Ha,Hb)
J(1’,2’)
J(2’,3’)
J(3’,4’)
J(4’,5’a)
J(4’,5’b)
J(5’a,5’b)
8.57
8.18
–
–
6.17
5.23
4.94
4.45
3.86
3.76
7.98
7.79
–
–
–
–
–
–
4.44
4.40
6.13
5.71
4.92
4.11
3.70
3.60
11.9
2.8
6.6
3.7
6.0
4.25
4.21
6.07
5.50
4.78
4.06
3.71
3.59
11.8
2.9
6.7
4.0
6.4
4.88
4.84
6.24
5.53
5.02
4.23
3.80
3.78
14.7
2.9
6.7
3.9
4.8
4.84
4.78
6.25
5.74
5.07
4.25
3.72
3.64
12.5
2.6
6.5
3.6
5.6
4.94
4.87
6.31
5.82
5.12
4.29
3.74
3.63
12.6
2.4
6.4
3.4
5.9
–
5.99
5.07
4.86
4.33
3.71
3.71
–
–
2.8
6.2
2.3
3.7
4.0
2.9
6.3
2.6
4.4
4.4
6.3
10.8
6.2
10.6
4.8
11.1
5.7
10.9
5.8
10.8
a
11.3
)
a) Not assigned.
Table 4. Selected 13C-NMR Chemical Shifts [ppm] of the Adenosine Monomers 7, 8, 10 – 13, and 17 in
CDCl3
7
8
10
11
12
13
17
C(2)
C(4)
C(5)
C(6)
154.73
151.83
126.44
152.08
141.95
–
91.75
84.86
81.54
87.22
63.44
146.91
144.87
122.56
147.38
138.14
–
91.18
84.93
81.48
86.90
63.16
153.55
151.50
125.63
154.71a)
152.52a)
59.40
90.14
82.67
81.80
86.87
146.35
145.89
121.58
148.43a)
146.76a)
59.53
89.86
83.28
81.74
86.43
151.84
153.83
124.89
154.48a)
154.58a)
58.41
89.88
83.73
80.68
86.68
152.22
150.31
125.08
155.23
153.32
36.65
90.15
83.02
81.37
153.08
149.64
121.95
152.16
150.01
36.74
90.29
83.12
81.55
C(8)
CH2ꢀC(8)
C(1’)
C(2’)
C(3’)
C(4’)
C(5’)
87.31
62.75
87.62
62.78
63.08
63.16
62.69
a) Assignments may be interchanged.
Data of N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylidene-8-{[(4-meth-
oxyphenyl)diphenylmethoxy]methyl}-N6-methyladenosine (10). White solid. Rf (cyclohexane/AcOEt
2 :1) 0.71. M.p. 68 – 788. [a]2D5 ¼ ꢀ21.1 (c ¼ 1.0, CHCl3). UV (CHCl3): 241 (20270), 285 (18030). IR
(ATR): 3059w, 3028w, 2955w, 2931w, 2865w, 1673m, 1590m, 1575s, 1509m, 1491w, 1447m, 1416w, 1370w,
1344m, 1317m, 1307m, 1250s, 1213m, 1179m, 1154m, 1129m, 1062s, 1038s, 975m, 917m, 899m, 866m, 822s.
1H-NMR (300 MHz, CDCl3): see Table 3; additionally, 7.51 – 7.15 (17 arom. H); 6.88 – 6.85 (2 arom. H);
3.81 (s, MeN); 3.79 (s, MeO); 1.57 (sept., J ¼ 6.8, Me2CH); 1.48, 1.35 (2s, Me2C); 0.83 (d, J ¼ 6.8,
Me2CH); 0.79, 0.78 (2s, Me2CSi); ꢀ 0.04 (s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 4;
additionally, 172.29 (s, C¼O); 159.02, 143.57, 143.50, 136.44, 134.54 (5s); 130.63 (2d); 130.61 (d);

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Helvetica Chimica Acta – Vol. 92 (2009)
128.72 (2d); 128.54 (4d); 128.14 (4d); 127.99 (2d); 127.40 (2d); 114.37 (s, Me2C); 113.47 (2d); 88.10 (s,
Ph2C); 55.37 (q, MeO); 35.88 (q, MeN); 34.20 (d, Me2CH); 27.37, 25.67 (2q, Me2C); 25.35 (s, Me2CSi);
20.40 (q, Me2CSi); 18.57, 18.53 (2q, Me2CH); ꢀ 3.30, ꢀ 3.34 (2q, Me2Si). HR-MALDI-MS: 892.4064
([M þ Na]þ, C50H59N5NaO7Siþ; calc. 892.4081).
