Synthesis of thymidine, uridine, and 5-methyluridine nucleolipids: Tools for a tuned lipophilization of oligonucleotides

Article abstract of DOI:10.1002/hlca.201200573

Three pyrimidine nucleosides, uridine (1), 5-methyluridine (6), and 2′-deoxythymidine (11), were converted to amphiphilic nucleolipids. Compounds 1 and 6 were lipophilized by introduction of symmetric ketal moieties with various carbon chain lengths (i.e., 5-17). Two ketal derivatives, 2b and 7a, were additionally further hydrophobized by N(3)-farnesylation. 2′-Deoxythymidine was alkylated at N(3) with a cetyl (=hexadecyl) residue, either directly or, after complete orthogonal protection of the sugar OH groups, by Mitsunobu reaction with hexadecan-1-ol. Some of the nucleolipids were subsequently converted to their 2-cyanoethyl phosphoramidites (5′ or 3′), one of which was used for an exemplary synthesis of a lipo-oligonucleotide. The sequence of this lipo-oligonucleotide is an encoded manifestation of Pythagoras' law, created with a key table in which the letters of the alphabet, the numbers from 0 to 9 as well as the mostly used mathematical symbols are allocated to a ribonucleic acid triplet of the genetic code. Copyright

Full text of DOI:10.1002/hlca.201200573

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Helvetica Chimica Acta – Vol. 96 (2013)
Synthesis of Thymidine, Uridine, and 5-Methyluridine Nucleolipids: Tools for
a Tuned Lipophilization of Oligonucleotides
by Emma Werz, Rebecca Viere, Gina Gassmann, Sergei Korneev, Edith Malecki, and
Helmut Rosemeyer*)
Organic Chemistry I - Bioorganic Chemistry, Institute of Chemistry of New Materials, Fachbereich
Biologie/Chemie, University of Osnabrꢀck, Barbarastr. 7, D-49076 Osnabrꢀck
(e-mail: hrosemey@uni-osnabrueck.de)
Dedicated to Prof. Dr. Jꢀrgen Liebscher, Berlin, and Cluj, Romania
Three pyrimidine nucleosides, uridine (1), 5-methyluridine (6), and 2’-deoxythymidine (11), were
converted to amphiphilic nucleolipids. Compounds 1 and 6 were lipophilized by introduction of
symmetric ketal moieties with various carbon chain lengths (i.e., 5 – 17). Two ketal derivatives, 2b and 7a,
were additionally further hydrophobized by N(3)-farnesylation. 2’-Deoxythymidine was alkylated at
N(3) with a cetyl (¼ hexadecyl) residue, either directly or, after complete orthogonal protection of the
sugar OH groups, by Mitsunobu reaction with hexadecan-1-ol. Some of the nucleolipids were
subsequently converted to their 2-cyanoethyl phosphoramidites (5’ or 3’), one of which was used for
an exemplary synthesis of a lipo-oligonucleotide. The sequence of this lipo-oligonucleotide is an encoded
manifestation of Pythagorasꢁ law, created with a key table in which the letters of the alphabet, the
numbers from 0 to 9 as well as the mostly used mathematical symbols are allocated to a ribonucleic acid
triplet of the genetic code.
1. Introduction. – In several recent reports, we described the synthesis of lipo-
oligonucleotides and their incorporation into artificial lipid bilayers with the aim of a
new DNA biosensor technology [1][2]. In this context, we could show that an
equilibrium exists obviously between bilayer-bound DNA duplexes and nanoscale
aggregates, which freely diffuse within the cis compartment of an optically transparent
microfluidic sample carrier with perfusion capabilities [1]. It is conceivable that the bias
of this equilibrium depends i) on the lipophilicity of the hydrophobic head group of the
lipo-oligonucleotide, and ii) on the hydrophilicity as well as on the chain length of the
appending oligonucleotide moiety, a relation which we have earlier defined as
amphiphilic ratio [3]. We found that a particular DNA dodecamer can be immobilized
within an artificial lipid bilayer, composed of 1-palmitoyl-2-oleyl-sn-glycero-3-phos-
phoethanol-amine (POPE)/1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC)
8 :2 (w/w), most efficiently, when the terminal lipophilic part of the lipo-oligonucleo-
tide contains a double-chained lipid with a sufficient alkyl chain length [1][4][5]; on the
other hand, a relatively short and mono-tailed lipid, e.g., geranyl or farnesyl groups,
attached to the 5’-terminal nucleotide residue of the lipo-oligonucleotide, leads to a
relatively easy wash-out of the bilayer-immobilized dodecamer [2]. One has to keep in
mind, however, that appending extremely lipophilic nucleolipid moieties to a short
DNA sequence might promote the formation of high-molecular-weight aggregates of
ꢂ 2013 Verlag Helvetica Chimica Acta AG, Zꢀrich

Helvetica Chimica Acta – Vol. 96 (2013)
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the lipo-oligonucleotides in favor of a lipid-bilayer incorporation. We, therefore,
prepared a series of phosphoramidite building blocks of 2’-deoxythymidine, uridine,
and 5-methyluridine for an automated solid-phase DNA synthesis, carrying symmetric
ketal moieties with varying alkyl chain lengths [4][5] or single-chained lipids at the
pyrimidine base. One of the phosphoramidites prepared will be used for the
representative synthesis of a lipo-oligonucleotide. In the following, all phosphorami-
dites will be used for the synthesis of lipo-oligonucleotides with a standardized DNA
chain length, which is not an easy task regarding their purification. The oligomers will
then be immobilized in an artificial lipid bilayer. The retention times, tR values, of the
lipo-oligonucleotides within this bilayer upon perfusion will be studied later. We expect
useful insight into the equilibrium mentioned above and, therewith, into new
possibilities for an optimization of our novel DNA biosensor technique [6]. In a
further study, we will prepare lipo-oligonucleotides with a selected lipophilic head
group (nucleolipid) but with DNA sequences of various chain lengths and study their
stability within a lipid bilayer towards perfusion. siRNSs carrying nucleolipids as those
reported here may show a significantly improved delivery in vivo [7]; cholesterol
residues, which have often been used for this purpose, bind very tightly into bilayer
membranes, thus hampering an effective transfection of an appending nucleic acid.
2. Results and Discussion. – 2.1. Hydrophobization of Uridine (1) and 5-
Methyluridine (6) by Long-Chain Ketal Groups. Uridine (1) and 5-methyluridine (6)
were reacted with symmetrical long-chain ketones in acidic medium (DMF) and gave
the ketals 2a – 2e and 7a – 7c, respectively. For this purpose, two different synthetic
protocols [3][8] were applied (see Exper. Part). Partly, the compounds were then
directly converted to their phosphoramidites 3 and 8, respectively, or first N(3)-
farnesylated and then phosphitylated to furnish 5 (Scheme 1) and 10 (Scheme 2),
respectively. All compounds were characterized by multinuclear NMR and UV
spectroscopy as well as by elemental analyses. Assignments of 13C-NMR resonances
was performed with the help of DEPT-135 spectra as well as by spectra simulation.
The novel phosphoramidites represent terminator molecules which can be attached
once to the 5’-terminus of an oligonucleotide chain lending them a tuned lipophilicity as
well as a protection against enzymatic 5’-exonucleolytic degradation.
Fig. 1 displays the Rf values of the various uridine- and methyluridine-containing
ketals as a function of the carbon-chain length. It is obvious that the lipophilicity of the
various ketals are not as strongly dependent from the alkyl-chain length as expected;
the additional introduction of an all-(E) farnesyl (¼(all-E)-3,7,11-trimethyldodeca-
2,6,10-trienyl) residue, however, enhances the lipophilicity of the resulting nucleolipid
significantly. A similar result had been found for cyclic ketal derivatives of 5-
fluorouridine [3].
Fig. 2 shows the chemical-shift differences (Dd) of 13C-NMR resonances of C(1a’’)
and C(1b’’) (for definition, see Exper. Part, General) of the corresponding ketal
moieties as a function of the total carbon-chain length. It reveals that the longer the
alkyl chain length gets, the higher is the difference of the chemical shifts of those C-
atoms most adjacent to the pseudo-stereogenic center at the ketal C-atom.
From the particular 13C-NMR chemical shifts (see Exper. Part) of C(1a’’) and
C(1b’’) of the ketals 2a – 2e and 7a – 7c, it can be seen that the increasing Dd values

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Helvetica Chimica Acta – Vol. 96 (2013)
Scheme 1
result from a change of the C(1b’’) (Cexo) resonances towards higher field, while the
C(1a’’) (Cendo) resonances remain almost constant. It is, therefore, assumed that steric
interactions, arising from contacting Van der Waals radii of closely spaced H-atoms,
lead to this increased shielding of the C-atoms attached to these H-atoms [9]. The steric
perturbation of the CꢀH bond involved causes the charge to drift towards the C-atom.
The bonding orbitals at the C-atom expand, and a paramagnetic shielding spara will arise
according to the KarplusꢀPople equation [10]. This points to decreasing
C(1a’’)ꢀC(ketal)ꢀC(1b’’) (F) bond angles with increasing alkyl-chain length due to
increasing Van der Waals interactions along the two C-chains. We tentatively assume
that, with increasing C-chain length (i.e., 2a ! 2e), both alkyl chains approach each
other more and more due to increasing Van der Waals interactions. This causes an

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875
Scheme 2
increasing steric perturbation of the C(1a’’)ꢀH and C(1b’’)ꢀH bonds with the above-
mentioned consequences for the 13C-NMR chemical shifts (Fig. 3).
This steric shift dst is, according to a model of Grant [11], depending on the
protonꢀproton repulsive force (FHH(rHH)) which is a function of the protonꢀproton
distance rHH and of the angle q between the HꢀH axis and the pertubated CꢀH bond:
dst ¼ const. FHH (rHH) cosq
2.2. Hydrophobization of 2’-Deoxythymidine by Long, Single-Chain Alkyl Groups
at N(3). In a further approach, we attempted the synthesis of thymidine derivative
carrying a long, single-chain long alkyl group at N(3) of the nucleobase. For this
purpose, 2’-deoxythymidine (11) was first reacted with cetyl bromide (1-bromohexa-
decane) under basic reaction conditions (K2CO3, DMF) and yielded the N(3)-cetyl

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Fig. 1. Rf Values of ketals 2a – 2e and 7a – 7c as a function of carbon-chain length
Fig. 2. Dd Values of 13C-NMR resonances of C(1’’) of ketals 2a – 2e and 7a – 7c as a function of carbon-
chain length

