Synthesis of novel nucleic acid mimics via the stereoselective intermolecular radical coupling of 3′-iodo nucleosides and formaldoximes

Article abstract of DOI:10.1021/jo961549c

A highly convergent free radical coupling of alkyl iodides and oximes, mediated by bis(trimethylstannyl) benzopinacolate (8), has been utilized to prepare a series of dimeric nucleosides as mimics of natural nucleic acids. The systematic optimization of the reaction conditions allowed for the single-step conversion of the appropriate iodides and oximes into the 2′-deoxy dimers 9 in moderate to excellent yields. For example, the reaction of 3′-deoxy-3′-iodo-5′-(triphenylmethyl)thymidine (6a) with 3′-O-(teri-butyldiphenylsilyl)-5′-O-(methyleneimino)thymidine (7a) in the presence of 8 in degassed benzene gave an 81percent yield of 3′-de(oxyphosphinico)-3′-(methyleneimino)-5′-O-(triphenyl- methyl)thymidylyl-(3′→5′)-3′-O-(tert-butyldiphenylsilyl) thymidine (9a). Similarly prepared were dimers containing both pyrimidine (thymine, 5-methylcytosine) and purine (adenine, guanine) bases. The reaction was highly stereoselective, giving only a single dimeric species having the riboconfiguration of the newly introduced C-3′-branched methylene moiety. Also prepared were dimers 16, incorporating 2′-O-methyl ribonucleosides in both halves of the dimer. This required the synthesis of 3′-deoxy-3′-iodo-2′-O-methyl nucleosides 12 as well as 2′-O-methyl-5′-O-methyleneimino nucleosides 15. For example, 5′-O-(teri-butyldiphenylsilyl)-3′-deoxy-3′-iodo-2′-O- methyl-5-methyluridine (12e) was prepared in 80percent yield by displacement of the corresponding inflate with Bu₄NI. Also prepared were the suitably protected 3′-deoxy-3′-iodo adenosine and guanosine derivatives. Compounds 15 were prepared in high yield by a regioselective Mitsunobu reaction to give the corresponding 5′-O-phthalimido nucleosides 13, which were subsequently converted to the requisite oximes 15. In the 2′-O-methyl series, the pinacolate coupling reaction proceeded with efficiency equal to that observed for the 2′-deoxy series 9, but with slightly less stereoselectivity, giving predominantly the C-3′ribo products 16, contaminated with 5-25percent of the epimeric material. Mixed base dimers containing both pyrimidine and purine bases at all possible positions, including purinepurine dimers were prepared. The hydroxylamine or methyleneimino (MI) backbone of several representative dimers so prepared was converted via methylation to give the corresponding methylenemethylimino (MMI)-linked compounds, which are novel phosphate surrogates for use in antisense oligonucleotides.

Full text of DOI:10.1021/jo961549c

8186
J . Org. Chem. 1996, 61, 8186-8199
Syn th esis of Novel Nu cleic Acid Mim ics via th e Ster eoselective
In ter m olecu la r Ra d ica l Cou p lin g of 3′-Iod o Nu cleosid es a n d
F or m a ld oxim es1
Balkrishen Bhat,*,2 Eric E. Swayze, Patrick Wheeler, Stuart Dimock, Michel Perbost,3 and
Yogesh S. Sanghvi
Isis Pharmaceuticals, Medicinal Chemistry Department, 2292 Faraday Avenue,
Carlsbad, California 92008
Received August 8, 1996X
A highly convergent free radical coupling of alkyl iodides and oximes, mediated by bis(trimethyl-
stannyl) benzopinacolate (8), has been utilized to prepare a series of dimeric nucleosides as mimics
of natural nucleic acids. The systematic optimization of the reaction conditions allowed for the
single-step conversion of the appropriate iodides and oximes into the 2′-deoxy dimers 9 in moderate
to excellent yields. For example, the reaction of 3′-deoxy-3′-iodo-5′-(triphenylmethyl)thymidine (6a )
with 3′-O-(tert-butyldiphenylsilyl)-5′-O-(methyleneimino)thymidine (7a ) in the presence of 8 in
degassed benzene gave an 81% yield of 3′-de(oxyphosphinico)-3′-(methyleneimino)-5′-O-(triphenyl-
methyl)thymidylyl-(3′f5′)-3′-O-(tert-butyldiphenylsilyl)thymidine (9a ). Similarly prepared were
dimers containing both pyrimidine (thymine, 5-methylcytosine) and purine (adenine, guanine) bases.
The reaction was highly stereoselective, giving only a single dimeric species having the ribo-
configuration of the newly introduced C-3′-branched methylene moiety. Also prepared were dimers
16, incorporating 2′-O-methyl ribonucleosides in both halves of the dimer. This required the
synthesis of 3′-deoxy-3′-iodo-2′-O-methyl nucleosides 12 as well as 2′-O-methyl-5′-O-methyleneimino
nucleosides 15. For example, 5′-O-(tert-butyldiphenylsilyl)-3′-deoxy-3′-iodo-2′-O-methyl-5-methyl-
uridine (12e) was prepared in 80% yield by displacement of the corresponding triflate with Bu4NI.
Also prepared were the suitably protected 3′-deoxy-3′-iodo adenosine and guanosine derivatives.
Compounds 15 were prepared in high yield by a regioselective Mitsunobu reaction to give the
corresponding 5′-O-phthalimido nucleosides 13, which were subsequently converted to the requisite
oximes 15. In the 2′-O-methyl series, the pinacolate coupling reaction proceeded with efficiency
equal to that observed for the 2′-deoxy series 9, but with slightly less stereoselectivity, giving
predominantly the C-3′ribo products 16, contaminated with 5-25% of the epimeric material. Mixed
base dimers containing both pyrimidine and purine bases at all possible positions, including purine-
purine dimers were prepared. The hydroxylamine or methyleneimino (MI) backbone of several
representative dimers so prepared was converted via methylation to give the corresponding
methylenemethylimino (MMI)-linked compounds, which are novel phosphate surrogates for use in
antisense oligonucleotides.
In tr od u ction
broad class of compounds have focused on the chemical
modification of the backbone,5 sugar,6 and base7 func-
tionalities of natural DNA (1) and have resulted in
significant progress toward establishing oligonucleotides
as viable therapeutic agents. In the arena of backbone
modifications, our focus of research has been on the
replacement of the natural phosphodiester linkage with
a nitrogen-containing, neutral, achiral isostere. Our
studies have led us to investigate the chemical and
biophysical properties of several different backbones,8
Oligonucleotide-based antisense strategies represent
a unique paradigm for the treatment of a wide variety
of human diseases states. The novel utility of these
agents resides in their ability to selectively prevent the
expression of a particular disease-associated gene in a
sequence specific manner.4 Successful drug development
based on this technology requires the synthesis and use
of chemically modified oligonucleotides that render sta-
bility to nucleolytic digestion, enhance cellular uptake,
and hybridize with high affinity and specificity toward
the target mRNA. Ongoing synthetic studies into this
(5) Sanghvi, Y. S.; Cook, P. D. In Nucleosides and Nucleotides as
Antitumor and Antiviral Agents; Chu, C. K., Baker, D. C., Eds.; Plenum
Press: New York, 1993; pp 311-324, and references cited therein.
(6) Sanghvi, Y. S.; Cook, P. D. In Carbohydrate Modifications in
Antisense Research; Sanghvi, Y. S., Cook, P. D., Eds.; ACS Symposium
Series 580; American Chemical Society: Washington, DC, 1995; pp
1-22, and references cited therein.
(7) Sanghvi, Y. S. In Antisense Research and Applications; Crooke,
S. T., Lebleu, B., Eds.; CRC Press: Boca Raton, FL, 1993; pp 273-
288, and references cited therein.
X Abstract published in Advance ACS Abstracts, October 15, 1996.
(1) Dedicated to Professor Nelson J . Leonard on the occasion of his
80th birthday.
(2) Author to whom correspondence should be addressed.
(3) Current address: Hewlett-Packard, 3500 Deer Creek Rd. 25-
u5, Palo Alto, CA 94304.
(4) Selected books and reviews published in 1996: (a) Methods in
Molecular Medicine: Antisense Therapeutics; Agrawal, S., Ed.; Humana
Press Inc., Totowa, NJ , 1996. (b) Bioorganic Chemistry: Nucleic Acids;
Hecht, S. M., Ed.; Oxford University Press: New York, 1996. (c)
Perspectives in Drug Discovery and Design: Antisense Therapeutics-
Progress and Prospects; Trainor, G. L., Ed.; ESCOM: Leiden, The
Netherlands, 1996. (d) Crooke, S. T. Chem. Ind. 1996, 3, 90-93. (e)
Crooke, S. T.; Bennett, C. F. Annu. Rev. Pharmacol. Toxicol. 1996,
36, 107-129.
(8) (a) Vasseur, J .-J .; Debart, F.; Sanghvi, Y. S.; Cook, P. D. J . Am.
Chem. Soc. 1992, 114, 4006-4007. (b) Sanghvi, Y. S.; Cook, P. D.
Nucleosides Nucleotides 1995, 14, 859-862. (c) Debart, F.; Vasseur,
J .-J .; Sanghvi, Y. S.; Cook, P. D. Bioorg. Med. Chem. Lett. 1992, 2,
1479-1482. (d) Sanghvi, Y. S.; Vasseur, J .-J .; Debart, F.; Cook, P. D.
Coll. Czech. Commun. 1993, 58, 158-162. (e) Haly, B.; Bellon, L. B.;
Mohan, V.; Sanghvi, Y. S. Nucleosides Nucleotides 1996, 15, 1383-
1395. (f) De Mesmaeker, A.; Waldner, A.; Sanghvi, Y. S.; Lebreton, J .
Biorg. Med. Chem. Lett. 1994, 4, 395-398.
S0022-3263(96)01549-6 CCC: $12.00 © 1996 American Chemical Society

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8187
and we have selected the methylene(methylimino) (MMI,
4) (Figure 1) linkage as a lead backbone modification for
advanced studies in antisense constructs.9
Replacement of the phosphate backbone of an oligo-
nucleotide with the MMI backbone has several distinct
advantages in terms of its antisense properties. It
provides a very high degree of nuclease resistance, the
nuclease stability, as the hydroxylamine linkage will
obviously not be a substrate for natural nucleases.
Furthermore, we have found that an MMI linkage confers
nuclease stability to the adjacent phosphodiester,6 which
allows the use of alternating phosphodiesters and MMI
linkages in an antisense oligomer. The resulting alter-
nating MMI oligomers demonstrate good affinity and
specificity for complementary RNA, while reducing the
net negative charge of the oligomer by more than 50%.
We have also found in preliminary in vitro studies that
MMI oligonucleotides of this type maintain or increase
biological activity relative to the parent phosphorothioate
oligomers.10 Additionally, significant benefits may be
realized in the economy of large-scale synthesis in
solution.
In preliminary communications, we have reported two
simple synthetic entries into construction of the MMI-
linked thymidine dimers. The first report8a described an
efficient coupling of 3′-C-formyl nucleoside with a 5′-O-
amino nucleoside to furnish an oxime-linked dimer,
which upon reduction, followed by in situ methylation,
provided the MMI backbone. The foregoing procedure
required the preparation of 3′-C-styryl nucleosides,11
available in 30-60% yield, after labor-intensive chroma-
tography. Such purifications become prohibitive for
large-scale applications in terms of time and cost in-
volved, and we therefore investigated alternative meth-
F igu r e 1. Modified oligonucleotides.
It has been proposed by Hart et. al.17 that this radical
then combines with the stable radical 8a , which is
hydrolyzed to provide the observed N,O-dialkyl hydroxyl-
amine. Recognizing the potential application of this
methodology to a highly convergent synthesis of MMI
dimers, we utilized this approach to prepare the meth-
ylene imino (MI)-linked dimer 9a (Scheme 1), although
in modest 30% yield.18 This reaction allows the instal-
lation of a key C-C bond in a chemo-, regio-, and
stereoselective manner between two nucleosides, and
since the hydroxylamine linkage can be readily methyl-
ated, provides an attractive approach for the synthesis
of MMI dimers. The simplicity of this procedure encour-
aged us to further investigate the reaction in detail, with
an aim to improve the coupling yield of 2′-deoxynucleo-
sides and extend the methodology to the preparation of
dimers bearing bases other than thymine.
ods to construct the desired nucleosidic dimers.
A
particularly attractive and germane methodology which
could be adapted for this purpose was initially reported
by Hart and Seely12 and involves the one-carbon homolo-
gation of an alkyl iodide with O-benzyl formaldoxime to
yield an O-benzylhydroxylamine via an intermolecular,
nonchain radical process. In this reaction pathway
(Figure 2), bis(trimethylstannyl)benzopinacolate13 (8) is
decomposed thermally to provide the presumably stable
stannyl ketyl radical 8a ,14 which then can decompose to
afford benzophenone and a trimethylstannyl radical.15
Alkyl iodides react with stannyl radicals extremely
rapidly16 to irreversibly give the tin iodide, and an alkyl
radical, which can then be trapped, in this case by an
oxime, to provide a presumed N-centered radical species.
While this study was in progress, we also became
interested in the synthesis of MMI dimers modified at
the 2′-position of the sugar with methoxy groups, as the
stability of hybrids of 2′-O-Me RNA (3) with complemen-
tary RNA (2) is considerably higher (∆Tm ∼ 1.5 °C/
modification) than that of the corresponding DNA-RNA
duplexes.19 This increased stability has been attributed
to hydrophobic interactions20 between substituents in the
minor groove and especially to the 3′-endo sugar confor-
mation predominantly adopted by 2′-O-methyl nucleo-
sides, which results in a decrease in the entropic motions
of the sugar, while maintaining a preorganized structure
with RNA-like character.21 Additionally, chimeric anti-
sense oligonucleotides containing 3 show enhanced sta-
bility toward nuclease digestion, higher binding affinity
toward target mRNA,22 and in some cases have shown
improved properties relative to their deoxy predecessors
in vitro and in vivo.23 The potential benefits of a
combination of the MMI backbone and 2′-O-methyl sugar
modification in a single molecule, such as 2′-O-Me MMI
(9) (a) Morvan, F.; Sanghvi, Y. S.; Perbost, M.; Vasseur, J .-J .; Bellon,
L. J . Am. Chem. Soc. 1996, 118, 255-256. (b) Sanghvi, Y. S.; Bellon,
L.; Morvan, F.; Hoshiko, T.; Swayze, E.; Cummins, L.; Freier, S.; Dean,
N.; Monia, B.; Griffey, R.; Cook, P. D. Nucleosides Nucleotides 1995,
16, 1087-1090.
(10) Sanghvi, Y. S.; Bellon, L.; Hoshiko, T.; Swayze, E.; Cummins,
L.; Freier, S.; Dean, N.; Monia, B.; Cook, P. D. First International
Anitsense Conference of J apan. (OP-17) Dec 4-7, 1994, Kyoto, J apan.
(11) (a) Sanghvi, Y. S.; Bharadwaj, R.; Debart, F.; De Mesmaeker,
A. Synthesis 1994, 1163-1166. (b) Sanghvi, Y. S.; Ross, B.; Bharadwaj,
R.; Vasseur, J .-J . Tetrahedron Lett. 1994, 35, 4697-4700.
(12) Hart, D. J .; Seely, F. L. J . Am. Chem. Soc. 1988, 110, 1631-
1633.
(17) Hart, D. J .; Krishnamurthy, R.; Pook, L. M.; Seely, F. L.
Tetrahedron Lett. 1993, 34, 7819-7822.
(18) Debart, F.; Vasseur, J .-J .; Sanghvi, Y. S.; Cook, P. D. Tetrahe-
dron Lett. 1992, 33, 2645-2648.
(19) Lesnik, E. A.; Guinosso, C. J .; Kawasaki, A. M.; Sasmor, H.;
Zounes, M.; Cummins, L. L.; Ecker, D. J .; Cook, P. D.; Freier, S. M.
Biochemistry 1993, 32, 7832-7838, and references cited therein.
(20) Lubini, P.; Zurcher, W.; Egli, M. Chem. Biol. 1994, 1, 39-45.
(21) Griffey, R. H.; Lesnik, E.; Freier, S. M.; Sanghvi, Y. S.; Teng,
K.; Kawasaki, A.; Guinosso, C.; Wheeler, P.; Mohan, V.; Cook, P. D.
In ref 6; pp 212-224.
(13) Hillgartner, H.; Neumann, W. P.; Schroeder, B. Liebigs. Ann.
Chem. 1975, 586-599.
(14) Neumann, W. P; Schroeder, B.; Ziebarth, M. Liebigs. Ann.
Chem. 1975, 2279-2292.
(15) Neuman, W. P.; Hillgartner, H.; Baines, K. M.; Dicke, R.;
Vorspohl, K.; Kobs, U.; Nussbeutel, U. Tetrahedron 1989, 45, 951-
960.
(16) (a) Curran, D. P.; J asperse, C. P.; Totleben, M. J . J . Org. Chem.
1991, 56, 7169-7172. (b) Curran, D. P.; Chen, M.-H.; Kim, D. J . Am.
Chem. Soc. 1989, 111, 6265-6276.

