U.S. patent application number 12/417750 was filed with the patent office on 2010-03-18 for method for preparing oligonucleotides.
This patent application is currently assigned to GIRINDUS AG. Invention is credited to Ilaria Adamo, Francoise Debart, Cecile Dueymes, Jean-Louis Imbach, Meinolf Lange, Fritz Link, Albert Meyer, Francois Morvan, Andreas Schonberger, Jean-Jacques Vasseur.
Application Number | 20100069623 12/417750 |
Document ID | / |
Family ID | 30011111 |
Filed Date | 2010-03-18 |
United States Patent
Application |
20100069623 |
Kind Code |
A1 |
Adamo; Ilaria ; et
al. |
March 18, 2010 |
Method for preparing oligonucleotides
Abstract
A solution phase synthesis method for preparing an
oligonucleotide, wherein at least some of the reagents are solid
supported. The method suitable for large-scale synthesis comprises
coupling a protected compound with a nucleotide derivative having a
protection group in the presence of a solid supported activator to
give an elongated oligonucleotide with a P(III)-internucleotide
bond; optionally processing the elongated oligonucleotide by
capping by reaction with a solid supported capping agent and/or by
oxidizing or sulfurizing by reaction of the oligonucleotide with a
solid supported oxidizing or sulfurization reagent; and removing
the protection group. The coupling may include reacting a
3'-protected compound of formula: ##STR00001## with a nucleotide
derivative having a 5'-protection group, or reacting a 5'-protected
compound of formula ##STR00002## with a nucleotide derivative
having a 3'-protection group.
Inventors: |
Adamo; Ilaria; (Fagagna,
IT) ; Dueymes; Cecile; (Rodez, FR) ;
Schonberger; Andreas; (Muden/Aller, DE) ; Imbach;
Jean-Louis; (Montpellier, FR) ; Meyer; Albert;
(Perols, FR) ; Morvan; Francois; (Castelnau le
Lez, FR) ; Debart; Francoise; (Combaillaux, FR)
; Vasseur; Jean-Jacques; (Combaillaux, FR) ;
Lange; Meinolf; (Halle/Westf, DE) ; Link; Fritz;
(Bergisch-Gladbach, DE) |
Correspondence
Address: |
Solvay;c/o B. Ortego - IAM-NAFTA
3333 Richmond Avenue
Houston
TX
77098-3099
US
|
Assignee: |
GIRINDUS AG
Bergisch-Gladbach
DE
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE
Paris Cedex 16
FR
UNIVERSITY OF MONTPELLIER II
Montpellier Cedex 5
FR
|
Family ID: |
30011111 |
Appl. No.: |
12/417750 |
Filed: |
April 3, 2009 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10522854 |
Nov 8, 2005 |
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PCT/EP03/08447 |
Jul 30, 2003 |
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12417750 |
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60399412 |
Jul 31, 2002 |
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Current U.S.
Class: |
536/25.31 ;
536/25.3 |
Current CPC
Class: |
C07H 21/02 20130101;
Y02P 20/582 20151101; C07H 21/00 20130101; C07H 21/04 20130101;
Y02P 20/55 20151101 |
Class at
Publication: |
536/25.31 ;
536/25.3 |
International
Class: |
C07H 21/04 20060101
C07H021/04 |
Foreign Application Data
Date |
Code |
Application Number |
Jul 31, 2002 |
EP |
02017211.0 |
Claims
1. A method for preparing an oligonucleotide comprising the steps
of a) providing a 3'-protected compound having the formula:
##STR00007## wherein B is a heterocyclic base, R.sub.2 is H, a
protected 2'-hydroxyl group, F, a protected amino group, an O-alkyl
group, an O-substituted alkyl, a substituted alkylamino or a
C4'-O2' methylene linkage, R.sub.3 is OR'.sub.3, NHR''.sub.3,
NR''.sub.3R'''.sub.3, a 3'-protected nucleotide, or a 3'-protected
oligonucleotide, R'3 is a hydroxyl protecting group, R'.sub.3,
R'''.sub.3 are independently an amine protecting group; b) reacting
said compound with a nucleotide derivative having a 5'-protection
group in the presence of a solid supported activator to give an
elongated oligonucleotide with a P(III)-internucleotide bond; c)
optionally processing the elongated oligonucleotide with a
P(III)-internucleotide bond by either or both of steps cl) and c2)
in any sequence: cl) capping by reacting with a solid supported
capping agent; c2) oxidizing or sulfurizing by reacting the
oligonucleotide with a solid supported oxidizing reagent; d)
removing the 5'-protection group by treatment with a solid
supported agent or removing the 5'-protection group with a removal
agent followed by addition of a solid supported scavenger; and e)
repeating steps a) to d) at least once.
2. The method of claim 1, wherein the nucleotide derivative having
a 5'-protection group of step b) has the following formula:
##STR00008## wherein X is a P(III)-function, B is a heterocyclic
base, R.sub.2 is H, a protected 2'-hydroxyl group, F, a protected
amino group, an O-alkyl group, an O-substituted alkyl, a
substituted alkylamino or a C4'-O2' methylene linkage, R.sub.5 is a
hydroxyl protecting group, a 5'-protected nucleotide, or a
5'-protected oligonucleotide.
3. A method for preparing an oligonucleotide comprising the steps
of a) providing a 5'-protected compound having the formula:
##STR00009## wherein B is a heterocyclic base, R.sub.2 is H, a
protected 2'-hydroxyl group, F, a protected amino group, an O-alkyl
group, an O-substituted alkyl, a substituted alkylamino or a
C4'-O2' methylene linkage, R.sub.3 is OH, NH.sub.2, R.sub.5 is a
hydroxyl protecting group, a 5'-protected nucleotide or a
5'-protected oligonucleotide; b) reacting said compound with a
nucleotide derivative having a 3'-protection group in the presence
of a solid supported activator to give an elongated oligonucleotide
with a P(III)-internucleotide bond; c) optionally processing the
elongated oligonucleotide with a P(III)-internucleotide bond by
either or both of steps cl) and c2) in any sequence; cl) capping by
reacting with a solid supported capping agent; c2) oxidizing or
sulfurizing by reacting the oligonucleotide with a solid supported
oxidizing reagent; d) removing the 3'-protection group by treatment
with a solid supported agent or removing the 3'-protection group
with a removal agent followed by addition of a solid supported
scavenger; and e) repeating steps a) to d) at least once.
4. The method of claim 3, wherein the nucleotide derivative having
a 3'-protection group has the following formula: ##STR00010##
wherein X is a P(III)-function, B is a heterocyclic base, R.sub.2
is H, a protected 2'-hydroxyl group, F, a protected amino group, an
O-alkyl group, an O-substituted alkyl, a substituted alkylamino or
a C4'-O2' methylene linkage, R.sub.3 is OR'.sub.3, NHR''.sub.3,
NR''.sub.3R'''.sub.3, a 3'-protected nucleotide or a 3'-protected
oligonucleotide, R'3 is a hydroxyl protecting group, R''.sub.3,
R'''.sub.3 are independently an amine protecting group, R'3 is a
hydroxyl protecting group, a 3'-protected nucleotide or a
3'-protected oligonucleotide.
5. The method of claim 1, wherein the nucleotide derivative of step
b) is a phosphoramidite or a H-phosphonate.
6. The method of claim 1 wherein the solid supported activator of
step b) is selected from the group consisting of a solid support
bearing a pyridinium salt, a cation exchange solid support with an
optionally substituted pyridinium salt, a cation exchange solid
support with an optionally substituted imidazolium salt, a solid
support bearing an optionally substituted azole (imidazol,
triazole, tetrazole), a salt of a weak base anion exchange resin
with a strong acid, a weak cation exchange resin (carboxylic) in
its protonated form, a solid support bearing an optionally
substituted phenol, a solid support bearing a carboxylic acid
chloride/bromide, a sulfonic acid chloride/bromide, a
chloroformate, a bromoformate, a chlorosulfite, a bromosulfite, a
phosphorochloridate, a phosphorbromidate and a solid support bound
carbodiimide.
7. The method of claim 1, wherein the solid supported oxidizing
reagent is selected from the group consisting of solid supported
periodate, permanganate, osmium tetroxide, dichromate,
hydroperoxide, substituted alkylamine oxide, percarboxylic acid and
persulfonic acid.
8. The method of claim 1, wherein the solid supported oxidizing
reagent is a solid supported sulfurization reagent.
9. The method of claim 8, wherein the solid supported sulfurization
reagent is selected from the group consisting of a solid supported
tetrathionate, a solid supported alkyl or aryl sulfonyl disulfide,
a solid supported optionally substituted dibenzoyl tetrasulfide, a
solid supported bis(alkyloxythiocarbonyl)tetrasulfide, a solid
supported optionally substituted phenylacetyl disulfide, a solid
supported N-[(alkyl or aryl)sulfanyl]alkyl or aryl substituted
succinimide, and a solid supported (2-pyridinyldithio)alkyl or
aryl.
10. The method of claim 1, wherein the solid supported capping
agent is a solid supported activated acid, preferably a carboxylic
acid chloride, carboxylic acid bromide, azolide, substituted
azolide, anhydride or chloroformate or phosphorochloridate, or a
solid supported phosphoramidite, or a solid supported H-phosphonate
monoester.
11. The method of claim 1, wherein the 5'-protection is a
dimethoxytrityl group (DMTr) or a monomethoxytrityl group (MMTr)
and the solid supported agent of step d) is a cationic ion
exchanger resin in the H.sup.+ form or solid supported ceric
ammonium nitrate.