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877
Fig. 3. Sketch of the ketal moiety demonstrating the steric clash of
HꢀC(1a’’) and HꢀC(1b’’)
derivative 12. Its UV maximum (267 nm) resembled that of compound 11, and
established N- and not O-alkylation.
In the following, 2’-deoxythymidine was N(3)-alkylated with hexadecan-1-ol (cetyl
alcohol) applying Mitsunobu reaction conditions. In a preceeding publication [4], we
showed that, for a Mitsunobu alkylation [12] of a nucleoside, the latter should be fully
protected at all OH functions to avoid side reactions. Therefore, we first protected the
5’-OH group of 2’-deoxythymidine (!13; Scheme 3), followed by protection of the 3’-
OH group with a tert-butyl(diphenyl)silyl (TBDPSi) group (!14). When a Mitsunobu
reaction was performed (Ph3P, THF, diisopropyl azodicarboxylate (DIAD), cetyl
alcohol, room temperature) with the 5’-protected compound 13, subsequent ESI mass
spectrum of the product isolated exhibited a correct molecular-ion peak ([M þ H]þ
713.5 Da). 1H-NMR Analysis, however, showed clearly two sets of signals of
corresponding to CH2 groups as well as a signal of an additional OH group besides
that of 3’-OH. Repeated chromatography as well as intensive drying at 408 in high
vacuum gave the same results with respect to ESI mass spectrometry and NMR
spectroscopy. Therefore, it was assumed that a relatively stable adduct of the N(3)-cetyl
compound 13 with 1 equiv. of cetyl alcohol had been formed.
Next, we performed a Mitsunobu reaction on the fully protected compound 14. This
reaction was performed under various reaction conditions. The best results were
obtained when all reagents (14, DIAD, Ph3P, THF) were mixed at room temperature,
and then stirred further overnight at room temperature. In this case, the yield obtained
after purification of the reaction product 15 amounts to moderate 50%. All new
compounds provided expected NMR spectra as well as elemental analyses values, and
they did not exhibit aggregation reactions with cetyl alcohol.
Next, compound 15 was desilylated by reaction with Bu4NF (TBAF) in THF to
yield compound 16, which was then phosphitylated to give the phosphoramidite 17.
Compound 17 can be used for the solid-phase synthesis of oligonucleotides, which carry
one or more lipophilization sites at any pre-determined position of the sequence
(Scheme 3).
2.3. Representative Lipo-Oligonucleotide Synthesis Using the Phosphoramidite 8a.
To test the practical applicability of lipophilic phosphoramidites as described above, we
used compound 8a for the preparation of a 24-mer carrying the nucleolipid 7a at the 5’-
terminus. For this purpose, we have chosen a special sequence which is derived from the
Pythagorasꢁ law with the help of the following encoding Table.
This Table presents an exemplary code for alphabetical letters, numbers from 0 to 9
and the most frequently used mathematical symbols in form of ribonucleic acid triplets
of the genetic code. The code presented in the Table represents one possible key. This

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Scheme 3
allocation can be principally changed; the number of permutations N for the
assignments is:
N ¼ n!/(n ꢀ k)! ¼ 64! ꢁ 1.3 · 1089
where n is the number of triplets and k is the number of symbols.

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Table. Encryption Table to Encode a Message into RNA
2. Base
U
C
A
G
1. Base
U
C
UUU ꢂ A
UUC ꢂ B
UUA ꢂ C
UUG ꢂ D
CUU ꢂ Q
CUC ꢂ R
CUA ꢂ S
CUG ꢂ T
AUU ꢂ 6
AUC ꢂ 7
AUA ꢂ 8
AUG ꢂ 9
UCU ꢂ E
UCC ꢂ F
UCAꢂ G
UCG ꢂ H
CCU ꢂ U
CCC ꢂ V
CCAꢂ W
CCG ꢂ X
ACU ꢂ /
UAU ꢂ I
UAC ꢂ J
UAA ꢂ K
UAG ꢂ L
CAU ꢂ Y
CAC ꢂ Z
CAA ꢂ 0
CAG ꢂ 1
AAU ꢂ :
AAC ꢂþ
AAA ꢂ -
UGU ꢂ M
UGC ꢂ N
UGA ꢂ O
UGG ꢂ P
CGU ꢂ 2
CGC ꢂ 3
CGA ꢂ 4
CGG ꢂ 5
A
G
AGU ꢂ !
p
ACC ꢂ S
ACA ꢂ¼
AGC ꢂ
AGA ꢂ sin
AGG ꢂ cos
GGU ꢂ1
GGC ꢂ D
GGA ꢂ L
GGG ꢂ @
2
*
ACG ꢂ
AAG ꢂ
GUU ꢂ tan
GCU ꢂ p
GCC ꢂ a
GCAꢂ b
GCG ꢂ>
GAU ꢂ (
GAC ꢂ )
Ð
GUC ꢂ
GUA ꢂ j
GUG ꢂ<
GAA ꢂ exp
GAG ꢂ g
Pythagorasꢁ law, in an encoded form using the above-mentioned encryption code, is
given by the RNA sequence 18.
5’-(UUU AAG AAC UUC AAG ACA UUA AAG) (18)
A back-transcription into a corresponding DNA following the regular base-pairing
rules gives 19:
3’-d(AAA TTC TTG AAG TTC TGT AAT TTC) (19)
Using the phosphoramidite 8a, the lipo-oligonucleotide 20 as well as its cyanine-5-
labelled complementary strand 21 were synthesized:
5’-d[(7a)(AAA TTC TTG AAG TTC TGT AAT TTC)] (20)
5’-d[(Cy-5)(GAA ATT ACA GAA CTT CAA GAA TTT)] (21)
Experiments towards spotting the lipo-oligonucleotide onto silanized glass plates to
produce an non-visible microdot [13] with a hidden message, which can be visualized by
addition of 21, are in progress and will be published in due course. Moreover, the
production of lipo-oligonucleotide-covered Wilhelmy plates for a specific nucleic acid
isolation from a library, using a special Dipcoater technique [14], will be described later.
The authors thank Mrs. Marianne Gather-Steckhan for recording the NMR spectra and Mrs. Anja
Schuster for the elemental analyses, as well as the team of the Ionovation GmbH, Osnabrꢀck, for valuable
discussions.

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Experimental Part
General. Starting compounds and solvents were purchased from the appropriate suppliers and were
used as obtained. Column chromatography (CC): silica gel 60 (SiO2; Merck, Germany). TLC: Aluminum
sheets, SiO2 60 F254, 0.2-mm layer (Merck, Germany). M.p.: Stuart-SMP3 apparatus (Fa. Bibby Scientific
Ltd., UK-Staffordshire); uncorrected. UV Spectra: Cary 6000i spectrophotometer (Varian, D-
Darmstadt); lmax in nm, e in mꢀ1 cmꢀ1. NMR Spectra: AMX-500 spectrometer (Bruker, D-Rheinstetten);
1
1H: 500.14, 13C: 125.76, and 31P: 101.3 MHz; d in ppm rel. to Me4Si as internal standard for H and 13C
nuclei, and external 85% H3PO4, J in Hz. Elemental analyses (C, H, N) of crystallized compounds were
performed on a VarioMICRO instrument (Fa. Elementar, D-Hanau).
2’,3’-O-(1-Pentylhexylidene)uridine (¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxymethyl)-2,2-di-
pentylfuro[3,4-d][1,3]dioxol-4-yl]pyrimidine-2,4(1H,3H)-dione; 2a). Uridine (1; 0.76 g, 3.1 mmol) was
dissolved in anh. DMF (10 ml), and undecan-6-one (0.80 ml, 3.9 mmol) as well as 4m HCl in 1,4-dioxane
(4 ml) and triethyl orthoformate (HC(OEt)3; 1 ml) were added. The mixture was stirred for 24 h at r.t.
Subsequently, the soln. was partitioned between CH2Cl2 (75 ml) and a sat. aq. NaHCO2 soln. (50 ml).
The org. phase was washed with dist. H2O (100 ml) and separated. After drying (Na2SO4), the solvent
was evaporated. Purification was performed by CC (SiO2 60; column: 2 ꢃ 22 cm). A stepwise elution
with 750 ml of CH2Cl2/MeOH 99 :1, followed by 250 ml of CH2Cl2/MeOH 95 :5 gave one main zone, from
which, after evaporation and drying in high vacuum, 2a (1.1 g, 2.69 mmol, 87%) was isolated. Colorless
foam. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.19. UV (MeOH): 260 (9.200). 1H-NMR (500.13 MHz,
3
3
(D6)DMSO): 11.32 (s, HꢀN(3)); 7.77 (d, J(6,5) ¼ 8.2, HꢀC(6)); 5.83 (d, J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.62
(dd, 3J(5,6) ¼ 8.0, 4J(5,HN(3)) ¼ 1.7, HꢀC(5)); 5.01 (t, 3J(OH,5’) ¼ 5.04, HOꢀC(5’)); 4.89 (dd, 3J(2’,1’) ¼
2.8, 3J(2’,3’) ¼ 6.6, HꢀC(2’)); 4.74 ((dd, 3J(3’,4’) ¼ 3.5, 3J(3’,2’) ¼ 6.6, HꢀC(3’)); 4.06 (Yq, 3J(4’,5’) ¼
3J(4’,3’) ¼ 4.4, HꢀC(4’)); 3.56 (m, CH2(5’)); 1.67 (m, CH2(1a’’)); 1.52 (m, CH2(1b’’)); 1.44 – 1.20 (m,
CH2(2a’’ – 4a’’, 2b’’ – 4b’’)); 0.86 (m, Me(5a’’,5b’’)). 13C-NMR (125.76 MHz, (D6)DMSO): 163.06 (C(4));
150.26 (C(2)); 141.94 (C(6)); 116.631 (C(ketal)); 101.65 (C(5)); 91.20 (C(1’)); 86.66 (C(4’)); 83.79
(C(3’)); 80.73 (C(2’)); 61.34 (C(5’)); 36.34 (C(1’’)); 31.34 (C(3a’’)); 31.25 (C(3b’’)); 23.19 (C(2a’’)); 22.51
(C(2b’’)); 21.91 (C(4a’’)); 21.89 (C(4b’’)); 13.76 (C(5’’)). Anal. calc. for C20H32N2O6 (396.48): C 60.59, H
8.14, N 7.07; found: C 60.20, H 8.11, N 6.97.
2’,3’-O-(1-Nonyldecylidene)uridine (¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxymethyl)-2,2-di-
nonylfuro[3,4-d][1,3]dioxol-4-yl]pyrimidine-2,4(1H,3H)-dione; 2b). Uridine (1; 0.76 g, 3.1 mmol) was
dissolved in anh. DMF (10 ml), and nonadecan-10-one (1.11 g, 3.9 mmol), 4m HCl in 1,4-dioxane (4 ml),
and HC(OEt)3 (1 ml), as well as CH2Cl2 (6 ml), were added consecutively. The mixture was stirred for
24 h at r.t. Subsequently, the mixture was partitioned between an aq. sat. NaHCO3 soln. (100 ml) and
CH2Cl2 (100 ml). The org. layer was washed with dist. H2O (100 ml), separated, dried (Na2SO4), and
then evaporated to dryness. Purification of the raw product was performed by stepped-gradient CC (SiO2
60, column: 6.5 ꢃ 10 cm). A stepwise elution with 800 ml of CH2Cl2/MeOH 99 :1, followed by 200 ml of
CH2Cl2/MeOH 95 :5 gave one main zone, from which, after evaporation and drying in high vacuum, 2b
(1.50 g, 2.95 mmol, 95%) was isolated. Colorless foam. M.p. 69.88. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.21.
UV (MeOH): 260 (9.600). 1H-NMR (500.13 MHz, (D6)DMSO): 11.33 (s, HꢀN(3)); 7.76 (d, 3J(6,5) ¼ 8.0,
HꢀC(6)); 5.82 (d, 3J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.62 (d, 3J(5,6) ¼ 8.0, HꢀC(5)); 5.02 (m, HOꢀC(5’)); 4.89 (dd,
3J(2’,1’) ¼ 2.5, 3J(2’,3’) ¼ 6.5, HꢀC(2’)); 4.73 (dd, 3J(3’,4’) ¼ 3.5, 3J(3’,2’) ¼ 6.5, HꢀC(3’)); 4.05 (Yq,