8188 J . Org. Chem., Vol. 61, No. 23, 1996
Bhat et al.
hydrazine, and subsequent derivatization of 5′-O-amino-
3′-O-(tert-butyldiphenylsilyl)thymidine so obtained with
formaldehyde to furnish 7a in high yield. Reaction of a
1:1:1 mixture of 6a , 7a , and 8 in degassed benzene
resulted in the formation of a single dimeric nucleoside
9a in 25% yield. The configuration of the dimer 9a was
1
determined to be 3′-ribo-type by 2D H NMR techniques
and was described in our initial communication of this
result.18 We believe that the stereospecifity in the
formation of 9a is due to a preferred sugar conformation,
which, along with the steric effect of the 1′-nucleobase
and 5′-substituent, promote a selective, unhindered R-
attack on the C3′-radical center.
F igu r e 2. Pinacolate-mediated reaction pathway.
The proposed reaction pathway shown in Figure 2
suggests several approaches toward optimization of the
yields obtained from the reaction. If the persistent
radical 8a couples with the N-centered radical to provide
an N,O-acetal, as suggested by Hart,17 then an increase
in the amount of 8 (and therefore 8a ) present may result
in more efficient trapping of the N-centered radical and
better yields. We found that this was indeed the case,
as increasing the amount of 8 to 2 and 3 equiv improved
the yield from 25% to 30% and 35%, respectively (Table
1, entries 1-3). We also noticed the formation of varying
amounts of the reduced product 3′-deoxy-5′-(triphenyl-
methyl)thymidine (6, X ) H) in the reaction mixture, as
well as traces of unreacted oxime 7a when lower amounts
of 8 were utilized. This reduced derivative presumably
arises from hydrogen abstraction by the alkyl radical
(from an unknown source), and the hydrogen abstraction
is in direct competition with the formation of product via
addition of the radical to 7a . In order to assure complete
utilization of the oxime, we utilized a slight excess of the
iodide 6a , along with 3 equiv of 8 (Table 1, entry 4). This
resulted in complete consumption of both 6a and 7a and
gave a 52% yield of isolated dimer 9a , along with small
amounts of 3′-deoxy nucleoside, after direct chromatog-
raphy of the reaction mixture (ether, then a MeOH/
CH2Cl2 gradient).
A number of examples in the literature describe phenyl
selenides12,27 and thionocarbonates28 as radical precursors
in carbohydrate and nucleoside chemistry. Therefore, we
prepared the 3′-phenyl selenide,29 and 3′-phenyl and
4-fluorophenyl thiocarbonate8a derivatives of 6 following
the literature procedures. Reaction of these nucleosides
(entries 5-7) under the conditions of entry 4 resulted in
poor to moderate yield of the desired dimer 9b, along with
substantial amounts of unreacted starting materials and
increased formation of the 3′-deoxy product 6 (R )
TBDPS, X ) H). We also varied the solvent to tert-butyl
alcohol and 1,4-dioxane (entries 8, 9), which not un-
expectedly decreased the yield of 9b and increased the
amount of reduced product 6 (X ) H) formed.
(5), encouraged us to extend our studies of this radical
coupling reaction to the preparation of dimers of the type
5. Herein we describe in detail a systematic synthesis
study in which we have optimized the radical coupling
methodology to prepare the MMI dimers of type 4,
resulting in a dramatic improvement in yield compared
to our original communication. We also describe the
extension of this methodology to other nucleosides,
including the 2′-O-methyl series, resulting in the prepa-
ration of purine-containing mixed base dimers 4 and 5.
In addition, many of the requisite 3′-deoxy-3′-iodo nucleo-
sides were unknown, and we have developed an efficient
synthesis of these versatile radical precursors, as well as
practical large-scale synthesis of the 5′-oxime ribonucleo-
side radical acceptors.
Resu lts a n d Discu ssion
In previous studies on the synthesis of 3′-C-substituted
nucleosides, we11 and others24 have demonstrated that
control of the stereochemistry at the C3′-position of a
nucleoside was possible via a radical reaction. In general,
these studies have found that a C-3′ radical of a deoxy
nucleoside (usually thymidine) affords mainly the 3′-ribo
diastereomer, which results from selective attack of the
radical trap from the R-face of the 3′-radical. With this
consideration in mind, we envisioned the use of the O,O-
bis(trimethylstannyl)benzopinacol (8)-mediated radical
coupling reaction pathway (Figure 2) as a means to
construct the desired nucleosidic dimers in a stereo-
specific manner from simple nucleosides in a single step.
Our initial attempts at utilizing this approach focused
on the preparation of a T*T deoxy MI dimer (* )
3′-CH2NHO-5′) and required as synthons the known 3′-
deoxy-3′-iodo nucleosides 6a 25 and 6b,8a as well as oxime
7a . We have recently reported the functionalization of
2′-deoxy nucleosides to the 5′-phthalimido derivatives via
a selective Mitsunobu reaction.26 The oxime 7a was
readily prepared from 5′-O-phthalimidothymidine by
silylation, cleavage of the phthalimide with methyl-
When we employed an aqueous KF workup30 in lieu of
direct chromatography (entry 10), we obtained a marked
increase in yield, isolating 81% of the dimer 9a instead
of the 52% without this treatment. This indicates the
presence of an adduct which is efficiently hydrolyzed in
aqueous KF to give the desired dimer in high yields and
(22) (a) Monia, B. P.; Lesnik, E. A.; Gonzalez, C.; Lima, W. F.;
McGee, D.; Guinosso, C. J .; Kawasaki, A. M.; Cook, P. D.; Freier, S.
M. J . Biol. Chem. 1993, 268, 14514-14522. (b) Cummins, L. L.; Owens,
S. R.; Risen, L. M.; Lesnik, E. A.; Freier, S. M.; McGee, D.; Guinosso,
C. J .; Cook, P. D. Nucleic Acids Res. 1995, 23, 2019-2024. (c) Agrawal,
S.; Tamsamani, J . In ref 4a; Chapter 14, pp 247-270, and references
cited therein.
(23) Zhao, Q.; Temsamani, J .; Iadarola, P. L.; J iang, Z.; Agrawal,
S. Biochem. Pharmacol. 1996, 51, 173-182.
(24) (a) Chu, C. K.; Doboszewski, B; Schmidt, W.; Ullas G. V. J . Org.
Chem. 1989, 54, 2767-2769. (b) Fiandor, J .; Tam, S. Y. Tetrahedron
Lett. 1990, 31, 597-600. (c) Becouarn, S.; Czernecki, S.; Valery, J .-M.
Tetrahedron Lett. 1995, 36, 873-876.
(25) Verheyden, J . P. H.; Moffatt, J . G. J . Org. Chem. 1970, 35,
2868-2877.
(26) Perbost, M.; Hoshiko, T.; Morvan, F.; Swayze, E.; Griffey, R.
H.; Sanghvi, Y. S. J . Org. Chem. 1995, 60, 5150-5156.
(27) Stork, G.; Suh, H.-S.; Kim, G. J . Am. Chem. Soc. 1991, 113,
7054-7056.
(28) (a) Barton, D. H. R.; J aszberenyi, J . Cs. Tetrahedron Lett. 1989,
30, 2619-2622. (b) Robins, M. J .; Wilson, J . S.; Hansske, F. J . Am.
Chem. Soc. 1983, 105, 4059-4065. (c) Barton, D. H. R.; J ang, D.-O.;
J aszberenyi, J . Cs. Tetrahedron Lett. 1990, 31, 4681-4684.
(29) J oshi, B. V.; Rao, T. S.; Reese, C. B. J . Chem. Soc., Perkin Trans.
1 1992, 2537-2544.
(30) Leibner, J . E.; J acobus, J . J . Org. Chem. 1979, 44, 449-450.