12. A method for preparing an oligonucleotide comprising the steps
of a) providing a compound having the formula: ##STR00011## wherein
B is a heterocyclic base, R.sub.2 is H, a protected 2'-hydroxyl
group, F, a protected amino group, an O-alkyl group, an
O-substituted alkyl, a substituted alkylamino or a C4'-O2'
methylene linkage, R.sub.3 is OR'.sub.3, NHR''.sub.3,
NR''.sub.3R'''.sub.3, a 3'-protected nucleotide or a 3'-protected
oligonucleotide; and R.sub.5 is a P(III)-function, R'.sub.3 is a
hydroxyl protecting group, R''.sub.3, R'''.sub.3 are independently
an amine protecting group, or R.sub.5 is a hydroxyl protecting
group, a protected nucleotide or a protected oligonucleotide and
R.sub.3 is a P(III)-function; b) reacting said compound with a
nucleotide derivative having a 3' or 5'-free OH-- group in the
presence of a solid supported activator to give an elongated
oligonucleotide with a P(III)-internucleotide bond; c) optionally
processing the elongated oligonucleotide with a
P(III)-internucleotide bond by either or both of steps cl) and c2)
in any sequence: cl) capping by reacting with a solid supported
capping agent; c2) oxidizing or sulfurizing by reacting the
oligonucleotide with a solid supported oxidizing reagent; d)
removing the 3' or 5'-protection group by treatment with a solid
supported agent or removing the 5'-protection group with a removal
agent followed by addition of a solid supported scavenger; and e)
repeating steps a) to d) at least once.
13. The method of claim 3, wherein the nucleotide derivative of
step b) is a phosphoramidite or a H-phosphonate.
14. The method of claim 3 wherein the solid supported activator of
step b) is selected from the group consisting of a solid support
bearing a pyridinium salt, a cation exchange solid support with an
optionally substituted pyridinium, a cation exchange solid support
with an optionally substituted imidazolium salt, a solid support
bearing an optionally substituted azole (imidazol, triazole,
tetrazole), a salt of a weak base anion exchange resin with a
strong acid, a weak cation exchange resin (carboxylic) in its
protonated form, a solid support bearing an optionally substituted
phenol, a solid support bearing a carboxylic acid chloride/bromide,
a sulfonic acid chloride/bromide, a chloroformate, a bromoformate,
a chlorosulfite, a bromosulfite, a phosphorochloridate, a
phosphorbromidate and a solid support bound carbodiimide.
15. The method of claim 3, wherein the solid supported oxidizing
reagent is selected from the group consisting of solid supported
periodates, permanganates, osmium tetroxides, dichromates,
hydroperoxides, substituted alkylamine oxides, percarboxylic acid,
and persulfonic acid.
16. The method of claim 3, wherein the solid supported oxidizing
reagent is a solid supported sulfurization reagent.
17. The method of claim 16, wherein the solid supported
sulfurization reagent is selected from the group consisting of a
solid supported tetrathionate, a solid supported alkyl or aryl
sulfonyl disulfide, a solid supported optionally substituted
dibenzoyl tetrasulfide, a solid supported
bis(alkyloxythiocarbonyl)tetrasulfide, a solid supported optionally
substituted phenylacetyl disulfide, a solid supported N-[(alkyl or
aryl)sulfanyl]alkyl or aryl substituted succinimide and a solid
supported (2-pyridinyldithio)alkyl or aryl.
18. The method of claim 3, wherein the solid supported capping
agent is a solid supported activated acid, preferably a carboxylic
acid chloride, carboxylic acid bromide, azolide, substituted
azolide, anhydride or chloroformate or phosphorochloridate, or a
solid supported phosphoramidite, or a solid supported H-phosphonate
monoester.
19. The method of claim 3, wherein the 3'-protection is a silyl
group and the solid supported agent of step d) is a solid-supported
ammonium fluoride, or the 3'-protection is levuiinic acid, and the
solid supported agent of step d) is a solid supported hydrazine or
a solid supported hydrazinium.
20. A method for sulfurization of an oligonucleotide with a P(III)
internucleotide bond comprising the step of oxidizing with a solid
supported sulfurization agent consisting of solid supported amine
and a tetrathionate having the formula S.sub.4O.sub.6.sup.-2 or a
cyanoethylthiosulfate having the formula
(NC--CH.sub.2--CH.sub.2--S--SO.sub.3.sup.-).
Description
[0001] The present invention relates to a method for preparing
oligonucleotides.
[0002] The synthesis of oligonucleotides has been the subject of
investigations for a long period of time. Automated synthesis
procedures have been developed and apparatus for the automated
syntheses are commercially available. Most of these procedures have
been developed for rather small quantities of oligonucleotides (in
the range of mg). These amounts are sufficient for most
investigational purposes.
[0003] Especially with the development of antisense therapeutics,
large scale synthesis lip became a matter of considerable
importance. Although relative large scale amounts of
oligonucleotides have been obtained by scale-up of solid phase
synthesis procedures, these technologies show major limitations
especially high costs for reagents and materials, e.g. the solid
phase bound starting oligonucleotide.
[0004] With scale-up, the reaction time of each step of the
synthesis increases.
[0005] Furthermore oligonucleotides synthesis by standard solid
phase synthesis results in a contamination of the desired full
length compound by failure sequences arising from incomplete
reaction during the synthesis cycle. At large scales the
purification of the crude oligonucleotide involves complicated
isolation and chromatographic purification of the final
product.
[0006] In general, synthesis methods for oligonucleotides consist
of a four-step procedure for the elongation of the
oligonucleotide
1. Coupling
2. Capping
3. Oxidation
[0007] 4. Deprotection of the protected hydroxyl group for the next
reaction cycle.
[0008] One object of the present invention is to provide a method
for the preparation of oligonucleotides suitable for large scale
(kilogram to tons) synthesis.
[0009] A further object of the present invention is to provide a
method for the preparation of oligonucleotides avoiding complicated
purification steps, especially chromatographic purifications,
especially during synthesis cycles.
[0010] A further object of the invention is to provide a method for
the preparation of oligonucleotides allowing an effective
convergent synthesis.
[0011] In one embodiment this object is solved by a liquid phase
synthesis method, comprising the steps of [0012] a) providing a
3'-protected compound having the formula;
[0012] ##STR00003## [0013] wherein [0014] B is a heterocyclic base
[0015] R.sub.2 is H, a protected 2'-hydroxyl group, F, a protected
amino group, an O-alkyl group, an O-substituted alkyl, a
substituted alkylamino or a C4'--O2' methylen linkage
[0016] R.sub.3 is OR'.sub.3, NHR''.sub.3, NR''.sub.3R'''.sub.3, a
3'-protected nucleotide or a 3'-protected oligonucleotide,
[0017] R'.sub.3 is a hydroxyl protecting group,
[0018] R''.sub.3, R'''.sub.3 are independently an amine protecting
group, [0019] b) reacting said compound with a nucleotide
derivative having a 5'-protection group in the presence of a solid
supported activator to give an elongated oligonucleotide with a
P(III)-internucleotide bond [0020] c) optionally processing the
elongated oligonucleotide with a P(III)-internucleotide bond by
either or both of steps c1) and c2) in any sequence [0021] c1)
capping, preferably by reacting with a solid supported capping
agent [0022] c2) oxidizing, preferably by reacting the
oligonucleotide with a solid supported oxidizing reagent [0023] d)
removing the 5'-protection group.
[0024] The method of the present invention is a solution phase
synthesis wherein at least some of the reagents are solid
supported. "Solid supported" covers covalently bound reagents and
reagents bound to a solid support by ionic forces.
[0025] In a preferred embodiment, step d) is effected by treatment
with a solid supported agent or removing the 5'-protection group
with a removal agent followed by addition of a solid supported
scavenger or followed by extraction.
[0026] In most cases coupling occurs of a 5'-OH-synthon with a
3'-phosphorous-synthon. Alternatively coupling of a
5'-phosphorous-synthon with a 3'-OH-synthon is also possible.
Therefore in a further embodiment the invention comprises a method
comprising the steps of [0027] a) providing a 5'-protected compound
having the formula:
[0027] ##STR00004## [0028] wherein [0029] B is a heterocyclic base
[0030] R.sub.2 is H, a protected 2'-hydroxyl group, F, a protected
amino group, an O-alkyl group, an O-substituted alkyl, a
substituted alkylamino or a C4'--O2' methylen linkage [0031]
R.sub.3 is OH, NH.sub.2 [0032] R.sub.5 is a hydroxyl protecting
group, a 5'-protected nucleotide or a 5'-protected oligonucleotide
[0033] b) reacting said compound with a nucleotide derivative
having a 3'-protection group in the presence of a solid supported
activator to give an elongated oligonucleotide with a
P(III)-internucleotide bond [0034] c) optionally processing the
elongated oligonucleotide with a internucleotide bond by either or
both of steps c1) and c2) in any sequence [0035] c1) capping,
preferably by reacting with a solid supported capping agent [0036]
c2) oxidizing, preferably by reacting the oligonucleotide with a
solid supported oxidizing reagent [0037] d) removing the
3'-protection group.
[0038] In a preferred embodiment, step d) is effected by treatment
with a solid supported agent or removing the 3'-protection group
with a removal agent followed by addition of a solid supported
scaenger or followed by extraction.
[0039] In further embodiments, it is possible to couple a
3'-phosphorous synthon with a 3'-OH synthon to form a non-natural
3'-3'-internucleosidic linkage. For the synthesis of non-natural
5'-5'-internucleosidic linkages it is possible to react a
5'-phosphorous synthon with a 5'-OH synthon. These non-natural
internucleosidic linkages show increased nuclease resistance.
Step a)
[0040] B, the heterocyclic base can be a natural nucleobase or a
modified one including a non-base residue. The natural nucleobasis
are adenine, guanine, thymine, cytosine and uracil. In general
these bases need protection groups during the synthesis. Suitable
protected nucleobases are known to persons skilled in the art for
example N-4-benzoylcytosine, N-6-benzoyl adenine, N-2-isobutiryl
guanine, N-4-acetyl or isobutyril cytosine, N-6-phenoxyacetyl
adenine, N-2-tert-butyl phenoxyacetyl guanine. Suitable non-base
residues include for example Hydrogen, H leading to the
1',2'-dideoxyribose (dSpacer from Glen Research) which can be used
as linker or to mimic abasic sites in an oligonucleotide (Takeshita
et al., J. Biol. Chem., 1987, 262, 10171).
[0041] Furthermore, it is also possible to use isomers of
nucleosides such as L, D, .alpha., .beta. and the like.
