Deoxyribonucleoside cyclic N-acylphosphoramidites as a new class of monomers for the stereocontrolled synthesis of oligothymidylyl-and oligodeoxycytidylyl- phosphorothioates

Article abstract of DOI:10.1021/ja991773u

A simple and straightforward synthesis of the pyrimidine 2'- deoxyribonucleoside cyclic Nacylphosphoramidites R(p)-1 and Sp-1 is described. Specifically, (±)-2-amino-1-phenylethanol 2 was chemoselectively N-acylated to 4 by treatment with ethyl fluoroacet

Full text of DOI:10.1021/ja991773u

J. Am. Chem. Soc. 2000, 122, 2149-2156
2149
Deoxyribonucleoside Cyclic N-Acylphosphoramidites as a New Class
of Monomers for the Stereocontrolled Synthesis of Oligothymidylyl-
and Oligodeoxycytidylyl- Phosphorothioates
Andrzej Wilk, Andrzej Grajkowski, Lawrence R. Phillips,† and Serge L. Beaucage*
Contribution from the DiVision of Therapeutic Proteins, Center for Biologics EValuation and Research,
Food and Drug Administration, 8800 RockVille Pike, Bethesda, Maryland 20892, and Laboratory of Drug
DiscoVery Research and DeVelopment, DeVelopmental Therapeutics Program, National Cancer Institute,
Frederick, Maryland 21701
ReceiVed May 28, 1999
Abstract: A simple and straightforward synthesis of the pyrimidine 2′-deoxyribonucleoside cyclic N-
acylphosphoramidites RP-1 and SP-1 is described. Specifically, (()-2-amino-1-phenylethanol 2 was chemo-
selectively N-acylated to 4 by treatment with ethyl fluoroacetate 3 followed by reaction with hexaethylphosphorus
triamide to afford the cyclic N-acylphosphoramidite 5 as a mixture of diastereomeric rotamers (5a and 5b).
Condensation of N4-benzoyl-5′-O-(4,4′-dimethoxytrityl)-2′-deoxycytidine 8 with 5 in the presence of 1H-
tetrazole gave, after silica gel chromatography, pure RP-1 and SP-1. 31P NMR studies indicated that when
RP-1 or SP-1 is reacted with 3′-O-acetylthymidine and N,N,N′,N′-tetramethylguanidine in CD3CN, the
dinucleoside phosphotriester SP-9 or RP-9 is formed in near quantitative yield with total P-stereospecificity
(δP 144.2 or 143.9 ppm, respectively). Sulfurization of SP-9 or RP-9 generated the P-stereodefined dinucleoside
phosphorothioate RP-11 or SP-11 (δP 71.0 or 71.2 ppm, respectively). The 2′-deoxycytidine cyclic
N-acylphosphoramidite derivatives RP-1 and SP-1 were subsequently applied to the solid-phase synthesis of
[RP,RP]- and [SP,SP]-trideoxycytidilyl diphosphorothioate d(CPSCPSC), and [RP,SP,RP]-tetradeoxycytidilyl
triphosphorothioate d(CPSCPSCPSC). Following deprotection, reversed-phase (RP) HPLC analysis of these
oligonucleotide analogues showed a single peak for each oligomer. By comparison, RP-HPLC analysis of
purified P-diastereomeric d(CPSCPSC) and d(CPSCPSCPSC) prepared from standard 2-cyanoethyl deoxyribo-
nucleoside phosphoramidites exhibited 4 and 8 peaks, respectively, each peak corresponding to a specific
P-diastereomer (see Figure 3A). The thymidine cyclic N-acylphosphoramidite derivatives RP-14 and SP-14
were also prepared, purified, and used successfully in the solid-phase synthesis of [RP]11-d[(TPS)11T]. Thus,
the application of deoxyribonucleoside cyclic N-acyl phosphoramidites to P-stereocontrolled synthesis of
oligodeoxyribonucleoside phosphorothioates may offer a compelling alternative to the methods currently used
for such syntheses.
Oligodeoxyribonucleoside phosphorothioates (PS-ODNs) have
been and continue to be extensively studied as potential
therapeutic agents against various types of cancer and infectious
diseases in humans.1 Given that these oligonucleotide analogues
are P-chiral, each of the n internucleotidic phosphorothioate
linkages adopts either a RP or a SP configuration. Chemically
synthesized PS-ODNs are therefore mixtures of 2n stereoisomers,
the ratio RP:SP of these varying between 1:1 and 3:2.2 Most
studies addressing the biological activity, pharmacokinetic
properties, and toxicology of PS-ODNs have been performed
with oligonucleotides having undefined phosphorus chirality.
Recently, stereopure RP-oligodeoxyribonucleoside phosphoro-
thioates were prepared enzymatically and then shown to possess
a lower stability to nucleases endogenous to human serum than
the parent PS-ODNs with undefined P-chirality.3 Conversely,
chemically synthesized stereopure SP-oligodeoxyribonucleoside
phosphorothioates have demonstrated superior stability to these
nucleases than P-diastereomeric PS-ODNs.4 Thus, further
investigation into the biological, pharmacokinetic, and toxico-
logical properties of P-stereopure PS-ODNs requires improved
chemical methods to synthesize these biomolecules and increase
their availability for clinical studies.
Over the years, a number of methods have been developed
for the preparation of PS-ODNs with defined P-chirality.
Specifically, nucleoside oxathiaphospholane derivatives,5 cyclic
phosphoramidites such as nucleoside indol-oxazaphosphorines6
or xylose-derived oxazaphosphorinanes,7 and nucleoside bicyclic
(3) Tang, J. Y.; Roskey, A.; Li, Y.; Agrawal, S. Nucleosides Nucleotides
1995, 14, 985-990.
(4) Koziolkiewicz, M.; Wojcik, M.; Kobylanska, A.; Karwowski, B.;
Rebowska, B.; Guga, P.; Stec, W. J. Antisense Nucleic Acid Drug DeV.
1997, 7, 43-48.
(5) (a) Stec, W. J.; Grajkowski, A.; Koziolkiewicz, M.; Uznanski, B.
Nucleic Acids Res. 1991, 19 5883-5888. (b) Stec, W. J.; Grajkowski, A.;
Kobylanska, A.; Karwowski, B.; Koziolkiewicz, M.; Misiura, K.; Okruszek,
A.; Wilk, A.; Guga, P.; Boczkowska, M. J. Am. Chem. Soc. 1995, 117,
12019-12029. (c) Karwowski, B.; Guga, P.; Kobylanska, A.; Stec, W. J.
Nucleosides Nucleotides 1998, 17, 1747-1759. (d) Stec, W. J.; Karwowski,
B.; Boczkowska, M.; Guga, P.; Koziolkiewicz, M.; Sochacki, M.; Wiec-
zorek, M. W.; Blaszczyk, J. J. Am. Chem. Soc. 1998, 120, 7156-7167.
(6) (a) Wang, J.-C.; Just, G. Tetrahedron Lett. 1997, 38, 3797-3800.
(b) Wang, J.-C.; Just, G. Tetrahedron Lett. 1997, 38, 705-708.
* To whom correspondence should be addressed. Telephone: (301)-827-
5162. FAX: (301)-480-3256. E-mail: beaucage@phosphoramidite.cber.
nih.gov.
† National Cancer Institute.
(1) (a) Crooke, S. T.; Bennett, C. F. Annu. ReV. Pharmacol. Toxicol.
1996, 36, 107-129. (b) Beaucage, S. L.; Iyer, R. P. Tetrahedron 1993, 49,
6123-6194.
(2) (a) Wilk, A.; Stec, W. J. Nucleic Acids Res. 1995, 23, 530-534. (b)
Wyrzykiewicz, T. K.; Cole, D. L. Bioorg. Chem. 1995, 23, 33-41.