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8189
Sch em e 1. In ter m olecu la r Cou p lin g of 2′-Deoxy Nu cleosid es
Ta ble 1. Op tim iza tion of P in a cola te-Med ia ted Nu cleosid e Cou p lin g
% unreactedb
molar ratioa
exp no.
6:7:8
B
B′
R
X
solvent
6
7
% productb
9
1
2
3
4
5
6
7
8
9
1:1:1
1:1:2
1:1:3
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
Tr
Tr
Tr
Tr
TBDPS
TBDPS
TBDPS
TBDPS
TBDPS
Tr
I
I
I
I
C6H6
C6H6
C6H6
C6H6
C6H6
C6H6
C6H6
t-BuOH
1,4-dioxane
C6H6
0
0
0
0
34
9
10
27
19
0
5
5
0
25c
30c
35
1.5:1:3
1.5:1:3
1.5:1:3
1.5:1:3
1.5:1:3
1.5:1:3
1.2:1:3
1:3:2
0
52d
7
SePh
OC(S)OPh
OC(S)OPh-F
I
I
I
I
59
53
54
24
45
0
38
37
35e
22e
81f
84f
10
11
TBDPS
C6H6
0
72
All experiments were carried out on approximately 1 mmol scale. Based on NMR data. c 5% of 2′,3′-dideoxy compound observed by
a
b
NMR. Isolated yield after direct chromatography of the crude reation mixture. e 14% of 2′,3′-dideoxy nucleoside was observed in NMR.
d
f Isolated yield after aqeous KF workup and chromatography.
provides support for the pathway depicted in Figure 2.
The coupling was further optimized by reducing the
amount of pinacolate 8 to 2 equiv and increasing the ratio
of oxime 7a to 3 equiv, resulting in complete consumption
of 6b, total suppression of the formation of reduced
product 6 (X ) H, R ) TBDPS), and isolation of 9b in
84% yield (entry 11). The higher relative concentration
of 7a serves to increase the rate of addition of the alkyl
radical to 7a , thereby overwhelming the competing
hydrogen abstraction pathway. The excess 7a was easily
recovered (99%, based on oxime not converted to product)
and could be recycled in subsequent reactions with no
reduction in yields. It should be noted that we could
obtain only a modest 48% yield of 9a by the syringe pump
addition of Bu3SnH/AIBN to a solution of 6a (1 equiv)
and 7a (3 equiv), demonstrating the superiority of the
pinacolate-mediated procedure in the synthesis dimer 9a .
These results taken together clearly indicate that use of
radical precursor 6, acceptor 7, and pinacolate 8 in a ratio
of 1:3:2, combined with an aqueous KF workup, gave the
best outcome and resulted in a dramatic improvement
in yield over our initial report. It is also noteworthy that
the 81% of 9 (entry 10) obtained in a single step is far
superior to the 30% obtained via our previous sequence
in four steps from the radical precursor. This material
can be reductively methylated to the MMI backbone in
high yield and then appropriately functionalized and
incorporated into oligonucleotides using standard
methodology.8a
11, an 81% yield of the T*T dimer 9a was obtained,
indicating there is no effect of changing the 5′-protection
between Tr and TBDPS. We next extended this reaction
to the preparation of mixed-base dimers. The 2′-deoxy-
5-methylcytidine iodide 6c was prepared in high yield
by triazolation31 of 6a , followed by displacement with
ammonia. Reaction of 6c and 7a under our optimized
conditions resulted in a 58% yield of the desired MeC*T
dimer 9c, along with a 97% recovery of unreacted oxime.
A preparation of 5′-O-(tert-butyldimethylsilyl)-2′,3′-dideoxy-
3′-iodoadenosine has been reported utilizing Ph3P/I2/
imidazole;32 however, this procedure gave, in our hands,
traces of the presumed 3′-iodo nucleosides and predomi-
nantly N-6-triphenylphosphine adducts. We made sev-
eral attempts to prepare the desired 3′-iodides from base-
protected purines (5′-TBDPS-dABz, 5′-TBDPS-dAdmf, and
5′-TBDPS-dGdmf), using the conditions used for the
synthesis of 6a and 6b, Ph3P/I2/base,33 and various
triflation/displacement conditions (vide infra), but were
unsuccessful. Reaction of the purine 3′-thiocarbonates
under the optimized conditions resulted in the formation
of a ca. 40% yield of dimer, which could not be separated
from ca. 20% of the corresponding 3′-deoxygenated
nucleoside. We were able to demonstrate the compat-
ibility of this reaction with purine nucleosides by the use
(31) Divakar, K. J .; Reese, C. B. J . Chem. Soc., Perkin Trans 1. 1982,
1171.
(32) Yu, D.; d’Alarcao, M. J . Org. Chem. 1989, 54, 3240-3442.
(33) (a) Millar, J . G.; Underhill, E. W. J . Org. Chem. 1986, 51, 4726-
4728. (b) Huang, J .; McElroy, E. B.; Widlanski, T. S. J . Org. Chem.
1994, 59, 3520-3521. (c) Bringmann, G.; Schneider, S. Synthesis 1983,
139-141.
When we substituted the trityl-protected iodide 6a for
6b, otherwise using identical conditions to those in entry

8190 J . Org. Chem., Vol. 61, No. 23, 1996
Bhat et al.
Sch em e 2. Syn th esis of 2′-O-Meth yl Nu cleosid ic
from the adjacent 2′-methoxy group was preventing
efficient formation of the activated phosphorus species
at 3′, we attempted an inversion of a 3′-triflate with
iodide, which was successfully employed on carbohydrate
precursors.36 The reaction of nucleosides 11a and 11e
with trifluoromethanesulfonic anhydride in anhydrous
CH2Cl2 at -10 °C furnished corresponding 3′-triflates,
which were stable enough to be isolated after careful
aqueous workup. The crude triflates were then smoothly
displaced upon heating with Bu4NI in toluene or xylene
to furnish 67% of 12a and 80% of 12e.
Ra d ica l P r ecu r sor sa
Since our studies on the pinacolate-mediated coupling
reaction indicated that 3′-iodides were the ideal radical
precursors for this reaction, we attempted to prepare the
corresponding 3′-iodopurines via this sequence. 2′-O-
Methyladenosine 10b was protected by the reaction of
nucleoside with N,N′-dimethylacetamide diethylacetal in
MeOH at rt for 24 h to give corresponding acetamidine
protected derivative 10c in nearly quantitative yield,
which on dimethoxytritylation afforded 70% of 11b. For
the N-2 protection of the guanosine analog, two separate
approaches were taken. 2′-O-Methylguanosine (10d ) was
reacted under transient protection conditions with tri-
methylsilyl chloride in pyridine for 8 h, followed by
addition of isobutyryl chloride to furnish the correspond-
ing N-2 protected analog 10e in 70% yield, and 10d was
reacted with N,N-dimethylformamide diethylacetal in
MeOH at rt for 24 h, which furnished 10f in 97% yield
after crystallization. Subsequent tritylation of com-
pounds 10e and 10f furnished corresponding 5′-protected
derivatives 11c and 11d in 80-90% yields. As with 11a
the reaction of the purines 11b-d and 11k with trifluoro-
methanesulfonic anhydride furnished corresponding 3′-
triflates, which were converted to 3′-iodo nucleosides
12b-d and 12k in 58-80% isolated yields upon heating
with Bu4NI in toluene or xylene. Because of problems
associated with the loss of the DMT protecting group in
the radical reaction and subsequent reductive methyl-
ation (vide infra) under acidic conditions, we also pre-
pared the corresponding 5′-TBDPS protected purine
derivatives. After silylation of 10b and 10d and then
protection of the N-6 and N-2 positions with the dmf
group to furnish 11h and 11j, respectively, compounds
12f and 12g were prepared by reaction with triflic
anhydride and subsequent treatment with Bu4NI to
afford the 3′-iodo derivatives in good yield.
a
Reagents and conditions: (i) N,N′-dimethylacetamide dim-
ethylacetal/MeOH; rt, 24 h; (ii) iBuCl/TMSCl/pyridine; rt, 12 h;
(iii) N,N ′-dimethylformamide diethylacetal/MeOH; rt, 24 h; (iv)
DMTCl/DMAP/pyridine; rt, 16 h; (v) t-BuPh2SiCl/DMAP/pyridine;
rt, 15-20 h; (vi) Tf2O/pyridine/CH2Cl2, -10 °C; (vii) Bu4NI/toluene,
80 or 110 °C; (viii) 1,1,1,3,3,3-hexafluoro-2-propanol, rt, 5 h.
of oximes 7b and 7c. Oxime 7b was prepared from the
5′-O-phthalimido derivative26 in a manner similar to that
used for 7a . The guanosine derivative 7c was prepared
via a Mitsunobu reaction on N,N-dimethylformamidine
(dmf) protected 2′-deoxyguanosine34 (vide infra), which
profoundly changes the reactivity of the guanine base.35
Reaction of 6a and 7b resulted in a 59% yield of the
desired T*A dimer 9d , with recovery of 83% of unreacted
7b. Reaction of 6a and 7c, however, resulted in a
mixture of two dimeric and one oxime byproducts, along
with unreacted 7c. We surmised that the dmf protecting
group was being partially cleaved under the reaction
conditions and treated this mixture with NH4OH/dioxane
to completely remove the protecting group. This resulted
in the formation of only two major products, and the base
unprotected dimer 9e was obtained in 46% yield, along
with 91% of unreacted 7c. Our ability to stereospecifi-
cally synthesize the foregoing mixed base dimers con-
taining four types of nucleic acid bases in a single step
from readily available precursors clearly demonstrates
the utility of this reaction for the preparation of various
heterodimers.
As discussed earlier in the introduction of this paper,
due to the biological implications of 2′-O-methyl RNA (3),
we concentrated our research effort on the synthesis of
2′-O-methyl MMI dimer 5. This required the synthesis
of the 3′-deoxy-3′-iodo nucleosides 12. The reaction of
2′-O-methyl-5-methyluridine (10a ) with 4,4′-dimethoxy-
trityl chloride or tert-butyldiphenylsilyl chloride plus a
catalytic amount of DMAP in pyridine gave correspond-
ing 5′-protected derivatives 11a and 11e, respectively,
in excellent yields (Scheme 2). A first attempt at the
iodination of 11e was made utilizing the conditions
effective for the preparation of 6b; however, only a 27%
yield of product was obtained. We next investigated
several related iodination procedures, including Ph3P/I2/
imidazole,33a Ph3P/I2/pyridine,33b and Ph3P/ICH2CH2I/
DCE33c without success. Reasoning that steric hindrance
The structures of 3′-iodonucleosides 12 were confirmed
by a broad array of spectroscopic and analytical data
1
including H NMR, 13C NMR, FAB MS, and elemental
1
analysis. In the H NMR spectra, a distinct downfield
chemical shift of the H3′ was observed by about 0.4 to
0.5 ppm from its precursors, which suggested the pres-
ence of an electron-withdrawing group at the 3′-position.
In the 13C NMR spectra, the C3′ resonance appears at
ca. 26 ppm, which is indicative of the substitution of
iodine for hydroxyl, as the “heavy atom effect” of iodine
replaces the purely electronegative effect of oxygen.37 The
nucleophilic displacement of 3′-triflates with iodide is
expected to proceed with total inversion of configuration
giving the xylo-3′-iodo nucleoside derivatives. In order
to unequivocally prove this stereochemistry by 2D NMR
spectroscopy, compounds 12a -c were detritylated under
(36) Binkley, R. W.; Ambrose, M. G.; Hehemann, D. G. J . Org. Chem.
1980, 45, 4387-4391.
(37) Silverstein, R. M.; Bassler, G. C.; Morrill, T. C. Spectrometric
Identification of Organic Compounds; J ohn Wiley & Sons: New York,
1981; p 267.
(34) McBride, L. J .; Kierzek, R.; Beaucage, S. L.; Caruthers, M. H.
J . Am. Chem. Soc. 1986, 108, 2040-2048.
(35) A thorough investigation of this potentially useful observation
is ongoing, and detailed results will be reported in due course.

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8191
Sch em e 3. Syn th esis of 2′-O-Meth yl Nu cleosid ic Ra d ica l Accep tor sa
a
Reagents and conditions: (i) Ph3P/DEAD/PhthNOH/THF or DMF, rt, 1-3 h; (ii) t-BuPh2SiCl/imidazole/DMF, rt, 24 h; (iii) H3CNHNH2/
CH2Cl2, -10 °C-rt, 0.5-1 h; (iv) HCHO,MeOH/EtOAc, 10 °C-rt, 2-4 h; (v) 1,2,4-triazole/POCl3/Et3N/CH3CN; (vi) NaH/benzamide/
dioxane; (vii) NH3/dioxane, rt, 1-2 h.
mild conditions using hexafluoro-2-propanol38 at room
temperature for 1-4 h to furnish corresponding 5′-
hydroxy derivatives 12h -j in 75-85% yield. The samples
were studied in DMSO-d6, and in each case, two-
dimensional TOCSY data was used to assign the 1H
spectrum, and a two-dimensional NOESY was used to
confirm the stereochemistry. The 3′ proton of each
compound was inferred to be on the R-face of the sugar
through the lack of any observable NOE between the 3′
proton and H6 of the pyrimidine or H8 of the purine. A
strong NOE was evident between the 2′ sugar proton and
the H6 or H8, as well as a weak NOE between the 1′
proton and H6 or H8. A weak NOE between H3′ and
H1′ of each compound provided unequivocal proof of the
xylo configuration of the 3′-iodide. Specifically, for 12h ,
there were strong NOE’s from H6 to H2′ and the thymine
methyl, from H3′ to H4′ and between H5′ and H5′′. Weak
NOE’s were observable between H6 and H1′, and from
H1′ to H2′, H3′, H4′, and the 2′ methoxy. For 12i,
moderate NOE was observed from H1′ to H8, H2′, H3′,
H4′, and the 2′ methoxy group, and from H3′ to H2′, H4′,
and the 2′ methoxy group. For 12j, strong NOE was
observed between H8 and H2′, and between H3′ and H4′.
Moderate NOE was observed from H1′ to H2′, H4′, and
the 2′ methoxy, and a weak NOE was evident between
the H1′ and H3′. We believe that we are providing the
first reliable method to synthesize 2′-O-methyl-3′-iodo
nucleosides in modest to very high yields.
The synthesis of the 2′-O-methyl nucleoside formal-
doximes as the radical acceptors (Scheme 3) was carried
out via a regiospecific Mitsunobu reaction of the primary
5′-hydroxyl group with N-hydroxyphthalimide,39 in a
manner similar to that previously described by us for the
preparation of 5′-O-amino-2′-deoxy nucleosides.26 Reac-
tion of 10a with N-hydroxyphthalimide in presence of tri-
phenylphosphine and diethyl azodicarboxylate (DEAD)
in THF gave a 69% yield the corresponding 2′-O-methyl-
5′-phthalimido derivative 13a , which crystallized directly
from the reaction mixture. Reaction of 10b under similar
conditions in DMF provided the 2′-O-methyladenosine
analog in 70% yield, after precipitation of the product
from a heterogeneous ether/water mixture. We26 and
others40 have encountered difficulty in achieving a selec-
tive Mitsunobu reaction at the 5′-hydroxyl of guanosine
derivatives, as N-3,5′-cyclonucleosides are formed, with
intramolecular attack of the N-3 lone pair at the activated
5′-carbon being preferred to intermolecular attack by the
desired nucleophile. O-6 Alkylation has also been ob-
served under Mitsunobu conditions, which further com-
plicates the synthesis of 5′-substituted guanosine deriva-
tives via a Mitsunobu reaction.41 In the course of
investigating various protecting groups for the N-2 of the
guanine nucleobase, we observed that N-2 dmf protection
completely suppresses undesirable side reactions at N-3
and O-6 and gives exclusively the desired 5′-substitution
reaction. In this manner, 2′-O-methylguanosine (10f)
was reacted with N-hydroxyphthalimide in presence of
Ph3P and DEAD in dry DMF, to afford a 93% yield of
14c, which crystallized directly from the reaction mix-
ture. The structure was confirmed by its 1H NMR, in
which the NH signal in anhydrous DMSO-d6 appeared
as a sharp singlet at 11.37 ppm, exactly at the same place
as in 10f. The chemical shifts of formamidine proton and
H-8 also remained the same. However, a downfield
chemical shift was observed for 4′ and 5′ protons by about
1.0 ppm, suggesting that the phthalimido group was
attached at the 5′-position because of the magnetic
anisotropic effect42 of two amide carbonyl groups of the
phthalimido group onto the 4′ and 5′ protons. The
regioselectivity of the Mitsunobu reaction on 10f is, we
believe, due to the change in the electronics of the
nucleobase induced by the dmf moiety at the N-2 posi-
tion.35
The 5′-phthalimido derivatives 13a-c were then treated
with tert-butyldiphenylsilyl chloride and imidazole in
anhydrous DMF for 24-48 h to give corresponding 3′-
silyl derivatives 14a -c in 90-95% yield. In general we
(38) Leonard, N. J .; Neelima. Tetrahedron Lett. 1995, 36, 7833-
7836.
(39) (a) Mitsunobu, O. Synthesis 1981, 1-28. (b) Hughes, D. in
Organic Reactions; L. A. Paquette et. al., Eds.; J ohn Wiley & Sons:
New York, 1992; Vol. 42, pp 355-656.
(40) (a) Gao, X.; Gaffney, B. L.; Hadden, S.; J ones, R. A. J . Org.
Chem. 1986, 51, 755. (b) Kimura, J .; Fujisawa, Y.; Yoshizawa, T.;
Fukuda, K.; Mitsunobu, O. Bull. Chem. Soc. J pn. 1979, 52, 1191-
1196.
(41) Himmelsbach, F.; Schulz, B. S.; Trichtinger, T.; Charubala, R.;
Pfleiderer, W. Tetrahedron, 1984, 40, 59-72.
(42) Vul’fson, S. G.; Nikolaev, V. F.; Vereshehagin, A. N. Bull. Acad.
Sci. USSR Div. Chem. Sci. 1985, 34, 732.