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3J(4’,5’) ¼ 3J(4’,3’) ¼ 4.2, HꢀC(4’)); 3.57 (m, CH2(5’)); 1.66 (m, CH2(1a’’)); 1.51 (m, CH2(1b’’)); 1.30 – 1.20
(m, CH2(2a’’ – 8a’’, 2b’’ – 8b’’)); 0.85 (m, Me(9a’’,9b’’)). 13C-NMR (125.76 MHz, (D6)DMSO): 163.11
(C(4)); 150.28 (C(2)); 141.98 (C(6)); 116.63 (C(ketal)); 101.67 (C(5)); 91.23 (C(1’)); 86.69 (C(4’)); 83.82
(C(3’)); 80.70 (C(2’)); 61.35 (C(5’)); 36.38 (C(1a’’)); 36.29 (C(1b’’)); 31.21 (C(7a’’)); 31.19 (C(7b’’)); 29.09
(C(3a’’)); 29.04 (C(3b’’)); 28.86 (C(4a’’)); 28.83 (C(4b’’)); 28.80 (C(5’’)); 28.59 (C(6a’’)); 28.58 (C(6b’’));
23.52 (C(2a’’)); 22.88 (C(2b’’)); 22.01 (C(8a’’)); 22.00 (C(8b’’)); 13.85 (C(9’’)). Anal. calc. for C28H48N2O6
(508.69): C 66.11, H 9.51, N 5.51; found: C 65.86, H 9.50, N 5.21.
2’,3’-O-(1-Tridecyltetradecylidene)uridine (¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxymethyl)-
2,2-ditridecylfuro[3,4-d][1,3]dioxol-4-yl]pyrimidine-2,4(1H,3H)-dione; 2c). Heptacosan-14-one (0.40 g,
1 mmol) was added to a soln. of anh. THF (14 ml), 1 (1.22 g, 5 mmol), TsOH (0.19 g, 1 mmol), and
HC(OEt)3 (0.85 ml, 5.1 mmol). The mixture was refluxed for 24 h (758), and then Et3N (0.6 ml) was
added. To this mixture, ice-cold 4% aq. NaHCO3 (50 ml) was added, and the mixture was stirred for
15 min at r.t. The mixture was washed with 100 ml of CH2Cl2 and 100 ml of dist. H2O. The org. layer was
dried (Na2SO4), filtered, and the solvent was evaporated. Compound 2c was precipitated by addition of
ice-cold MeOH on ice; the material was filtered and dried in high vacuum overnight: 2c (65.6%, 0.41 g,
0.66 mmol). Colorless solid. M.p. 90.18. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.24. UV (CH2Cl2): 260
(9.340). 1H-NMR (500 MHz, (D6)DMSO): 11.32 (d, 4J(HN(3),5) ¼ 1.89, HꢀN(3)); 7.76 (d, 3J(6,5) ¼ 8.2,
3
3
4
HꢀC(6)); 5.82 (d, J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.61 (dd, J(5,6) ¼ 8.2, J(5,HN(3)) ¼ 2.2, HꢀC(5)); 5.01 (t,
3J(HOꢀC(5’),5’) ¼ 5.4, HOꢀC(5’)); 4.88 (dd, 3J(2’,1’) ¼ 2.5, 3J(2’,3’) ¼ 6.6, HꢀC(2’)); 4.73 (dd, 3J(3’,4’) ¼
3.5, J(3’,2’) ¼ 6.6, HꢀC(3’)); 4.05 (Yq, J(4’,5’) ¼ 3J(4’,3’) ¼ 4.4, HꢀC(4’)); 3.55 (m, CH2(5’)); 1.66 (m,
CH2(1a’’)); 1.51 (m, CH2(1b’’)); 1.42 – 1.19 (m, CH2(2a’’ – 12a’’, 2b’’ – 12a’’)); 0.85 (m, Me(13a’’,13b’’)).
13C-NMR (125.76 MHz, (D6)DMSO): 163.07 (C(4)); 150.26 (C(2)); 141.94 (C(6)); 116.62 (C(ketal));
101.66 (C(5)); 91.22 (C(1’)); 86.68 (C(4’)); 83.81 (C(3’)); 80.68 (C(2’)); 61.34 (C(5’)); 36.38 (C(1a’’));
36.22 (C(1b’’)); 31.21 (C(11’’)); 29.05 (C(3a’’)); 28.99 (C(3b’’)); 28.96 – 28.59 (C(4’’) – C(10’’)); 22.48
(C(2a’’)); 22.86 (C(2b’’)); 22.00 (C(12’’)); 13.84 (C(13’’)). Anal. calc. for C36H64N2O6 (620.90): C 69.64, H
10.39, N 4.51; found: C 69.77, H 10.74, N 3.92.
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2’,3’-O-(1-Pentadecylhexadecylidene)uridine (¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxy-
methyl)-2,2-dipentadecylfuro[3,4-d][1,3]dioxol-4-yl]pyrimidine-2,4(1H,3H)-dione; 2d). Hentriacontan-
16-one (0.45 g, 1.0 mmol) was added to a soln. of anh. THF (14 ml), 1 (1.22 g, 5 mmol), TsOH (0.19 g,
1.0 mmol), and HC(OEt)3 (0.85 ml, 5.1 mmol). This mixture was refluxed for 24 h (758), and Et3N
(0.6 ml) was added. The resulting mixture was poured into an aq. ice-cold 4% NaHCO3 soln. (50 ml) and
stirred for 15 min at r.t. The mixture was washed with CH2Cl2 (100 ml) and dist. H2O (100 ml), dried
(Na2SO4), filtered, and the solvent was evaporated. The residue was triturated with ice-cold MeOH on
ice which gave 2d (0.36 g, 0.54 mmol, 53.7%). Slightly yellowish solid which was dried in high vacuum.
M.p. 938. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.26. UV (CH2Cl2): 260 (8.350). 1H-NMR (500 MHz,
(D6)DMSO): 11.32 (s, HꢀN(3)); 7.77 (d, 3J(6,5) ¼ 8.0, HꢀC(6)); 5.83 (d, 3J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.62 (d,
3J(5,6) ¼ 8.0, HꢀC(5)); 5.01 (t, 3J(HOꢀC(5’),5’) ¼ 5.0, HOꢀC(5’)); 4.88 (dd, 3J(2’,1’) ¼ 2.5, 3J(2’,3’) ¼ 6.5,
HꢀC(2’)); 4.73 (dd, 3J(3’,4’) ¼ 3.5, 3J(3’,2’) ¼ 6.3, HꢀC(3’)); 4.05 (Yq, 3J(4’,5’) ¼ 3J(4’,3’) ¼ 4.4, HꢀC(4’));
3.55 (m, CH2(5’)); 1.66 (m, CH2(1a’’)); 1.51 (m, CH2(1b’’)); 1.41 – 1.16 (m, CH2(2a’’ – 14a’’, 2b’’ – 14a’’));
0.85 (m, Me(15a’’,15b’’)). 13C-NMR (125.76 MHz, (D6)DMSO): 162.69 (C(4)); 150.03 (C(2)); 141.49
(C(6)); 116.52 (C(acetal)); 101.45 (C(5)); 91.02 (C(1’)); 86.44 (C(4’)); 83.62 (C(3’)); 80.50 (C(2’)); 61.18
(C(5’)); 36.32 (C(1a’’)); 36.06 (C(1b’’)); 30.90 (C(13’’)); 28.77 (C(3a’’)); 28.73 (C(3b’’)); 28.66 – 28.28
(C(4’’) – C(12’’)); 23.18 (C(2a’’)); 22.63 (C(2b’’)); 21.66 (C(14’’)); 13.46 (C(15’’)). Anal. calc. for
C40H72N2O6 (677.01): C 70.96, H 10.72, N 4.14; found: C 71.08, H 11.06, N 3.74.
2’,3’-O-(1-Heptadecyloctadecylidene)uridine (¼1-[(3aR,4R,6R,6aR)-2,2-Diheptadecyltetrahydro-6-
(hydroxymethyl)furo[3,4-d][1,3]dioxol-4-yl]pyrimidine-2,4(1H,3H)-dione; 2e). Pentatriacontan-18-one
(0.5 g, 0.99 mmol) was added to a soln. of anh. THF (14 ml), 1 (1.22 g, 5 mmol), TsOH (0.19 g,
1.0 mmol), and HC(OEt)3 (0.85 ml, 5.1 mmol). The mixture was refluxed for 24 h at 758. Then, Et3N
(0.6 ml) was added, and the resulting mixture was poured into an ice-cold aq. 4% NaHCO3 soln. (50 ml).
This soln. was stirred for 15 min at r.t. The org. layer was washed with CH2Cl2 (100 ml) and dist. H2O
(100 ml), dried (Na2SO4), filtered, and the solvent was evaporated. The residue was triturated with ice-
cold MeOH on ice, which gave the solid product. The colorless product was dried overnight in high
vacuum to afford 2e (0.45 g, 0.61 mmol, 61.4%). M.p. 89.78. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.21. UV