Data of N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylidene-8-{[(4-meth-
oxyphenyl)diphenylmethoxy]methyl}-1-methyladenosine (11). Colourless glass. Rf (cyclohexane/AcOEt
2 :1) 0.26. [a]2D5 ¼ ꢀ25.6 (c ¼ 1.3, CHCl3). UV (CHCl3): 241 (24340), 277 (11920), 305 (12000). IR
(ATR): 3058w, 3028w, 2956w, 2867w, 1645s, 1607m, 1578m, 1542m, 1509m, 1489w, 1463w, 1447m, 1416w,
1391m, 1372m, 1346w, 1307m, 1250s, 1213m, 1178m, 1155m, 1060s, 1032s, 1002w, 970m, 928w, 901w.
1H-NMR (300 MHz, CDCl3): see Table 3; additionally, 8.16 – 8.13 (m, 2 arom. H); 7.54 – 7.20 (m, 15 arom.
H); 6.78 – 6.75 (m, 2 arom. H); 3.78 (s, MeO); 3.71 (s, MeN); 1.61 (sept., J ¼ 6.9, Me2CH); 1.46, 1.33 (2s,
Me2C); 0.87 (d, J ¼ 6.9, Me2CH); 0.83 (s, Me2CSi); 0.05, 0.04 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3):
see Table 4; additionally, 177.84 (s, C¼O); 158.79, 143.71, 143.64, 136.24, 134.85 (5s); 131.78 (d); 130.48
(2d); 129.78 (2d); 128.56, 128.54 (4d); 128.06 (2d); 127.97, 127.96 (4d); 127.12 (2d); 114.46 (s, Me2C);
113.33 (2d); 87.86 (s, Ph2C); 55.34 (q, MeO); 36.82 (q, MeN); 34.22 (d, Me2CH); 27.38, 25.73 (2q, Me2C);
25.35 (s, Me2CSi); 20.44 (q, Me2CSi); 18.63, 18.61 (2q, Me2CH); ꢀ 3.18, ꢀ 3.26 (2q, Me2Si). HR-
MALDI-MS: 892.4069 ([M þ Na]þ, C50H59N5NaO7Siþ; calc. 892.4081).
N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-8-(hydroxymethyl)-2’,3’-O-isopropylidene-
N6-methyladenosine (12). A soln. of 10 (1.637 g, 1.88 mmol) in CH2Cl2 (10 ml) was treated with Et3SiH
(2.4 ml, 15.0 mmol) and Cl2CHCOOH (1.9 ml, 22.6 mmol), and stirred for 15 min at 258. The mixture was
neutralised with sat. aq. NaHCO3 soln., and the aq. layer was extracted with CH2Cl2. The combined org.
layers were dried (Na2SO4) and evaporated. FC (cyclohexane/AcOEt 2 :1 ! 1:1) gave 12 (884 mg,
79%). White solid. Rf (cyclohexane/AcOEt 2 :1) 0.24. M.p. 55 – 608. [a]2D5 ¼ ꢀ24.1 (c ¼ 0.75, CHCl3). UV
(CHCl3): 286 (15280). IR (ATR): 3375w, 3346w, 2956w, 2868w, 1671m, 1590s, 1575s, 1458m, 1447m,
1418w, 1372m, 1344m, 1321s, 1275m, 1251m, 1210m, 1155m, 1130m, 1079s, 1044s, 971w, 911w, 866m, 828s.
1H-NMR (400 MHz, CDCl3): see Table 3; additionally, 7.45 – 7.42 (m, 2 arom. H); 7.32 – 7.27 (m, 1 arom.
H); 7.20 – 7.16 (m, 2 arom. H); 3.78 (s, MeN); 3.52 (dd, J ¼ 6.4, 5.9, OH); 1.62, 1.38 (2s, Me2C); 1.61 (sept.,
J ¼ 6.9, Me2CH); 0.86 (d, J ¼ 6.9, Me2CH); 0.83 (s, Me2CSi); 0.05 (s, Me2Si). 13C-NMR (100 MHz,
CDCl3): see Table 4; additionally, 172.32 (s, C¼O); 136.34 (s); 130.75 (d); 128.71 (2d); 128.00 (2d);
115.00 (s, Me2C); 35.89 (q, MeN); 34.17 (d, Me2CH); 27.33, 25.49 (2q, Me2C); 25.56 (s, Me2CSi); 20.44,
20.40 (2q, Me2CSi); 18.54 (q, Me2CH); ꢀ 3.34 (q, Me2Si). HR-MALDI-MS: 598.3056 ([M þ H]þ,
C30H44N5O6Siþ; calc. 598.3061).