8192 J . Org. Chem., Vol. 61, No. 23, 1996
Bhat et al.
Sch em e 4. In ter m olecu la r Ra d ica l Cou p lin g of
The reaction of benzoyl protected iodide 12k with
benzoyl protected oxime 15b in an attempt to obtain a
fully base protected A*CMe dimer, gave an intractable
mixture of products. Reaction of 12a with the benzoyl
protected oxime 15b gave a less complicated mixture
which contained debenzoylated oxime 15c as the major
component. Presumably, the persistent radical 8a pro-
motes cleavage of the benzoyl protecting group of both
12k and 15b, and the resulting radicals react in several
ways to give a mixture of products. Using unprotected
oxime 15c alleviated this problem, and reaction of 12a
with nucleoside 15c furnished the T*CMe dimer 16b in
75% yield. Next, we attempted the reaction of purine
analog 12b with 15a which gave 16c in 52% yield and
attested to the stability of the acetamidine protecting
group to these reaction conditions. Reaction of the 2′-
O-methylguanosine-derived iodide 12c with 15a afforded
a modest 40% yield of the Gibu*T dimer 16d , while
reaction with 15c gave 55% of the Gibu*C dimer 16e. The
successful synthesis of 16c-e was particularly satisfying,
in that it demonstrated that this methodology is compat-
ible with the use of 3′-iodopurines as radical precursors,
expanding the scope of the reaction. When compound
12c was reacted with 15d under the same conditions, a
lower yield (30%) of corresponding Gibu*A dimer 16f was
obtained. Similarly, compound 16g was obtained in 40%
yield from 12b and 15d . A careful examination of the
products revealed that the partial loss of protecting
groups, such as isobutyryl and DMT was taking place,
undoubtedly contributing to the reduction of isolated
product.
2′-O-Meth yl Nu cleosid es
utilized the 3′-O-silyl derivatives after organic-aqueous
workup directly for further transformation because silyl
byproducts were the only impurities present and did not
interfere in the subsequent hydrazinolysis. Deprotection
of phthalimido derivatives 14a -c with methylhydrazine
gave corresponding intermediate nucleosides, which were
found to be somewhat unstable if left unused for more
than several days, even if stored in the freezer. However,
the structure of each of these 5′-O-amino intermediates
was confirmed by 1H NMR and FAB MS. Because of
their unstable character, the 5′-O-amino nucleosides were
immediately reacted with aqueous formaldehyde in MeOH/
EtOAc to provide the corresponding formaldoxime de-
rivatives 15a , 15d , and 15e in 70-80% overall yields
from the unsubstituted nucleosides 10a ,b,f. The struc-
1
tures were confirmed by H NMR, which indicated the
complete disappearance of the hydroxylamine proton
signal, and the appearance of the methylene protons as
two distinct doublets, each showing geminal coupling
with J values of 7-8 Hz. As it has been demonstrated
that presence of a 5-methyl group on the cytosine residue
improved the antisense properties of oligonucleotides
compared to unsubstituted cytidine,43 the 5-methyl-
cytidine derivatives 15b and 15c were prepared via
triazolation of 18a according to the literature procedure,28
followed by either displacement with sodium benzamide44
to give 15b, or with anhydrous ammonia in dioxane to
afford 15c in excellent yields.
With a full complement of 2′-O-methyl radical precur-
sors 12 and acceptors 15 in hand, we began a detailed
study of the ability of these synthons to be coupled into
nucleosidic dimers (Scheme 4). The coupling of iodide
12a (1 equiv) and oxime 15a (3.0 equiv) in the presence
of 8 (2 equiv), followed by an aqueous KF workup and
chromatography, afforded a 50% yield of the dimer 16a ,
along with unreacted oxime (90%, based on amount not
converted to product). We observed several minor DMT-
containing (by TLC charring) side products in this
reaction, presumably arising from less efficient addition
to the oxime 15a , allowing the incipient 3′-radical to react
via undesired pathways. Hart has observed side reac-
tions involving various adducts with 8a ,17 and in order
to minimize this potential problem, we lowered the
effective concentration of 8a via the syringe pump
addition of 8 to a mixture of 12a and 15a over 24 h. This
procedure succeeded in reducing the incidence of side
products and increased the yield of 16a to 70%, along
with a 90% recovery of unreacted oxime.
In order to address this issue we subsequently utilized
5′-O-TBDPS protected 3′-iodo nucleosides 12e-g as radi-
cal precursors. The coupling of iodide 12e (1.2 equiv) and
oxime 15a (1.0 equiv) in the presence of 8 (3 equiv) was
far less efficient than the corresponding reaction on the
2′-deoxy compounds (Table 1, entry 10), as a ca. 40%
yield of the desired dimer was obtained, along with
significant amounts of 3′-deoxygenated product and un-
reacted 15a . However, when the reaction was performed
with a 1:3:2 ratio of 12e:15a :8, an 84% yield of dimer
16h was obtained, along with unreacted oxime (95%,
based on amount not converted to product). These
conditions are identical to those which gave only a 50%
yield of the DMT-protected dimer and demonstrate the
superiority of 5′-silyl protection to 5′-DMT protection for
this reaction. This excellent yield prompted us to use a
similar procedure with purine nucleosides. Reaction 12f
and 12g with 15d and 15f gave the desired MI-dimers
16i-k in 30-40% yields. A partial loss of the dmf group
was observed under the radical conditions, undoubtedly
contributing to the lower yields, and made a tedious
chromatographic purification necessary. The dimer 16i
was obtained in pure form; however, satisfactory elemen-
tal analyses for 16j and 16k could not be obtained. The
FAB+ MS of product obtained in the case of 16j (homo-
geneous on TLC) shows an m/ e 1176 (M + H+, 100%),
indicating the presence of the desired dimer, and also
an m/ e 1121 (50%), corresponding to material having lost
a single dmf protecting group.
The structures of these 2′-O-methyl MI dimers 16 were
confirmed by extensive NMR studies, and an interesting
observation was revealed through 400 MHz 1H NMR
spectroscopy, which indicated the presence of a dimeric
nucleosidic impurity. This impurity displayed reso-
nances very similar to the major component (in many
(43) Sanghvi, Y. S.; Hoke, G. D.; Freier, S. M.; Zounes, M. C.;
Gonzalez, C.; Cummins, L.; Sasmor, H.; Cook, P. D. Nucleic Acids Res.
1993, 21, 3197-3203.
(44) Perbost, M.; Sanghvi, Y. S. J . Chem. Soc., Perkin Trans. 1. 1994,
2051-2052.
1
cases the product appears homogeneous by 200 MHz H

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8193
Sch em e 5
Sch em e 6. Syn th esis of 2′-O-Meth yl MMI Dim er sa
NMR), but was present in every dimer investigated, with
the ratio varying for different dimers (5-25%). It should
be pointed out that these compounds were all purified
by column chromatography and were homogenous on
TLC. We attribute this impurity to the presence of the
xylo or â-diastereomer of the MI-dimer, having the
inverted stereochemistry at the C-3′ of the upper nucleo-
side of the dimer. This result can be anticipated by the
fact that during the homolytic fission of 3′-iodo nucleo-
side, a planar C-3′ radical is generated. The unpaired
electron in a C-centered radical generally occupies an
orbital which has mainly p-character,45 therefore allowing
attack from both faces. It is known in the literature that
the presence of functional groups adjacent to the radical
center exert a marked steric effect on the stereochemical
outcome of the reaction, directing the incoming group to
the most accessible lobe of the π radical.46 Our results
are consistent with this explanation, as for the 2′-deoxy
series the R-face of the incipient C-3′ radical is unsub-
stituted, while the â-face is shielded by the nucleobase
as well as the 5′-substituent. This results in the observed
exclusive formation of the 3′-C-ribo dimer. For the C-3′
radical derived from a 2′-O-methyl nucleoside, however,
the methoxy group adjacent to the radical center exerts
a steric effect which counters that of nucleobase and the
5′-substituent, resulting in less selective attack of the
incoming oxime and the observed mixtures of products.
The basis for the high stereoselectivity of radical
addition reactions at the 3′-position of nucleosides has
been attributed to the presence of bulky 5′-protecting
groups as well as the nucleobase.24a We wished to
investigate whether, if the steric constraint at the 5′-
position was reduced, the resulting pinacolate-mediated
coupling reaction would result in a higher isomeric ratio
of the corresponding MI dimers. Toward this end, the
iodide 12h was reacted with 15a under our standard
conditions to furnish the T*T dimer 16l in 68% yield.
Surprisingly, the ratio of 16l to the presumed isomeric
impurity did not change significantly from the ca. 85:15
mixture of ribo- and xylo-diastereomers seen for 16h .
This suggests that the bulky group at the 5′-position has
little or no effect on the stereochemical outcome during
free radical-mediated C-C bond formation at the C-3′
position of nucleosides and indicates the nucleobase as
the more important steric director.
a
Reagents and conditions: (i) HCHO/NaBH3CN/AcOH, 45 min;
(ii) Et3N‚3HF/Et3N/THF, rt, 24 h; (iii) DMTCl/DMAP/pyridine, rt,
24 h; (iv) NH4OH/dioxane, rt, 24 h; (v) TBAF on silica gel/THF,
rt, 24 h; (vi) 1,1,1,3,3,3-hexafluoro-2-propanol, rt, 3 h.
NMR spectrum of 18 is simplified relative to the dimers
16, due to the presence of only a single carbohydrate
moiety. This enabled us to conclusively prove the stereo-
chemistry of both the major and minor components of 18
by employing 2D NMR techniques. TOCSY and NOESY
spectra were used to assign each of the chemical shifts
for the major and minor products in the one-dimensional
1H spectrum. The spectrum of the major product was
consistent only with a structure having the H3′ on the
â-face of the furanose ring, shown by the strong NOE
between H6 and H3′, thereby conclusively establishing
the stereochemistry of the 3′-position as having the ribo-
configuration. The spectrum of the minor product was
consistent only with a structure having inverted stereo-
chemistry at the 3′-position. No NOE was observed
between H6 and H3′, whereas moderate NOE was
observed from H3′ to both H1′ and the 2′-O-methyl group,
as well as a strong NOE between H3′ and H4′.
Finally, the representative dimers 16h and 16d were
converted to desired MMI-dimers (Scheme 6) by reacting
with formaldehyde and sodium cyanoborohydride in
acetic acid8a to give 19a and 19c, respectively. The
resulting MMI dimer 19c was treated with DMTCl to
give 19d , because the DMT protecting group was lost
during methylation. Desilylation of 19a gave the fully
deprotected T*T dimer 19b, at which point the ratio of
epimers obtained via the pinacolate mediated coupling
reaction to form 16h could be readily established as 86:
14 by integration of the H6 protons. These isomers were
also inseparable, both by TLC and reverse phase HPLC.
We also sought to extend the one-carbon homologation
reported by Hart12 to the iodides 12, which may be useful
synthons for the preparation of biologically active nucleo-
sides. Thus, the reaction of 12a with O-benzylform-
aldoxine (17, 3 equiv) in degassed benzene at 80 °C in
presence of 8 gave the 3′-(benzyloxyamino)methyl analog
18, along with the corresponding 3′-epimer as a 5:1
mixture in 40% yield (Scheme 5). Potentially, a cleavage
of the N-O bond or debenzylation of 18 would result in
1
The H NMR of the mixture 19b was studied in D2O at
310 K, and TOCSY and NOESY spectra were used to
assign all resonances in the H spectrum and study the
stereochemistry of the isomers. The spectra were con-
sistent with the proposed structure for the major isomer,
two â-nucleosides connected 3′f5′ by an MMI linkage.
This was demonstrated by moderate NOE’s from the H1′
of the upper nucleoside unit to its own H2′, H4′, TH6,
and the 2′-O-methyl. Also observed was NOE transfer
1
1
the synthesis of novel C-branched nucleosides. The H
(45) Rahman, A.-U.; Shah, Z. in Stereoselective Synthesis in Organic
Chemistry; Springer-Verlag: New York, 1993; pp 458-502.
(46) Giese, B. Angew. Chem., Int. Ed. Engl. 1983, 22, 753-764.