[0042] A suitable protection for the 2'-hydroxyl-group include but
are not limited to tert-butyl dimethylsilyl (TBDMS),
triisopropylsilyloxymethyl (TOM), fluorophenyl-metoxypiperidinyl
(FPMP).
[0043] Suitable protecting groups for the 3'-hydroxyl-group include
but are not limited to tert-butyl dimethylsilyl (TBDMS), levulinyl,
benzoyle. This compound is then reacted with a nucleotide
derivative with a 3'-phosphorous-synthon. The nucleotide derivative
preferably has the following formula
##STR00005##
wherein
[0044] X is a P(III)-function
[0045] B is a heterocyclic base
[0046] R.sub.2 is H, a protected 2'-hydroxyl group, F, a protected
amino group, an O-alkyl group, an O-substituted alkyl, a
substituted alkylamino or a C4'--O2' methylen linkage
[0047] R.sub.5 is a hydroxyl protecting group, a 5'-protected
nucleotide or a 5'-protected oligonucleotide.
[0048] In the second embodiment, the nucleotide derivative
preferably has the following formula
##STR00006##
wherein
[0049] X is a P(III)-function
[0050] B is a heterocyclic base
[0051] R.sub.2 is H, a protected 2'-hydroxyl group, F, a protected
amino group, an O-alkyl group, an O-substituted alkyl, a
substituted alkylamino or a C4'--O2' methylen linkage
[0052] R.sub.3=, OR'.sub.3, NR''.sub.3, NR''.sub.3R'''.sub.3, a
3'-protected nucleotide or a 3'-protected oligonucleotide,
[0053] R'.sub.3 is a hydroxyl protecting group,
[0054] R''.sub.3, R'''.sub.3 are independently an amine protecting
group,
[0055] R'.sub.3 is a hydroxyl protecting group, a 3'-protected
nucleotide or a 3'-protected oligonucleotide
Step b): The Coupling Step
[0056] In step b) the coupling of the nucleotide or
oligonucleotides occurs. The chemistry of the reaction depends on
the type of activated phosphorous compound.
[0057] Several methods for coupling nucleotides are known. The most
common methods are via phosphoramidite and via H-phosphonate. In
each of these cases the phosphor is in an activated state which
allows coupling with the free hydroxyl group of the other part.
[0058] In phosphoramidite chemistry (Beaucage et al., Tetrahedron,
1992, 48, 2223-2311: Beaucage and Caruthers in unit 3.3 of Current
Protocols in Nucleic Acid Chemistry, Wiley) a nucleoside or
oligonucleotide-3'-O-phosphoramidite where the P(III) phosphorus is
substituted with a dialkylamine (phosphite activating group) and a
phosphorus protecting group (including but not limited to
2-cyanoethyl, methyl) is reacted with 5'-hydroxyl nucleoside or
oligonucleotide in presence of an activator to create a phosphite
triester internucleosidic linkage.
[0059] In H-phosphonate chemistry (Froehler, Methods in Molecular
Biology. Protocols for oligonucleotides and analogs, Humana Press,
1993, 63-80; Stromberg and Stawinski, in unit 3.4 of Current
Protocols in Nucleic Acid Chemistry, Wiley) a nucleoside or
oligonucleotide-3'-O--H-phosphonate is reacted with a 5'-hydroxyl
nucleoside or oligonucleotide in presence of an activator to create
a H-phosphonate diester internucleosidic linkage.
[0060] Suitable activators for the coupling step in phosphoramidite
chemistry include, but are not limited to a solid support bearing a
pyridinium salt, for example a solid support covalently linked to
pyridine e.g. poly(vinyl)-pyridinium or the pyridinium is a counter
ion of a cation exchange solid support. The cation exchange support
can be a strong or a weak exchanger, for example a sulfonic acid or
a carboxylic acid. The pyridinium salt can also be a substituted
pyridinium salt, for example dichloropyridinium. It can further be
a solid support bearing an optionally substituted azole (imidazole,
triazole, tetrazole), or is the salt of a weak base anion exchange
resin with a strong acid, or a weak cation exchange resin
(carboxylic) in its protonated form (see U.S. Pat. No. 5,574,146),
or a solid support bearing an optionally substituted phenol (see W.
Dabkowski and al., Tet Lett, 2000, 41, 7535-7539).
[0061] The use of imidazole is less preferred.
[0062] For the H-phosphonate method the suitable activators
include, but are not limited to solid supports bearing a carboxylic
acid chloride, sulfonic acid chloride, a chloroformate, a
chlorosulfite or a phosphorochloridate or the respective
Br-compounds. Further compounds are disclosed in WO 01/64702 A1,
page 6, line 36 to page 8, line 5, incorporated by reference and C
B Reese and Q Song, Nucleic Acid Res., 1999, 27, 963-971.
Step c) Capping and Oxidizing
[0063] Capping is understood as a reaction wherein a reagent reacts
with remaining protected compounds of step a). As the capping agent
is preferably solid supported, the 3'-protected compound can be
removed together with the solid supported capping agent.
[0064] For the capping step suitable reagents suitable capping
agents include, but are not limited to activated acids for example
carboxylic acid, chloride or sulfonic acid chloride, carboxylic
acid bromide, azolide, substituted azolide, anhydride or
chloroformate or phosphorochloridate, or a solid supported
phosphoramidate, or a solid supported H-phosphonate monoester. The
acid group is preferably an acid group covalently bound to a solid
support. Commercially available cationic exchanger resins can be
used as a starting material for synthesizing the solid supported
carboxylic acids or sulfonic acids.
[0065] The oxidizing reaction is used to oxidize the
P(III)-internucleotide bond to a P(V)-internucleotide bond. Capping
can be performed before oxidizing and vice versa. Depending on the
reagents capping and oxidizing may also be combined in one
step.
[0066] In case of H-phosphonate chemistry, the oxidizing step is
preferably done in every second or third cycle or at the end of
synthesis only. In phosphoamidite chemistry removal of the excess
of 5' nucleoside oligonucleotide can be facsilated by a hydrolysis
step, for example with water.
[0067] For the oxidizing step the oxidizing reagent can be any
oxidizing reagent used for prior art solid phases, preferably in
the form of solid supported agent, either covalently bound or bound
by ionic forces. Suitable reagents are solid supported periodates,
permanganates, osmium tetroxides, dichromates, hydroperoxides,
substituted alkylamine oxides, percarboxylic acid and persulfonic
acid.
[0068] These compounds are negatively charged, therefore they can
be solid supported by a suitable ion exchanger for example an ion
exchanger bearing ammonium groups. These substances could be bound
to solid support consisting for example of an amino, alkyl amino,
dialkyl amino or trialkyl amino anion exchanger.
[0069] In oligonucleotides synthesis for investigational purposes
and especially for antisense therapeutics phosphorthioate analogs
are used. In this case the oxidizing is a sulfurization. As a solid
supported oxidizing reagent a solid supported sulfurization reagent
is used, for example a solid supported tetrathionate, a solid
supported alkyl or aryl sulfonyl disulfide, a solid supported
optionally substituted dibenzoyl tetrasulfide, a solid supported
bis(alkyloxythlocarbonyl)tetrasuifide, a solid supported optionally
substituted phenylacetyl disulfide, a solid supported N-[(alkyl or
aryl)sulfanyl]alkyl or aryl substituted succinimide and a solid
supported (2-pyridinyldithio)alkyl or aryl.
[0070] Very preferred is a solid supported cyanoethylthiosulfate
(NC--CH.sub.2--CH.sub.2S--SO.sub.3.sup.-), available according to
the procedure in U.S. Pat. No. 3,506,676 or a solid supported
tetrathionate.
Step d) Deprotection
[0071] Suitable 5'-protection group include, but are not limited to
trityl groups, preferably a dimethoxytrityl group (DMTr) or a
monomethoxytrityl group (MMTr). These protection groups are used in
conventional prior art solid phase oligonucleotides synthesis.
Other suitable 5'-protection groups include, but are not limited to
tert-butyl dimethylsilyl (TBDMS), levulinyl, benzoyle,
fluorenemethoxycarbonyl (FMOC), the
9-phenylthioxanthen-9-yl(S-pixyl).
[0072] In the second embodiment, in step d) the 3'-protection group
is removed. Suitable 3'-protection groups include, but are not
limited to 3'-O-tent butyl dimethyl silyl (TBDMS), 3'-O-acetate,
3'-O-levulinyl groups. They can be removed by a solid-supported
ammonium fluoride, solid-supported ammonium hydroxide or
solid-supported hydrazine.
[0073] In step d) of the first embodiment, the 5'-protection group
is removed. Thereafter the oligonucleotides can either be used or
the oligonucleotide corresponds to the 3'-protected compound of
step a) to repeat the cycle.
[0074] The use of solid supported reagents for the removal of the
DMTr-protection group for a completely synthesized oligonucleotide
has already been reported in U.S. Pat. No. 5,808,042. The content
of this document is incorporated by reference. Surprisingly the
methods disclosed in U.S. Pat. No. 5,808,042 can also be applied in
a solution phase synthesis as described in the present
application.
[0075] Suitable reagents are also disclosed in synthetic
communications 24 (17) 1994, 2323-2428.
[0076] In step d) of the second embodiment, the 3'-protection group
is removed. Thereafter the oligonucleotides can either be used or
the oligonucleotide corresponds to the 5'-protected compound of
step a) to repeat the cycle.
Step e): Repetition
[0077] In most cases the methods will be repeated at least once.
When starting from monomeric oligonucleotides the method of the
present invention will result in a dimer. Repeating the method of
the present invention will elongate the dimer to a trimer. By
repeating the method of the invention several times n-mers can be
synthesized.
[0078] As the yield of a synthesis is not 100%, the overall yield
of correct oligonucleotides decreases with the number of cycles.
Depending on the yield of a single cycle, oligonucleotides can be
synthesized of at least up to 100 nucleotides in sufficient yield,
but longer oligonucleotides are also possible.