N6-Benzoyl-8-(chloromethyl)-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylidene-N6-
methyladenosine (13). A soln. of 12 (785 mg, 1.31 mmol) in CH2Cl2 (6.5 ml) was cooled to 08, treated with
EtNiPr2 (342 ml, 1.97 mmol) and MsCl (101 ml, 1.31 mmol), stirred at 258 for 18 h, treated with LiCl
(56 mg, 1.31 mmol), and stirred for 3 h. The mixture was diluted with CH2Cl2 and washed with H2O. The
combined org. layers were dried (Na2SO4) and evaporated. FC (cyclohexane/AcOEt 4 :1) gave 13
(755 mg, 94%). White solid. Rf (cyclohexane/AcOEt 4 :1) 0.36. M.p. 45 – 558. [a]2D5 ¼ ꢀ23.0 (c ¼ 0.7,
CHCl3). UV (CHCl3): 293 (15390). IR (ATR): 2957w, 2868w, 1673m, 1575s, 1461m, 1447m, 1417w,
1374m, 1350m, 1317s, 1277m, 1251m, 1211m, 1177w, 1154m, 1130m, 1080s, 1059s, 1043s, 1024m, 971w,
913w, 866m, 825s. 1H-NMR (400 MHz, CDCl3): see Table 3; additionally, 7.46 – 7.43 (m, 2 arom. H); 7.32 –
7.28 (m, 1 arom. H); 7.22 – 7.17 (m, 2 arom. H); 3.80 (s, MeN); 1.63, 1.40 (2s, Me2C); 1.58 (sept., J ¼ 6.9,
Me2CH); 0.84 (d, J ¼ 6.9, Me2CH); 0.80, 0.79 (2s, Me2CSi); ꢀ 0.01, ꢀ 0.02 (2s, Me2Si). 13C-NMR
(100 MHz, CDCl3): see Table 4; additionally, 172.42 (s, C¼O); 136.27 (s); 130.80 (d); 128.76 (2d); 128.01
(2d); 114.62 (s, Me2C); 35.87 (q, MeN); 34.22 (d, Me2CH); 27.38, 25.57 (2q, Me2C); 25.43 (s, Me2CSi);
20.43, 20.40 (2q, Me2CSi); 18.58, 18.57 (2q, Me2CH); ꢀ 3.35 (q, Me2Si). HR-MALDI-MS: 616.2706
([M þ H]þ, C30H43ClN5O5Siþ; calc. 616.2722).
5’-O-[Dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylidene-N6-methyladenosine-8-methyl-
(81 ! 5’-S)-2’,3’-O-isopropylidene-5’-thiouridine (15). A soln. of 13 (684 mg, 1.11 mmol) and 14 [1]
(380 mg, 1.11 mmol) in dry degassed MeOH (3.5 ml) was cooled to 08, treated with a freshly prepared
1.27m soln. of MeONa in MeOH (3.5 ml, 4.44 mmol), and stirred at 258 for 19 h. The mixture was diluted
with sat. aq. NH4Cl soln. and H2O, and extracted four times with CH2Cl2. The combined org. layers were
dried (Na2SO4) and evaporated. FC (CH2Cl2/MeOH 95 :5) gave 15 (827 mg, 96%). White solid. Rf

Helvetica Chimica Acta – Vol. 92 (2009)
1179
(CH2Cl2/MeOH 95 :5) 0.34. M.p. 192 – 1958. [a]2D5 ¼ ꢀ20.9 (c ¼ 0.7, CHCl3). UV (CHCl3): 266 (22080).
IR (ATR): 3314w, 2956w, 2865w, 1692s, 1621s, 1582w, 1535w, 1498w, 1456w, 1421w, 1373s, 1329w, 1296w,
1274m, 1259m, 1210m, 1156w, 1076s, 972w, 921w, 828w. 1H-NMR (400 MHz, CDCl3): see Table 5;
additionally, 7.30 (d, J ¼ 8.1, HꢀC(6/I)); 5.71 (d, J ¼ 8.1, HꢀC(5/I)); 3.14 (d, J ¼ 4.7, MeNHꢀC(6/II));
1.54 (sept., J ¼ 6.9, Me2CH); 1.60, 1.51, 1.40, 1.27 (4s, 2 Me2C); 0.82 (d, J ¼ 6.9, Me2CH); 0.77, 0.76 (2s,
Me2CSi); ꢀ 0.04, ꢀ 0.06 (2s, Me2Si). 13C-NMR (100 MHz, CDCl3): see Table 6; additionally, 114.87,
113.83 (2s, 2 Me2C); 34.23 (d, Me2CH); 27.65 (q, MeNHꢀC(6/II)); 27.31, 27.20, 25.54, 25.38 (4q, 2 Me2C);
25.35 (s, Me2CSi); 20.42, 20.40 (2q, Me2CSi); 18.59, 18.56 (2q, Me2CH); ꢀ 3.34, ꢀ 3.36 (2q, Me2Si). HR-
MALDI-MS: 776.3454 ([M þ H]þ, C35H54N7O9SSiþ; calc. 776.3473).