8194 J . Org. Chem., Vol. 61, No. 23, 1996
Bhat et al.
F igu r e 3. 2D NOESY spectrum of 19e.
from the upper TH6 to H2′, H3′, and TCH3. Moderate
NOE is seen between the MMI N-methyl and the 2′-O-
methyl of the upper nucleoside. In the lower nucleoside,
NOE is observed from the H1′ to H2′, TH6, 2′-O-methyl
and from TH6 to H2′, H3′, and TCH3. As was the case
for the mixture 18, the key NOE contact is that observed
between H6 and H3′ for the upper nucleoside, which
unequivocally establishes the stereochemistry of the 3′-
position of the major isomer as having the ribo-configu-
ration.
The epimeric mixture of 19b was treated with DMTCl
in pyridine to give a 14:86 mixture of epimers 20a and
20b, respectively, which could be resolved on TLC, and
were separable by careful column chromatography. TOC-
SY and NOESY spectra were used to assign the chemical
shifts and to search for clues to define the chemical
structure. For both compounds, it was necessary to run
the spectra at 313 K in order to better increase chemical
shift dispersion and allow for structure determination.
For the upper nucleoside of the minor product 20a ,
moderate-to-strong NOE′s were observed from H1′ to H2′,
H3′, and H4′. The H6 proton showed a strong NOE to
the H2′, and a weaker NOE to the H1′ and one of the
3′-methylene protons (H3′′). The H1′ to H3′ NOE found
for upper sugar of 20a is consistent with that seen for
the minor component in 18, and unequivocally estab-
lished the structure of the minor product in the pinacolate
coupling reaction as the 3′-C-epimer, having the xylo-
configuration at the 3′-position of the upper unit. The
stereochemistry of the major product 20b, although
known from the NOESY of 19b, could not be determined
unambiguously from a 2D NMR experiment on 20b. The
upper furanose has strong NOE’s from H6 to H2′ and
TCH3 and from H1′ to H2′, the 2′-O-methyl, H4′, and
either the H3′ or H3′′. The H3′ resonance of the upper
sugar was superimposed upon one of the 3′-methylene
protons (H3′′), and therefore the observed NOE contact
to this resonance from H6 cannot be used to determine
the stereochemistry.
In order to perform detailed 2D NMR studies on the
G*T MMI dimer without interference from protons of the
protecting groups, the fully deprotected dimer 19e was
synthesized from 19d through a series of deprotection
reactions. It is noteworthy that the G*T dimer 16d was
formed in a 20:1 ratio over its corresponding 3′-epimer,
which could be separated by chromatography, giving a
1
single compound for study. The H NMR of compound
19e was studied in DMSO-d6 solution at 293, 310, 333,
and 353 K. TOCSY and NOESY (Figure 3) spectra at
310 and 353 K were used to assign all resonances in the
1H spectrum. Only the 5′-5′′ and 3′-methylene pairs
remained without unequivocal definitions. The spectra
were consistent with the proposed structure, as demon-
strated by strong NOE’s from GH8 to GH1′, GH2′, and
GH3′, from GH2′ to GH3′ and GH1′, and from GH1′ to
GH4′. The lower ribo showed positive NOE from TH6
to its H1′, H2′, and H3′, as well as between H1′ and H2′,
H1′ and H4′, and from the 2′-O-methyl to H1′ and H2′.
The experimental data was interpreted in terms of a two-
state equilibrium between a North-type puckered ring
and a South-type puckered ring using the PSEUROT
methodology of Altona.47 This methodology incorporates
the vicinal coupling constants of ring protons as a means
to estimate proton-proton torsion angles and then

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8195
Ta ble 2. P SEUROT Ca lcu la tion s for th e Su ga r
Con for m a tion s in 19e
the dmf protected guanosine derivative. The use of the
dmf protecting group on the guanine nucleobase results
in exclusive reaction at the 5′-position, rendering the N1,
N3, and O6 unreactive under Mitsunobu conditions,
which may have profound implications for other trans-
formations of guanine derivatives.35 Use of the oximes
15 as traps for non-nucleosidic radicals has not been
explored, but the addition of a variety of C-centered
radicals can be envisaged, which would result in the
formation of a variety of novel 5′-O-amino nucleoside
derivatives.
upper sugar
lower sugar
(3′-methylene G-nucleoside)
(T-nucleoside)
310 K
333 K
353 K
333 K
353 K
J (1′2′)
J (2′3′)
J (3′4′)
1.8
5.5
9.0
1.9
5.6
7.9
1.9
5.7
8.0
5.1
4.1
4.7
4.9
5.1
5.6
%N
%S
90
10
77
23
78
22
46
54
52
48
PN ) 36.6; PS ) 237.8;
φN ) 34.0; φS ) 52.0
PN ) 20.4; PS ) 156.1;
φN ) 38.0; φS ) 33.0
Utilizing the pinacolate-mediated one-carbon homolo-
gation reported by Hart and Seely,12 a highly convergent
method for assembling complex nucleosidic dimers as
mimics of natural nucleic acids has been developed. To
our knowledge, this is the first example of the assembly
of nucleosidic dimers via free radical methods, and
although we have only investigated the assembly of
dimers, it is feasible that higher order homologues could
be constructed through this approach.49 The results
detailed herein describe the optimization of this reaction
for the 2′-deoxy series, resulting in an improvement of
yield of dimer 9a from 25% to over 80%. This result
compares very favorably with our previously reported
route, which requires four transformations in 30% overall
yield to obtain 9a , whereas the pinacolate-mediated
coupling reaction gives an 81% yield of identical material
in a single step. The utility of this reaction for the
preparation of mixed base dimers, in both the deoxy
series and 2′-O-methyl series, has been demonstrated.
Of special importance toward our goal of incorporating
these dimers into antisense oligonucleotides 4 and 5, is
the ability to incorporate all four types of natural
nucleosides into both the top and bottom portions of the
dimers 9 and 16. Our results suggest that the highest
yields are obtained for homopyrimidine dimers, with fair
and modest yields obtained for heterodimers and homo-
purine dimers, respectively.
translates this information into the corresponding endo-
cyclic torsion angle in terms of the pseudorotational
parameters, phase angle (P), and maximum puckering
amplitude (φ). The conformation of the two ribose rings
of 19e were analyzed on the basis of the vicinal J -
3
3
couplings J 1′2′, . Standard parameters
3J 2′3′, and J 3′4′
were adjusted to account for changes in the electro-
negativity and structure due to the 2′-methoxy moiety
in both sugars and the MMI at the 3′-position.48 Initial
conditions for the PSEUROT calculation were suggested
by previous work indicating that a ribonucleoside modi-
fied with a 3′-ribo C-C bond prefers to adopt a 3′-endo
conformation.21 Table 2 compiles the vicinal proton-
proton coupling constants (3J HH) derived from those
spectra for use in determining the conformation of the
MMI-ribose ring, and the results of the PSEUROT
3
calculations. It was not possible to determine all J HH
values for each molecule at every temperature, and
pseudorotation was only calculated where data was
obtainable. These results support the hypothesis that
the 2′-O-methyl-3′-ribo-CH2-modified ribose ring (upper
unit) strongly favors the north-type pucker, with 80-90%
of the population adopting a C3′-endo form. The calcula-
tions for the lower unit support a pseudorotational
equilibrium more typical of RNA, with 50% of the
population in the northern conformation.
In general, we found that reactions using 5′-O-TBDPS
protected substrates were cleaner than those employing
the corresponding 5′-O-DMT protected derivatives, mak-
ing purification of dimers 9 or 16 easier. Furthermore,
base protection is not required and is often detrimental
to the success of the reaction. The use of unprotected
nucleobases becomes a problem only in the case of
guanine, as unprotected G derivatives are insoluble in
benzene. This can be overcome by treating the crude
product mixture with NH4OH, so as to effect complete
removal of the protecting group. This strategy is exem-
plified in the synthesis of 9e. The reaction occurs with
remarkable stereoselectivity, as no traces of any isomers
resulting from â-face attack were evident for the 2′-deoxy
series 9. In the 2′-O-methyl series 16, reasonable stereo-
selectivity is still maintained, even upon removal of the
bulky 5′-protecting group, indicating that the â-linked
nucleobase is the predominant steric factor governing the
outcome of the reaction. Finally, as a representative
example, the 2′-O-methyl dimer 16d was converted to the
corresponding MMI dimer and then completely depro-
tected to afford the unsubstituted G*T MMI dimer 19d .
Con clu sion s
In summary, we have developed an efficient and high-
yielding synthesis of nucleosidic radical precursors and
acceptors and demonstrated the use of these synthons
in a highly convergent radical coupling reaction to afford
nucleosidic dimers. The 3′-iodo-2′-O-methyl nucleosides
12 were conveniently prepared from the corresponding
unprotected nucleoside via activation of the 3′-hydroxyl
as the triflate, followed by displacement with iodide. This
reaction occurs with inversion of configuration at C-3′,
giving the xylo-iodo nucleosides. These hitherto unknown
iodo nucleosides are potentially versatile precursors in
a variety of free radical as well as ionic transformations.
An extremely efficient synthesis of the requisite 5′-O-
methylene(imino) nucleosides 15 has also been developed,
which relies on a regioselective Mitsunobu reaction of the
5′-hydroxyl group of the parent nucleosides. This reac-
tion gives very high yields of the phthalimides 13 for the
5-methyluridine and adenosine derivatives, as well as for
1
The structure of this dimer was confirmed by H NMR
(47) Altona, C.; Sundarlingam, M. J . Am. Chem. Soc. 1972, 94,
8205-8212. PSEUROT Version 6.2 was obtained from Professor C.
Altona, Gorlaeus Laboratories, Leiden, The Netherlands.
(48) (a) Altona, C.; Ippel, J . H.; Westra Hoekzema, A. J . A.; Erkelens,
C.; Groesbeek, M.; Donders, L. A. Magn. Reson. Chem. 1989, 27, 564.
(b) Altona, C.; Francke, R.; de Haan, R.; Ippel, J . H.; Daalmans, G. J .;
Westra Hoekzema, A. J . A.; vanWijk, J . Magn. Reson. Chem. 1994,
32, 670.
methods, and the pseudorotational parameters were
calculated. The results indicate that both sugar units
adopt predominantly an RNA-like sugar pucker, with the
(49) Cook, P. D.; Sanghvi, Y. S.; Kung, P.-P. PCT Int. Appl. WO
95/18623, J uly 13, 1995.