[0079] For most cases oligonucleotides having that size will not be
needed. An antisense therapy oligonucleotides are normally in the
range of 8-36 nucleotides, more preferably 12-30, most commonly in
the range of the 16-26 nucleotides.
[0080] In contrast to prior art, convergent synthesis strategies
are fully compatible with the synthesis method of the present
invention. Convergent synthesis methods are methods wherein small
oligonucleotides are synthesized first and the small
oligonucleotides are then combined for synthesizing larger blocks.
By this method the number of coupling reactions can be
significantly reduced. Thereby the overall yield of the
oligonucleotide is increased.
[0081] In prior art, each synthesis of a small oligonucleotide had
to start from the solid support bound nucleic acid which was rather
expensive. Therefore convergent synthesis strategies have not found
much application in oligonucleotide synthesis.
[0082] Convergent synthesis has the further advantage, that the
reaction product is essentially free of (n-1)mers. In prior art
synthesis, the purification of oligonucleotides with a length of n
from oligonucleotides with a length of n-1 is the most difficult in
purification of the oligonucleotide. By convergent synthesis, these
(n-1)mers are nearly avoided, because larger fragments are
combined.
[0083] In a preferred embodiment, the method of the present
invention uses dimers or trimers as the compounds in step a) and/or
b).
[0084] During the synthesis cycles, reagents are mostly added in a
solid supported form. These solid supported reagents are preferably
removed after reaction or after each reaction step. Depending on
the type of reagent it is in some cases possible to remove two or
more of the solid supported reagents together.
[0085] In a preferred embodiment, coupling and at least final
oxidizing steps are done by solid supported reagents.
[0086] As the synthesis is intended for the production of large
amounts of oligonucleotides it is preferred that the solid
supported reagent is recycled. This recycling is obviously easier
if the solid supported reagents are removed separately after each
reaction.
[0087] The solid supported reagents can be removed by methods like
filtration or centrifugation. Because of the ease of handling,
filtration is the preferred way of removing the solid supported
reagents.
[0088] A very preferred reagent for the sulfurization is a solid
supported anion exchange resin in complex with a tetrathionate
having the formula S.sub.4O.sub.6, preferably a quaternary ammonium
resin bearing tetrathionate as counter ion.
Purification
[0089] After the final synthesis cycle, it will in most cases be
necessary to make one or more additional purification steps. Such
purification steps for crude oligonucleotide synthesis products are
known in prior art solid phase synthesis.
[0090] It is necessary to remove the remaining protection groups
especially from the heterocyclic bases and optionally remaining
protecting groups on the sugar or phosphorous backbone.
[0091] In a preferred embodiment, in case of the use of MMT or DMT
as a protection group, the oligonucleotide is purified by binding
to an ion exchanger and the protection group is removed while the
oligonucleotide is bound to the exchanger. After removal of the
protection groups, the oligonucleotide is released from the ion
exchanger.
[0092] The invention will be further exemplified with the following
examples.
EXAMPLE 1
Synthesis of the dimer 5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl
phosphite triester
[0093] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phosphoramidite with 5'-OH-T-3'-O-TBDMS using the DOWEX 50W X8
pyridinium form.
Analytical Scale.
[0094] 5'-OH-T-3'-O-TBDMS (11 mg, 32.5 mmol) and
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (41 mg, 55.25 mmol, 1.7
eq) are dissolved in anhydrous acetonitrile (550 ml). The solution
is transferred under argon in a NMR tube containing the DOWEX 50W
X8 pyridinium form (100 mg, 0.30 mmol pyrH.sup.+, 9.2 eq). The
reaction is followed by .sup.31P NMR. Before the NMR experiment
deuterated acetonitrile (50 ml) is added. The yield is determined
by .sup.31P NMR. After 3 h the desired dimer T-T phosphite triester
is obtained with 100% of yield compared to 5'-OH-T-3'-O-TBDMS. The
crude is a mixture of 5'-O-DMTr-T-3'-cyanoethyl phosphoramidite
(.sup.31P NMR (CD.sub.3CN) .delta. 149.14, 149.07, 14.7%),
5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl phosphite triester (.delta.
140.53, 70.2%), 5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate
(.delta. 8.74, 15.1%).
EXAMPLE 2
Synthesis of the dimer 5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl
phosphite triester
[0095] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phosphoramidite with 5'-OH-T-3'-O-TBDMS using the
poly(4-vinylpyridinum p-toluenesulfonate) (Aldrich).
Analytical Scale.
[0096] 5'-OH-T-3'-O-TBDMS (11 mg, 32.5 mmol) and
5'O-DMTr-T-3'-cyanoethyl phosphoramidite (41 mg, 55.25 mmol, 1.7
eq) are dissolved in anhydrous acetonitrile (550 ml). The solution
is transferred under argon in a NMR tube containing the
poly(4-vinylpyridinum p-toluenesulfonate) (100 mg, 0.33 mmol
tos.sup.-, 10.3 eq). The reaction is followed by .sup.31P NMR.
Before the NMR experiment deuterated acetonitrile (50 ml) is added.
The yield is determined by .sup.31P NMR. After 1 h 45 the desired
dimer T-T phosphite triester is obtained with 82% of yield compared
to 5'-OH-T-3'-O-TBDMS. The crude is a mixture of
5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl phosphite triester (.sup.31P
NMR (CD.sub.3CN) .delta. 140.54, 48.2%), 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.77, 51.8%).
EXAMPLE 3
Synthesis of the dimer 5'-OH-T-T-3'-O-TBDMS cyanoethyl
phosphorothloate triester
[0097] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phosphoramidite with 5'-OH-T-3'-O-TBDMS using the DOWEX 50W X8
pyridinium form.
[0098] A solution of 5'-OH-T-3'-O-TBDMS (124 mg, 0.35 mmol) and
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (441 mg, 0.59 mmol, 1.7
eq) in anhydrous acetonitrile (6 ml) is added to DOWEX 50W X8
pyridinium form (1 g, 3 mmol pyrH.sup.+, 9.5 eq). The resulting
mixture is shaken for 4 h 45. The reaction is followed by .sup.31P
NMR and the yield is also determined by .sup.31P NMR. The desired
dimer 5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl phosphite triester is
obtained with 100% of yield compared to 5'-OH-T-3'-O-TBDMS. The
crude is a mixture of 5'-O-DMTr-T-3'-cyanoethyl phosphoramidite
(.sup.31P NMR (CD.sub.3CN) .delta. 149.17, 449.10, 5.4%),
5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl phosphite triester (.delta.
140.57, 140.54, 68.3%), 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.75, 8.71, 26.3%).
[0099] Sulfurization: The DOWEX 50W X8 resin is filtered off and
the resulting solution is added to AMBERLYST A26 tetrathionate form
(1.44 g, 2.44 mmol S.sub.4O.sub.6.sup.2-, 7 eq.). The reaction is
followed by .sup.31P NMR and the yield is also determined by
.sup.31P NMR. After 20 h the desired dimer 5'-O-DMTr-T-T-3'-O-TBDMS
cyanoethyl phosphorothioate triester is obtained with 97% of yield.
The crude is a mixture of 5'-O-DMTr-T-3'-cyanoethyl
thiophosphoramidate (.sup.31P NMR (CD.sub.3CN) .delta. 71.16,
4.0%), 5'-O-DMTr-T-T-3'-O-TBDMS cyanoethyl phosphorothioate
triester (d 68.28, 68.23, 69.5%), 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (d 8.75, 8.71, 26.5%). MALDI-TOF MS (negative
mode, trihydroxyacetophenone as matrix) ammonia treatment of an
aliquot gives 5'-OH-T-T-3'-O-TBDMS phosphorothioate diester:
[M-H].sup.- m/z.sub.exp=978.12, m/z.sub.calc=977.13.
[0100] Detritylation: The AMBERLYST A26 is filtered off and the
solvent are evaporated. The crude is dissolved in 4 ml of
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled in an ice bath. To
this solution is added 1 ml of a solution of benzene sulfonic acid
10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred
15 min at 0.degree. C. The reaction is washed with 10 ml of a
saturated solution of NaHCO.sub.3, the organic layer is separated,
dried (Na.sub.2SO.sub.4), evaporated, and purified on a silica gel
column. The desired dimer T-T is eluted with
CH.sub.2Cl.sub.2/CH.sub.3OH (95/5). The appropriates fractions are
collected and evaporated to give 230 mg of a white foam in a yield
of 83% compared to 5'-OH-T-3'-O-TBDMS. .sup.31P NMR (CD.sub.3CN)
.delta. 68.29, 68.19. MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M+H].sup.+ m/z.sub.exp=730.46,
m/z.sub.calc=730.82. The spectrophotometric purity (97%) is
determined by HPLC at 260 nm.
EXAMPLE 4
Synthesis of the trimer 5'-OH-T-T-T-3'-O-TBDMS cyanoethyl
phosphorothioate triester
[0101] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phosphoramidite with the dimer 5'-OH-T-T-3'-O-TBDMS cyanoethyl
phosphorothioate triester using the DOWEX 50W X8 pyridinium
form.
[0102] A solution of 5'-OH-T-T-3'-O-TBDMS cyanoethyl
phosphorothioate triester (230 mg, 0.31 mmol) and
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (399 mg, 0.54 mmol, 1.7
eq) in anhydrous acetonitrile (8 ml) is added to DOWEX 50W X8
pyridinium form (1 g, 3 mmol pyr.sup.+, 9.5 eq). The resulting
mixture is shaken for 5 h. The reaction is followed by .sup.31P NMR
and the yield is also determined by .sup.31P NMR. The desired
trimer 5'-O-DMTr-T-T-T-3'-O-TBDMS cyanoethyl phosphite triester is
obtained with 100% of yield compared to the dimer
5'-OH-T-T-3'-O-TBDMS cyanoethyl phosphorothioate triester. The
crude is a mixture of 5'-O-DMTr-T-3'-cyanoethyl phosphoramidite
(.sup.31P NMR (CD.sub.3CN) .delta. 149.16, 149.10, 17.7%),
5'-O-DMTr-T-T-T-3'-O-TBDMS cyanoethyl phosphite triester (.delta.