10.1021/ja991773u CCC: $19.00 © 2000 American Chemical Society
Published on Web 02/24/2000

2150 J. Am. Chem. Soc., Vol. 122, No. 10, 2000
Wilk et al.
Scheme 1
Scheme 3
5b as a consequence of partial double-bond character of the
C-N bond linking the 2-fluoroacetyl group to the oxazaphos-
pholane ring.10 Further, we found the ratio of these rotamers to
vary with solvent polarity.11 Other factors contributing to the
1
complexity of NMR data are H and 13C spin-spin couplings
to phosphorus and fluorine. In this regard, the proton-decoupled
31P NMR spectrum of 5 in C6D6 or DMSO-d6 is simpler to
analyze.
Scheme 2
Because 5 possesses two chiral centers, two sets of two signals
at ∼120 and ∼130 ppm are observed due to the tricoordinated
phosphorus atom (RP and SP). Each set of signals (RP or SP)
can be assigned to the two rotamers, one of which appears as
a singlet (5a) and the other (5b) as a doublet. Given the large
coupling constants (JPF ) 50-75 Hz) associated with the signal
observed for 5b in solvents of differing polarity, it is likely that
these signals result from “through-space” 31P-19F spin-spin
coupling.12 Additional evidence in support of these spectral
assessments was obtained from an experiment involving base-
induced cyclization of 2-[N-(2,2,2-trifluoroacetyl)amino]ethyl
phosphordichloridite 6 to the chloro N-acylphosphoramidite
derivative 7 as a mixture of rotamers (7a and 7b) in CD3CN
(Scheme 3). Proton-decoupled 31P NMR analysis of this mixture
showed signals at 178 ppm (singlet assigned to the dichloridite
6), 151 ppm (singlet corresponding to rotamer 7a), and 146 ppm
(quartet attributed to rotamer 7b which has its fluorine atoms
crowded near the phosphorus atom).13 The quartet (characterized
by a 31P-19F spin-spin coupling constant JPF ) 74 Hz)
indicates through-space or nonbonded interactions between the
phosphorus and fluorine nuclei. To the best of our knowledge,
a “through-bond” 4JPF would be expected to be less than 5 Hz.14
Our observations are consistent with those reported in the
oxazaphospholidines8 have been used for this purpose. To date,
only nucleoside oxathiaphospholane derivatives have enabled
the synthesis of PS-ODNs with total P-stereospecificity. We
now wish to report deoxyribonucleoside cyclic N-acylphos-
phoramidites, such as RP-1 and SP-1 (Scheme 1), as a promising
new class of monomers in the P-stereospecific synthesis of PS-
ODNs.
Results and Discussion
The synthesis of RP-1 and SP-1 begins with the preparation
of cyclic N-acylphosphoramidite 5 (Scheme 2). Commercial
(()-2-amino-1-phenylethanol 2 was reacted with ethyl fluoro-
acetate 3 (1.3 equiv) at 130 °C until ethanol had completely
distilled off to afford the crude amido alcohol 4 in near
quantitative yields. Heating recrystallized 4 with hexaethylphos-
phorus triamide (1 equiv) at 120 °C until N,N-diethylamine had
distilled off9 was followed by distillation of the material left
under high-vacuum to give 5 as a viscous liquid. The cyclic
N-acylphosphoramidite 5 was characterized by NMR spectros-
copy and accurate mass determination. 1H and 13C NMR spectra
of 5 are quite complex due to the presence of rotamers 5a and
(10) Multiplicity of 1H, and 13C NMR signals associated with tertiary
amide rotamers is well-documented in the literature; for example, see: (a)
Abraham, R. J.; Loftus, P. In Proton and Carbon-13 NMR Spectroscopy -
An Integrated Approach; Heyden: London, 1980; pp 171-174. (b) Edwards,
O. E.; Dvornik, D.; Kolt, R. J.; Blackwell, B. A. Can. J. Chem. 1992, 70,
1397-1405. (c) Hoye, T. R.; Renner, M. K. J. Org. Chem. 1996, 61, 2056-
2064. (d) Wilk, A.; Grajkowski, A.; Phillips, L. R.; Beaucage, S. L. J. Org.
Chem. 1999, 64, 7515-7522.
(11) A striking example of chemical shift dependence upon solvent
polarity is illustrated by the 31P NMR spectra of 5 in C6D6 and DMSO-d6
(data shown as Supporting Information). The signal intensity of rotameric
species 5a in C6D6 (123.5 and 133.1 ppm) is reduced by at least a factor of
5 in DMSO-d6.
(7) (a) Jin, Y.; Just, G. J. Org. Chem. 1998, 63, 3647-3654. (b) Jin, Y.;
Biancotto, G.; Just, G. Tetrahedron Lett. 1996, 37, 973-976.
(8) (a) Iyer, R. P.; Guo, M.-J.; Yu, D.; Agrawal, S. Tetrahedron Lett.
1998, 39, 2491-2494. (b) Guo, M.-J.; Yu, D.; Iyer, R. P.; Agrawal, S.
Bioorg. Med. Chem. Lett. 1998, 8, 2539-2544 and references therein.
(9) This reaction was carried out essentially as described in the literature;
see: (a) Mizrakh, L. I.; Polonskaya, L. Yu.; Kozlova, L. N.; Babushkina,
T. A.; Bryantsev, B. I. Zh. Obshch. Khim. 1975, 45, 1469-1473. (b)
Pudovik, M. A.; Terent’eva, S. A.; Medvedeva, M. D.; Pudovik, A. N. Zh.
Obshch. Khim. 1973, 43, 679.
(12) Proton-coupled 19F NMR analysis of 5 exhibited two sets (one for
P and the other for SP) of two signals. Each set of signals was composed
R
of a triplet attributed to rotamer 5a and two triplets assigned to rotamer 5b.
The signals associated with 5b (12 lines for overlapping RP-5b and SP-5b)
resulted from 31P-19F spin-spin coupling; the coupling constants JFP (53
and 70 Hz in C6D6) were identical to the JPF measured from the
corresponding 31P NMR spectrum (data shown in Experimental section and
as Supporting Information).
(13) Data shown as Supporting Information.

P-Stereospecific Synthesis of PS-ODNs
J. Am. Chem. Soc., Vol. 122, No. 10, 2000 2151
literature; through-space 31P-19F spin-spin couplings were
found for (o-trifluoromethylphenyl) phosphines with JPF values
ranging from 51 to 56 Hz in chlorobenzene.15 Finally, through-
space 19F-19F spin-spin couplings have been extensively
studied16 in 1,8-difluoronaphthalene and 4,5-difluorophenan-
threne derivatives. In these compounds, the intramolecular pairs
of fluorine atoms crowded near each other exhibited large
coupling constants (JFF ) 59-177 Hz).17-19
amidite derivatives.23 Thus, column dimensions, amount of
sorbent, elution solvent(s), and flow rates must be optimized to
ensure the best chromatographic resolution of P-stereodefined
phosphoramidite derivatives within the shortest period of time.
Although the silica gel-induced decomposition products of RP-1
and SP-1 have not yet been completely characterized, small
amounts (less than 5%) of hydrolyzed SP-1 (presumably its
H-phosphonate derivative) and deoxyribonucleoside 8 can be
generated during chromatography. A fraction of these decom-
position products co-elute with the slower-moving RP-1. When
purified and isolated as amorphous solids, cyclic N-acylphos-
phoramidites RP-1 and SP-1 exhibit stability comparable to that
of the parent 2-cyanoethyl 2′-deoxycytidine phosphoramidite
in either long-term storage or in acetonitrile solution. Selection
criteria for the oxazaphospholane N-(2-fluoroacetyl) and C-5
phenyl groups of deoxyribonucleoside cyclic N-acylphosphor-
amidites were thus based on the excellent solid-state and solution
stability of RP-1 and SP-1, their coupling efficiency in solid-
phase oligonucleotide synthesis, and the relative ease of
oligonucleotidic phosphate/phosphorothioate triester deprotec-
tion.