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(CH2Cl2): 260 (9.320). H-NMR (500 MHz, (D6)DMSO, 608): 11.16 (s, HꢀN(3)); 7.74 (d, J(6,5) ¼ 8.0,
HꢀC(6)); 5.84 (d, 3J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.60 (d, 3J(5,6) ¼ 8.2, HꢀC(5)); 4.88 (m, HꢀC(2’), HOꢀC(5’),
2 H); 4.75 (dd, 3J(3’,4’) ¼ 3.5, 3J(3’,2’) ¼ 6.5, HꢀC(3’)); 4.07 (Yq, 3J(4’,5’) ¼ 3J(4’,3’) ¼ 4.3, HꢀC(4’));
3.53 – 3.63 (m, CH2(5’)); 1.68 (m, CH2(1a’’)); 1.53 (m, CH2(1b’’)); 1.43 – 1.19 (m, CH2(2a’’ – 16a’’, 2b’’ –
16b’’)); 0.86 (m, Me(17a’’,17b’’)). 13C-NMR (125.76 MHz, (D6)DMSO): 162.69 (C(4)); 150.03 (C(2));
141.50 (C(6)); 116.52 (C(acetal)); 101.45 (C(5)); 91.02 (C(1’)); 86.44 (C(4’)); 83.62 (C(3’)); 80.50 (C(2’));
61.18 (C(5’)); 36.32 (C(1a’’)); 36.05 (C(1b’’)); 31.19 (C(15’’)); 28.76 (C(3a’’)); 28.72 (C(3b’’)); 28.79 –
28.25 (C(4’’) – C(14’’)); 23.17 (C(2a’’)); 22.62 (C(2b’’)); 21.66 (C(16’’)); 13.46 (C(17’’)). Anal. calc. for
C44H80N2O6 (733.12): C 72.09, H 11.00, N 3.82; found: C 71.70, H 11.14, N 3.81.
5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-2’,3’-O-(1-pentylhexylidene)uridine
(¼2-Cyanoethyl [(3aR,4R,6R,6aR)-6-(2,4-Dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydro-2,2-dipen-
tylfuro[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidite; 3a). Compound 2a (0.214 g,
0.3 mmol) was dissolved in dist. CH2Cl2 (15 ml). Under Ar, EtN(iPr)2 (125 ml, 0.72 mmol) and
(chloro)(2-cyanoethoxy)(diisopropylamino)phosphine (156 ml, 0.6 mmol) were then added, and the
mixture was stirred for 17 min at r.t. The reaction was quenched by addition of an ice-cold aq. 5%
NaHCO3 soln. (12 ml), and the mixture was extracted with CH2Cl2 (15 ml). The combined org. layers
were dried (1 min, Na2SO4), filtered, evaporated to dryness (258), and the raw product was further dried
in high vacuum at r.t. CC (SiO2 60, column: 2 ꢃ 10 cm, CH2Cl2/acetone 8 :2, containing 8 drops of Et3N
per l) gave one main zone which was pooled, evaporated, and dried in high vacuum: 3a (0.13 g,
0.22 mmol, 71%). Colorless oil stored at ꢀ 208. Rf (SiO2 60; CH2Cl2/acetone 8 :2) 0.66. 31P-NMR
(202.45 MHz, CDCl3): 149.40 (PR), 149.30 (PS).
5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-2’,3’-O-(1-nonyldecylidene)uridine
(¼2-Cyanoethyl [(3aR,4R,6R,6aR)-6-(2,4-Dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydro-2,2-dino-
nylfuro[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidite; 3b). Compound 2b (0.153 g,
0.3 mmol) was converted to 3b as described for 3a. Yield: 0.157 g (0.22 mmol, 73%). Colorless oil stored
at ꢀ 208. Rf (silica 60; CH2Cl2/acetone 8 :2) 0.89. 31P-NMR (202.45 MHz, CDCl3): 149.46 (PR), 149.37
(PS).
5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-2’,3’-O-(1-heptadecyloctadecylidene)-
uridine (¼2-Cyanoethyl [(3aR,4R,6R,6aR)-6-(2,4-Dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydro-
2,2-diheptadecylfuro[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidite; 3e). Compound
2e (0.22 g, 0.3 mmol) was converted to 3e as described for 3a. Yield: 0.1 g (0.17 mmol, 57%). Colorless oil
stored at ꢀ 208. Rf (SiO2 60; CH2Cl2/acetone 8 :2) 0.81. 31P-NMR (202.45 MHz, CDCl3): 149.46 (PR),
149.38 (PS).
2’,3’-O-(1-Nonyldecylidene)-3-[(2E,6E)-3,7,11-trimethyl-2,6,10-dodecatrien-1-yl]uridine
(¼1-
[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxymethyl)-2,2-dinonylfuro[3,4-d][1,3]dioxol-4-yl]-3-[(2E,6E)-
3,7,11-trimethyldodeca-2,6,10-trien-1-yl]pyrimidine-2,4(1H,3H)-dione; 4b). Compound 2b (0.5 g,
0.98 mmol) was dissolved in anh. DMF (14 ml), and K2CO3 (1 g, 7.24 mmol) was added. Subsequently,
under Ar, (E,E)-farnesyl bromide (0.35 ml, 1.1 mmol) was added dropwise within 10 min. The mixture
was stirred for 24 h at r.t. under the exclusion of light. Then, the mixture was filtered and partitioned
between dist. H2O (225 ml) and CH2Cl2 (150 ml). The org. phase was separated, dried (Na2SO4), and
filtered. The soln. was evaporated to dryness and further dried in high vacuum. CC (SiO2 60, column: 2 ꢃ
27 cm, CH2Cl2 and MeOH, 99 :1) and evaporation of the main fractions gave 4b (0.533 g, 0.75 mmol,
77%). Colorless oil. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.59. UV (MeOH): 260 (7010). 1H-NMR
(500.13 MHz, (D6)DMSO): 7.81 (d, 3J(6,5) ¼ 8.0, HꢀC(6)); 5.87 (d, 3J(1’,2’) ¼ 2.2, HꢀC(1’)); 5.74 (d,
3J(5,6) ¼ 8.0, HꢀC(5)); 5.11 (t, 3J(HOꢀC(5’),5’) ¼ 6.5, HOꢀC(5’)); 5.08 – 5.00 (m, HꢀC(2’’’,6’’’,10’’’));
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4.87 (dd, 3J(2’,1’) ¼ 2.5, J(2’,3’) ¼ 6.6, HꢀC(2’)); 4.73 (dd, 3J(3’,4’) ¼ 3.0, J(3’,2’) ¼ 6.5, HꢀC(3’)); 4.41 –
4.38 (m, CH2(1’’’)); 4.09 (Yq, 3J(4’,5’) ¼ 3J(4’,3’) ¼ 4.2, HꢀC(4’)); 3.61 – 3.51 (m, CH2(5’)); 2.03 (m,
CH2(5’’’)); 2.00 – 1.92 (m, CH2(8’’’,9’’’)); 1.92 – 1.87 (m, CH2(4’’’)); 1.73 (s, Me(13’’’)); 1.69 – 1.66 (m,
CH2(1a’’)); 1.63 (s, Me(12’’’)); 1.54 (s, Me(14’’’)); 1.51 (m, CH2(1b’’)); 1.42 – 1.18 (m, CH2(2a’’ – 8a’’, 2b’’ –
8b’’)); 0.85 (m, Me(9a’’,9b’’)). 13C-NMR (125.76 MHz, (D6)DMSO): 161.55 (C(4)); 150.20 (C(2)); 140.18
(C(6)); 138.81 (C(3’’’)); 134.45 (C(7’’’)); 130.47 (C(11’’’)); 124.01 (C(6’’’)); 123.49 (C(10’’’)); 118.69
(C(2’’’)); 116.56 (C(ketal)); 100.87 (C(5)); 92.09 (C(1’)); 86.79 (C(4’)); 83.99 (C(3’)); 80.72 (C(2’)); 61.28
(C(5’)); 39.04 (C(8’’’)); 38.74 (C(4’’’)); 38.17 (C(1’’’)); 36.36 (C(1a’’)); 36.31 (C(1b’’)); 31.19 (C(7a’’));