Table 5. Selected 1H-NMR Chemical Shifts [ppm] and Coupling Constants [Hz] of the A*[s]U(*) Dimers
4, 5, 15, and 23 in CDCl3
15
4
23
5
15
4
23
5
(96 mm)
(113 mm) (96 mm) (123 mm)
Uridine unit (I)
HꢀN(3/I)
10.49
–
5.64
4.89
4.65
10.58
–
5.63
4.88
4.58
12.14
2.31
5.70
5.19
4.88
11.72
2.27
5.62a)
5.18
4.93
4.13
2.95
2.95
MeꢀC(6/I)
HꢀC(1’/I)
HꢀC(2’/I)
HꢀC(3’/I)
HꢀC(4’/I)
HaꢀC(5’/I)
HbꢀC(5’/I)
J(1’,2’/I)
J(2’,3’/I)
J(3’,4’/I)
J(4’,5’a/I)
J(4’,5’b/I)
2.4
6.5
4.1
5.8
6.4
2.4 0.8
6.6 6.4
4.1 3.9
6.4 7.9
5.5 5.7
0.8
6.3
4.0
6.9
6.9
4.27 – 4.22 4.23 – 4.19 4.18
2.96
2.91
3.01
2.90
2.99
2.90
b
J(5’a,5’b/I) 14.0 13.8 12.8
)
Adenosine unit (II)
MeNHꢀC(6/II) 6.74
6.90
–
8.29
–
7.20
8.34
–
H2NꢀC(6/II)
HꢀC(2/II)
–
7.16
8.23
4.25
3.98
6.18
5.23
5.08
4.51
3.95
3.76
8.32
4.28
4.08
6.24
5.91
5.11
b
CHaꢀC(8/II)
CHbꢀC(8/II)
HꢀC(1’/II)
HꢀC(2’/II)
HꢀC(3’/II)
HꢀC(4’/II)
HaꢀC(5’/II)
HbꢀC(5’/II)
4.23 – 4.19 4.10
J(Ha,Hb/II) 14.5 14.7
)
14.8
4.04
6.08
5.25
5.09
4.10
6.39
5.97
5.11
4.23
3.59
3.48
J(1’,2’/II)
J(2’,3’/II)
J(3’,4’/II)
J(4’,5’a/II)
J(4’,5’b/II)
1.9
6.3
3.0
5.1 1.6
5.8 6.2
1.1 3.0
5.0
5.9
0.9
4.27 – 4.22 4.50
6.8 < 1.0 6.9 < 1.0
6.2 < 1.0 6.4 < 1.0
3.67
3.54
3.95
3.77
J(5’a,5’b/II) 10.5 12.5 10.5 10.5
a) Assignment may be interchanged with HꢀC(5/I). b) Not assigned.
2’,3’-O-Isopropylidene-N6-methyladenosine-8-methyl-(81 ! 5’-S)-2’,3’-O-isopropylidene-5’-thiouri-
dine (4). In a polyethylene flask, a soln. of 15 (502 mg, 0.65 mmol) in THF (3.2 ml) was treated with
(HF)3 · Et3N (1.1 ml, 19.4 mmol) and stirred at 258 for 24 h. The mixture was treated with 1m aq. NaOH
soln. until the pH reached ca. 8, diluted with H2O, and extracted four times with AcOEt. The combined
org. layers were dried (Na2SO4) and evaporated. FC (CH2Cl2/MeOH 95 :5) gave 4 (400 mg, 98%). White
solid. Rf (CH2Cl2/MeOH 95 :5) 0.27. M.p. 1808 (sintering from 1508). [a]2D5 ¼ ꢀ72.3 (c ¼ 0.6, CHCl3). UV
(CHCl3): 267 (21800). IR (ATR): 3305w, 3204w, 2986w, 2936w, 1690s, 1622s, 1583w, 1539w, 1499w, 1454w,
1373s, 1331m, 1299w, 1258m, 1212s, 1077s, 1011m, 851m. 1H-NMR (400 MHz, CDCl3): see Table 5;
additionally, 7.28 (d, J ¼ 8.1, HꢀC(6/I)); 6.73 (br. d, J ¼ 11.1, HOꢀC(5’/II)); 5.70 (d, J ¼ 8.1, HꢀC(5/I));
3.13 (br. s, MeNHꢀC(6/II)); 1.63, 1.47, 1.36, 1.23 (4s, 2 Me2C). 13C-NMR (100 MHz, CDCl3): see Table 6;
additionally, 114.86, 114.03 (2s, 2 Me2C); 28.25 (q, MeNHꢀC(6/II)); 27.92, 27.12, 25.50, 25.28 (4q,