Condensation of commercial N4-benzoyl-5′-O-(4,4′-dimeth-
oxytrityl)-2′-deoxycytidine 8 with 5 (1.1 equiv) and 1H-tetrazole
(1.1 equiv) was carried out in dry acetonitrile for 20 min at 25
°C. The crude reaction products were purified by chromatog-
raphy on silica gel 60 (230-400 mesh) to afford RP-1 and SP-
120 as white amorphous solids.21 Although pure (>99%), the
relatively low yield of these cyclic N-acylphosphoramidites (26
and 22%, respectively) is due to only modest stability of RP-1
and SP-1 toward silica gel chromatography. The stability of
deoxyribonucleoside cyclic N-acylphosphoramidites during
chromatography depends, in part, on the nature of the N-acyl
and C-5 functional groups of the oxazaphospholane ring.22
Typically, the stability of deoxyribonucleoside cyclic N-acylphos-
phoramidites toward silica gel decreases in the following
order: N-propionyl > N-acetyl > N-(2-methoxyacetyl) > N-(2-
fluoroacetyl) . N-(2,2,2-trifluoroacetyl). Stability also decreases
with the following substitution in the C-5 group of the
oxazaphospholane ring: phenyl > allyl > H. The most critical
feature in the purification of RP-1 and SP-1 by silica gel
chromatography is minimizing the contact time of these cyclic
N-acylphosphoramidites with silica gel. However, this must be
performed in a manner that would not compromise the
chromatographic resolution of these P-stereopure phosphor-
The 2′-deoxycytidine cyclic N-acylphosphoramidites RP-1 and
SP-1 were characterized by NMR spectroscopy, accurate mass
1
determination, and HPLC. Much like the H and 13C NMR
spectra of 5, those of RP-1 and SP-1 are difficult to interpret
due to the presence of rotamers (RP-1a and RP-1b, SP-1a and
SP-1b) and 1H/13C spin-spin couplings to phosphorus and
fluorine. As demonstrated in the case of 5, proton-decoupled
31P NMR spectra of RP-1 and SP-1 are more amenable to
interpretation. Typically, a signal (doublet) is observed at ∼130
ppm in CD3CN and assigned to the rotamer RP-1b or SP-1b
that has the fluorine and phosphorus atoms near to each other
(Scheme 1 and Figure 1).24 This doublet originates from a
through-space 31P-19F spin-spin coupling and is characterized
by a large coupling constant (JPF ∼131 Hz). Additionally, a
singlet is present at ∼134 ppm and attributed to the rotamer
RP-1a or SP-1a that has the fluorine and the phosphorus atoms
distal to each other; no 31P-19F spin-spin coupling could be
measured for that rotamer. A proton-coupled 19F NMR spectrum
of SP-1 revealed two signals at -224 ppm and -219 ppm in
C6D6 relative to fluorotrichloromethane that was used as an
external standard.13 The signal at -224 ppm (set of two triplets)
is tentatively assigned to the rotamer SP-1a given the small 19F-
(14) Hund, R.-D.; Behrens, U.; Ro¨schenthaler, G.-V. Phosphorus, Sulfur,
Silicon 1992, 69, 119-127.
(15) Miller, G. R.; Yankowsky, A. W.; Grim, S. O. J. Chem. Phys. 1969,
51, 3185-3190.
(16) (a) Everett, T. S. In Chemistry of Organic Fluorine Compounds II
- A Critical ReView, ACS Monograph 187; Hudlicky´, M., Pavlath, A. E.,
Eds.; American Chemical Society: Washington, DC, 1995; pp 1037-1086.
(b) Servis, K. L.; Fang, K.-N. J. Am. Chem. Soc. 1968, 90, 6712-6717. (c)
Chambers, R. D.; Sutcliffe, L. H.; Tiddy, G. J. T. Trans. Faraday Soc.
1970, 66, 1025-1038. (d) Hilton, J.; Sutcliffe, L. H. Prog. Nucl. Magn.
Reson. Spectros. 1975, 10, 27-39. (e) Matthews, R. S.; Preston, W. E.
Org. Magn. Reson. 1980, 14, 258-263. (f) Matthews, R. S. Org. Magn.
Reson. 1982, 18, 226-230.
(17) Mallory, F. B.; Mallory, C. W.; Fedarko, M.-C. J. Am. Chem. Soc.
1974, 96, 3536-3542.
(18) Mallory, F. B.; Mallory, C. W.; Ricker, W. M. J. Am. Chem. Soc.
1975, 97, 4770-4771.
(19) Mallory, F. B.; Mallory, C. W.; Ricker, W. M. J. Org. Chem. 1985,
50, 457-461.
(20) The P-stereochemistry of these deoxyribonucleoside cyclic N-
acylphosphoramidites has been tentatively assigned on the basis that the
relative RP-HPLC mobility of [RP,SP,RP]-d(CPSCPSCPSC) prepared from RP-1
and SP-1 corresponded to that reported for a d(CPSCPSCPSC) diastereomer
of identical P-stereochemistry that was assigned according to known
procedures (see ref 2a). Assuming that base-assisted coupling of the 5′-OH
function of nucleosides and nucleotides with RP-1 or SP-1 occurred with
inversion of configuration at phosphorus, and sulfurization of the resulting
phosphite triester proceeded with retention of configuration, our tentative
P-stereochemical assignments for RP-1 and SP-1 seem justified. NMR
experiments are currently underway to confirm the absolute P-stereochem-
istry of RP-1 and SP-1. In addition, the stereochemistry of these N-
acylphosphoramidites at C-5 of the oxazaphospholane ring has been
determined by an alternate synthesis of RP-1 and SP-1 using enantiomerically
pure 2-amino-1-phenylethanol, and comparing chromatographic and 31P
NMR properties. It is still unclear why only RP-1 and SP-1, out of potentially
four diastereomers, can be isolated.
4
31P spin-spin coupling constant JFP ) 2.1 Hz measured for
that rotamer. The signal observed at -219 ppm (set of two
triplets) is attributed to the rotamer SP-1b, as it probably resulted
from a through-space 19F-31P spin-spin coupling; a large
coupling constant (JFP ) 181 Hz) was measured for that signal.
(23) Complete elution of deoxyribonucleoside cyclic N-acylphosphor-
amidites from silica gel columns should be accomplished within 2 h to
minimize decomposition.
(24) Both RP-1 and SP-1 used for the reactions performed in NMR tubes
(Figure 1) have been scrupulously purified. Specifically, RP-1 has been
purified twice to prevent its contamination with small amounts of 8 generated
by the slow decomposition of SP-1 during silica gel chromatography. The
presence of 8 during the activation of RP-1 with TMG would lead to the
formation of the corresponding (3′-3′)-dinucleoside phosphite triester. Given
the similarity of the 31P NMR chemical shift of this phosphite triester with
that of RP-9 and SP-9, its presence may incorrectly be viewed as an apparent
lack of coupling stereospecificity during the preparation of SP-9.
(21) HPTLC-RP2F (Analtech): RP-1, Rf (CHCl3:CH3CN 2:1 v/v) )
0.51; SP-1, Rf (CHCl3:CH3CN 2:1 v/v) ) 0.71.
(22) Numbering nomenclature of the oxygen, phosphorus, and nitrogen
atoms of the oxazaphospholane ring is 1, 2, and 3, respectively. See:
Phosphor-Verbindungen II, Houben-Weyl - Methoden der organischen
Chemie, Band E2; Georg Thieme Verlag Stuttgart: New York, 1982; pp
1125-1126.

2152 J. Am. Chem. Soc., Vol. 122, No. 10, 2000
Wilk et al.