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31.16 (C(7b’’)); 29.07 (C(3a’’)); 29.02 (C(3b’’)); 28.83 (C(4a’’)); 28.78 (C(4b’’)); 28.58 (C(5a’’)); 28.56
(C(5b’’)); 28.58 (C(6a’’); 28.59 (C(6b’’)); 26.09 (C(5’’’)); 25.62 (C(9’’’)); 25.34 (C(12’’’)); 23.48 (C(2a’’));
22.83 (C(2b’’)); 21.99 (C(8’’)); 17.41 (C(15’’’)); 16.06 (C(14’’’)); 15.66 (C(13’’’)); 13.81 (C(9’’)). Anal. calc.
for C43H72N2O6 (713.04): C 72.43, H 10.18, N 3.93; found: C 72.59, H 10.58, N 3.96.
5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-2’,3’-O-(1-nonyldecylidene)-3-[(2E,6E)-
3,7,11-trimethyl-2,6,10-dodecatrien-1-yl]uridine (¼2-Cyanoethyl [(3aR,4R,6R,6aR)-6-{2,4-Dioxo-3-
[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]-3,4-dihydropyrimidin-1(2H)-yl}tetrahydro-2,2-dino-
nylfuro[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidoite; 5b). Compound 4b (0.214 g,
0.3 mmol) was converted to 5b as described for 3a. Yield: 0.253 g (0.26 mmol, 87%). Colorless oil stored
at ꢀ 208. Rf (SiO2 60; CH2Cl2/acetone 8 :2) 0.97. 31P-NMR (202.45 MHz, CDCl3): 149.34 (PR), 149.31
(PS).
5-Methyl-2’,3’-O-(1-nonyldecylidene)uridine (¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxy-
methyl)-2,2-dinonylfuro[3,4-d][1,3]dioxol-4-yl]-5-methylpyrimidine-2,4(1H,3H)-dione; 7a). Anh. 5-
methyluridine (6; 0.77 g, 3 mmol) was dissolved in dry DMF (10 ml). Then, nonadecan-10-one (1.13 g,
4 mmol), dissolved in CH2Cl2 (10 ml), HC(OEt)3 (1 ml), and 4m HCl in 1,4-dioxane (4 ml) were added.
The mixture was stirred at r.t. for 24 h. Subsequently, the mixture was partinioned between an aq. sat.
Na2CO3 soln. (100 ml) and CH2Cl2 (100 ml). The org. phase was separated, dried (Na2SO4), filtered, and
evaporated to dryness. Traces of DMF were removed by repeated evaporation from CH2Cl2. The residue
was dried in high vacuum overnight. The resulting colorless foam was purified by CC (SiO2 60, column:
6.5 ꢃ 10 cm; CH2Cl2/MeOH 95 :5) to give one main zone which was pooled; the solvent was evaporated,
and the residue was dried in high vacuum: 7a (1.3 g, 83%). Colorless oil. Rf (SiO2 60; CH2Cl2/MeOH
95 :5) 0.31. UV (MeOH): 265 (10600). 1H-NMR ((D6)DMSO): 11.34 (s, HꢀN(3)); 7.63 (s, HꢀC(6)); 5.83
(d, 3J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.02 (t, 3J(HOꢀC(5’),5’) ¼ 5.0, HOꢀC(5’)); 4.88 (dd, 3J(2’,1’) ¼ 3.0, 3J(2’,3’) ¼
6.5, HꢀC(2’)); 4.75 (dd, 3J(3’,2’) ¼ 6.5; 3J(3’,4’) ¼ 3.5, HꢀC(3’)); 4.02 (m, 3J(4’,3’) ¼ 3.5, 3J(4’,5’) ¼ 4.5,
HꢀC(4’)); 3.56 (m, CH2(5’)); 1.76 (s, Me); 1.66 (m, CH2(1a’’)); 1.52 (m, CH2(1b’’)); 1.38 (m, CH2(2a’’));
1.24 (m, CH2(3a’’ – 8a’’, 2b’’ – 8b’’)); 0.85 (m, Me(9a’’,9b’’)). 13C-NMR ((D6)DMSO): 163.66 (C(4));
150.27 (C(2)); 137.50 (C(6)); 116.77 (C(ketal)); 109.38 (C(5)); 90.52 (C(1’)); 86.24 (C(4’)); 83.50 (C(3’));
80.58 (C(2’)); 61.31 (C(5’)); 36.33 (C(1a’’)); 36.28 (C(1b’’)); 31.17 (C(7a’’)); 31.16 (C(7b’’)); 29.06
(C(3a’’)); 29.01 (C(3b’’)); 28.83 (C(4a’’)); 28.81 (C(4b’’)); 28.80 (C(5’’)); 28.77 (C(6a’’)); 28.55 (C(6b’’));
23.48 (C(2a’’)); 22.86 (C(2b’’)); 21.97 (C(8a’’)); 21.96 (C(8b’’)); 13.82 (C(9a’’)); 13.81 (C(9b’’)); 11.94
(MeꢀC(5)). Anal. calc. for C29H50N2O6 (522.73): C 66.63, H 9.64, N 5.36; found: C 66.47, H 9.272, N 5.25.
5-Methyl-2’,3’-O-(1-pentadecylhexadecylidene)uridine (¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hy-
droxymethyl)-2,2-dipentadecylfuro[3,4-d][1,3]dioxol-4-yl]-5-methylpyrimidine-2,4(1H,3H)-dione; 7b).
Hentriacontan-16-one (0.45 g, 1 mmol) was added to a soln. of 6 (1.29 g, 5 mmol), TsOH (0.19 g,
1 mmol), and HC(OEt)3 (0.83 ml, 5 mmol) in THF (14 ml). This mixture was heated to 758 under reflux
for 24 h. Then, Et3N (0.6 ml) was added, and the resulting mixture was poured into an ice-cold aq. 4%
NaHCO3 soln. (50 ml). After stirring for 15 min at r.t., the mixture was partitioned between CH2Cl2
(100 ml) and H2O (100 ml). The org. layer was separated, dried (Na2SO4), filtered, and the solvent was
evaporated. The resulting oil was triturated with ice-cold MeOH on an ice bath, which led to
precipitation of 7b as a colorless solid. The latter was filtered off, and the filtrate was evaporated to yield
another portion of solid 7b. Total yield: 0.509 g (74%) as a yellowish solid. M.p. < 708. Rf (SiO2 60;
CH2Cl2/MeOH 95 :5) 0.24. UV (CH2Cl2): 263 (12250). 1H-NMR ((D6)DMSO): 11.09 (s, HꢀN(3)); 7.58
(s, HꢀC(6)); 5.83 (d, 3J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.01 (t, 3J(HOꢀC(5’),5’) ¼ 5.0, HOꢀC(5’)); 4.89 (dd,
3J(2’,1’) ¼ 2.8, 3J(2’,3’) ¼ 6.6, HꢀC(2’)); 4.77 (dd, 3J(3’,2’) ¼ 6.6, 3J(3’,4’) ¼ 3.5, HꢀC(3’)); 4.05 (Yq,
3J(4’,5’) ¼ 3J(4’,3’) ¼ 4.4, HꢀC(4’)); 3.60 (m, CH2(5’)); 1.79 (s, MeꢀC(5)); 1.66 (m, CH2(1a’’)); 1.52 (m,
CH2(1b’’)); 1.43 – 1.19 (m, CH2(2a’’ – 14a’’, 2b’’ – 14b’’)); 0.85 (m, Me(15a’’,15b’’))). 13C-NMR
((D6)DMSO): 163.14 (C(4)); 149.91 (C(2)); 136.94 (C(6)); 116.59 (C(ketal)); 109.07 (C(5)); 90.50
(C(1’)); 86.03 (C(4’)); 83.31 (C(3’)); 80.38 (C(2’)); 61.12 (C(5’)); 36.32 (C(1a’’)); 36.03 (C(1b’’)); 30.74
(C(13’’)); 28.63 (C(3a’’)); 28.61 (C(3b’’)); 28.44 – 28.10 (C(4’’) – C(12’’)); 23.02 (C(2a’’)); 22.52 (C(2b’’));
21.48 (C(14’’)); 13.24 (C(15’’)); 11.33 (MeꢀC(5)). Anal. calc. for C41H74N2O6 (691.04): C 71.26, H 10.79, N
4.05; found: C 72.39, H 11.48, N 3.33.
2’,3’-O-(1-Heptadecyloctadecylidene)-5-methyluridine (¼1-[(3aR,4R,6R,6aR)-2,2-Diheptadecylte-
trahydro-6-(hydroxymethyl)furo[3,4-d][1,3]dioxol-4-yl]-5-methylpyrimidine-2,4(1H,3H)-dione; 7c).

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Helvetica Chimica Acta – Vol. 96 (2013)
Pentatriacontan-18-one (0.50 g, 1 mmol) was added to a soln. of 6 (1.29 g, 5 mmol), TsOH (0.19 g,
1 mmol), and HC(OEt)3 (0.83 ml, 5 mmol) in THF (10 ml). This mixture was heated to 758 under reflux
for 24 h. Then, Et3N (0.6 ml) was added, and the mixture was poured into an ice-cold aq. 4% NaHCO3
soln. (50 ml). After stirring for 15 min at r.t., the mixture was partitioned between CH2Cl2 (100 ml) and
H2O (100 ml). The org. layer was separated, dried (Na2SO4), filtered, and the solvent was evaporated.
The resulting oil was triturated with cold MeOH which led to precipitation of raw 7c. The product was
filtered off, and the filtrate was evaporated to yield a further crop of 7c. Total yield: 0.5 g (68%). M.p.
728. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.19. UV (CH2Cl2): 263 (14380). 1H-NMR ((D6)DMSO): 11.31 (s,
HꢀN(3)); 7.62 (s, HꢀC(6)); 5.84 (d, 3J(1’,2’) ¼ 2.5, HꢀC(1’)); 5.02 (t, 3J(HOꢀC(5’),5’) ¼ 6.5, HOꢀC(5’));
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3
4.88 (dd, 3J(2’,1’) ¼ 2.5, J(2’,3’) ¼ 6.6, HꢀC(2’)); 4.75 (dd, 3J(3’,2’) ¼ 6.6, J(3’,4’) ¼ 3.5, HꢀC(3’)); 4.02
3
3
(dd, J(4’,5’) ¼ 4.2, J(4’,3’) ¼ 4.2, HꢀC(4’)); 3.57 (m, CH2(5’)); 1.76 (s, MeꢀC(5)); 1.66 (m, CH2(1a’’));
1.51 (m, CH2(1b’’)); 1.37 (m, CH2(2a’’)); 1.24 (m, CH2(3a’’ – 16a’’, 2b’’ – 16b’’)); 0.85 (m, CH2(17a’’,17b’’)).
13C-NMR ((D6)DMSO): 163.33 (C(4)); 150.04 (C(2)); 137.14 (C(6)); 116.64 (C(ketal)); 109.18 (C(5));
90.48 (C(1’)); 86.09 (C(4’)); 83.38 (C(3’)); 80.44 (C(2’)); 61.18 (C(5’)); 36.31 (C(1a’’)); 36.06 (C(1b’’));
30.90 (C(15’’)); 28.75 (C(3a’’)); 28.71 (C(3b’’)); 28.59 – 28.27 (C(4’’) – C(14’’)); 23.17 (C(2a’’)); 22.63
(C(2b’’)); 21.66 (C(16’’)); 13.46 (C(17’’)); 11.56 (MeꢀC(5)). Anal. calc. for C45H82N2O6 (747.14): C 72.34,
H 11.06, N 3.75; found: C 72.39, H 11.48, N 3.33.
5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-5-methyl-2’,3’-O-(1-nonyldecylide-
ne)uridine (¼2-Cyanoethyl [(3aR,4R,6R,6aR)-Tetrahydro-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-
1(2H)-yl)-2,2-dinonylfuro[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidoite; 8a).
Compound 7a (0.157 g, 0.3 mmol) was converted to 8a as described for 3a (0.155 g, 71%). Colorless
oil stored at ꢀ 208. Rf (SiO2 60; CH2Cl2/acetone 8 :2) 0.88. 31P-NMR (202.45 MHz, CDCl3): 149.36 (PR),
149.22 (PS).
5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-2’,3’-O-(1-heptadecyloctadecylidene)-
5-methyluridine (¼2-Cyanoethyl [(3aR,4R,6R,6aR)-2,2-Diheptadecyltetrahydro-6-(5-methyl-2,4-dioxo-
3,4-dihydropyrimidin-1(2H)-yl)furo[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidoite;
8c). Compound 7c (0.214 g, 0.3 mmol) was converted to 8c as described for 3a (0.20 g, 0.21 mmol, 70%).
Colorless oil stored at ꢀ 208. Rf (silica 60; CH2Cl2/acetone 8 :2) 0.87. 31P-NMR (101.25 MHz, CDCl3):
149.31 (PR), 149.17 (PS).
5-Methyl-2’,3’-O-(1-nonyldecylidene)-3-[(2E,6E)-3,7,11-trimethyl-2,6,10-dodecatrien-1-yl]uridine
(¼1-[(3aR,4R,6R,6aR)-Tetrahydro-6-(hydroxymethyl)-2,2-dinonylfuro[3,4-d][1,3]dioxol-4-yl]-5-meth-
yl-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]pyrimidine-2,4(1H,3H)-dione; 9a). Compound 7a
(0.52 g, 1 mmol) was dissolved in dry DMF (14 ml), and anh. K2CO3 (1 g, 7.24 mmol) was added. Then,
(E,E)-farnesyl bromide (0.35 ml, 1.1 mmol) was added dropwise, and the mixture was stirred under Ar
for 24 h under the exclusion of light. Then, the mixture was partitioned between H2O (200 ml) and
CH2Cl2 (100 ml). The org. layer was separated, dried (Na2SO4), filtered, and the solvent was evaporated.
Traces of DMF were removed by drying in high vacuum overnight. CC (SiO2 60, column: 2 ꢃ 21 cm;
CH2Cl2/MeOH, 99 :1) gave one main zone which was pooled and evaporated to dryness. Further drying
in high vacuum gave 9a (0.5 g, 68%). Colorless oil. Rf (SiO2 60; CH2Cl2/MeOH 95 :5) 0.66. UV (MeOH):
266 (8700). 1H-NMR ((D6)DMSO): 7.68 (s, HꢀC(6)); 5.89 (d, 3J(1’,2’) ¼ 2.5, HꢀC(1’))); 5.12 (t,
3J(HOꢀC(5’),5’) ¼ 5.0, HOꢀC(5’)); 5.07 – 5.00 (m, HꢀC(2’’’,6’’’,10’’’)); 4.85 (dd, 3J(2’,1’) ¼ 2.8, 3J(2’,3’) ¼
3
3
6.6, HꢀC(2’)); 4.76 (dd, J(3’,2’) ¼ 6.6, J(3’,4’) ¼ 3.5, HꢀC(3’)); 4,39 (m, CH2(1’’’)); 4.06 (m, HꢀC(4’));
3.62 – 3.52 (m, CH2(5’)); 2.03 (m, CH2(5’’’)); 1.99 – 1.92 (m, CH2(8’’’,9’’’)); 1.92 – 1.86 (m, CH2(4’’’)); 1.81
(s, MeꢀC(5)); 1.74 (s, Me(13’’’)); 1.69 – 1.64 (m, CH2(1a’’)); 1.63 (s, Me(12’’’)); 1.54 (s, Me(14’’’)); 1.52 (m,
CH2(1b’’)); 1.43 – 1.17 (m, CH2(2a’’ – 8a’’, 2b’’ – 8b’’)); 0.85 (m, Me(9a’’,9b’’)). 13C-NMR ((D6)DMSO):
162.27 (C(4)); 150.09 (C(2)); 138.71 (C(6)); 135.71 (C(3’’’)); 134.42 (C(7’’’)); 130.45 (C(11’’’)); 123.98
(C(6’’’)); 123.46 (C(10’’’)); 118.75 (C(2’’’)); 116.74 (C(ketal)); 108.57 (C(5)); 91.42 (C(1’)); 86.34 (C(4’));
83.64 (C(3’)); 80.61 (C(2’)); 61.25 (C(5’)); 38.98 (C(8’’’)); 38.76 (C(4’’’)); 38.52 (C(1’’’)); 36.30 (C(1’’)); 31.
15 (C(7a’’)); 31.13 (C(7b’’)); 29.03 (C(3a’’)); 28.97 (C(3b’’)); 28.80 (C(4a’’)); 28.74 (C(4b’’)); 28.55
(C(5a’’)); 28.52 (C(5b’’)); 26.06 (C(6a’’)); 25.55 (C(6b’’)); 25.32 (C(5’’’)); 23.44 (C(9’’’)); 22.80 (C(12’’’));
21.95 (C(2a’’)); 21.93 (C(2b’’)); 17.37 (C(8’’)); 16.03 (C(15’’’)); 15.64 (C(14’’)); 13.79 (C(13’’’)); 13.78
(C(9’’)); 12.59 (MeꢀC(5)). Anal. calc. for C44H74N2O6 (727.07): C 72.69, H 10.26, N 3.85; found: C 72.67,
H 9.925, N 3.76.