2 Me2C). HR-MALDI-MS: 634.2281 ([M þ H]þ, C27H36N7O9Sþ; calc. 634.2295).

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Helvetica Chimica Acta – Vol. 92 (2009)
Table 6. Selected 13C-NMR Chemical Shifts [ppm] of the A*[s]U(*) Dimers 4, 5, 15, and 23 in CDCl3
15
4
23
5
15
4
23
5
Uridine unit (I)
Adenosine unit (II)
C(2/I)
C(4/I)
C(5/I)
C(6/I)
150.44
150.46 152.26a) 152.47a)
C(2/II)
C(4/II)
C(5/II)
C(6/II)
C(8/II)
153.10
149.48b)
118.90
155.13
148.58
152.80 152.52 152.23
c
163.78
102.98
142.19
163.76 163.03
103.02 103.79
163.27
103.56
)
150.55 149.71
119.31 118.38 118.67
155.37 155.48 155.75
147.75 149.46 148.63
28.25 29.14 28.74
92.41 88.58 88.47
82.84 83.09 82.89
81.81 82.32 81.76
142.11 151.94a) 151.41a)
MeꢀC(6/I)
C(1’/I)
C(2’/I)
C(3’/I)
C(4’/I)
–
–
20.57
20.55
92.24
84.79
84.47
91.89
34.63
CH2ꢀC(8/II) 28.14
94.01
84.41
83.25
93.80 92.21
84.35 85.07
83.06 84.81
C(1’/II)
C(2’/II)
C(3’/II)
C(4’/II)
C(5’/II)
90.25
83.18
82.39
88.12a) 85.98 90.10
86.23a) 85.84 88.22 85.72
63.01
C(5’/I)
33.88
33.93 35.15
63.45 63.03 63.40
a) Assignments may be interchanged. b) Broad signal. c) Not visible.
N6-Benzoyl-8-(chloromethyl)-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-O-isopropylideneade-
nosine (17). A soln. of 16 [1] (5.085 g, 8.71 mmol) in CH2Cl2 (29 ml) was cooled to 08, treated with
Et2NiPr (1.97 ml, 11.3 mmol) and MsCl (809 ml, 10.45 mmol), allowed to warm to 258, and stirred for 19 h.
Evaporation and FC (cyclohexane/AcOEt 3 :7 ! 1 :1) gave 17 (4.249 g, 81%). White solid. Rf
(cyclohexane/AcOEt 1:1) 0.64. M.p. 75 – 858. [a]2D5 ¼ ꢀ10.5 (c ¼ 1.0, CHCl3). UV (CHCl3): 287
(21110). IR (ATR): 3104w, 2957w, 2867w, 1698m, 1609s, 1583m, 1526w, 1485m, 1460m, 1429m, 1373m,
1357m, 1248s, 1212m, 1156m, 1074s, 1001w, 970w, 925w, 828s. 1H-NMR (300 MHz, CDCl3): see Table 3;
additionally, 9.03 (br. s, NH); 8.01 – 7.98 (m, 2 arom. H); 7.63 – 7.48 (m, 3 arom. H); 1.63, 1.41 (2s, Me2C);
1.56 (sept., J ¼ 6.9, Me2CH); 0.83 (d, J ¼ 6.9, Me2CH); 0.79, 0.78 (2s, Me2CSi); ꢀ 0.01, ꢀ 0.02 (2s,
Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 4; additionally, 164.39 (s, C¼O); 133.58 (s); 132.86 (d);
128.91 (2d); 127.83 (2d); 114.42 (s, Me2C); 34.24 (d, Me2CH); 27.43, 25.63 (2q, Me2C); 25.47 (s, Me2CSi);
20.50, 20.47 (2q, Me2CSi); 18.66 (q, Me2CH); ꢀ 3.22 (q, Me2Si). HR-MALDI-MS: 602.2549 ([M þ H]þ,
C29H41ClN5O5Siþ; calc. 602.2565).
6-(Chloromethyl)-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’-3’-O-isopropylideneuridine (19). A
soln. of 18 (3.377 g, 7.40 mmol) in CH2Cl2 (37 ml) was cooled to 08, treated with EtNiPr2 (1.98 ml,
11.1 mmol) and MsCl (687 ml, 8.87 mmol), allowed to warm to 258, and stirred for 18 h. Evaporation and
FC (cyclohexane/AcOEt 2 :1) gave 19 (2.834 g, 81%). White solid. Rf (cyclohexane/AcOEt 2 :1) 0.32.