Scheme 4
coupling was observed for the signal corresponding to rotamer
SP-1a at 133.0 ppm.13 Thus, the equivalence of JFP and JPF
proves that the 31P and 19F NMR signals observed for SP-1b in
C6D6 at 126 ppm and -219 ppm, respectively, result from a
31P-19F spin-spin coupling. Although the absolute magnitude
of JFP and JPF for RP-1b and SP-1b is larger in C6D6 than in
CD3CN, the relative magnitudes of JFP and JPF are identical for
either RP-1b or SP-1b whether measured in C6D6, CD3CN, or
a mixture of these solvents (data not shown).
Unlike standard deoxyribonucleoside phosphoramidites, RP-1
and SP-1 are not activated by weak acids; however, similar to
deoxyribonucleoside oxathiaphospholane derivatives,5 they readily
react with base-activated nucleophiles. For example, when SP-1
is mixed with 3′-O-acetylthymidine (1.1 equiv) in CD3CN in a
NMR tube, addition of N,N,N′,N′-tetramethylguanidine (TMG,
1% v/v) leads to rapid (<5 min) formation of the dinucleoside
phosphite triester RP-9 (Scheme 4 and Figure 1) in essentially
quantitative yields with total P-stereospecificity. The 31P NMR
spectrum of RP-9 showed only a single line (143.9 ppm),
indicative of P-stereopurity. Sulfurization of RP-9 with 3H-1,2-
benzodithiol-3-one 1,1-dioxide25,26 afforded the P-stereodefined
dinucleoside phosphorothioate triester SP-11 (δP 71.2 ppm) with
complete stereospecificity (Figure 1).26 Substituting N2-iso-
Figure 1. 31P NMR (121 MHz, CD3CN) spectra of: (A) SP-1 as a
mixture of rotamers SP-1a and SP-1b; (B) RP-9 generated from SP-1
and 3′-O-acetylthymidine in the presence of TMG; (C) Sp-11 obtained
by sulfurization of RP-9 with 3H-1,2-benzodithiol-3-one 1,1-dioxide;
(D) RP-1 as a mixture of rotamers RP-1a and RP-1b; (E) SP-9 generated
from RP-1 and 3′-O-acetylthymidine in the presence of TMG; (F) RP-
11 obtained by sulfurization of SP-9 with 3H-1,2-benzodithiol-3-one
1,1-dioxide; (G) RP-9 from (B) and SP-9 from (E) mixed together; (H)
SP-11 from (C) and RP-11 from (F) mixed together.
(25) (a) Beaucage, S. L.; Iyer, R. P.; Egan, W.; Regan, J. B. Ann. New
York Acad. Sci. 1990, 616, 483-485. (b) Iyer, R. P.; Phillips, L. R.; Egan,
W.; Regan, J. B.; Beaucage, S. L. J. Org. Chem. 1990, 55, 4693-4699. (c)
Regan, J. B.; Phillips, L. R.; Beaucage, S. L. Org. Prep. Proced. Int. 1992,
24, 488-492.
(26) 3H-1,2-Benzodithiol-3-one 1,1-dioxide is unstable in the presence
of TMG in the NMR tube. Consequently, more than the normally required
amount of sulfur-transfer reagent is necessary for complete sulfurization.
Due to extensive base-catalyzed decomposition of the sulfurizing reagent,
variable amounts of oxidized, instead of sulfurized, dinucleoside phospho-
triester is detected by 31P NMR spectroscopy.
By comparison, the 31P NMR signal assigned to SP-1b in C6D6
is a doublet at 126 ppm with a JPF ) 182 Hz. Because of 31P
NMR signal broadening, no through-bond 31P-19F spin-spin

P-Stereospecific Synthesis of PS-ODNs
J. Am. Chem. Soc., Vol. 122, No. 10, 2000 2153
butyryl-3′-O-acetyl-2′-deoxyguanosine for 3′-O-acetylthymidine
in Scheme 4 cleanly produced the P-stereodefined dinucleoside
phosphite triester RP-10 (δP 143.9 ppm). After sulfurization,
the corresponding dinucleoside phosphorothioate triester SP-
12 (δP 71.2 ppm) was obtained.13 Under these conditions, O6-
phosphitylation or other modification of the guanine nucleobase
could not be detected. The dinucleotide analogue SP-12 was
separated from excess N2-isobutyryl-3′-O-acetyl-2′-deoxygua-
nosine by silica gel chromatography prior to being treated with
concentrated NH4OH for 10 h at 55 °C. Following detritylation,
RP-HPLC analysis of the deprotected dimer RP-13 revealed that
two major products had been formed. One corresponded to RP-
13 (single peak with tR ) 12.6 min, >95%), whereas the other
(single peak with tR ) 16.4 min) was identified as benzamide.13
This side-product was produced by ammonolysis of N4-
benzoylcytosine during deprotection. The identity of RP-13 was
further confirmed, after deprotection, by comigration with one
of the two RP-HPLC peaks associated with P-diastereomeric
d(CPSG) that was prepared from commercial 2-cyanoethyl
phosphoramidites (data not shown).
Given that solid-phase coupling reactions usually occur with
substantially slower kinetics than those performed in solution,
both RP-1 and SP-1 were separately condensed with commercial
N-protected 2′-deoxyguanosine linked to long-chain alkylamine
controlled pore glass (LCAA-CPG). The condensation reaction
required a higher concentration of TMG (5%, v/v) in acetonitrile
to achieve coupling rates comparable to those obtained in
solution phase. Following sulfurization, the solid-phase-linked
dimer was acidified, and the coupling efficiency of RP-1 and
SP-1 was estimated on the basis of the spectrophotometric
measurement of the 4,4′-dimethoxytrityl cation absorbance at
498 nm. A coupling efficiency of ∼98% was thus determined.
Each P-stereopure dinucleoside phosphorothioate was released
from the support and fully deprotected by treatment with
concentrated NH4OH for 10 h at 55 °C. The RP-HPLC profiles
of RP-13 and SP-13 are, as expected, very similar to those
obtained from solution-phase synthesis of RP-13 and SP-13.13
Both RP-13 and SP-13 show as a single homogeneous peak (tR
) 12.6 and 13.4 min, respectively) indicative of high P-
stereopurity. Benzamide appeared as a single peak (tR ) 16.4
min) and a small amount (<5%) of 2′-deoxyguanosine (tR )
9.6 min) was detected in accordance with the results of the trityl
assay performed prior to alkaline deprotection. The identities
of minor RP-HPLC peaks (tR ) 10.6 min, <3%, tR ≈ 12, 17.8,
and 21.5 min, each representing less than 1% of the total peak
area) are still unknown. However, these results show that
formation of side-products during the solid-phase preparation
of either RP-13 or SP-13 is minimal.13
Cleavage of the amidated benzyl thiophosphate-protecting
group from SP-11 (RP-11) or SP-12 (RP-12) by concentrated
NH4OH is essentially complete within 10 h at 55 °C and is
likely to proceed by more than one mechanism. For example,
cyclo-deesterification of the amidated benzyl thiophosphate
protecting group may follow path a (Figure 2) with the
simultaneous formation of an oxazoline derivative. It has been
reported that heating a 2-acetamidoethyl phosphite triester at
140-145 °C under vacuum leads to formation of 2-methyl-2-
oxazoline.27 It could therefore be argued that a cyclo-deesteri-
fication reaction could also occur when the leaving group is a
thiophosphate instead of an H-phosphonate diester derivative.