140.85, 140.68, 140.37, 140.30, d 68.07, 68.02, 68.3%),
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (88.7, 8.68,
14%).
[0103] Sulfurization: The DOWEX 50W X8 pyridinium form is filtered
off and the resulting solution is added to AMBERLYST A26
tetrathionate form (1.3 g, 2.44 mmol S.sub.4O.sub.6.sup.2-, 7 eq.).
The reaction is followed by .sup.31P NMR and the yield is also
determined by .sup.31P NMR. After 45 h the desired trimer
5'-O-DMTr-T-T-T-3'-O-TBDMS cyanoethyl phosphorothioate triester is
obtained with 100% of yield. MALDI-TOF MS (negative mode,
trihydroxyacetophenone as matrix) [M-H].sup.- m/z.sub.exp=1297.89,
m/z.sub.calc=1296.38 after 30 min of ammonia treatment to remove
the cyanoethyl protecting group. The crude is a mixture of
5'-O-DMTr-T-3'-cyanoethyl thiophosphoramidate (.sup.31P NMR
(CD.sub.3CN) d 72.04, 71, 17, 14.0%), 5'-O-DMTr-T-T-T-3'-O-TBDMS
cyanoethyl phosphorothioate triester (d 68.17, 68.12, 68.07, 67.96,
67.80, 67.58, 73.8%), 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (d 8.76, 8.71, 12.2%).
[0104] Detritylation: The AMBERLYST A26 is filtered off and the
solvent are evaporated. The crude is dissolved in 4 ml of
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled in an ice bath. To
this solution is added 1 ml of a solution of benzene sulfonic acid
10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred
45 min at 0.degree. C. The reaction is washed with 10 ml of a
saturated solution of NaHCO.sub.3, the organic layer is separated,
dried (Na.sub.2SO.sub.4), evaporated, and purified on a silica gel
column. The desired trimer T-T-T is eluted with
CH.sub.2Cl.sub.2/CH.sub.3OH (95/5). The appropriates fractions are
collected and evaporated to give 221 mg of a white foam in a yield
of 63% compared to the dimer 5'-OH-T-T-3'-O-TBDMS cyanoethyl
phosphorothioate triester. .sup.31P NMR (CD.sub.3CN) .delta. 68.53,
68.38, 68.34, 67.74, 67.54. MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M+H].sup.+ m/z.sub.exp=1103.91,
m/z.sub.calc=1104.15. The spectrophotometric purity (93%) is
determined by HPLC at 260 nm.
EXAMPLE 5
Synthesis of the dimer 5'-OH-T-dA.sup.Bz-3'O-TBDMS cyanoethyl
phosphorothioate triester
[0105] Coupling procedure of 5'-O-DMTr-T-3'-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-TBDMS using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich).
[0106] A solution of 5'-OH-dA.sup.Bz-3'-O-TBDMS (176 mg, 0.38 mmol)
and 5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (560 mg, 0.75 mmol, 2
eq) in anhydrous acetonitrile (6 ml) is added to
poly(4-vinylpyridinum p-toluenesulfonate) (1.15 g, 3.84 mmol
tos.sup.-, 10.2 eq). The resulting mixture is shaken for 4 h 30
min. The reaction is followed by .sup.31P NMR and the yield is also
determined by .sup.31P NMR. The desired dimer
5'-O-DMTr-T-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite triester is
obtained with 100% of yield compared to the 5'-OH-de-3'-O-TBDMS.
The crude is a mixture of 5'-O-DMTr-T-3'-cyanoethyl phosphoramidite
(.sup.31P NMR (CD.sub.3CN) .delta. 149.10, 149.05, 12.3%),
5'-O-DMTr-T-A.sup.Bz-3'-O-TBDMS cyanoethyl phosphite triester
(.delta. 140.52, 140.37, 50%), 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.72, 8.69, 37.7%).
[0107] Sulfurization: The poly(4-vinylpyridinum p-toluenesulfonate)
is filtered off and the resulting solution is added to AMBERLYST
A26 tetrathionate form (1.55 g, 2.63 mmol S.sub.4O.sub.6.sup.2-, 7
eq.). The reaction is followed by .sup.31P NMR. The reaction
mixture is shaken for 24 h 30. The desired dimer
5'-O-DMTr-T-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphorothioate
triester is isolated after filtration of the resin, evaporation of
the solvent, and column chromatography (silica gel;
CH.sub.2Cl.sub.2/MeOH (50/1)). Yield: 325 mg, 0.28 mmol, 76%.
.sup.31P NMR (CD.sub.3CN) .delta. 68.34, 68.15. MALDI-TOF (positive
mode, trihydroxyacetophenone as matrix) [M+H].sup.+
m/z.sub.exp=1144.22, m/z.sub.calc=1146.32.
[0108] Detritylation: The 5'-O-DMTr-T-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester is dissolved in 10 ml of
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled in an ice bath. To
this solution is added 1 ml of a solution of benzene sulfonic acid
10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred
35 min at 0.degree. C. The reaction is washed with 20 ml of a
saturated solution of NaHCO.sub.3, the organic layer is separated,
dried (Na.sub.2SO.sub.4), evaporated, and purified on a silica gel
column. The desired dimer T-dA.sup.Bz is eluted with
CH.sub.2Cl.sub.2/CH.sub.3OH (95/5). The appropriates fractions are
collected and evaporated to give a white foam. Yield: 223 mg, 0.26
mmol, 71%. .sup.31P NMR (CD.sub.3CN) .delta. 68.06, 67.89.
MALDI-TOF MS (positive mode, trihydroxyacetophenone as matrix)
[M-H].sup.+ m/z.sub.exp=842.18, m/z.sub.calc=843.95; (negative
mode, trihydroxyacetophenone as matrix) ammonia treatment of an
aliquot gives 5'-OH-T-dA-3'-O-TBDMS phosphorothioate diester:
[M-H].sup.- m/z.sub.exp=685.38, m/z.sub.calc=684.77.
EXAMPLE 6
Synthesis of the trimer 5'-O-DMTr-dA.sup.Bz-T-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester
[0109] Coupling procedure of 5'-O-DMTr-de-3'-cyanoethyl
phosphoramidite with the dimer 5'-OH-T-A.sup.Bz-3'-O-TBDMS
phosphorothioate triester using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich).
[0110] A solution of the dimer 5'-OH-T-dA.sup.Bz-3'-O-TBDMS
phosphorothioate triester (223 mg, 0.26 mmol) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl phosphoramidite (432 mg, 0.50
mmol, 1.9 eq) in anhydrous acetonitrile (20 ml) is added to
poly(4-vinylpyridinum p-toluenesulfonate) (0.8 g, 2.7 mmol
tos.sup.-, 10.3 eq). The resulting mixture is shaken for 6 h 30.
The reaction is followed by .sup.31P NMR and the yield is also
determined by .sup.31P NMR. The desired trimer
5'-O-DMTr-dA.sup.Bz-T-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester is obtained with 62% of yield compared to the dimer
5'-OH-T-dA.sup.Bz-3'-O-TBDMS phosphorothioate triester. The crude
is a mixture of 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl phosphoramidite
(.sup.31P NMR (CD.sub.3CN) d 149.14, 8.4%),
5'-O-DMTr-dA.sup.Bz-T-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester .delta. (140.90, 140.77, 67.85, 67.79, 43.3%),
5'-OH-T-dA.sup.Bz-3'-O-TBDMS phosphorothioate triester (.delta.
68.03, 67.89, 13.4%), 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.71, 8.66, 34.9%).
[0111] Sulfurization: The poly(4-vinylpyridinum p-toluenesulfonate)
is filtered off and the resulting solution is added to AMBERLYST
A26 tetrathionate form (0.78 g, 1.33 mmol S.sub.4O.sub.6.sup.2-, 5
eq.). The reaction is followed by .sup.31P NMR and the yield is
also determined by .sup.31P NMR. After 14 h 30 the desired trimer
5'-O-DMTr-dA.sup.Bz-T-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate triester is obtained with 100% of yield. The crude
is a mixture of 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl
thiophosphoramidate (.sup.31P NMR (CD.sub.3CN) d 71.88, 71.21,
10%), 5'-O-DMTr-dA.sup.Bz-T-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate triester (25.9%) and 5'-OH-T-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester (16.2%) (.delta. 68.08, 68.05,
67.93, 67.89, 67.85, 67.79, 67.57), 5'-O-DMTr-T-3'-cyanoethyl
phosphorothioate diester (.delta. 57.38, 4.8%),
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogenophosphonate (.delta.
8.75, 8.70, 43.11%). MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M+H].sup.+ m/z.sub.exp=1631.68,
m/z.sub.calc=1632.77; (negative mode, trihydroxyacetophenone as
matrix) ammonia treatment of an aliquot gives 5'-OH-T-dA-3'-O-TBDMS
phosphorothioate diester: [M-H].sup.- m/z.sub.exp=1316.45,
m/z.sub.calc=1316.43.
EXAMPLE 7
Synthesis of the dimer 5'-O-DMTr-dC.sup.Bz-T-3'-O-Lev cyanoethyl
phosphite triester
[0112] Coupling procedure of 5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl
phosphoramidite with 5'-OH-T-3'-O-Lev using the DOWEX 50W XS
pyridinium form.
Analytical Scale.
[0113] 5'-OH-T-3'-O-Lev (20 mg, 58.9 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl phosphoramidite (83.4 mg, 100
mmol, 1.7 eq) are dissolved in anhydrous acetonitrile (550 ml). The
solution is transferred under argon in a NMR tube containing the
DOWEX 50W X8 pyridinium form (181 mg, 0.54 mmol pyrH.sup.+, 9.2
eq). The reaction is followed by .sup.31P NMR. Before the NMR
experiment deuterated acetonitrile (50 ml) is added. The yield is
determined by .sup.31P NMR. After 6 h the desired dimer T-dC.sup.Bz
phosphite triester is obtained with 100% of yield compared to
5'-OH-T-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl phosphoramidite (.sup.31P NMR
(CD.sub.3CN) .delta. 149.36, 149.32, 11%),
5'-O-DMTr-T-dC.sup.Bz-3'-O-TBDMS cyanoethyl phosphite triester
(.delta. 140.52, 140.39, 70%), 5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.90, 8.58, 19%).