M.p. 78 – 888. [a]D25 ¼ ꢀ3.8 (c ¼ 0.9, CHCl3). UV (CHCl3): 268 (17270). IR (ATR): 3196w (br.), 3095w,
3066w, 2957w, 2868w, 1690s, 1625w, 1459m, 1378s, 1250m, 1209m, 1185w, 1157m, 1131m, 1079s, 1060s,
1
980m, 936w, 874s, 827s. H-NMR (300 MHz, CDCl3): see Table 7; additionally, 10.05 (br. s, NH); 1.58
(sept., J ¼ 6.9, Me2CH); 1.53, 1.33 (2s, Me2C); 0.84 (d, J ¼ 6.9, Me2CH); 0.81 (s, Me2CSi); 0.06, 0.05 (2s,
Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 113.88 (s, Me2C); 34.18 (d, Me2CH);
27.33, 25.43 (2q, Me2C); 25.37 (s, Me2CSi); 20.45, 20.39 (2q, Me2CSi); 18.55 (q, Me2CH); ꢀ 3.21 (q,
Me2Si). HR-MALDI-MS: 497.1849 ([M þ Na]þ, C21H35ClN2NaO6Siþ; calc. 497.1851).
5’-O-[Dimethyl(1,1,2-trimethylpropyl)silyl]-2’-3’-O-isopropylidene-6-methyluridine (20). A suspen-
sion of 19 (2.838 g, 5.97 mmol), MgO (2.420 g, 60.05 mmol) and 10% Pd/C (640 mg, 0.6 mmol) in AcOEt
(60 ml) was stirred under H2 (1 atm) for 4 h at 258. Filtration through Celite, evaporation, and FC
(cyclohexane/AcOEt 2 :1 ! 1 :1) gave 20 (2.338 g, 89%). White solid. Rf (AcOEt) 0.50. M.p. 115.8 –
116.28. [a]2D5 ¼ þ17.2 (c ¼ 1.3, CHCl3). UV (CHCl3): 261 (11720). IR (ATR): 3193w (br.), 3058w,
2957w, 2937w, 2867w, 1686s, 1626w, 1447m, 1372s, 1327w, 1310w, 1250m, 1209m, 1185w, 1158m, 1131m,
1080s, 1062s, 1006w, 974w, 935w, 875m, 826s. 1H-NMR (300 MHz, CDCl3): see Table 7; additionally, 10.04
(br. d, J ¼ 1.6, NH); 1.58 (sept., J ¼ 6.9, Me2CH); 1.52, 1.32 (2s, Me2C); 0.84 (d, J ¼ 6.9, Me2CH); 0.81 (s,
Me2CSi); 0.06, 0.05 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 113.68 (s, Me2C);

Helvetica Chimica Acta – Vol. 92 (2009)
1181
Table 7. Selected 1H-NMR Chemical Shifts [ppm] and Coupling Constants [Hz] of the Uridine Monomers
19 – 22 in CDCl3
19
20
21
22
19
20
21
22
HꢀC(5)
5.83
4.43
4.32
–
5.81
5.25
4.82
4.15
3.80
3.76
5.55
–
–
2.32
5.69
5.21
4.81
4.12
3.78
3.74
5.58
–
–
2.32
5.65
5.25
5.02
4.22
3.86
3.79
5.57
–
–
2.31
5.65
5.23
4.86
4.12
3.23
3.23
CHaꢀC(6)
CHbꢀC(6)
MeꢀC(6)
HꢀC(1’)
HꢀC(2’)
HꢀC(3’)
HꢀC(4’)
HaꢀC(5’)
HbꢀC(5’)
J(Ha,Hb)
13.1
–
–
–
J(1’,2’)
J(2’,3’)
J(3’,4’)
J(4’,5’a)
J(4’,5’b)
J(5’a,5’b)
1.1
6.4
4.4
5.3
7.0
1.1
6.4
4.3
5.6
7.0
2.4
6.5
4.1
3.1
4.6
1.0
6.4
3.8
7.2
7.2
a
11.0
11.1
12.1
)
a) Not assigned.
Table 8. Selected 13C-NMR Chemical Shifts [ppm] of the Uridine Monomers 19 – 22 in CDCl3
19
20
21
22
19
20
21
22
C(2)
C(4)
C(5)
C(6)
150.51
162.94
104.82
150.86
41.15
–
150.77
163.43
103.09
153.38
–
151.39a)
162.76
103.63
152.98a)
–
150.92
163.41
103.28
153.16
–
C(1’)
C(2’)
C(3’)
C(4’)
C(5’)
91.88
84.33
82.01
89.77
63.94
91.84
84.35
82.22
89.71
64.06
92.30
83.57
80.71
87.97
62.90
92.12
85.02
84.49
88.35
31.54
CH2ꢀC(6)
MeꢀC(6)
20.51
20.57
20.47
a) Assignments may be interchanged.
34.19 (d, Me2CH); 27.31, 25.40 (2q, Me2C); 25.37 (s, Me2CSi); 20.45, 20.39 (2q, Me2CSi); 18.59, 18.54 (2q,
Me2CH); ꢀ 3.22 (q, Me2Si). HR-MALDI-MS: 463.2229 ([M þ Na]þ, C21H36N2NaO6Siþ; calc. 463.2240).