8196 J . Org. Chem., Vol. 61, No. 23, 1996
Bhat et al.
equiv) in dry CH2Cl2 (5 mL/mmol) at -10 °C under an inert
atmosphere was added a solution of trifluoromethanesulfonic
anhydride (2 equiv) in CH2Cl2 (5 mL/mmol) dropwise over 0.5
h. After stirring an additional 0.25 h, a solution of ap-
propriately protected 3′-hydroxyl nucleoside (1 equiv, azeo-
troped with dry pyridine) in dry CH2Cl2 (5 mL/mmol) was
added dropwise over 0.5 h, and the solution was stirred at -10
°C for an additional 2 h. The reaction mixture was diluted
with an equal volume of ice cold 10% aqueous NaHCO3 with
vigorous stirring, and the mixture was allowed to warm to rt.
The organic phase was removed, dried (MgSO4), diluted with
toluene (5 mL/mmol), concentrated, and azeotroped with dry
toluene (3 × 5 mL/mmol). To the resulting foam were added
Bu4NI (2 equiv) and dry toluene (30 mL/mmol), and the
resulting mixture was heated for 0.5 h at 80 °C in an oil bath
with vigorous stirring, at which point all solid had dissolved
and a dark red oil separated. The resulting mixture was
dissolved by dilution with EtOAc and washed with water (15
mL/mmol), 1:1 5% aqueous NaHSO3 and 5% aqueous Na2SO3
(2 × 15 mL/mmol), dried (MgSO4), concentrated, and chro-
matographed to provide the iodide.
3′-Deoxy-5′-O-(4,4′-d im eth oxytr ip h en ylm eth yl)-3′-iod o-
2′-O-m et h yl-5-m et h ylu r id in e (12a ). From 5′-O-(4,4′-
dimethoxytrityl)-2′-O-methyl-5-methyluridine (5.75 g, 10 mmol)
according to general procedure A was obtained 4.41 g (64%)
of 12a after chromatography (30% to 50% EtOAc/hexane): Rf
0.38 (50% EtOAc/hexane); 1H NMR (CDCl3) δ 9.91 (s, 1H),
7.55-7.20 (m, 10H), 6.85 (d, 4H), 5.85 (s, 1H, H-1′), 4.37 (s,
1H), 4.31 (d, 1H), 3.93 (m, 1H), 3.79 (s, 6H), 3.60-3.50 (m,
1H), 3.56 (s, 3H), 3.20 (m, 1H), 1.83 (s, 3H); 13C NMR (CDCl3)
δ 164.16, 158.53, 150.35, 144.23, 136.14, 135.44, 135.25,
130.06, 128.12, 127.77, 126.88, 113.06, 110.06, 92.48, 90.17,
86.55, 80.00, 68.56, 58.32, 55.09, 26.84, 12.32. Anal. Calcd
for C32H33N2O7I‚0.4CH2Cl2: C, 54.16; H, 4.74; N, 3.90.
Found: C, 54.27; H, 4.58; N, 3.73.
3′-Deoxy-5′-O-(4,4′-d im eth oxytr ip h en ylm eth yl)-3′-iod o-
2-N-isobu tyr yl-2′-O-m eth ylgu a n osin e (12c). From 5 g
(8.26 mmol) of 11c according to general procedure A was
obtained 3.8 g (59%) of 12b after chromatography (80%
EtOAc/hexane): 1H NMR (DMSO-d6) δ 12.14 (s, 1H), 11.67
(s, 1H), 7.96 (s, 1H), 7.42-7.20 (m, 9H), 7.17-6.86 (m, 4H),
5.85 (d, J ) 2.1 Hz, 1H), 4.74 (bs, 2H), 3.87-3.86 (m, 1H),
3.73 (s, 6H), 3.32-3.08 (m, 5H), 2.85-2.70 (m, 1H), 1.12-1.03
(m, 6H); MS (FAB+) m/ e 780 (M + H). Anal. Calcd for
C36H38N5O7I‚0.25C6H14: C, 56.25; H, 5.16; N, 8.75. Found: C,
56.48; H, 5.24; N, 8.68.
6-N-Ben zoyl-3′-d eoxy-5′-O-(4,4′-d im et h oxyt r ip h en yl-
m eth yl)-3′-iod o-2′-O-m eth yla d en osin e (12k ). From N-6-
benzoyl-5′-O-(4,4′-dimethoxytrityl)-2′-O-methyladenosine (0.69
g, 1 mmol) according to general procedure A was obtained 0.47
g (58%) of 12k after chromatography (50% to 70% EtOAc/
hexane): Rf 0.34 (50% EtOAc/hexane); 1H NMR (CDCl3) δ 9.12
(s, 1H), 8.81 (s, 1H), 8.37 (s, 1H), 8.03 (d, 2H), 7.65-7.15 (m,
9H), 6.85 (d, 4H), 6.18 (s, 1H, H-1′), 4.68 (s, 1H), 4.39 (d, 1H),
3.94 (dd, 1H), 3.80 (s, 6H), 3.66 (dd, 1H), 3.63 (s, 3H), 3.21
(dd, 1H); 13C NMR (CDCl3) δ 164.52, 158.61, 158.57, 152.71,
151.09, 149.37, 144.36, 141.46, 135.64, 135.35, 133.61, 132.72,
130.10, 130.03, 128.81, 128.10, 127.86, 127.79, 126.96, 123.38,
113.16, 92.76, 89.73, 86.61, 80.48, 68.58, 58.38, 55.20, 26.60.
Anal. Calcd for C39H36N6O6I‚0.4CH2Cl2‚0.5EtOAc: C, 56.79;
H, 4.70; N, 8.00. Found: C, 56.60; H, 4.64; N, 8.01.
upper unit being essentially locked into the northern
conformation. This suggests that preorganized structures
of type 5 will adopt a conformation which is more
favorable for hybridization with the target mRNA, po-
tentially increasing their affinity, specificity, and thereby
their usefulness in the design of superior antisense
oligonucleotides.
Exp er im en ta l Section
Gen er a l. Unless otherwise noted, materials were obtained
from commercial suppliers and were used as provided. 2′-O-
Methyl-5-methyluridine, 5′-O-(4,4′-dimethoxytriphenylmethyl)-
2′-O-methyl-5-methyluridine, 5′-O-(4,4′-dimethoxytriphenyl-
methyl)-N-2-isobutyryl-2′-O-methylguanosine, and N-6-benzoyl-
5′-O-(4,4′-dimethoxytriphenylmethyl)-2′-O-methyladenosine were
purchased from RI Chemicals, CA (714-288-1548). 2′-O-
Methylguanosine and 2′-O-methyladenosine were purchased
from Summit Pharmaceuticals Corp., N.J . (201-585-9687).
Other general experimental procedures were carried out as
described previously.26
NMR Sp ectr oscop y. 1H NMR spectra for all compounds
were recorded either at 399.94 MHz on a Varian Unity 400
NMR spectrometer or at 199.975 MHz on a Varian Gemini
200 NMR spectrometer. All multidimensional and variable
temperature spectra were collected on the Unity 400 NMR.
The compound 19d was studied at a concentration of 1.6 mM
in 600 µL of DMSO-d6. One-dimensional 1H NMR spectra
were recorded at the sample temperatures 293, 310, 333, and
353 K. All one-dimensional measurements were performed
under the same conditions and processed identically: 5200 Hz
sweep width, 32K time domain, zero-filling to 64K. Where
possible, the data were studied unapodized, but in some
instances the standard Varian VnmrS resolution enhancement
method was invoked, using a line broadening of -1.01 and a
gaussian filter of 0.945. All subspectra were observed to be
first order. Proton resonances were assigned from two-
dimensional spectra run at 310 and 353 K. TOCSY and
NOESY spectra were run at 310 K with a 20 ms spin-lock and
a 650 ms mixing time, respectively, with 1K by 512 complex
points being collected in a phase-sensitive manner. Similar
experiments were carried out at 353 K, with 2K by 512
complex points collected in a phase-sensitive manner. In each
case, the data was apodized with a squared cosine and zero-
filled to 2K × 1K complex points before Fourier transforma-
tion. The 13C spectra were recorded on the same instrument,
at a frequency of 100.57 MHz, using a sweep width of 30441
Hz, an acquisition time of 0.50 s, and processed by apodizing
with 2 Hz line-broadening and zero-filling to 32K. The 13C
spectrum was assigned with the aid of a 1H{13C} HMQC at
293 K. For this experiment 1K complex points were collected
in the directly-detected dimension over a sweep width of 3200
Hz. A total of 240 increments were collected in a phase-
sensitive manner in the indirectly-detected dimension, over a
sweep-width of 22 kHz. The data was apodized with a squared
cosine in the 1H dimension and a gaussian in t1.
One-dimensional 1H spectra for 12h , 12i, 12j, 18a , 20a , and
20b were all recorded at 293 K using identical parameters for
acquisition and processing: 14336 complex points were col-
lected over a sweep width of 7 kHz. Data was zero-filled to
64K points and apodized with 0.30 Hz line-broadening before
Fourier transform. Two-dimensional spectra were acquired
with sweep widths adjusted to optimize resolution across the
spectral range of each sample, ranging from 4 kHz to 5200
Hz in each dimension. Data sets of 1K by 256 points were
acquired for 12h and 12j, 1K by 512 points for 12i and 20b.
Data sets of 2K by 512 data points were collected for 18 and
20b to allow adequate resolution. Data was collected at 313
K for 20a and 20b to enhance chemical shift dispersion. All
data was phase-sensitive, processed under conditions other-
wise identical to the methods used in the TOCSY and NOESY
work outlined above. 1H NMR data for 19b was collected at
310 K in deuterium oxide, using the same series of experiments
described above.
5′-O-(ter t-Bu tyld ip h en ylsilyl)-3′-d eoxy-3′-iod o-5-m eth -
yl-2′-O-m eth ylu r id in e (12e). A solution of 11e (7.0 g, 13.7
mmol) and dry pyridine (1.9 g, 24.6 mmol) in anhydrous
CH2Cl2 (80 mL) was cooled under vigorous stirring to -10 °C
in an inert atmosphere for about 20 min. A solution of triflic
anhydride (5.1 g, 17.7 mmol) in CH2Cl2 (30 mL) was slowly
added via a syringe (15 min.). The reaction was complete in
35 min after the addition. To this cold solution was added
MeOH (1 mL) and then saturated NaHCO3, and the organic
layer was separated and washed with brine (2 × 15 mL)
followed by drying over Na2SO4. Solvent was removed under
reduced pressure and the residue azeotroped with toluene (2
× 20 mL). The residual gum was dissolved in p-xylene (100
mL), to this was added Bu4NI (5.6 g,15.1 mmol), and the
reaction mixture was heated at 140 °C in a preheated bath.
Gen er a l P r oced u r e A. Syn th esis of 3′-Iod o-2′-O-m eth -
yl Nu cleosid es (11 f 12). To a solution of pyridine (4.3