Helvetica Chimica Acta – Vol. 96 (2013)
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5’-O-{[Bis(1-methylethyl)amino](2-cyanoethoxy)phosphino}-5-methyl-2’,3’-O-(1-nonyldecylidene)-
3-[(2E,6E)-3,7,11-trimethyl-2,6,10-dodecatrien-1-yl]uridine (¼2-Cyanoethyl [(3aR,4R,6R,6aR)-Tetrahy-
dro-6-{5-methyl-2,4-dioxo-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]-3,4-dihydropyrimidin-
1(2H)-yl}-2,2-dinonylfuro[3,4-d][1,3]dioxol-4-yl]methyl Bis(1-methylethyl)phosphoramidoite; 10a).
Compound 9a (0.22 g, 0.3 mmol) was converted to 10a as described for 3a (0.2 g, 0.22 mmol, 77.9%).
Colorless oil stored at ꢀ 208. Rf (SiO2 60; CH2Cl2/acetone 8 :2) 0.97. 31P-NMR (202.45 MHz, CDCl3):
149.28 (PR), 149.26 (PS).
2’-Deoxy-3-hexadecyl-3,4-dihydrothymidine (¼ 3-Hexadecyl-1-[(2R,4S,5R)-tetrahydro-4-hydroxy-5-
(hydroxymethyl)furan-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione; 12). 2’-Deoxythymidine (11, 0.98 g,
4.05 mmol) was dissolved in anh. DMF (24 ml). After heating to 488 on a water bath, K2CO3 (1.465 g,
10.6 mmol) was added under N2. After stirring for 10 min, 1-bromohexadecane (1.1 ml, 4.5 mmol) was
added portionwise during 5 h. Stirring was continued for further 23 h. Then, the mixture was filtered, and
the residue was washed with CH2Cl2. The filtrate was dried (Na2SO4), filtered, and evaporated to
dryness. CC (SiO2 60, 6.5 ꢃ 13 cm; stepwise elution with i) CH2Cl2/MeOH 98 :2, ii) CH2Cl2/MeOH 96 :4,
iii) CH2Cl2/MeOH 95 :5) gave one main zone which was evaporated and then dried in high vacuum to
give 12 (1.03 g, 2.67 mmol, 66%). Amorphous foam. Tglasstransition 106 – 1128. Rf (SiO2; CH2Cl2/MeOH
1
9 :1): 0.26. log P: 8.60 ꢄ 0.56. H-NMR ((D6)DMSO): 1.484 (Yq, 3J(H,H) ¼ 7.2, CH2(2’’’)); 1.235 (m,
3
CH2(3’’’ – 15’’’)); 0.851 (t, J(16’’’,15’’’) ¼ 6.9, Me(16’’’)); 7.745 (s, HꢀC(6)); 1.816 (s, Me(7)); 6.201 (Yt,
3J(1’,HaꢀC(2’)) ¼ 6.9, 3J(1’,HbꢀC(2’)) ¼ 6.8, HꢀC(1’)); 2.094 (ddd, 2J(HaꢀC(2’),HbꢀC(2’)) ¼ ꢀ11.6,
3
3
3
3J(HaꢀC(2’),1’) ¼ 6.7, J(HbꢀC(2’),1’) ¼ 6.6, J(HaꢀC(2’),3’) ¼ 4.9, J(HbꢀC(2’),3’) ¼ 5.0, CH2(2’)); 4.240
(Yq, HꢀC(3’)); 5.218 (d, 3J(HOꢀC(3’),3’) ¼ 3.4, HOꢀC(3’)); 3.538 – 3.623 (m, 2J(HaꢀC(5’),HbꢀC(5’)) ¼
ꢀ15.0, CH2(5’)); 5.005 (t, 3J(OHꢀC(5’),5’) ¼ 3.9, HOꢀC(5’)); 3.744 – 3.799 (m, HꢀC(4’), CH2(1’’’)).
13C-NMR ((D6)DMSO): 40.92 ((C(1’’’)); 26.939 (C(2’’’)); 26.251 (C(3’’’)); 28.5967 (C(4’’’)); 28.767 –
28.928 (C(5’’’ – 12’’’)); 28.560 (C(13’’’)); 31.200 (C(14’’’)); 21.992 (C(15’’’)); 13.846 (C(16’’’)); 150.289
(C(2)); 162.532 (C(4)); 108.386 (C(5)); 134.605 (C(6)); 12.820 (C(7)); 84.697 (C(1’)); 135 40.08 (C(2’));
70.230 (C(3’)); 87.311 (C(4’)); 61.188 (C(5’)). Anal. calc. for C26H46N2O5 (466.654): C 66.92, H 9.94, N
6.00; found: C 66.70, H 10.01, N 5.77.
5’-O-[Bis(4-methoxyphenyl)phenylmethyl]-2’-deoxy-3,4-dihydrothymidine (¼1-[(2R,4S,5R)-5-
{[Bis(4-methoxyphenyl)(phenyl)methoxy]methyl}tetrahydro-4-hydroxyfuran-2-yl]-5-methylpyrimidine-
2,4(1H,3H)-dione; 13) [15]. Anh. 11 (1.94 g, 8 mmol) was evaporated from dry pyridine and then
dissolved in dry pyridine (40 ml). Then, 4,4’-dimethoxytrityl chloride (3.52 g, 10.4 mmol) was added, and
the mixture was stirred under N2 for 24 h. After subsequent addition of MeOH, stirring was continued for
30 min. After addition of an ice-cold 5% aq. NaHCO3 soln. and further stirring for 30 min, the mixture
was extracted three times with H2O, followed by extraction with CH2Cl2. The org. layer was dried
(Na2SO4, 30 min), filtered, evaporated, and dried in high vacuum. The residue was chromatographed
(SiO2 60, column: 4 ꢃ 24 cm; stepwise elution with CH2Cl2/MeOH 99 :1, 97:3, and 95 :5). After removal
of the solvent, 13 (3.36 g, 6.2 mmol, 77%) was isolated as a slightly yellowish foam. Tglasstransition 80 – 878. Rf