Indeed, when N- and 5′-O-deblocked RP- or SP-1228 (Figure 2)
was heated in the absence of NH4OH in acetonitrile:H2O (1:1
Figure 2. Possible pathways for the deprotection of internucleotidic
phosphorothioate triester by treatment with concentrated NH4OH at 55
°C using N- and 5′-O-deblocked RP-12 or SP-12 as a model. Path a:
thermolytic cyclo-deesterification; path b: ammonolysis of the 2-fluo-
roacetyl group followed by cyclo-deesterification; path c: P-deesteri-
fication via SN2 attack of ammonia and/or hydroxide at phosphorus;
path d: P-deesterification via SN2 attack of ammonia at the benzylic
carbon.
o
v/v) for 1 h at 85 C, RP-13 or SP-13 was produced in yields
similar to those obtained under ammonolysis conditions (in
accordance with the results of RP-HPLC analysis of the
deprotection reaction).13 Under the reaction conditions used, path
a is a viable mechanism for thiophosphate deprotection of SP-
11 (RP-11) or SP-12 (RP-12).
Alternatively, ammonolysis of the 2-fluoroacetamido group
could be envisioned to generate an aminoalkylated thiophosphate
triester intermediate via path b (Figure 2), which could then
readily induce cyclo-deesterification with concomitant formation
of a highly reactive aziridine intermediate.29 Cyclo-deesterifi-
cation of aminoalkylated phosphotriesters is well-documented
(28) Typically, N- and 5′-O-deblocked SP-12 was prepared by condensing
SP-1 with dGibu-LCAA-CPG in the presence of TMG in acetonitrile as
recommended in the Experimental Section. Following sulfurization and
detritylation, the solid-phase-linked dimer was exposed to pressurized
ammonia gas ( ∼10 bar) for 10 h at 25 °C (see ref 37). Under these
conditions, the dimer is released from the support and N-deprotected without
significant loss (<10%) of the amidated benzyl thiophosphate-protecting
group. Ammonia free N- and 5′-O-deblocked SP-12 was then eluted from
CPG using MeCN-H2O (1:1 v/v) for further experimentation.
(27) Mizrakh, L. I.; Polonskaya, L. Yu.; Babushkina, T. A.; Bryantsev,
B. I. Zh. Obshch. Khim. 1975, 45, 549-552.
(29) Brown, D. M.; Osborne, G. O. J. Chem. Soc. 1957, 2590-2593.

2154 J. Am. Chem. Soc., Vol. 122, No. 10, 2000
Wilk et al.
in the literature.10d,29,30 In agreement with predictions, we found
that incubation of the fluoroacetamido alcohol 4 with concen-
trated NH4OH at 55 °C for 10 h leads to substantial ammonoly-
sis of the 2-fluoroacetamido group ( ∼25%) as revealed by RP-
HPLC analysis of the reaction. These findings strongly support
path b as a concurrent cleavage mechanism of the amidated
benzyl thiophosphate-protecting group from SP-11 (RP-11) or
SP-12 (RP-12) by concentrated NH4OH.
Another possibility is an SN2-type nucleophilic attack at
phosphorus by ammonia and/or hydroxide ion that could lead
to displacement of the amidated benzyl thiophosphate-protecting
group with inversion of configuration at phosphorus (path c,
Figure 2).31 This nucleophilic attack at phosphorus would also
produce internucleotide bond cleavage with the generation of
either 2′-deoxycytidine or 2′-deoxyguanosine along with their
corresponding amidated or aminoalkylated phosphorothioate
diesters.31 Although this pathway cannot be ruled out, our results
do not support it as being an operative mechanism in P-
deprotection of SP-11 (RP-11) or SP-12 (RP-12).
Finally, an SN2 attack by ammonia at the benzylic carbon
atom could displace the internucleotide thiophosphate function
(path d, Figure 2). It is well-known that deprotection of benzyl
phosphate and benzyl phosphorodithioate derivatives can be
readily achieved by treatment with thiophenolates,32 presumably
via SN2 attack by the thiolate at the benzylic carbon atom.
Although ammonia is a harder base than thiolates,33 it has been
reported to stereospecifically demethylate a dinucleoside methyl
phosphorothioate triester to the corresponding phosphorothioate
diester.34 It is therefore conceivable that concentrated NH4OH
could cleave a benzylic thiophosphate protecting group under
the conditions used for removing the methyl thiophosphate-
protecting group.
Deprotection of the amidated benzyl thiophosphate-protecting
group from SP-11 (RP-11) or SP-12 (RP-12) under basic
conditions is indeed complex considering the many pathways
that could lead to the formation of SP-13 or RP-13. However,
deprotection mechanisms according to paths a and b (Figure 2)
are the most likely canadidates on the basis of RP-HPLC
analysis of the deprotection reactions studied. Conversely,
deprotection mechanisms according to paths c and d cannot, at
this point, be conclusively confirmed or rejected.
To demonstrate the utility of RP-1 and SP-1, the stereo-
controlled synthesis of [RP, RP]- and [SP, SP]-trideoxycytidilyl
diphosphorothioate d(CPSCPSC), and [RP, SP, RP]-tetradeoxy-
cytidilyl triphosphorothioate d(CPSCPSCPSC) was attempted using
a modified solid-phase protocol (see Experimental Section).
Thus, the P-stereodefined 5′-O-DMTr-deoxyribonucleotide ana-
logues were released from the solid support, N- and P-
deprotected, and then purified by RP-HPLC. Following removal
of the 5′-O-DMTr group from each purified oligonucleotides
by treatment with 80% acetic acid, RP-HPLC chromatograms
Figure 3. Panel A: RP-HPLC chromatogram of purified P-diastereo-
meric d(CPSCPSCPSCPSC) synthesized from standard solid-phase phos-
phoramidite chemistry using 3H-1,2-benzodithiol-3-one 1,1-dioxide as
a sulfur-transfer reagent. Panel B: RP-HPLC chromatogram of purified
[RP,SP,RP]-d(CPSCPSCPSC) synthesized from deoxyribonucleoside cyclic
N-acylphosphoramidites RP-1 and SP-1 according to solid-phase
techniques and by the use of 3H-1,2-benzodithiol-3-one 1,1-dioxide
as a sulfur-transfer reagent. Panel C: RP-HPLC chromatogram of
purified P-diastereomeric d(CPSCPSCPSCPSC) spiked with purified
[RP,SP,RP]-d(CPSCPSCPSCPSC).
of [RP, RP]- and [SP, SP]-d(CpsCpsC),13 and [RP, SP, RP]-
d(CPSCPSCPSC) showed a single peak for each oligonucleotide
analogue (Figure 3, panel B). For comparison, solid-phase
syntheses of P-diastereomeric d(CPSCPSC) and d(CPSCPSCPSC)
were also performed using standard 2-cyanoethyl deoxyribo-
nucleoside phosphoramidites and 3H-1,2-benzodithiol-3-one 1,1-
dioxide25 as the sulfur-transfer reagent. These oligomers were
then deprotected and purified under conditions identical to those
described above for the related P-stereodefined oligonucleotides.
RP-HPLC analysis of P-diastereomeric d(CPSCPSC)13 and
d(CPSCPSCPSC) exhibited four and eight peaks, respectively, each
peak corresponding to a specific P-diastereomer (Figure 3, panel
A). The conspicuous absence of peaks corresponding to any of
the seven diastereomers and the sole appearance of [RP, SP, RP]-
d(CPSCPSCPSC) in Figure 3 (panel B) thus demonstrates that
the new synthesis of the PS-ODN was achieved with complete
P-stereospecificity.