EXAMPLE 8
Synthesis of the dimer 5'-OH-dC.sup.Bz-T-3'-O-Lev cyanoethyl
phosphorothioate triester
[0114] Coupling procedure of 5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl
phosphoramidite with 5'-OH-T-3'-O-Lev using the DOWEX 50W X8
pyridinium form.
[0115] A solution of 5'-OH-T-3'-O-Lev (119 mg, 0.35 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl phosphoramidite (496 mg, 0.60
mmol, 1.7 eq) in anhydrous acetonitrile (10 ml) is added to DOWEX
50W X8 pyridinium form (1.1 g, 3.3 mmol pyrH.sup.+, 9.4 eq). The
resulting mixture is shaken for 5 h 30 min. The reaction is
followed by .sup.31P NMR and the yield is also determined by
.sup.31P NMR. The desired dimer 5'-O-DMTr-dC.sup.Bz-T-3'-O-Lev
cyanoethyl phosphite triester is obtained with 100% of yield
compared to 5'-OH-T-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-T-dC.sup.Bz-3'-O-Lev cyanoethyl phosphite triester
(.sup.31P NMR (CD.sub.3CN) .delta. 140.59, 140.45, 64%),
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (.delta.
8.68, 8.66, 36%).
[0116] Sulfurization: The DOWEX 50W X8 resin is filtered off and
the resulting solution is added to AMBERLYST A26 tetrathionate form
(1.44 g, 2.44 mmol S.sub.4O.sub.6.sup.2-, 7 eq.). The reaction is
followed by .sup.31P NMR. The reaction mixture is shaken for 16 h.
The desired dimer 5'-O-DMTr-dC.sup.Bz-T-3'-O-Lev cyanoethyl
phosphorothioate triester is isolated after filtration of the
resin, evaporation of the solvent and column chromatography (silica
gel; CH.sub.2Cl.sub.2/MeOH (97/3)). The crude is a mixture of
5'-O-DMTr-T-dC.sup.Bz-3'-O-Lev cyanoethyl phosphorothioate triester
(.sup.31P NMR (CD.sub.3CN) .delta. 68.05, 67.89, 83.7%),
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (.delta.
8.63, 16.3%). The spectrophotometric purity determined by HPLC at
260 nm is 80%.
Detrytilation of the dimer 5'-O-DMTr-dC.sup.Bz-T-3'-O-Lev
cyanoethyl phosphorothioate triester with the DOWEX 50 W X8 H.sup.+
form
Aldrich
[0117] To the mixture of the dimer 5'-O-DMTr-dC.sup.Bz-T-3'-O-Lev
cyanoethyl phosphorothioate triester (121 mmol estimated) and
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate diester (44 mmol
estimated) in solution in 10 ml of CH.sub.2Cl.sub.2/MeOH (7/3) is
added the DOWEX 50 W X8H.sup.+ form (1.4 g, 7 mmol H.sup.+, 58
eq/dimer). The reaction is followed by reverse phase HPLC. After 15
min the detritylation is complete. The resin is filtered off and
the solvents are evaporated. The desired dimer
5'-OH-dC.sup.Bz-T-3'-O-Lev cyanoethyl phosphorothioate triester is
purified by precipitation from CH.sub.2Cl.sub.2/MeOH (9/1) in
diethylether. .sup.31P NMR (CD.sub.3OD) .delta. 68.24, 67.90,
MALDI-TOF MS (positive mode, trihydroxyacetophenone as matrix)
[M-H].sup.+ m/z.sub.exp=803.11 m/z.sub.calc=803.76. The
spectrophotometric purity (97%) is determined by HPLC at 260
nm.
EXAMPLE 9
Synthesis of the dimer 5'-OH-T-T-3'-O-Lev cyanoethyl
phosphorothioate triester
[0118] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phospharamidite with 5'-OH-T-3'-O-Lev using the DOWEX 50W X8
pyridinium form.
[0119] A solution of 5'-OH-T-3'-O-Lev (100 mg, 0.29 mmol) and
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (547 mg, 0.73 mmol, 2.5
eq) in anhydrous acetonitrile (10 ml) is added to DOWEX 50W X8
pyridinium form (0.9 g, 2.7 mmol pyrH.sup.+, 9.3 eq). The resulting
mixture is shaken for 10 h. The reaction is followed by .sup.31P
NMR and by reverse phase HPLC. The excess of
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite is hydrolysed with 500 ml
of water The desired dimer 5'-O-DMTr-T-T-3'-O-Lev cyanoethyl
phosphite triester is obtained with 100% of yield compared to
5'-OH-T-3'-O-Lev. The crude is a mixture of 5'-O-DMTr-T-T-3'-O-Lev
cyanoethyl phosphite triester (HPLC % Area=55%) and
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (HPLC %
Area=45%).
[0120] Sulfurization: The DOWEX 50W X8 resin is filtered off and
the resulting solution is added to AMBERLYST A26 tetrathionate form
(0.8 g, 1.5 mmol S.sub.4O.sub.6.sup.2-, 5 eq.). The reaction is
followed by .sup.31P NMR and by reverse phase HPLC. After 15 h the
desired dimer 5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphorothioate
triester is obtained with 100% of yield. The crude is a mixture of
5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphorothioate triester
(.sup.31P NMR d 68.04, HPLC % Area=57%), 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (d 8.77, HPLC % Area=43%).
Detrytilation of the dimer 5'-O-DMTr-T-T-3'-O-Lev cyanoethyl
phosphorothioate triester with the DOWEX 50 W X8H.sup.+ form
Aldrich
[0121] The AMBERLYST A26 resin is filtered off and the solvents are
evaporated. To the mixture of the dimer 5'-O-DMTr-T-T-3'-O-Lev
cyanoethyl phosphorothioate triester (0.29 mmol estimated) and
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (0.22 mmol
estimated) in solution in 20 ml of CH.sub.2Cl.sub.2/MeOH (7/3) is
added the DOWEX 50 W X8H.sup.+ form (3.7 g, 18.5 mmol H.sup.+, 64
eq/dimer). The reaction is followed by reverse phase HPLC. After 30
min the detritylation of the dimer is complete. The resin is
filtered off and the solvents are evaporated. The desired dimer
5'-OH-T-T-3'-O-Lev cyanoethyl phosphorothioate triester is purified
by precipitation from CH.sub.2Cl.sub.2/MeOH (9/1) in diethylether.
.sup.31P NMR (CD.sub.3CN) d 67.88, 67.73. MALDI-TOF MS (positive
mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=713.79 m/z.sub.calc=714.66. The purity (95%) is
determined by HPLC.
EXAMPLE 10
Synthesis of dimer 5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester dimer
[0122] Coupling procedure of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-TBDMS using the DOWEX 50W X8 pyridinium
form:
[0123] 5'-OH-dA.sup.Bz-3'-O-TBDMS (100 mg, 0.21 mmol) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite (311 mg, 0.36
mmol, 1.7 eq) are dissolved in anhydrous acetonitrile (15 ml). The
solution is transferred under argon in a flask containing the DOWEX
50W X8 pyridinium form (655 mg, 1.97 mmol pyrH.sup.+, 9.2 eq) and
is shaken for 4 h 30 min. The reaction is followed by .sup.31P NMR.
The yield is determined by .sup.31P NMR. The desired dA-dA
phosphite triester dimer is obtained with 92% of yield compared to
the 5'-OH-dA.sup.Bz-3'-O-TBDMS. The crude is a mixture of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl phosphoramidite (.sup.31P NMR
(CD.sub.3CN) .delta. 149.25, 149.13; 27.7%),
51-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester (.delta. 140.75, 140.38; 53.9%),
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogenophosphonate (.delta.
8.69, 8.64; 18.5%).
[0124] Sulfurization: To a solution of
5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS phosphite triester dimer
(0.2 mmol) in anhydrous acetonitrile is added AMBERLYST A26
tetrathionate form (5.4 eq., 1.14 mmol S.sub.4O.sub.6.sup.2-, 0.63
g). The reaction mixture is shaken for 20 h. The reaction is
followed by .sup.31P NMR. The yield is determined by .sup.31P NMR.
After filtration of the resins the desired dimer dA-dA
phosphorothioate triester is obtained with 88% of yield compared to
the 5'-OH-dA.sup.Bz-3'-O-TBDMS. The crude is a mixture of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl thiophosphoramidate (.sup.31P NMR
(CD.sub.3CN) .delta. 71.85, 71.22; 29.0%),
5'-O-DMTr-A.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphorothioate
(.delta. 68.08, 68.01; 51.5%), 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.66, 8.59; 19.5%).
EXAMPLE 11
Synthesis of the dimer 5'-OH-dC.sup.Bz-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester
[0125] Coupling procedure of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-TBDMS using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0126] 5'-OH-dA.sup.Bz-3'-O-TBDMS adenosine (100 mg, 0.21 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite (365 mg, 0.43
mmol, 2. eq) are dissolved in anhydrous acetonitrile (15 ml). The
solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (655 mg, 2.17 mmol
tos.sup.-, 10.2 eq) and is shaken for 5 h 50 min. The reaction is
followed by .sup.31P NMR. The yield is determined by .sup.31P NMR.
The desired dC-dA phosphite triester dimer is obtained with 100% of
yield compared to the 5'-OH-dA.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphite triester (.sup.31P NMR (CD.sub.3CN) (.delta. 140.55,
140.49; 53.9%), 5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (.delta. 8.67; 18.5%).
[0127] Sulfurization: To a solution of
5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester dimer (0.21 mmol) in anhydrous dichloromethane is added
AMBERLYST A26 tetrathionate form (0.63 g, 1.14 mmol
S.sub.4O.sub.6.sup.2-, 5.3 eq.). The reaction mixture is shaken for
14 h 30 min. The reaction is followed by .sup.31P NMR. The yield is
determined by .sup.31P NMR. After filtration of the resins the
desired phosphorothioate triester dimer is obtained with 100% of
yield compared to the 5'OH-dA.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dC.sup..times.z-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate (.sup.31P NMR (CD.sub.3CN) (d 68.14,
68.07; 50.6%), 5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (d 8.67; 49.4%). Purification is attempted on
a silica gel column, which is treated with triethylamine.