886
Helvetica Chimica Acta – Vol. 96 (2013)
(SiO2; CH2Cl2/MeOH 96 :4) 0.28. log P: 4.88 ꢄ 0.51. 1H-NMR ((D6)DMSO): 11.299 (s, HꢀN(3)); 7.500
(s, HꢀC(6)); 1.462 (s, Me(7)); 6.209 (Yt, 3J(1’,HaꢀC(2’)) ¼ 7.0, 3J(1’,HbꢀC(2’)) ¼ 6.7, HꢀC(1’)); 2.162
(ddd, 2J(HaꢀC(2’),HbꢀC(2’)) ¼ ꢀ13.4, 3J(HaꢀC(2’),1’) ¼ 6.3, 3J(HaꢀC(2’),3’) ¼ 3.6, HaꢀC(2’)); 2.241
(ddd, 2J(HbꢀC(2’),HaꢀC(2’)) ¼ ꢀ13.5, 3J(HbꢀC(2’),1’) ¼ 6.8, HbꢀC(2’)); 4.305 – 4.341 (m, HꢀC(3’));
5.298 (d, 3J(HOꢀC(3’),3’) ¼ 4.3, HOꢀC(3’)); 3.890 (dd, 3J(4’,3’) ¼ 3.4, HꢀC(4’)); 3.173 – 3.237 (m,
3
2J(HaꢀC(5’),HbꢀC(5’)) ¼ ꢀ10.7, CH2(5’)); 3.736 (s, 2 Me(1’’)); 6.893 (d, J(3’’,4’’) ¼ 7.5, HꢀC(3’’), 4 H);
3
7.391 (d, J(8’’,9’’) ¼ 7.6, HꢀC(8’’), 2 H); 7.217 – 7.325 (m, 4 HꢀC(4’’), 2 HꢀC(9’’), HꢀC(10’’)). 13C-NMR
((D6)DMSO): 150.271 (C(2)); 163.546 (C(4)); 109.470 (C(5)); 135.229 (C(6)); 11.595 (C(7)); 83.717
(C(1’)); 39.41 (C(2’)); 70.463 (C(3’)); 85.561 (C(4’)); 63.696 (C(5’)); 54.962 (C(1’’)); 158.078 (C(2’’));
113.160 (C(3’’)); 129.634 (C(4’’)); 135.570 (C(5’’)); 85.769 (C(6’’)); 144.622 (C(7’’)); 127.346 (C(8’’));
127.778 (C(9’’)); 126.681 (C(10’’)). Anal. calc. for C31H32N2O7 (544.595): C 68.35, H 5.92, N 5.14; found: C
68.02, H 5.91, N 4.99.
5’-O-[Bis(4-methoxyphenyl)phenylmethyl]-2’-deoxy-3’-O-[(1,1-dimethylethyl)diphenylsilyl]-3,4-di-
hydrothymidine (¼1-[(2R,4S,5R)-5-{[Bis(4-methoxyphenyl)(phenyl)methoxy]methyl}-4-{[(1,1-dime-
thylethyl)diphenylsilyl]oxy}tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione; 14). Com-
pound 13 (0.47 g, 0.88 mmol) was dissolved in anh. DMF (7 ml). Then, 1H-imidazole (0.18 g, 2.64 mmol)
was added. To the mixture, (tert-butyl)(diphenyl)silyl chloride (TBDPSiCl; 1.32 mmol, 0.35 ml) was
added dropwise under cooling in an ice bath (N2 atm.). After 22 h, the reaction was quenched by addition
of MeOH (4 ml). After stirring for 30 min at r.t., to the mixture was added a 5% aq. NaHCO3 soln., and
the mixture was extracted twice with AcOEt. After washing with H2O, the org. layer was dried (Na2SO4,
30 min), filtered, evaporated, and then dried in high vacuum. The residue was purified by CC (SiO2 60,
column: 4 ꢃ 15 cm; equilibrated with petroleum ether (PE)/AcOEt 2.1, containing 3% of Et3N). Elution
with PE/AcOEt 2.1, followed by PE/AcOEt 1.1, gave one main zone, from which 14 (514 mg, 76%) was
isolated. Colorless amorphous solid. Rf (SiO2, PE/AcOEt 1:1) 0.54. Tglasstransition 61.7 – 70.28. log P:
11.54 þ / ꢀ 0.75. 1H-NMR ((D6)DMSO): 11.287 (s, HꢀN(3)); 1.410 (s, Me(7)); 6.249 (Yt,
3J(1’,HbꢀC(2’)) ¼ 7.0, 3J(1’,HaꢀC(2’)) ¼ 6.8, HꢀC(1’)); 2.203 (ddd, 2J(HaꢀC(2’),HbꢀC(2’)) ¼ ꢀ13.4,
3J(HaꢀC(2’),1’) ¼ 6.0, 3J(HaꢀC(2’),3’) ¼ 2.9, HbꢀC(2’)); 2.126 (ddd, 2J(HbꢀC(2’),HaꢀC(2’)) ¼ ꢀ13.7,
3J(HbꢀC(2’),1’) ¼ 6.7, HbꢀC(2’)); 4.443 (Yq, HꢀC(3’)); 4.010 (m, (HꢀC(4’)); 2.912 (dd,
2
2J(HaꢀC(5’),HbꢀC(5’)) ¼ ꢀ14.9, HaꢀC(5’)); 3.027 (dd, J(HbꢀC(5’),HaꢀC(5’)) ¼ 13.4, HbꢀC(5’)); 3.719
3
3
(s, 2 Me(1’’)); 6.8 (dd, J(3’’,4’’) ¼ 4.3, 4 HꢀC(3’’)); 7.096 (Yq, J(H,H) ¼ 8.3, 4 HꢀC(4’’)); 7.322 – 7.408
(m, 2 HꢀC(8’’), 2 HꢀC(9’’), HꢀC(10’’)); 7.194 – 7.221 (m, HꢀC(6), 4 HꢀC(2*)); 7.507, 7.562 (2d,
3J(H,H) ¼ 6.9, HꢀC(3*), 2 ꢃ 2 H); 7.471 – 7.485 (m, 2 HꢀC(4*)); 0.980 (s, 3 Me(6*)). 13C-NMR
((D6)DMSO): 150.787 (C(2)); 164.026 (C(4)); 110.070 (C(5)); 135.639 (C(6)); 12.132 (C(7)); 84.377
(C(1’)); 39.33 (C(2’)); 73.801 (C(3’)); 85.903 (C(4’)); 63.717 (C(5’)); 55.540 (C(1’’)); 158.630 (C(2’’));
113.664 (C(3’’)); 130.080 (C(4’’)); 135.970 (C(5’’)); 86.392 (C(6’’)); 144.995 (C(7’’)); 128.019 (C(8’’));
128.201 (C(9’’)); 127.214 (C(10’’)); 133.150 (C(1*)); 135.715 (C(2*)); 128.397 (C(3*)); 130.542 (C(4*));
19.059 (C(5*)); 27.148 (C(6*)). Anal. calc. for C47H50N2O7Si · 0.5 H2O (782.995): C 71.21, H 6.44, N 3.54;
found: C 71.48, H 6.41, N 3.35.
5’-O-[Bis(4-methoxyphenyl)phenylmethyl]-2’-deoxy-3’-O-[(1,1-dimethylethyl)diphenylsilyl]-3-hexa-
decyl-3,4-dihydrothymidine (¼1-[(2R,4S,5R)-5-{[Bis(4-methoxyphenyl)(phenyl)methoxy]methyl}-4-
{[(1,1-dimethylethyl)diphenylsilyl]oxy}tetrahydrofuran-2-yl]-3-hexadecyl-5-methylpyrimidine-2,4(1H,3H)-
dione; 15). The fully protected 14 (1.1 g, 1.4 mmol) was dissolved in THF (12 ml). At r.t., cetyl alcohol
(0.34 g, 1.4 mmol), Ph3P (0.55 g, 2.1 mmol), and diisopropyl azodicarboxylate (DIAD; 0.6 ml, 2.1 mmol)
were added. Stirring was continued overnight under N2 and under exclusion of light. Then, the mixture
was evaporated to dryness, and the residue was purified by CC (SiO2 60, column: 4 ꢃ 20 cm; PE/AcOEt
6 :1, containing 5% of Et3N). Evaporation of the main zone afforded a material which was redissolved in
cold AcOEt and extracted with H2O to remove traces of Et3N. After evaporation of the org. layer, the
residue was dried for several days in high vacuum to give 15 (1.03 g, 50%). Colorless foam. Rf (SiO2, PE/
1
3
AcOEt 6 :1) 0.45. log P: 20.82 þ / ꢀ 0.78. H-NMR ((D6)DMSO): 3.767 (t, J(1’’’,2’’’) ¼ 7.3, CH2(1’’’));
1.239 (m, CH2(2’’’ – 15’’’)); 0.854 (t, 3J(16’’’,15’’’) ¼ 6.7, Me(16’’’)); 1.470 (s, Me(7)); 6.306 (Yt,
3J(1’,HaꢀC(2’)) ¼ 7.0, 3J(1’,HbꢀC(2’)) ¼ 6.7, HꢀC(1’)); 2.249 (ddd, 2J(HaꢀC(2’),HbꢀC(2’)) ¼ ꢀ13.4,
3J(HaꢀC(2’),1’) ¼ 6.0, 3J(HaꢀC(2’),3’) ¼ 3.0, HaꢀC(2’)); 2.132 (ddd, 2J(HbꢀC(2’),HaꢀC(2’)) ¼ ꢀ13.8,
3J(HbꢀC(2’),1’) ¼ 6.6, HbꢀC(2’)); 4.465 (Yq, HꢀC(3’)); 4.049 (dd, 3J(4’,3’) ¼ 3.4, HꢀC(4’)); 2.947 (dd,