The coupling efficiency of pyrimidine deoxyribonucleoside
cyclic N-acylphosphoramidites was investigated further by
attempting the solid-phase synthesis of [RP]11-d[(TPS)11T] from
SP-14 under the conditions used for P-stereodefined d(CPS-
CPSCPSC). The crude 5′-O-DMTr-dodecamer analogue was
cleaved from the solid support, P-deprotected, and then analyzed
by RP-HPLC.13 Following removal of the 5′-O-DMTr group,
the crude oligodeoxyribonucleoside phosphorothioate was then
subjected to polyacrylamide gel electrophoresis (PAGE) under
denaturing conditions.13 Both RP-HPLC and PAGE show the
dodecanucleotide as a major product. In the PAGE analysis,
the band corresponding to the 12-mer accounts for ∼75% of
the combined intensity of all bands. These results indicate that
(30) (a) Wilk, A.; Srinivasachar, K.; Beaucage, S. L. J. Org. Chem. 1997,
62, 6712-6713. (b) Wilk, A.; Grajkowski, A.; Srinivasachar, K.; Beaucage,
S. L. Antisense Nucleic Acid Drug DeV. 1999, 9, 361-366.
(31) (a) van Boom, J. H.; Burgers, P. M. J.; van Deursen, P. H.; Arentzen,
R.; Reese, C. B. Tetrahedron Lett. 1974, 3785-3788. (b) Adamiak, R. W.;
Arentzen, R.; Reese, C. B. Tetrahedron Lett. 1977, 1431-1434. (c) Reese,
C. B.; Titmas, R. C.; Yau, L. Tetrahedron Lett. 1978, 2727-2730.
(32) (a) Daub, G. W.; van Tamelen, E. E. J. Am. Chem. Soc. 1977, 99,
3526-3528. (b) Brill, W. K.-D.; Nielsen, J.; Caruthers, M. H. J. Am. Chem.
Soc. 1991, 113, 3972-3980. (c) Caruthers, M. H.; Kierzek, R.; Tang, J. Y.
In Biophosphates and Their Analogues - Synthesis, Structure, Metabolism
and ActiVity; Bruzik, K. S., Stec, W. J., Eds; Elsevier: Amsterdam, 1987;
pp 3-21.
(33) Ho, T.-L. Chem. ReV. 1975, 75, 1-20.
(34) Wilk, A.; Uznanski, B.; Stec, W. J. Nucleic Acids Res. Symp. Ser.
No. 24 1991, 63-66.

P-Stereospecific Synthesis of PS-ODNs
J. Am. Chem. Soc., Vol. 122, No. 10, 2000 2155
dimethoxytrityl)-2′-deoxycytidine (Chem-Impex), N2-isobutyryl-5′-O-
(4,4′-dimethoxytrityl)-2′-deoxyguanosine (Chem-Impex), and 3′-O-
acetyl thymidine (Sigma) were used without additional purification.
DNA synthesis reagents were purchased from PE-Biosystems and used
according to the manufacturer’s recommendations. The sulfur transfer
reagent 3H-1,2-benzodithiol-3-one 1,1-dioxide was obtained from Glen
Research and used as recommended in the literature.25b,c
both thymidine and 2′-deoxycytidine cyclic N-acylphosphor-
amidites can confidently be used in the solid-phase synthesis
of much larger oligomers.
Flash chromatography on silica gel columns was performed using
Merck silica gel 60 (230-400 mesh), whereas analytical thin-layer
chromatography (TLC) was conducted on 2.5 cm × 7.5 cm glass plates
coated with a 0.25 mm thick layer of silica gel 60 F254 (Whatman) or
on HPTLC-RP2F reversed phase 10 cm × 10 cm glass plates coated
with a 0.15 mm thick layer of ethyl modified silica gel W/UV254
(Analtech). Analytical HPLC chromatography was achieved using a
4.6 mm × 250 mm Kromasil (Si-100, 5 µm) column (Supelco).
NMR spectra were recorded at 25 °C or as indicated at 7.05 T (300
MHz for 1H). 1H- and proton-decoupled 31P NMR spectra were obtained
using deuterated solvents. Unless noted otherwise, tetramethylsilane
In summary, the preparation of pyrimidine deoxyribonucleo-
side cyclic N-acylphosphoramidites is easily accomplished from
commercially available precursors. Chromatographic resolution
of these diastereomeric phosphoramidites to P-stereopure cyclic
N-acylphosphoramidites such as RP-1 and SP-1 on silica gel is
greatly facilitated by the difference in mobility of each dia-
stereomer and that of its epimer. Base-assisted condensation of
the 5′-OH function of a nucleoside or a nucleotide covalently
linked to a solid support with RP-1 or SP-1 leads to rapid and
efficient formation of an internucleoside phosphite triester
linkage. The phosphite triester function can be either oxidized
to a phosphate triester (PO) by treatment with tert-butyl
hydroperoxide35 or sulfurized by a sulfur-transfer reagent to a
P-stereodefined thiophosphate phosphotriester (PS). This ap-
proach permits completely stereocontrolled synthesis of chimeric
PO/PS-ODNs. In stark contrast, deoxyribonucleoside 3′-O-(2-
thio-1,3,2-oxathiaphospholane) derivatives allow only the for-
mation of polar P-stereodefined phosphorothioate diesters;5 an
additional set of four deoxyribonucleoside 3′-O-(2-oxo-spiro-
4,4-pentamethylene-1,3,2-oxathiaphospholane) monomers is
required for the stereocontrolled synthesis of chimeric PO/PS-
ODNs.5c,d
The cyclic N-acylphosphoramidite approach to oligonucleo-
tide synthesis is an attractive and versatile new concept in the
preparation of P-stereopure oligonucleoside phosphorothioates.
The method is currently being optimized to improve the
chromatographic recovery of deoxyribonucleoside cyclic N-
acylphosphoramidite monomers that will be used for incorporat-
ing the four standard nucleobases into DNA chains of at least
20 bases long. These oligonucleotides will include P-stereo-
defined and P-diastereomeric PS-ODNs, chimeric PO/PS-ODNs,
and unmodified oligomers. Results of these studies will be
reported in due course.
1
(TMS) was used as internal reference for H NMR spectra, and 85%
phosphoric acid in deuterium oxide as an external reference for 31P
NMR spectra. Proton-decoupled 13C NMR spectra were recorded in
either CDCl3, C6D6, or DMSO-d6 using TMS as an internal reference.
Proton-coupled 19F NMR spectra were recorded using fluorotrichlo-
romethane as an external reference. Chemical shifts δ are reported in
parts per million (ppm).
Nominal resolution and accurate mass electron-ionization (70 eV)
mass spectra were acquired from samples introduced directly into the
ion source via a solid’s direct exposure (high temperature) probe using
perfluorokerosene (PFK) as an internal standard. Nominal and accurate
mass fast ion (cesium) bombardment mass spectra were acquired from
samples dissolved in glycerol (to which aqueous sodium iodide was
added) and bombarded with 8 keV fast cesium ions using cesium iodide
or a mixture of cesium iodide and sodium iodide as a mass calibration
standard.
(()-2-[N-(2-Fluoroacetyl)]amino-1-phenylethanol (4). Commercial
(()-2-amino-1-phenylethanol 2 (5.48 g, 40.0 mmol) and ethyl fluoro-
acetate 3 (5.30 g, 50.0 mmol) were heated at 130 °C until the generated
ethanol had completely distilled off ( ∼2 h). Upon cooling to ambient
temperature, the reaction mixture solidified under high vacuum. The
crude product was recrystallized from CHCl3 to afford 4 (5.70 g, 28.9
mmol, 72%) as white crystals (mp 121-123 °C). 1H NMR (300 MHz,
DMSO-d6) δ 3.21 (ddd, J ) 13.4, 7.9, 5.5 Hz, 1H), 3.37 (m, 1H), 4.68
(m, 1H), 4.78 (d, J ) 47.1 Hz, 2H), 5.49 (d, J ) 4.3 Hz, 1H), 7.30 (m,
5H), 8.06 (t, J ) 5.5 Hz, 1H). 13C NMR (75 MHz, DMSO-d6) δ 54.2,
1
78.9, 87.9 (d, JCF ) 180 Hz), 133.8, 135.0, 135.9, 151.3, 175.0 (d,
2JCF ) 17.0 Hz). EI-HRMS: calcd for C10H12FNO2 (M+•) 197.0852,
found 197.0862.