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8197
The reaction was complete in 30 min. It was cooled to rt and
then diluted with EtOAc (250 mL) and washed with 5%
aqueous solution of sodium sulfite and sodium bisulfite (1:1).
The organic layer was dried over Na2SO4 and concentrated
followed by flash chromatography on silica gel using 60%
EtOAc/hexane. Removal of the solvent furnished 6.8 g (80%)
of 12e as a colorless foam: 1H NMR (DMSO-d6) δ 11.50 (s,
1H), 7.23-7.43 (m, 11H), 5.78 (d, J ) 4.0 Hz, 1H), 4.6 (bs,
1H), 4.40-4.43 (m, 1H), 3.89 (bs, 2H), 3.42 (s, 3H), 1.59 (s,
3H), 1.04 (s, 9H); MS (FAB+) m/ e 621 (M + H). Anal. Calcd
for C27H33N2O5SiI: C,52.26; H, 5.36; N, 4.51. Found: C, 52.55;
H, 5.41; N, 4.48.
5′-O-(ter t-Bu t yld ip h en ylsilyl)-3′-d eoxy-6-N-[(d im et h -
yla m in o)m eth ylen e]-3′-iod o-2′-O-m eth yla d en osin e (12f).
From 11h (5.3g, 9.2 mmol), pyridine (3.65 g, 46.1 mmol), triflic
anhydride (3.0 g, 11 mmol), and Bu4NI (5.2 g, 14.0 mmol)
according to the method used for 12e was obtained 3.8 g (60%)
of 12f after chromatography on silica gel using 80:15:3-5%
MeOH in EtOAc:hexane: 1H NMR (DMSO-d6) δ 8.93 (s, 1H),
8.45 (s, 1H), 8.24 (s, 1H), 7.73-7.39 (m, 10H), 6.07 (d, J ) 2.8
Hz, 1H), 4.89-4.87 (m, 1H), 4.76-4.74 (m, 1H), 3.98-3.93 (m,
3H), 3.46 (s, 3H), 3.21 (s, 3H), 3.14 (s, 3H), 1.03 (s, 9H); MS
(FAB+) m/ e 685 (M + H). Anal. Calcd for C30H37N6O3SiI‚
0.25C6H12: C, 53.61; H, 5.71; N, 11.91. Found: C, 53.20; H,
5.58; N, 12.24.
5′-O-(ter t-Bu t yld ip h en ylsilyl)-3′-d eoxy-2-N-[(d im et h -
yla m in o)m eth ylen e]-3′-iod o-2′-O-m eth ylgu a n osin e (12g).
From 11j (5.0 g, 8.46 mmol), pyridine (3.36 g, 46 mmol), triflic
anhydride (3 g, 11 mmol), and Bu4NI (5.2 g, 14.0 mmol)
according to the method used for 12e was obtained 2.5 g (43%)
of 12g after chromatography on silica gel using 80:15:3-5%
MeOH in EtOAc:hexane: 1H NMR (DMSO-d6) δ 11.43 (s, 1H),
8.58 (s, 1H), 7.87 (s, 1H), 7.70-7.64 (m, 10H), 5.90 (d, J ) 2
Hz, 1H), 4.88 (bs, 1H), 4.70 (bs, 1H), 3.46 (s, 3H), 3.12 (s, 3H),
3.04 (s, 3H), 1.02 (s, 9H; MS (FAB+) m/ e 701 (M + H). Anal.
Calcd for C30H37N6O4SiI: C, 51.43; H, 5.32; N, 11.99. Found:
C, 51.56; H, 5.37; N, 11.98.
procedure B was obtained 74.3 g (98%) of product after
partitioning the concentrated reaction mixture between ice
water (3 L) and ether (3 L) and collection and drying of the
resulting solid. The product contains traces (0.125 equiv by
1H NMR and combustion analysis) of Ph3PdO, which does not
interfere in the silylation reaction: Rf 0.38 (10% MeOH/
CH2Cl2); 1H NMR (DMSO-d6) δ 8.36 (s, 1H), 8.12 (s, 1H), 7.81
(s, 4H), 6.02 (d, J ) 5.0 Hz, 1H), 5.50 (d, J ) 5.0 Hz, 1H),
4.6-4.3 (m, 4H), 4.3-4.2 (m, 1H), 3.33 (s, 3H); HRMS (FAB+,
CsI/NBA) calcd for C19H18N6O6 + Cs+ 559.0342, found 559.0355.
Anal. Calcd for C19H18N6O6‚0.125Ph3PdO (evident in 1H
NMR): C, 55.34; H, 4.34; N, 18.22. Found: C, 55.07; H, 4.45;
N, 17.98.
2-N -[(D im e t h y la m in o )m e t h y le n e ]-2′-O -m e t h y l-5′-
p h th a lim id ogu a n osin e (13c). 2-N-[(Dimethylamino)meth-
ylene]-2′-O-methylguanosine (10f, 6.39 g, 18.2 mmol) was
exhaustively dried (0.01 mmHg, 45 °C, several days over P2O5)
and then reacted according to general procedure B. After the
reaction was complete (by TLC), it was reduced to 1/3 its
original volume, and the solid was collected and dried to yield
8.85 g (93%) of hydrated 13c: Rf 0.23 (10% MeOH/CH2Cl2); 1H
NMR (DMSO-d6) δ 11.39 (s, 1H), 8.53 (s, 1H), 8.05 (s, 1H),
7.84 (br s, 4H), 5.92 (d, J ) 5.8 Hz, 1H), 5.52 (d, J ) 5.3 Hz,
1H), 4.5-4.1 (m, 5H), 3.14 (s, 3 H), 3.01 (s, 3H), 2.88 (s, 3 H);
HRMS (FAB+, CsI/NBA) calcd for C22H23N7O7 + Cs+ 630.0713,
found 630.0725. Anal. Calcd for C22H23N7O7‚1.5H2O: C,
50.38; H, 5.00; N, 18.69. Found: C, 50.57; H, 5.12; N, 18.81.
Gen er a l P r oced u r e C. Silyla tion of Nu cleosid es (13
f 14). The requisite nucleoside (1 equiv, dried over P2O5 in
vacuo) and imidazole (4.5 equiv) were dissolved in dry DMF
(5 mL/mmol) under an inert atmosphere, and TBDPSCl (1.5
equiv) was added. The reaction was stirred at room temper-
ature until complete by TLC (16-48 h), then poured into
EtOAc (15 mL/mmol) and water (15 mL/mmol). The organic
layer was washed with water (3 × 10 mL/mmol), dried
(MgSO4), and concentrated. On large scale, it proved more
convenient to concentrate the crude reaction mixture to a thin
syrup, partition the product between ether and water, and then
collect the resulting solid. This material could be purified by
column chromatography; however, the only impurities present
were silyl byproducts, which did not interfere in the subse-
quent conversion to the oximes via general procedure D.
3′-(t er t -Bu t yld ip h e n ylsilyl)-2-N -[(d im e t h yla m in o)-
m eth ylen e]-2′-O-m eth ylgu a n osin e (14c). From 13c (8.85
g, 16.9 mmol) according to general procedure C was obtained
10.6 g (84%) of 14c after filtration (0 to 10% MeOH/CH2Cl2)
of the crude material through a plug of silica: Rf 0.36 (10%
Gen er a l P r oced u r e B. Mitsu n obu Rea ction of Nu cleo-
sid es (10 f 13). A mixture of the appropriate nucleoside (1
equiv), triphenylphosphine (1.15 equiv), and N-hydroxy-
phthalimide (1.15 equiv) was dried under vacuum over P2O5
for 18 h prior to use. To this mixture under an inert
atmosphere is added dry THF (for T) or DMF (for A and Gdmf
)
(10 mL/mmol) and then diethyl azodicarboxylate (1.15 equiv)
dropwise with stirring to the solution at rt. The rate of
addition is maintained such that the resulting deep red
coloration is just discharged before addition of the next drop.
After the addition is complete (5-45 min, depending on
starting nucleoside and scale), the reaction is stirred until
shown to be complete by TLC. The solvent was evaporated in
vacuo to approximately 1/3 the starting volume, and if a solid
was obtained (T, Gdmf) it was collected, otherwise (A) the
resulting solution was partitioned between water and ether
and the resulting solid collected, washed well with ether, and
dried to yield the desired product. This material was pure in
some cases, but usually contained traces of triphenylphosphine
oxide and/or diethyl hydrazinedicarboxylate, which could be
removed by column chromatography. However, these impuri-
ties did not interfere with the subsequent reactions (general
procedure C), and the crude material could therefore be carried
directly to the next step.
2′-O-Meth yl-5′-O-p h th a lim id o-5-m eth ylu r id in e (13a ).
2′-O-Methyl-5-methyluridine (4.08 g, 15 mmol) was reacted
according to general procedure B. After the reaction was
complete (by TLC), the solids were collected, washed well with
ether, and dried to yield 3.06 g (49%) of pure product. The
combined filtrates were concentrated then purified by column
chromatography (0 to 4% MeOH/CH2Cl2) to provide an ad-
ditional 2.50 g (40%), giving a combined yield of 5.56 (89%) of
13a : Rf 0.25 (5% MeOH/CH2Cl2); 1H NMR (DMSO-d6) δ 11.36
(s, 1H), 7.87 (br s, 4H), 7.58 (s, 1H), 5.89 (d, J ) 5.7 Hz, 1H),
5.43 (d, J ) 5.7 Hz, 1H), 4.5-3.8 (m, 6H), 3.34 (s, 3H), 1.79 (s,
3H). Anal. Calcd for C19H19N3O8‚0.5H2O: C, 53.52; H, 4.73;
N, 9.85. Found: C, 53.51; H, 4.49; N, 9.84.
1
MeOH/CH2Cl2); H NMR (DMSO-d6) δ 11.35 (s, 1H), 8.43 (s,
1H), 8.04 (s, 1H), 7.84 (br s, 4H), 7.5-7.7 (m, 4H), 7.3-7.4 (m,
6H), 6.02 (d, J ) 6.1 Hz, 1H), 4.5-4.7 (m, 1H), 4.0-4.5 (m,
4H) 3.05 (s, 3 H), 3.03 (s, 3H), 2.88 (s, 3 H), 1.06 (s, 9H); HRMS
(FAB+, CsI/NBA) calcd for C38H41N7O7Si + Cs+ 868.1891, found
868.1899. Anal. Calcd for C38H41N7O7Si‚0.5H2O: C, 61.27;
H, 5.68; N, 13.16. Found: C, 61.27; H, 5.82; N, 13.38.
Gen er a l P r oced u r e D. Syn th esis of Nu cleosid e 5′-
F or m a ld oxim es (14 f 15). The crude material obtained
from the silylation of the corresponding 5′-O-phthalimido
nucleoside was dissolved in dry CH2Cl2 (10 mL/mmol), and
methylhydrazine (1.2 equiv) was added dropwise at -10 to 0
°C. After 1 h, the mixture was filtered, the filtrates were
washed with CH2Cl2, the combined organics were washed with
water and brine and dried (Na2SO4), and the solution was
concentrated to yield the 5′-O-amino nucleoside, which was
used immediately without further purification. (The 5′-O-
amino nucleosides can be purified by column chromatography;
however, we have observed that they tend to decompose upon
standing). This residue was dissolved in 1:1 EtOAc/MeOH (15
mL/mmol), formaldehyde (20% w/w aqueous, 1.1 equiv) was
added, and the mixture was stirred 1 h at room temperature.
The solution was concentrated and then chromatographed or
crystallized to provide the 3′-silyl-5′-formaldoxime.
3′-O-(ter t-Bu t yld ip h en ylsilyl)-2-N-[(d im et h yla m in o)-
m e t h y le n e ]-2′-O -m e t h y l-5′-O -(m e t h y le n e im in o )g u a -
n osin e (15e). From 14c (10.6 g, 14.4 mmol) according to
general procedure D was obtained 9.21 g of 15e in essentially
quantitative yield after filtration (0 to 10% MeOH/CH2Cl2) of
2′-O-Meth yl-5′-O-p h th a lim id oa d en osin e (13b). From 2′-
O-methyladenosine (50.0 g, 178 mmol) according to general