Helvetica Chimica Acta – Vol. 96 (2013)
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2J(HaꢀC(5’),HbꢀC(5’)) ¼ ꢀ10.6, HaꢀC(5’)); 3.063 (dd, 2J(HbꢀC(5’),HaꢀC(5’)) ¼ ꢀ10.6, HbꢀC(5’)); 3.729
3
3
(s, 2 Me(1’’)); 6.805 (d, J(3’’,4’’) ¼ 4.4, 4 HꢀC(3’’)); 7.112 (Yt, J(H,H) ¼ 8.3, 4 HꢀC(4’’)); 7.334 – 7.420
(m, 2 HꢀC(8’’), 2 HꢀC(9’’), HꢀC(10’’)); 7.206 – 7.233 (m, HꢀC(6), 4 HꢀC(2*)); 7.521, 7.579 (2d,
3J(H,H) ¼ 6.9, 2 ꢃ 2 HꢀC(3*)); 7.445 – 7.481 (m, 2 HꢀC(4*)); 0.996 (s, 3 Me(6*)). 13C-NMR
((D6)DMSO): 40.17 (C(1’’’)); 26.54 (C(2’’’)); 26.23 (C(3’’’)); 28.55 (C(4’’’)); 28.77 – 28.87 (C(5’’’ –
12’’’)); 28.48 (C(13’’’)); 31.149 (C(14’’’)); 21.941 (C(15’’’)); 13.790 (C(16’’’)); 150.102 (C(2)); 162.340
(C(4)); 108.599 (C(5)); 134.967 (C(6)); 12.229 (C(7)); 84.802 (C(1’)); 39.32 (C(2’)); 73.149 (C(3’));
85.448 (C(4’)); 63.059 (C(5’)); 54.939 (C(1’’)); 113.062 (C(3’’)); 129.493 (C(4’’)); 135.042 (C(5’’)); 85.832
(C(6’’)); 144.388 (C(7’’)); 127.430 (C(8’’)); 127.690 (C(9’’)); 126.626 (C(10’’)); 133.937 (C(1*)); 135.121
(C(2*)); 127.802 (C(3*)); 129.948 (C(4*)); 18.467 (C(5*)); 26.32 (C(6*)). Anal. calc. for C63H82N2O7Si
(1007.420): C 75.11, H 8.20, N 2.78; found: C 74.71, H 8.16, N 2.66.
5’-O-[Bis(4-methoxyphenyl)(phenyl)methyl]-2’-deoxy-3-hexadecyl-3,4-dihydrothymidine (¼1-
[(2R,4S,5R)-5-{[Bis(4-methoxyphenyl)(phenyl)methoxy]methyl}tetrahydro-4-hydroxyfuran-2-yl]-3-hex-
adecyl-5-methylpyrimidine-2,4(1H,3H)-dione; 16). Compound 15 (0.56 g, 0.56 mmol) was dissolved in
THF (7 ml). To this soln., Bu4NF (TBAF; 5.5 ml), dissolved in THF, was added. The mixture was stirred
for 30 min at r.t. and evaporated to dryness. Purification was performed by CC (SiO2, column: 4 ꢃ 24 cm;
PE/AcOEt 2 :1, containing 3% of Et3N, followed by PE/AcOEt 1:1). Evaporation of the main zone gave
a material which was redissolved in cold AcOEt and extracted with H2O to remove traces of Et3N.
Evaporation of the org. phase in high vacuum gave 16 (0.336 g, 79%). Slightly orange foam. Rf (SiO2, PE/
1
3
AcOEt 2 :1) 0.43. log P: 14.17 þ / ꢀ 0.56. H-NMR ((D6)DMSO): 3.778 (t, J(1’’’,2’’’) ¼ 7.3, CH2(1’’’));
1.226 (m, CH2(2’’’ – 15’’’)); 0.841 (t, 3J(16’’’,15’’’) ¼ 6.8, Me(16’’’)); 7.546 (s, HꢀC(6)); 1.504 (s, Me(7));
3
3
2
6.241 (Yt, J(1’,HaꢀC(2’)) ¼ 6.8, J(1’,HbꢀC(2’)) ¼ 6.6, HꢀC(1’)); 2.200 (ddd, J(HaꢀC(2’),HbꢀC(2’)) ¼
ꢀ13.4, 3J(HaꢀC(2’),1’) ¼ 6.2, 3J(HaꢀC(2’),3’) ¼ 4.0, HaꢀC(2’)); 2.243 (ddd, 2J(HbꢀC(2’),HaꢀC(2’)) ¼
ꢀ13.5, 3J(HbꢀC(2’),1’) ¼ 6.7, HbꢀC(2’)); 4.314 – 4.349 (m, HꢀC(3’)); 5.296 (d, 3J(HOꢀC(3’),3’) ¼ 3.7,
HOꢀC(3’)); 3.908 (dd, 3J(4’,3’) ¼ 3.4, HꢀC(4’)); 3.189 – 3.250 (m, 2J(HaꢀC(5’),HbꢀC(5’)) ¼ ꢀ10.1,
CH2(5’)); 3.730 (s, 2 Me(1’’)); 6.878 (d, 3J(3’’,4’’) ¼ 7.5, 4 HꢀC(3’’)); 7.391 (d, 3J(8’’,9’’) ¼ 7.6,
2 HꢀC(8’’)); 7.217 – 7.325 (m, 4 HꢀC(4’’), 2 HꢀC(9’’), HꢀC(10’’)). 13C-NMR ((D6)DMSO): 40.54
(C(1’’’)); 26.901 (C(2’’’)); 26.238 (C(3’’’)); 28.585 (C(4’’’)); 28.740 – 28.990 (C(5’’’ – 12’’’)); 28.550
(C(13’’’)); 31.1872 (C(14’’’)); 21.981 (C(15’’’)); 13.836 (C(16’’’)); 150.194 (C(2)); 162.450 (C(4));
108.630 (C(5)); 134.252 (C(6)); 12.298 (C(7)); 84.812 (C(1’)); 39.63 (C(2’)); 70.351 (C(3’)); 85.555
(C(4’)); 60.654 (C(5’)); 113.173 (C(3’’)); 129.651 (C(4’’)); 135.389 (C(5’’)); 85.793 (C(6’’)); 144.632
(C(7’’)); 127.624 (C(8’’)); 127.792 (C(9’’)); 126.701 (C(10’’)). Anal. calc. for C47H64N2O7 · 1.5 AcOEt
(769.020): C 70.45, H 8.42, N 3.10; found: C 70.53, H 8.72, N 2.97.
5’-O-[Bis(4-methoxyphenyl)phenylmethyl]-3’-O-[[bis(1-methylethyl)amino](2-cyanoethoxy)phos-
phino]-2’-deoxy-3-hexadecyl-3,4-dihydrothymidine (¼(2R,3S,5R)-2-{[Bis(4-methoxyphenyl)(phenyl)-
methoxy]methyl}-5-(3-hexadecyl-5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-
yl 2-Cyanoethyl Bis(1-methylethyl)phosphoramidite; 17). Compound 16 (0.23 g, 3 mmol) was three times
co-evaporated from CH2Cl2 and subsequently dissolved in CH2Cl2 (15 ml). Then, Hꢀnigꢁs base (126 ml,
0.72 mmol) and (chloro)(2-cyanoethoxy)(diisopropylamino)phosphine (156 ml, 0.6 mmol) were added
under Ar. After stirring for 15 at r.t., a 5% aq. NaHCO3 soln. (12 ml) was added. The mixture was
extracted three times with CH2Cl2. The combined org. phases were dried (Na2SO4; 1 min!), filtered, and
evaporated to dryness (bath temp. ꢅ 258). The raw product was then subjected to flash chromatography
in a water-cooled column (SiO2, column: 2 ꢃ 10.5 cm, 0.5 bar N2 pressure). Elution with CH2Cl2/acetone
8 :2 gave a main zone which was evaporated and dried for 5 min in high vacuum to give 17 (119 mg, 41%).
Colorless glass (which can be stored under N2 at ꢀ 408) for months. Rf (SiO2; CH2Cl2/acetone 8 :2) 0.85/
0.93. 31P-NMR ((D6)DMSO): 147.413, 147.734.
Oligonucleotides. The oligonucleotides 20 and 21, and their MS analysis were performed by
Eurogentec S. A., Liege Science Park, Belgium.

888
Helvetica Chimica Acta – Vol. 96 (2013)
REFERENCES
[1] E. Werz, S. Korneev, M. Montilla-Martinez, R. Wagner, R. Hemmler, C. Walter, J. Eisfeld, K. Gall,
H. Rosemeyer, Chem. Biodiversity 2012, 9, 272.
[2] K. Kçstler, E. Werz, E. Malecki, M. Montilla-Martinez, H. Rosemeyer, Chem. Biodiversity 2013, 10,
39.
[3] E. Malecki, H. Rosemeyer, Helv. Chim. Acta 2010, 93, 1500.
[4] S. Korneev, H. Rosemeyer, Helv. Chim. Acta 2013, 96, 201.
[5] E. Malecki, V. Ottenhaus, E. Werz, M. Montilla-Martinez, C. Knies, H. Rosemeyer, Chem.
Biodiversity 2013, submitted.
[6] H. Rosemeyer, E. Malecki, S. Korneev, E. Werz, K. Gall, Reactive, ꢃLipophilic Nucleoside Building
Blocks for the Synthesis of Hydrophobic Nucleic Acidsꢁ, Europꢄische Patentanmeldung, 28.09. 2012,
EP12186576.0.
[7] C. Wolfrum, S. Shi, K. N. Jayaprakash, M. Jayaraman, G. Wang, R. K. Pandey, K. G. Rjeev, T.
Nakayama, K. Charrise, E. M. Ndungo, T. Zimmermann, V. Koteliansky, M. Manoharan, M. Stoffel,
Nat. Biotechnol. 2007, 25, 1149; M. Anaya, M. Kwak, A. J. Musser, K. Mꢀllen, A. Herrmann, Chem. –
Eur. J. 2010, 16, 12852.
˙ ˙
[8] L. Moreau, M. Camplo, M. Wathier, N. Taib, M. Laguerre, I. Bestel, M. W. Grinstaff, P. Barthelemy,
J. Am. Chem. Soc. 2008, 130, 14454.
[9] E. Breitmaier, W. Voelter, ꢃ13C-NMR Spectroscopy; Monographs in Modern Chemistryꢁ, Verlag
Chemie, Weinheim, New York, 1978, Vol. 5, pp. 72, 74.
[10] M. Karplus, J. A. Pople, J. Chem. Phys. 1963, 38, 2803.
[11] D. M. Grant, B. V. Cheney, J. Am. Chem. Soc. 1967, 89, 5315.
[12] K. C. Kumara Swamy, N. N. Bhuwan Kumar, E. Balaraman, K. V. P. Pavan Kumar, Chem. Rev. 2009,
109, 2551; T. Brossette, E. Klein, C. Creminon, J. Grassi, C. Mioskowski, L. Lebeau, Tetrahedron
2001, 57, 8129; F. Himmelsbach, B. S. Schulz, T. Trichtinger, R. Charubala, W. Pfleiderer,
´
Tetrahedron 1984, 40, 59; E. Quezada, D. Vina, G. Delogu, F. Borges, L. Santana, E. Uriarte,
Helv. Chim. Acta 2010, 93, 309; O. R. Ludek, C. Meier, Synlett 2005, 3145; O. R. Ludek, C. Meier,
Synlett 2006, 324.
[13] C. Taylor Clelland, V. Risca, C. Bancroft, Nature 1999, 399, 533.
[14] H. Rosemeyer, United States Patent US 7914991, ꢃNucleolipids and Use thereof and Devices for
Nucleic Acid Analysisꢁ, 29.03.2011.
[15] P. S. Pallan, P. von Matt, C. J. Wilds, K.-H. Altmann, M. Egli, Biochemistry 2006, 45, 8048; C.
Bleasdale, S. B. Ellwood, B. T. Golding, J. Chem. Soc., Perkin Trans. 1 1990, 803.
Received October 15, 2012