2-(N,N-Diethylamino)-3-(2-fluoroacetyl)-5-phenyl-1,3,2-oxaza-
phospholane (5). Recrystallized 4 (4.93 g, 25.0 mmol) and hexa-
ethylphosphorus triamide (6.20 g, 25.0 mmol) were heated at 120 °C
until ∼3.2 g of N,N-diethylamine was collected by distillation ( ∼3 h).
The reaction mixture was then distilled under high-vacuum to give 5.79
g of 5 (19.2 mmol, 76%) as a slightly yellow viscous liquid (bp 150
°C at 0.3 mmHg). 31P NMR (121 MHz, C6D6) δ 119.0 (d, JPF ) 70.5
Hz), 123.6, 128.7 (d, JPF ) 52.9 Hz), 133.1. 31P NMR (121 MHz,
DMSO-d6) δ 115.6 (d, JPF ) 57.6 Hz), 122.3, 125.4 (d, JPF ) 74.7
Experimental Section
Materials and Methods. Common chemicals and solvents were
purchased from various commercial sources and used without further
purification. Anhydrous pyridine and benzene were obtained from
Aldrich and used as received. Acetonitrile (Aldrich) and N,N,N′,N′-
tetramethylguanidine (Aldrich) were refluxed over calcium hydride,
and distilled prior to use. Phosphorus trichloride (Aldrich) was distilled
immediately prior to use. (()-2-Amino-1-phenylethanol, (R)-2-amino-
1-phenylethanol, and (S)-2-amino-1-phenylethanol were purchased from
Fluka and used as received. Ethyl fluoroacetate, N-(hydroxyethyl)-2,2,2-
trifluoroacetamide, hexaethylphosphorus triamide, and sublimed 1H-
tetrazole were purchased from Aldrich and used without further
purification. Protected nucleosides such as N4-benzoyl-5′-O-(4,4′-
2
Hz), 130.8.19F NMR (282 MHz, C6D6) δ -229.9 (t, JFH ) 46.6 Hz),
2
2
-229.3 (t, JFH ) 46.6 Hz), -225.4 (dt, JFP ) 70.3 Hz, JFH ) 47.4
2
Hz), -224.9 (dt, JFP ) 53.0 Hz, JFH ) 47.4 Hz). EI-HRMS: calcd
for C14H20FN2O2 P (M+•) 298.1247 found 298.1243.
2-[N-(2,2,2-Trifluoroacetyl)amino]ethyl phosphordichloridite (6).
N-(2-Hydroxyethyl)-2,2,2-trifluoroacetamide (23.57 g, 0.15 mol) and
anhydrous acetonitrile (35 mL) were placed in a flame-dried addition
funnel. The solution was added, dropwise over a period of 2 h, to a
500 mL flame-dried round-bottom flask containing a stirred solution
of freshly distilled phosphorus trichloride (24.76 g, 0.18 mol) in
anhydrous acetonitrile (180 mL). During the course of the addition, a
slight vacuum was applied through the dropping funnel to keep an
internal pressure of ∼750 mmHg, enabling removal of gaseous
hydrogen chloride that was generated. The reaction mixture was then
stirred for an additional 3 h at ∼40 mmHg. The remaining material
(35) 31P NMR analysis of the aqueous iodine oxidation of RP-9 or SP-9
revealed a considerable loss of the benzylic phosphate protecting group
during the course of the reaction. Our findings are in agreement with those
reported by others (see ref 32c) on the sensitivity of internucleosidic
o-methylbenzyl phosphite triesters to aqueous iodine. However, no prema-
ture loss of the benzylic phosphate-protecting group was observed when
tert-butylhydroperoxide, instead of aqueous iodine, was used for the
oxidation of RP-9 or SP-9.

2156 J. Am. Chem. Soc., Vol. 122, No. 10, 2000
Wilk et al.
was distilled under reduced pressure to give the colorless phosphor-
dichloridite 6 (34.83 g, 0.13 mol, 87%). Bp: 91-94 °C/0.2 mmHg.
1H NMR (300 MHz, C6D6) δ 2.85 (m, 2H), 3.62 (m, 2H). 13C NMR
(M + Cs+) 902.1618, found 902.1644; Sp-1: calcd for C41H41FN3O9P
(M + Cs+) 902.1618, found 902.1643.
General Procedure for Manual Solid-Phase Synthesis of [RP, RP]-
and [SP, SP]-d(CPSCPSC), [RP, SP, RP]-d(CPSCPSCPSC), and [RP]11-
d[(TPS)11T]. [RP, RP]-CPSCPSC: A standard DMT-dCBz-LCAA-CPG
column (0.2 µmol) was subjected to the following sequence of steps:
1, 2, 3, 2, 3, 4, 1, 2, 3, 2, 3, 5. Step 1: 3% TCA (w/v)/CH2Cl2 (3 mL,
1 min), followed by washing with dry MeCN (3 mL, 30 s). Step 2:
Sp-1, (5 mg, ∼5 µmol) and TMG (4 µL, ∼30 µmol) in dry MeCN
(200 µL), 5 min, followed by washing with MeCN (3 mL, 30 s). Step
3: 0.05 M 3H-1,2-benzodithiol-3-one 1,1-dioxide in MeCN (200 µL),
3 min, followed by washing with MeCN (3 mL, 30 s). Step 4: Ac2O/
2,6-lutidine/THF (1 mL), mixed with 1-methylimidazole/THF (1 mL),
2 min, followed by washing with MeCN (3 mL, 30 s). Step 5:
Concentrated NH4OH (1 mL, 10 h, 55 °C). [SP, SP]-CPSCPSC: identical
to the preparation of [RP,RP]-CPSCPSC except that RP-1 was used in
step 2. [RP, SP, RP]-CPSCPSCPSC: A standard DMT-dCBz-LCAA-CPG
column (0.2 µmol) was subjected to the following sequence of steps:
1, 2, 3, 2, 3, 4, 1, 2′, 3, 2′, 3, 4, 1, 2, 3, 2, 3, 5. Steps were identical to
those used for the preparation of [RP,RP]-CPSCPSC except that RP-1 was
used in step 2′ which otherwise was identical to step 2. [RP]11-
d[(TPS)11T]: A column filled with DMT-T covalently attached to
LCAA-CPG (0.2 µmol) through a succinyl-sarcosyl linker36 was
subjected to the following sequence of steps: (1, 2, 3, 2, 3, 4)10, 1, 2,
3, 2, 3, 5. Steps were identical to those used for the preparation of
[RP,RP]-CPSCPSC except that SP-14 was used in step 2.
2
(75 MHz, C6D6) δ 39.3 (d, JCP ) 3.9 Hz), 65.5 (d, JCP ) 9.7 Hz),
1
2
116.2 (q, JCF ) 288 Hz), 157.3 (q, JCF ) 36.7 Hz). 31P NMR (121
MHz, C6D6) δ 178.1. EI-HRMS: calcd for C4H5Cl2F3NO2P (M+•
-
HCl) 220.9621, found 220.9634. Upon prolonged standing (2 y) at -20
°C, phosphordichloridite 6 cyclized to the chloro phosphine 7 ( ∼60%)
which was isolated by distillation as a mixture of rotamers 7a and 7b.
Bp: 33-35 °C/0.2 mmHg. 1H NMR (300 MHz, C6D6) δ 2.85 (m, 1H),
3.06 (m, 1H), 3.67 (m, 1H), 3.89 (m, 1H). 13C NMR (75 MHz, C6D6)
2
1
δ 41.7, 43.0, 68.7 (d, JCP ) 7.7 Hz), 72.4, 116.0 (q, JCF ) 288 Hz),
1
116.3 (q, JCF ) 288 Hz), 157.2 (q, JCF ) 36.7 Hz), 157.3 (q, JCF
)
36.7 Hz). 31P NMR (121 MHz, C6D6) δ 145.9 (q, JPF ) 74.2 Hz), 151.4.
19F NMR (282 MHz, C6D6) δ -74.4, -71.9 (d, JFP ) 75.0 Hz). EI-
HRMS: calcd for C4H4ClF3NO2P (M+•) 220.9621, found 220.9622.