Chromatography leads to complete loss of the cyanoethyl group. The
dC.sup.Bz-dA.sup.Bz phosphorothioate dimer is eluted with
CH.sub.2Cl.sub.2/CH.sub.3OH (80/1). The appropriates fractions are
collected and evaporated to give a colorless oil. Yield: 185 mg,
0.14 mmol, 68%; .sup.31P NMR (CD.sub.3CN) d 57.58, 57.45; MALDI-TOF
MS (positive mode, trihydroxyacetophenone as matrix)
[M-DMTr+2H].sup.+ m/z.sub.exp=879.42, m/z.sub.calc=878.97.
EXAMPLE 12
Synthesis of the dimer 5'-OH-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester
[0128] Coupling procedure of
5'O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-TBDMS using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0129] 5'-OH-dA.sup.Bz-3'-O-TBDMS (102 mg, 0.22 mmol) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite (381 mg, 0.44
mmol, 2.05 eq) are dissolved in anhydrous dichloromethane (15 ml).
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (655 mg, 2.19 mmol
tos.sup.-, 10.1 eq) and is shaken for 5 h 40 min. The reaction is
followed by .sup.31P NMR. The yield is determined by .sup.31P NMR.
The desired dA-dA phosphite triester dimer is obtained with 100% of
yield compared to the 5'-OH-dA.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphite triester (.sup.31P NMR (CD.sub.3CN) (d 140.77, 140.46;
66.9%), 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d
8.50, 8.41; 33.1%).
[0130] Sulfurization: To a solution of
5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester dimer (0.22 mmol) in anhydrous dichloromethane is added
AMBERLYST A26 tetrathionate form (0.87 g, 1.14 mmol
S.sub.4O.sub.6.sup.2-, 5.4 eq.). The reaction mixture is shaken for
22 h. The reaction is followed by .sup.31P NMR. The yield is
determined by .sup.31P NMR. After filtration of the resins the
desired dA-dA phosphorothioate triester dimer is obtained with 100%
of yield compared to the 5'-OH-A.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate (.sup.31P NMR (CD.sub.3CN) (d 68.17, 67.89;
62.3%), 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogenophosphonate
(.delta. 8.45, 8.35; 37.7%).
[0131] Detritylation: To a solution of
5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate triester (0.22 mmol) in 10 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 0.63 ml (0.3 mmol, 1.4
eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 45 min
at 0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(Na.sub.2SO.sub.4), evaporated, and purified on a silica gel
column. The desired dA-dA dimer is eluted with
CH.sub.2Cl.sub.2/CH.sub.3OH (33/1). The appropriates fractions are
collected and evaporated to give a colorless oil. Yield: 73 mg, 76
mmol, 35%; .sup.31P NMR (CD.sub.3CN) .delta. 67.80, 67.71;
MALDI-TOF MS (positive mode, trihydroxyacetophenone as matrix)
[M-H].sup.+ m/z.sub.exp=957.01, m/z.sub.calc=957.07; HPLC
(spectrophotometrical purity at 260 nm=95%).
EXAMPLE 13
Synthesis of the dimer 5'-OH-dG.sup.IBu-dA.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester
[0132] Coupling procedure of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-TBDMS using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0133] 5'-OH-dA-3'-O-TBDMS (100 mg, 0.21 mmol) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite (352 mg, 0.42
mmol, 1.97 eq) are dissolved in anhydrous acetonitrile (20 ml). The
solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (655 mg, 2.19 mmol
tos.sup.-, 10.3 eq) and is shaken for 5 h 30 min. The reaction is
followed by .sup.31P NMR. The yield is determined by .sup.31P NMR.
The desired dG-dA phosphite triester dimer is obtained with 100% of
yield compared to the 5'-OH-dA.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphite triester (.sup.31P NMR (CD.sub.3CN) (.delta. 140.65,
140.45; 51.2%), 5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl
hydrogenophosphonate (.delta. 9.00, 8.81; 48.8%).
[0134] Sulfurization: To a solution of
5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester dimer (0.21 mmol) in anhydrous acetonitrile is added
AMBERLYST A26 tetrathionate form (0.63 g, 1.14 mmol
S.sub.4O.sub.6.sup.2-, 5.4 eq.). The reaction mixture is shaken for
2 h. The reaction is followed by .sup.31P NMR. The yield is
determined by .sup.31P NMR. After filtration of the resins the
desired dG-dA phosphorothioate triester dimer is obtained with 100%
of yield compared to the 5'-OH-dA.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate (.sup.31P NMR (CD.sub.3CN) (.delta. 68.15, 68.02;
50.4%), 5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl hydrogenophosphonate
(.delta. 8.91, 8.68; 49.6%).
[0135] Detritylation: To a solution of
5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate triester (0.21 mmol) in 10 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 0.5 ml (0.3 mmol, 1.4
eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 20 min
at 0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(Na.sub.2SO.sub.4), evaporated, and purified on a silica gel
column. The desired G-A dimer is eluted with
CH.sub.2Cl.sub.2/CH.sub.3OH (33/1). The appropriates fractions are
collected and evaporated to give a white foam. Yield: 95 mg, 0.1
mmol, 48% with respect of 5'-OH-dA-3'-O-TBDM; .sup.31P NMR
(CD.sub.3CN) .delta. 68.10, 67.87; HPLC (spectrophotometrical
purity at 260 nm=80%).
EXAMPLE 14
Synthesis of the dimer 5'-OH-dG.sup.IBu-dC.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester
[0136] Coupling procedure of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite with
5'OH-dC.sup.Bz-3'-O-TBDMS using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0137] 5'-OH-dC.sup.Bz-3'-O-TBDMS (100 mg, 0.22 mmol) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite (371 mg, 0.45
mmol, 2 eq) are dissolved in anhydrous acetonitrile (15 ml). The
solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (690 mg, 2.3 mmol
tos.sup.-, 10.3 eq) and is shaken for 5 h. The reaction is followed
by .sup.31P NMR. The yield is determined by .sup.31P NMR. The
desired dG-dC phosphite triester dimer is obtained with 100% of
yield compared to the 5'-OH-dC.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dG.sup.IBu-dC.sup.Bz-3'-O-TBDMS cyanoethyl
phosphite triester (.sup.31P NMR (CD.sub.3CN) (.delta. 141.73,
141.26; 62.1%), 5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl
hydrogeno-phosphonate (.delta. 9.05, 8.88; 37.9%).
[0138] Sulfurization: To a solution of
5'-O-DMTr-dG.sup.IBu-dC.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester dimer (0.22 mmol) in anhydrous acetonitrile is added
AMBERLYST A26 tetrathionate form (0.65 g, 1.3 mmol
S.sub.4O.sub.6.sup.2-, 5.4 eq.). The reaction mixture is shaken for
2 h. The reaction is followed by .sup.31P NMR. The yield is
determined by .sup.31P NMR. After filtration of the resins the
desired dG-dC phosphorothioate triester dimer is obtained with 100%
of yield compared to the 5'OH-dC.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dG.sup.IBu-dC.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate (.sup.31P NMR (CD.sub.3CN) (.delta. 68.12, 67.73;
61.2%), 5'O-DMTr-dG.sup.IBu-3'-cyanoethyl phosphorothioate diester
(.delta. 56.51, 56.39; 25.4%), 5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl
hydrogenophosphonate (d 9.04, 8.85; 25.4%). .sup.31P NMR d.
[0139] Detritytlation: To a solution of
5'-O-DMTr-dG.sup.IBu-dC.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate triester (0.22 mmol) in 10 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 0.5 ml (0.3 mmol, 1.4
eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 1 h at
0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(Na.sub.2SO.sub.4) and evaporated. The crude product is purified on
a silica gel column using CH.sub.2Cl.sub.2/CH.sub.3OH (33:1). The
appropriate fractions are collected and evaporated to give a
colorless oil. Yield: 99 mg, 0.1 mmol, 47%; .sup.31P NMR
(CD.sub.3CN) .delta. 67.82, 67.56; MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-H].sup.+ m/z.sub.exp=914.78,
m/z.sub.calc=914.03; HPLC (spectrophotometrical purity at 260
nm=84%).
EXAMPLE 15
Synthesis of 5'-O-DMTr-T-T-3'-O-DMTr-phosphorothioate diester
[0140] To a solution of 5'-O-DMTr-T-T-3'-O-DMTr H-phosphonate
diester (25 mg, 22 mmol) in dichloromethane is added AMBERLYST A26
tetrathionate form (170 mg, 0.29 mmol S.sub.4O.sub.6.sup.2-, 13
eq.) and 0.1 mL triethylamine. The reaction mixture shaken for 78
h. The title compound was isolated after filtration of the resin
and evaporation of the solvent. Yield: 28 mg, 22 mmol, 100%;
.sup.31P NMR (CD.sub.3CN) d 57.22; MALDI-TOF MS (negative mode,
trihydroxy-acetophenone as matrix) [M-H].sup.- m/z.sub.exp=1166.23,
m/z.sub.calc=1666.25.
EXAMPLE 16
Synthesis of 5'-O-DMTr-T-T-3'-O-TBDMS-phosphorothioate diester
[0141] To a solution of 5'-O-DMTr-T-T-3'-O-TBDMS H-phosphonate (55
mg, 58 mmol) in dichloromethane is added AMBERLYST A26
tetrathionate form (250 mg, 0.42 mmol S.sub.4O.sub.6.sup.2-, 7.3
eq.) and 0.2 mL triethylamine. The reaction mixture is shaken for
26 h. The title compound was isolated after filtration of the resin
and evaporation of the solvent. Yield: 63 mg, 58 mmol, 100%;
.sup.31P NMR (CD.sub.3CN) .delta. 57.78, 57.72; MALDI-TOF MS
(negative mode, trihydroxyacetophenone as matrix) [M-H].sup.-
m/z.sub.exp=977.04, m/z.sub.calc=977.13.