8198 J . Org. Chem., Vol. 61, No. 23, 1996
Bhat et al.
the crude material through a plug of silica: Rf 0.43 (10%
MeOH/CH2Cl2); H NMR (DMSO-d6) δ 11.19 (s, 1H), 8.47 (s,
3′-De(oxyp h osp h in ico)-3′-[m et h ylen e(m et h ylim in o)]-
5′-O-(t er t -b u t y ld ip h e n ylsily l)-2′-O-m e t h yl-5-m e t h y l-
u r id ylyl-(3′f5′)-3′-O-(ter t-bu tyld ip h en ylsilyl)-2′-O-m eth -
yl-5-m eth ylu r id in e (19a ). From 4.1 g (4.0 mmol) of 16h
according to general procedure F was obtained 2.93 g (70%)
of the desired MMI dimer, which required no chromatographic
1
1H), 7.94 (s, 1H), 7.5-7.7 (m, 4H), 7.4-7.5 (m, 6H), 6.96 (d, J
) 7.27 Hz, 1H), 6.55 (d, J ) 7.27 Hz, 1H), 6.02 (d, J ) 6.13
Hz, 1H), 4.4-4.5 (m, 1H), 4.0-4.3 (m, 4H) 3.06 (s, 3 H), 3.01
(br s, 6H), 1.06 (s, 9H) ppm. Anal. Calcd for C31H39N7O5Si‚
0.5H2O: C, 59.40; H, 6.43; N, 15.64. Found: C, 59.59; H, 6.33;
N, 15.61.
1
purification: Rf 0.65 (10% MeOH/CH2Cl2 ); H NMR (CDCl3)
δ 8.94 (s, 1H), 8.84 (s, 1H), 7.80-7.15 (m, 22H), 5.89 (s, 1H),
5.75 (s, 1H), 4.30-2.85 (m, 10H), 3.55 (s, 3H), 3.29 (s, 3H),
2.55-2.35 (m, 2H), 2.49 (s, 3H), 1.79 (s, 3H), 1.39 (s, 3H), 1.09
(s, 18H). Anal. Calcd for C56H71N5O11Si2‚H2O: C, 63.19; H,
6.91; N, 6.58. Found: C, 63.32; H, 6.83; N, 6.64.
3′-De(oxyp h osp h in ico)-3′-[m et h ylen e(m et h ylim in o)]-
2-N-isobu tyr yl-2′-O-m eth ylgu a n osylyl-(3′f5′)-3′-O-(ter t-
bu tyld ip h en ylsilyl)-2′-O-m eth yl-5-m eth ylu r id in e (19c).
From 0.50 g (0.42 mmol) of 16d according to general procedure
F was obtained 0.35 g (92%) of the detritylated MMI dimer
after chromatographic purification (70:15:15 EtOAc/hexane/
MeOH): 1H NMR (CDCl3) δ 12.20 (bs, 1H), 10.05 (bs, 1H), 9.80
(bs, 1H), 8.00 (s, 1H), 7.71-7.20 (m, 11H), 5.82 (m, 2H), 4.64
(bs, 1H), 4.13-2.60 (m, 21H), 2.49 (s, 3H), 1.82 (s, 3H), 1.22
(s, 6H), 1.08 (s, 9H); MS (FAB+) m/ e 903 (M + H). Anal.
Calcd for C44H57N8O11Si‚0.25H2O: C, 58.29; H, 6.39; N, 12.36.
Found: C, 57.95; H, 6.57; N, 12.14.
3′-De(oxyp h osp h in ico)-3′-[m et h ylen e(m et h ylim in o)]-
2′-O -m e t h y l-5-m e t h y lu r id y ly l-(3′f5′)-2′-O -m e t h y l-5-
m eth ylu r id in e (19b). To a solution of 19a (2.93 g, 2.68
mmol) in dry THF (25 mL) were added Et3N‚3HF (4.4 mL,
26.8 mmol) and Et3N (1.9 mL, 13.4 mmol). The resulting
solution was stirred at room temperature overnight, concen-
trated (0.1 mmHg) to a viscous syrup, chromatographed (0 to
10% MeOH/EtOAc), and then azeotroped with ethanol to
provide 1.32 g (86%) of 19b as a foam: Rf 0.40 (10% MeOH/
EtOAc); 1H NMR (DMSO-d6) δ 11.35 (s, 1H), 11.28 (s, 1H),
8.05 (s, 1H), 7.93 (s, 0.16H, minor isomer present in 14:86
ratio), 7.54 (s, 1H), 5.82 (d, 1H), 5.75 (s, 1H), 5.25 (t, 1H), 5.19
(d, 1H), 4.20-3.50 (m, 9H),3.40 (s, 3H), 3.28 (s, 3H), 2.91 (m,
1H), 2.67 (m, 1H), 2.57 (s, 3H), 2.43 (m, 1H), 1.78 (s, 3H), 1.73
(s, 1H). Anal. Calcd for C24H35N5O11‚0.5EtOH: C, 50.67; H,
6.46; N, 11.82. Found: C, 50.36; H, 6.25; N, 11.60.
Gen er a l P r oced u r e E . R a d ica l Cou p lin g R ea ct ion .
The appropriate 3′-deoxy-3′-iodo nucleoside (1 equiv) and 5′-
formaldoxime (3 equiv) were azeotroped with dry benzene (10
mL/mmol), and bis(trimethylstannyl) benzopinacolate (2 equiv)
and dry benzene (5 mL/mmol) were added. The mixture was
degassed (argon, 0.5 h) and heated to 80 °C in an oil bath for
16-24 h, at which point all iodide had been consumed (by
TLC). The solution was allowed to cool and stirred vigorously
with EtOAc (50 mL/mmol) and 10% aqueous KF (20 mL/mmol)
for 2 h. The organic layer was washed with 5% aqueous
NaHCO3 (20 mL/mmol), dried (MgSO4), concentrated, dis-
solved in the minimum amount of CH2Cl2, and applied to a
column of silica. Elution with 30% EtOAc/hexane (5 column
volumes) provided tin byproducts and benzophenone. The
unreacted oxime (75-99% of unreacted material recovered)
and the hydroxylamino-linked dimer were then obtained by
continued elution with the appropriate solvent system.
3′-De(oxyp h osp h in ico)-3′-(m et h ylen eim in o)-5′-O-(t r i-
p h e n y lm e t h y l)t h y m id y ly l-(3′f5′)-3′-O -(t er t -b u t y ld i-
p h en ylsilyl)-2′-d eoxya d en osin e (9d ). From 297 mg (0.5
mmol) of 6b and 775 mg (1.5 mmol) of 7b according to general
procedure F was obtained 515 mg (83% of unreacted material)
of the starting oxime, and 291 mg (59%) of 9d after elution of
the column with a gradient of 0% to 5% MeOH in 4:1
1
EtOAc/hexane: Rf 0.41 (5% MeOH in 4:1 EtOAc/hexane); H
NMR (CDCl3) δ 12.50 (s, 1H), 8.34 (s, 1H), 8.23 (s, 1H), 7.70-
7.10 (m, 26H), 6.55 (t, J ) 6.8 Hz, 1H), 6.45 (bs, 2H), 6.08 (t,
J ) 5.6 Hz, 1H), 5.98 (s, 1H), 4.50 (m, 1H), 4.07 (m, 1H), 3.94
(m, 1H), 3.47 (m, 2H), 3.28 (dd, 1H), 3.20 (dd, 1H), 2.84 (m,
2H), 2.45 (m, 3H), 2.19 (t, 2H), 1.52 (s, 1H), 1.09 (s, 9H). Anal.
Calcd for C56H60N8O7Si‚0.5H2O: C, 67.65; H, 6.18; N, 11.27.
Found: C, 67.77; H, 6.06; N, 11.35.
3′-De(oxyp h osp h in ico)-3′-[m et h ylen e(m et h ylim in o)]-
5′-O-(4,4′-d im e t h oxyt r ip h e n ylm e t h yl)-2′-O-m e t h yl-5-
m eth ylu r idylyl-(3′f5′)-2′-O-m eth yl-5-m eth ylu r idin e (20b)
a n d Its C-3′ Ep im er (20a ). The dimer 19b (1.70 g, 2.98
mmol) was azeotroped with dry pyridine (3×), dissolved in the
minimum amount of pyridine, and cooled to 0 °C, and 4,4′-
dimethoxytrityl chloride (1.53 g, 4.5 mmol) was added in 3
portions over 4 h. The reaction mixture was allowed to come
to rt with stirring overnight and then partitioned between
CH2Cl2 (50 mL) and 5% NaHCO3 (100 mL). The aqueous layer
was washed with CH2Cl2, and the combined organics were
washed with water and then dried (MgSO4), concentrated, and
azeotroped twice with toluene. The resulting residue was
chromatographed (0 to 5% MeOH/CH2Cl2) to provide 2.32 g
3′-De(oxyp h osp h in ico)-3′-(m eth ylen eim in o)-5′-O-(ter t-
bu tyldiph en ylsilyl)-2′-O-m eth yl-5-m eth ylu r id ylyl-(3′f5′)-
3′-O-(t er t -b u t yld ip h e n y lsilyl)-2′-O-m e t h y l-5-m e t h yl-
u r id in e (16h ). Compound 12e (1.22 g, 1.64 mmol), 15a (2.5
g, 4.15 mmol), and 8 (2.26 g, 3.27 mmol) in benzene (16 mL)
were reacted according to general procedure E. Continued
elution of the column with 50% EtOAc/hexane (10 column
volumes) gave the unreacted oxime 15a (1.80 g, 95% of
unreacted material), and elution with 10% MeOH/CH2Cl2
afforded 1.42 g (84%) of the hydroxylamino linked dimer 16h :
1
Rf 0.15 (5% MeOH/CH2Cl2 ); H NMR (CDCl3) δ 8.83 (s, 1H),
8.67 (s, 1H), 7.80-7.15 (m, 22H), 5.91 (s, 1H), 5.84 (d, J ) 2.3
Hz, 1H), 5.55 (t, 1H), 4.30-3.00 (m, 10H), 3.55 (s, 3H), 3.32
(s, 3H), 2.87 (m, 1H), 2.46 (m, 1H), 1.76 (s, 3H), 1.48 (s, 3H),
1.10 (s, 9H), 1.09 (s, 9H). Anal. Calcd for C55H69N5O11Si2: C,
63.99; H, 6.74; N, 6.78. Found: C, 63.65; H, 6.64; N, 6.58.
1
(89%) of a ca. 14:86 mixture of dimers (by H NMR): Rf 0.53
(10% MeOH/CH2Cl2). Anal. Calcd for C45H53N5O13‚0.5H2O:
C, 61.35; H, 6.18; N, 7.95. Found: C, 61.27; H, 6.13; N, 8.03.
A portion of this mixture (0.5 g) was carefully chromato-
graphed (5 × 15 cm, 2% MeOH in 4:1 EtOAc-hexane) to
provide the C-3′-epimer 20a : Rf 0.18 (2% MeOH in 4:1 EtOAc-
hexane); 1H NMR (CDCl3) δ 8.64 (s, 1H), 8.53 (s, 1H), 7.75 (s,
1H), 7.48 (s, 1H), 7.40-7.20 (m, 9H), 6.84 (m, 4H), 6.05 (d, J
) 6.0 Hz, 1H), 5.86 (s, 1H), 4.43 (t, 1H), 4.07 (m, 2H), 3.92 (m,
1H), 3.88 (s, 6H), 3.87-3.69 (m, 3H), 3.60 (s, 3H), 3.39 (s, 1H),
2.82 (m, 1H), 2.74 (m, 1H), 2.66 (m, 1H), 2.16 (s, 3H), 1.91 (s,
3H), 1.12 (s, 3H); 13C NMR (CDCl3) δ 163.54, 158.92, 150.40,
149.87, 143.29, 136.03, 135.35, 134.55, 130.49, 130.16, 129.10,
128.77, 127.94, 127.83, 127.74, 127.51, 113.20, 111.64, 110.63,
87.52, 83.41, 82.07, 78.78, 77.21, 70.35, 68.28, 62.17, 58.64,
58.34, 58.14, 55.29, 55.24, 45.45, 42.55, 12.40, 11.05; MS
(electrospray+) m/ e 872 (M + H+), 894 (M + Na+); MS
(electrospray
Gen er a l P r oced u r e F . Red u ctive Meth yla tion of MI
Dim er s. The appropriate base-unprotected MI dimer (1 equiv)
was dissolved in AcOH (10 mL/mmol) and cooled in a cool
water bath (not to freezing), and NaBH3CN (2 equiv) was
added in one portion, with vigorous stirring. To this suspen-
sion was added formaldehyde (20% aqueous, 15 equiv) in a
slow stream, the mixture was stirred for 5 min, and additional
portions of NaBH3CN (2 × 2 equiv) were added portionwise
over 10 min. The cool bath was removed, and the resulting
solution was allowed to warm to room temperature with
stirring over 1 h. The reaction mixture was poured into ice
cold water (50 mL/mmol), the resulting material was dissolved
with EtOAc (15 mL/mmol), and the organic phase was washed
with water (2 × 50 mL/mmol), 10% aqueous NaHCO3 (care-
fully, gas evolution) until the washings remained pH ) 8
(typically 1 × 15 mL/mmol), water (50 mL/mmol), and brine
and then dried (MgSO4). The solvent was removed, and the
syrup was azeotroped (2×) with dry MeCN to provide a foam
and then dried in vacuo.
-) m/ e 870 (M - H-), 906 (M + Cl-). Continued
elution of the column provided a substantial portion of mixed
fractions, followed by pure 20b: Rf 0.12 (2% MeOH in 4:1
EtOAc-hexane); 1H NMR (CDCl3) δ 9.11 (s, 1H), 9.06 (s, 1H),
7.85 (s, 1H), 7.47 (s, 1H), 7.44 (d, 2H), 7.35-7.20 (m, 7H), 6.82

Synthesis of Novel Nucleic Acid Mimics
J . Org. Chem., Vol. 61, No. 23, 1996 8199
(m, 4H), 5.89 (s, 1H), 5.81 (d, J ) 1.7, 1H), 4.16 (d, 1H), 4.03
(dd, 1H), 3.92 (m, 3H), 3.79 (s, 6H), 3.75 (m, 3H), 3.59 (s, 3H),
3.58 (s, 3H), 3.28 (d, 1H), 3.00 (m, 1H), 2.71 (m, 1H), 2.57 (s+m,
3H+1H), 1.88 (s, 3H), 1.36 (s, 3H); 13C NMR (CDCl3) δ 164.19,
163.65, 158.66, 150.22, 150.12, 144.27, 135.53, 135.46, 135.38,
130.17, 128.27, 127.92, 127.13, 113.16, 110.57, 110.22, 88.97,
87.76, 86.59, 86.00, 83.62, 83.30, 82.05, 77.21, 68.60, 62.54,
58.64, 58.21, 56.18, 55.24, 45.74, 39.01, 12.45, 11.92; MS
(electrospray+) m/ e 872 (M + H+), 894 (M + Na+); MS
(electrospray-) m/ e 870 (M - H-), 906 (M + Cl-).
3′-De(oxyp h osp h in ico)-3′-[m et h ylen e(m et h ylim in o)]-
5′-O-(4,4′-d im eth oxytr ip h en ylm eth yl)-2-N-isobu tyr yl-2′-
O-m eth ylgu an osylyl-(3′f5′)-3′-O-(ter t-bu tyldiph en ylsilyl)-
2′-O-m eth yl-5-m eth ylu r id in e (19d ). Compound 19c (348
mg, 0.38 mmol) was reacted with DMTCl (350 mg, 1.03 mmol)
in the presence of DMAP (30 mg) in a manner similar to that
described for the preparation of 20a and 20b, and the product
was purified by chromatography (5 to 7% MeOH/CH2Cl2) to
provide 345 mg (74%) of 19d : 1H NMR (CDCl3) δ 12.08 (bs,
1H), 11.60 (bs, 1H), 11.38 (bs, 1H), 8.03 (s, 1H), 7.62-7.08 (m,
21H), 6.80 (d, 4H), 6.00 (s, 1H), 5.78 (s, 1H), 4.20 (bs, 1H),
4.12-3.95 (m,3H), 3.76 (s, 6H), 3.50-2.58 (m, 19H), 2.25 (s,
3H), 1.60 (s, 3H), 1.20-1.15 (m, 6H), 1.00 (s, 9H); MS (FAB+)
m/ e 1206 (M + H). Anal. Calcd for C65H76N8O13Si‚0.5H2O:
C, 64.29; H, 6.39; N, 9.23. Found: C, 64.25; H, 6.41; N, 9.02.
3′-De(oxyp h osp h in ico)-3′-[m et h ylen e(m et h ylim in o)]-
2′-O-m e t h ylgu a n osylyl-(3′f5′)-2′-O-m e t h yl-5-m e t h yl-
u r id in e (19e). A solution of 19d (140 mg, 0.12 mmol) in
dioxane (2 mL) plus NH4OH (37%, 2 mL) was heated at 55 °C
in a sealed tube for 15 h. The solvent was removed, and the
residue was azeotroped with MeCN (3 × 10 mL) and then
dissolved in THF (2 mL) and treated with Bu4NF on silica gel
(0.32 g, contains 0.35 mmol of Bu4NF) with stirring for 20 h
at rt. The product was chromatographed (60:20:10 EtOAc/
hexane/MeOH and then 10% MeOH/CH2Cl2), and the resulting
product dissolved in 1,1,1,3,3,3-hexafluoro-2-propanol (3 mL)
and vigorously stirred for 3 h. MeOH (0.5 mL) was added,
the solvent removed, and the residue chromatographed (7-
12% MeOH/CH2Cl2) to provide 38 mg (77%) of 19e as a
colorless foam: 1H NMR (DMSO-d6) δ 8.00 (s, 1H), 7.52 (s,
1H), 6.38 (bs, 2H), 5.83 (s, 1H), 5.80 (s, 1H), 5.14 (bs, 1H), 5.00
(bs, 1H), 4.07-3.50 (m, 9H), 3.40 (s, 3H), 3.25 (s, 3H), 2.97
(m, 1H), 2.65 (m, 1H), 2.58 (s, 3H), 1.80 (s, 3H); 13C NMR
(DMSO-d6) δ 163.65, 155.58, 153.62, 150.47, 150.33, 135.77,
134.75, 116.67, 109.65, 86.39, 85.98, 85.85, 84.48, 82.28, 81.71,
71.20, 68.76, 61.15, 57.77, 57.34, 56.57, 45.50, 12.13. Anal.
Calcd for C24H34N8O10‚0.25H2O: C, 46.62; H, 5.73; N, 17.93.
Found: C, 46.48; H, 5.37; N, 17.91.
Ack n ow led gm en t. The authors would like to ac-
knowledge Dr. Ramesh Bharadwaj for the large scale
preparation of 8, and Boyd Conklin for the attempted
HPLC resolution of 19b. We thank Dr. P. Dan Cook
for his support and interest in this project. We also
acknowledge useful discussions with Professor Michael
J ung.
Su p p or tin g In for m a tion Ava ila ble: Full synthetic de-
tails and selected data for compounds 6c, 7a -c, 9a -c, 9e, 10c,
10e, 10f, 11a -k , 12b, 12d , 12h , 12i, 14a , 14b, 15a -d , 16a -
g, 16i-l, and 18 (21 pages). This material is contained in
libraries on microfiche, immediately follows this article in the
microfilm version of the journal, can be ordered from the ACS,
and can be downloaded from the Internet; see any current
masthead page for ordering information and Internet access
instructions.
J O961549C