N4-Benzoyl-5′-O-(4,4′-dimethoxytrityl)-3′-O-[3-(2-fluoroacetyl)-
5-phenyl-1,3,2-oxazaphospholanyl] -2′-deoxycytidine (RP-1 and SP-
1). To a solution of vacuum-dried 8 (1.90 g, 3.0 mmol) and
phosphinylating reagent 5 (980 mg, 3.3 mmol) in dry acetonitrile (15
mL) was added via syringe a 0.4 M solution of 1H-tetrazole in dry
acetonitrile (8.3 mL, 3.3 mmol). The reaction mixture was stirred at
room temperature (20 min) until only traces ( ∼1-2%) of unreacted 8
could be detected by HPTLC analysis. The reaction mixture was then
concentrated to a volume of ∼4 mL under reduced pressure, and applied
to the top of a silica gel (Merck 9385, 230-400 mesh, 60 Å, 45 g)
chromatography column (3.5 cm ID × 10 cm) equilibrated in CHCl3-
CH3CN (3:1). The column was eluted with a linear gradient of CHCl3-
CH3CN (3:1 v/v) to CHCl3-CH3CN (25:10) to afford pure SP-1 (300
mg, 0.35 mmol) and RP-1 (232 mg, 0.27 mmol) as white amorphous
solids. A mixture of RP-1 and SP-1 was also isolated (739 mg, 0.86
mmol).
Each ammoniacal solution collected from step 5 was concentrated
under reduced pressure, and the crude oligomer was purified “trityl
on” by RP-HPLC using a 5 µm Supelcosil LC-18S column (25 cm ×
4.6 mm) and a linear gradient of 1% MeCN/min, starting from 0.1 M
triethylammonium acetate pH 7.0, at a flow rate of 1 mL/min.
Appropriate fractions were pooled together, evaporated to dryness under
vacuum, and treated with aqueous 80% AcOH for 30 min. After
removal of excess acid under low pressure, the purified oligonucleotide
was dissolved in distilled water and further analyzed by RP-HPLC using
the same column and chromatographic conditions as those employed
for the purification of the crude oligonucleotide. RP-HPLC chromato-
gram of [RP, SP, RP]-CPSCPSCPSC is shown in Figure 3, whereas
chromatograms of [RP, RP]-CPSCPSC and [SP, SP]-CPSCPSC are
displayed as Supporting Information. In the case of unpurified [RP]11-
d[(TPS)11T], the “trityl on” RP-HPLC chromatogram and a photograph
of its “trityl off” PAGE profile are shown as Supporting Information.
An alternate route to the preparation of RP-1 and SP-1 relied on the
addition of anhydrous acetonitrile (5 mL) to vacuum-dried 8 (1.00 g,
1.58 mmol) and 1H-tetrazole (111 mg, 1.58 mmol). To the stirred
solution was added phosphoramidite 5 (520 mg, 1.75 mmol), dropwise
by syringe, over 15 min. Thin-layer chromatography was used to
monitor the reaction to completion. The reaction mixture was evaporated
to a foam under reduced pressure. Ethyl acetate (3 mL) was added to
the foamy residue, and the resulting suspension was applied to a short
silica gel (Merck 9385, 230-400 mesh, 60 Å, 67 g) chromatography
column (9.0 cm ID × 2 cm) equilibrated in EtOAc. The flask containing
crude RP-1 and SP-1 was rinsed with fresh EtOAc (2 mL), which was
added to the top of the column after the first EtOAc layer had dispersed
through the column. Further elution with EtOAc gave SP-1 (302 mg,
0.35 mmol) and RP-1 (359 mg, 0.42 mmol) as white foamy solids. As
above, a mixture of RP-1 and SP-1 was also isolated (198 mg, 0.23
mmol). HPTLC-RP2F (Analtech): RP-1, Rf (CHCl3:CH3CN 2:1 v/v)
) 0.51; SP-1, Rf (CHCl3:CH3CN 2:1 v/v) ) 0.71. Analytical HPLC
analysis of RP-1 and SP-1 was performed on a Supelco Kromasil (Si-
100, 5 µm) column (4.6 mm × 250 mm) using a linear gradient of
EtOAc (1%/min) from 70% EtOAc in hexane at a flow rate of 2.0
mL/min. Under these conditions, the retention time tR of SP-1 and RP-1
on the column is 8.4 and 17.4 min, respectively. 31P NMR (121 MHz,
CD3CN) RP-1 δ 131.1 (d, JPF ) 135 Hz), 135.9; SP-1 δ (ppm) 128.8
(d, JPF ) 128 Hz), 132.6. 31P NMR (121 MHz, C6D6): RP-1 δ 127.0
(d, JPF ) 188 Hz), 134.0; SP-1 δ (ppm) 126.0 (d, JPF ) 182 Hz), 133.0.
Acknowledgment. This research was supported in part by
an appointment to the Postgraduate Research Participation
Program at the Center for Biologics Evaluation and Research
administered by the Oak Ridge Institute for Science and
Education through an interagency agreement between the U.S
Department of Energy and the U.S Food and Drug Administra-
tion.
Supporting Information Available: 1H and 13C NMR
spectra of 4 and 5.31P NMR spectra of RP-1, SP-1, 5, 6, 7, RP-
9, SP-9, RP-10, RP-11, SP-11, SP-12, and SP-14. 19F NMR spectra
of SP-1, 5, and 7. RP-HPLC Chromatograms of RP-13 and SP-
13, [RP, RP]- and [SP, SP]-d(CPSCPSC), P-diastereomeric
d(CPSCPSC), “trityl on” [RP]11-d[(TPS)11T], and PAGE profile
of “trityl off”[RP]11-d[(TPS)11T] (PDF). This material is available
free of charge via the Internet at http://pubs.acs.org.
19F NMR (282 MHz, C6D6) RP-1 δ -218.3 (dt, JFP ) 189 Hz, 2JFH
)
4
2
46.6 Hz), -227 (dt, JFP ) 3.8 Hz, JFH ) 46.6 Hz); SP-1 δ -218.5
(dt, JFP ) 181 Hz, 2JFH ) 46.6 Hz), -224.2 (dt, 4JFP ) 2.1 Hz, 2JFH
)
46.6 Hz). FAB-HRMS: RP-1: calcd for C47H44FN4O9P (M + Na+)
881.2728, found 881.2687; SP-1: calcd for C47H44FN4O9P (M + Na+)
881.2728, found 881.2653.
5′-O-(4,4′-Dimethoxytrityl)-3′-O-[3-(2-fluoroacetyl)-5-phenyl-1,3,2-
oxazaphospholanyl] thymidine (RP-14 and SP-14). The deoxyribo-
nucleoside cyclic N-acylphosphoramidites RP-14 and SP-14 were
prepared under conditions identical to those used for the synthesis of
RP-1 and SP-1 and were isolated in similar yields. 31P NMR (121 MHz,
C6D6) RP-14 δ 131.1 (d, JPF ) 135 Hz), 135.9; SP-14 δ (ppm) 128.9
(d, JPF ) 131 Hz), 133.2. FAB-HRMS: RP-14: calcd for C41H41FN3O9P
JA991773U
(36) This CPG support was prepared as reported in the literature; see:
Brown, T.; Pritchard, C. E.; Turner, G.; Salisbury, S. A. J. Chem. Soc.,
Chem. Commun. 1989, 891-893.
(37) Boal, J. H.; Wilk, A.; Harindranath, N.; Max, E. E.; Kempe, T.;
Beaucage, S. L. Nucleic Acids Res. 1996, 24, 3115-3117.