2’,3’-O-Isopropylidene-6-methyluridine (21). A soln. of 20 (2.189 g, 4.97 mmol) in THF (50 ml) was
treated with Bu4F · 3 H2O (4.704 g, 14.9 mmol) and stirred for 19 h. Evaporation and FC (AcOEt) gave
21 (1.425 g, 96%). A sample for analysis was recrystallized from AcOEt. White solid. Rf (AcOEt) 0.43.
M.p. 149.0 – 150.68. [a]2D5 ¼ ꢀ32.7 (c ¼ 1.25, CHCl3). UV (CHCl3): 257 (10050). IR (ATR): 3349w (br.),
3164w (br.), 3091w, 3050w, 2989w, 2937w, 2858w, 2808w, 1719m, 1674s, 1619w, 1466m, 1448m, 1380s,
1369s, 1333w, 1309w, 1290w, 1274w, 1232w, 1205m, 1157m, 1113m, 1083m, 1052s, 1030s, 1012s, 980m, 928w,
916w, 868s, 853m, 839m, 816m. 1H-NMR (300 MHz, CDCl3): see Table 7; additionally, 9.76 (br. s, NH);
3.25 (br. s, OH); 1.55, 1.34 (2s, Me2C). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 114.30 (s,
Me2C); 27.43, 25.36 (2q, Me2C). HR-EI-MS: 283.0925 ([M ꢀ Me]þ, C12H15N2O6þ ; calc. 283.0925). Anal.
calc. for C13H18N2O6 (298.29): C 52.35, H 6.08, N 9.39; found: C 52.37, H 5.94, N 9.37.
5’-S-Acetyl-2’-3’-O-isopropylidene-6-methyl-5’-thiouridine (22). A soln. of 21 (1.198 g, 4.02 mmol) in
dry CH2Cl2 (40 ml) was cooled to 08, treated with 4-(dimethylamino)pyridine (DMAP; 737 mg,
6.03 mmol) and TsCl (843 mg, 4.42 mmol), allowed to warm to 258, and stirred for 4 h. After dilution
with sat. NH4Cl soln., the mixture was extracted three times with AcOEt. The combined org. layers were
dried (Na2SO4) and evaporated. A soln. of the residue in dry DMF (25 ml) was treated with AcSK
(1.153 g, 10.1 mmol) and heated to 708 for 1 h. The soln. was diluted with AcOEt and washed three times
with sat. aq. NH4Cl soln. The combined org. layers were dried (Na2SO4) and evaporated. FC
(cyclohexane/AcOEt 1:1 ! 1:2) gave 22 (1.116 g, 78%). Recrystallisation of a sample from MeCN gave
slightly red crystals suitable for X-ray analysis. Rf (cyclohexane/AcOEt 1:1) 0.19. M.p. 197.5 – 198.88.

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Helvetica Chimica Acta – Vol. 92 (2009)
[a]2D5 ¼ þ29.4 (c ¼ 1.1, CHCl3). UV (CHCl3): 258 (12663). IR (ATR): 3201w (br.), 3084w, 2990w, 2935w,
2819w, 1680s, 1626m, 1450w, 1443m, 1414w, 1383s, 1368s, 1309w, 1276m, 1239w, 1207m, 1175w, 1157m,
1136m, 1094s, 1079m, 1052s, 1034m, 1025m, 1015m, 997m, 983m, 971m, 953m, 911w, 868m, 842m, 829m,
809m. 1H-NMR (300 MHz, CDCl3): see Table 7; additionally, 10.16 (br. s, NH); 2.32 (s, AcS); 1.50, 1.31
(2s, Me2C). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 194.89 (s, MeC¼O); 113.86 (s, Me2C);
30.67 (q, MeC¼O); 27.15, 25.21 (2q, Me2C). HR-MALDI-MS: 379.0934 ([M þ Na]þ, C15H20N2NaO6Sþ;
calc. 379.0940). Anal. calc. for C15H20N2O6S (356.40): C 50.55, H 5.66, N 7.86; found: C 50.77, H 5.71, N
7.96.
X-Ray Analysis of 22. Dimensions of the analyzed crystal: cube 0.6 ꢄ 0.42 ꢄ 0.4 mm. C15H20N2O6S,
Mr 356.40, orthorhombic P212121; a ¼ 9.1667(2), b ¼ 12.6749(3), c ¼ 14.8909(4) ꢄ, V¼ 1730.13(7) ꢄ3,
Z ¼ 4, Dx ¼ 1.368 Mg/m3. The reflections were measured on a Bruker-Nonius-KappaCCD diffractometer
(graphite monochromator, MoKa radiation, l ¼ 0.71073) at 250 K. All the calculations were performed
using maXus (Bruker Nonius, Delft, and MacScience, Japan). The structure was solved by direct methods
and refined by full-matrix least-squares analysis (SHELXL-97) including an isotropic extinction
correction. All non-H-atoms were refined anisotropically (H-atoms isotropic, whereby H-positions are
based on stereochemical considerations).
2’,3’-O-Isopropylidene-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]adenosine-8-methyl-(81 ! 5’-S)-
2’,3’-O-isopropylidene-6-methyl-5’-thiouridine (23). A suspension of 22 (952 mg, 2.67 mmol) in dry
MeOH (26 ml) was heated to reflux until complete dissolution, cooled to 258, treated with K2CO3
(1.107 g, 8.01 mmol), stirred for 40 min, treated with 17 (1.608 g, 2.67 mmol), and stirred for 15 h at 258.
The mixture was treated with sat. aq. NH4Cl soln. and diluted with H2O. After evaporation of MeOH, the
residue was extracted four times with AcOEt. The combined org. layers were dried (Na2SO4) and
evaporated. FC (CH2Cl2/MeOH 95 :5) gave 23 (1.626 g, 78%). Rf (CH2Cl2/MeOH 90 :10) 0.54. M.p.
139 – 1428. [a]D25 ¼ ꢀ117.3 (c ¼ 0.8, CHCl3). UV (CHCl3): 263 (24730). IR (ATR): 3436w, 3346w, 3260w,
3220w, 2959w, 2866w, 2815w, 1687s, 1642s, 1594m, 1574w, 1458w, 1433m, 1417w, 1372s, 1331m, 1291m,
1251m, 1233m, 1216m, 1206m, 1154m, 1141m, 1085s, 1068s, 1056s, 977m, 966m, 934m, 896w, 872s, 853m,
828s. 1H-NMR (300 MHz, CDCl3): see Table 5; additionally, 5.58 (s, HꢀC(5/I)); 1.60, 1.49, 1.41, 1.29 (4s,
2 Me2C); 1.52 (sept., J ¼ 6.9, Me2CH); 0.80 (d, J ¼ 6.9, Me2CH); 0.75, 0.74 (2s, Me2CSi); ꢀ 0.05, ꢀ 0.07
(2s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 6; additionally, 113.83, 113.64 (2s, 2 Me2C); 34.25 (d,
Me2CH); 27.38, 27.25, 25.64, 25.35 (4q, 2 Me2C); 25.38 (s, Me2CSi); 20.48 (q, Me2CSi); 18.68, 18.66 (2q,
Me2CH); ꢀ 3.21 (q, Me2Si). HR-MALDI-MS: 798.3473 ([M þ H]þ, C35H53N7NaO9SSiþ; calc.
798.3292).
2’,3’-O-Isopropylideneadenosine-8-methyl-(81 ! 5’-S)-2’,3’-O-isopropylidene-6-methyl-5’-thiouridine
(5). In a polyethylene flask, a soln. of 23 (1.008 g, 1.30 mmol) in dry THF (4.5 ml) was treated with
(HF)3 · Et3N (3.5 ml, 65 mmol) and stirred at 258 for 14 h. The mixture was cooled to 08, treated with 1m
aq. NaOH soln. until the pH reached ca. 10 and extracted four times with CH2Cl2. The combined org.
layers were dried (Na2SO4) and evaporated. FC (CH2Cl2/MeOH 95 :5 ! 90 :10) gave 5 (754 mg, 92%).
White solid. Rf (CH2Cl2/MeOH 90 :10) 0.42. M.p. 160 – 1648. [a]2D5 ¼ ꢀ105.8 (c ¼ 1.1, CHCl3). UV
(CHCl3): 263 (25140). IR (ATR): 3326w (br.), 3190w (br.), 2986w, 2936w, 2868w, 2823w, 1688s, 1635s,
1604m, 1579m, 1444m, 1371s, 1332m, 1301m, 1266m, 1210s, 1156m, 1069s, 969m, 946m, 869s, 850s, 823m.
1H-NMR (300 MHz, CDCl3): see Table 5; additionally, 6.63 (dd, J ¼ 10.0, 1.0, HOꢀC(5’/II)); 5.52 (s,
HꢀC(5/I)); 1.63, 1.48, 1.36, 1.30 (4s, 2 Me2C). 13C-NMR (75 MHz, CDCl3): see Table 6; additionally,
113.95, 113.85 (2s, 2 Me2C); 27.96, 27.27 25.61, 25.42 (4q, 2 Me2C). HR-MALDI-MS: 656.2110 ([M þ
Na]þ, C27H35N6NaO9Sþ; calc. 656.2115).
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Received March 5, 2009