EXAMPLE 17
Synthesis of AMBERLYST A26 Tetrathionate Form
[0142] 10 g commercial Amberlyst A26 hydroxide form (Rohm &
Haas) is washed twice with 20 mL methanol and twice with 20 mL
dichloromethane and dried in vacuum. Potassium tetrathionate (30.35
g, 100 mmol, 3 eq.) is dissolved in 200 mL deionized water. The
solution is added to the resin and shaken for 20 hours. The
solution is decanted of. The resin is washed with 4 L deionized
water, twice with 100 mL methanol and twice with 100 mL
dichloromethane and dried under reduced pressure for 3 hours to
give 8.5 g of solid-supported tetrathionate. The reagents loading
was determined by elemental analysis, giving a value of 23.25% for
sulfur (4.24% for nitrogen, 45.74% for carbon and less than 100 ppm
for potassium). Loading: 1.81 mmol S.sub.4O.sub.6.sup.2- per gram
of resin.
EXAMPLE 18
Synthesis of Polymer-Supported Pyridinium
[0143] The commercially available strongly acidic ion-exchange
resin DOWEX 50W X8 H.sup.+ form (Fluke) is washed successively with
water, HCl 2M, water until pH 7, methanol and dichloromethane to
dry the resin. Then, the resin is stirred in a solution of pyridine
2M in acetonitrile or just washed with a slight flow of the
solution of pyridine 2M in acetonitrile for 15 minutes. Then, the
resin is washed with acetonitrile and dichloromethane and dried
under vacuum over P.sub.2O.sub.5. The reagents loading was
determined by elemental analysis, giving a value of 11.56% for
sulfur and 3.97% for nitrogen. Loading: 2.83 mmol pyrH.sup.+ per
gram of resin.
EXAMPLE 19
Preparation of Polystyrene-Bound Acid Chloride
[0144] The commercial polystyrene-bound carboxy acid RAPP Polymere
(5.0 g, 1.96 mmol/g, 100-200 mesh, 1% DVB) is suspended in
anhydrous CH.sub.2Cl.sub.2 (80 ml) and N,N-dimethylformamide (0.3
ml). Thionyl chloride (1.8 ml, 3.5 eq) are added under stirring and
the mixture is refluxed for 3 h. The resin is filtered under argon
and washed with dried CH.sub.2Cl.sub.2 (100 ml), ether (100 ml) and
dried under vacuum for 4 h.
[0145] IR (cm.sup.-1): 1775 (C.dbd.O, Acid chloride)
[0146] Elemental analysis: Cl 7.43% (w/100 g resin) (2.09
mmol/g)
[0147] Chloride titration: 2.1 mmol/g
EXAMPLE 20
Synthesis of 5'-O-DMTr-dA.sup.Bz-dC.sup.Bz-3'-O-Lev
H-phosphonate
[0148] A solution of 5'-O-DMTr-dA.sup.Bz-H-phosphonate TEA salt
(123.4 mg, 0.150 mmol) and of 3'-O-Lev-dC.sup.Bz (53.7 mg, 0.125
mmol) in 2.0 ml of CH.sub.2Cl.sub.2/py (1:1) is added to
polystyrene-bound acid chloride (388.8 mg, 2.1 mmol/g, 5.5 eq) that
is suspended in 2.5 ml of the same solvent. The mixture is shaken
for 1 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, dried over Na.sub.2SO.sub.4, the solvent
is evaporated and the pyridine is eliminated by coevaporation with
toluene. The isolated product was dried under vacuum. Yield
89%.
[0149] .sup.31P NMR (CD.sub.3CN) .delta. 10.03 ppm, 9.46 ppm.
[0150] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1134.13, m/z.sub.calc=1133.51.
[0151] The spectrophotometrical purity determined by HPLC is
93%.
EXAMPLE 21
Synthesis of 5'-O-DMTr-dA.sup.Bz-T-3'-O-Lev H-phosphonate
[0152] A solution of 5'-O-DMTr-dA.sup.Bz-H-phosphonate TEA salt
(123.4 mg, 0.150 mmol) and of 3'-O-Lev-T (42.5 mg, 0.125 mmol) in
2.0 ml of CH.sub.2Cl.sub.2/PY (1:1) is added to polystyrene-bound
acid chloride (550.0 mg, 2.1 mmol/g, 7.7 eq) that is suspended in
5.0 ml of the same solvent. The mixture is shaken for 30 min at
room temperature until the disappearance of the monomers. The
reaction is monitored by reverse phase HPLC. The resin is filtered,
washed with CH.sub.2Cl.sub.2. The pyridinium salt present in
solution is removed by aqueous extraction and the aqueous phase is
washed twice with CH.sub.2Cl.sub.2. The organic fractions are
collected, dried over Na.sub.2SO.sub.4, the solvent is evaporated
and the pyridine is eliminated by coevaporation with toluene. The
isolated product is dried under vacuum. Yield 88.5%
[0153] .sup.31P NMR (CD.sub.3CN) .delta. 10.02 ppm, 9.08 ppm.
[0154] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1043.02, m/z.sub.calc=1045.00.
[0155] The spectrophotometrical purity determined by HPLC is
98%.
EXAMPLE 22
Synthesis of 5'-O-DMTr-T-dC.sup.Bz-3'-O-TBDMS H-phosphonate
[0156] A solution of 5'-O-DMTr-T-H-phosphonate TEA salt (106.4 mg,
0.150 mmol) and of 3'-O-TBDMS-dC.sup.Bz (55.7 mg, 0.125 mmol) in
2.0 ml of CH.sub.2Cl.sub.2/py (1:1) is added to polystyrene-bound
acid chloride (555.0 mg, 2.7 mmol/g, 10 eq) that is suspended in
5.0 ml of the same solvent. The mixture is shaken for 2 h at room
temperature until the disappearance of the monomers. The reaction
is monitored by reverse phase HPLC. The resin is filtered, washed
with CH.sub.2Cl.sub.2. The pyridinium salt present in solution is
removed by aqueous extraction and the aqueous phase is washed twice
with CH.sub.2Cl.sub.2. The organic fractions are collected, dried
over Na.sub.2SO.sub.4, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 77.5%.
[0157] .sup.31P NMR (CD.sub.3CN) .delta. 10.50 ppm, 10.00 ppm.
[0158] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1038.69, m/z.sub.calc=1037.20.
[0159] The spectrophotometrical purity determined by HPLC is
94%.
EXAMPLE 23
Synthesis of 5'-O-DMTr-T-dC.sup.Bz-3'-O-TBDMS phosphorothioate TEA
salt
[0160] A solution of 5'-O-DMTr-T-dC.sup.Bz-3'-O-TBDMS H-phosphonate
(50 mg, 0.048 mmol) in 5.0 nil of CH.sub.2Cl.sub.2 and 0.2 ml TEA
is added to Amberlyst A26 tetrathionate form (141.0 mg, 1.7 mmol/g,
5 eq). The mixture is shaken over night, the resin is filtered and
the solvent is evaporated. The product is dried under vacuum. Yield
100%.
[0161] .sup.31P NMR (CD.sub.2Cl.sub.2) .delta. 59.17 ppm, 58.99
ppm.
[0162] The spectrophotometrical purity determined by HPLC is
95%.
EXAMPLE 24
Synthesis of 5'-O-DMTr-dA.sup.Bz-T-3'-O-Lev phosphate TEA salt
[0163] A solution of 5'-O-DMTr-dA.sup.Bz-T-3'-O-Lev H-phosphonate
(90 mg, 0.0863 mmol) in 5.0 ml of CH.sub.2Cl.sub.2 and 0.2 ml TEA
is added to (polystyrilmethyl)trimethylamonium metaperiodate
(NOVABIOCHEM) (173.0 mg, 2.5 mmol/g, 5 eq). The mixture is shaken
over night, the resin is filtered and the solvent is evaporated.
The product is dried under vacuum. Yield 100%.
[0164] .sup.31P NMR (CD.sub.2Cl.sub.2) .delta. -1.37 ppm.
[0165] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1059.31, m/z.sub.calc=1060.03.
[0166] The spectrophotometrical purity determined by HPLC is
87%.
EXAMPLE 25
Synthesis of 5'-O-DMTr-T-dA.sup.Bz-dC.sup.Bz-3'-O-Lev
H-phosphonate
Detritylation of 5'-O-DMTr-dA.sup.Bz-dC.sup.Bz-3'-O-Lev
H-phosphonate
[0167] The H-phosphonate dimer
5'-O-DMTr-dA.sup.Bz-dC.sup.Bz-3'-O-Lev (120 mg, 0.106 mmol) is
dissolved in 4.0 ml of CH.sub.2Cl.sub.2/MeOH (7:3) and cooled in an
ice bath. To this solution 1.0 ml of a solution of 10% BSA (benzene
sulfonic acid) in CH.sub.2Cl.sub.2/MeOH (7:3) is added drop wise
under stirring and the progress of the reaction is monitored by
TLC. After 15 min the mixture is quenched with a solution of
NaHCO.sub.3. The organic layer is washed with water to remove any
trace of base, then it is dried over Na.sub.2SO.sub.4 and the
solvent is evaporated. The product is purified by precipitation
from CH.sub.2Cl.sub.2 with ether and dried under vacuum. Yield
88%.
[0168] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=830.75, m/z.sub.calc=831.75.
[0169] The spectrophotometrical purity determined by HPLC is
91%.
Coupling
[0170] A solution of 5'-O-DMTr-T-H-phosphonate TEA salt (93.8 mg,
0.132 mmol) and of 5'-OH-dA.sup.Bz-dC.sup.Bz-3'-O-Lev H-phosphonate
(73.2 mg, 0.088 mmol) in 2.0 ml of CH.sub.2Cl.sub.2/py (1:1) is
added to polystyrene-bound acid chloride (503.0 mg, 2.1 mmol/g, 8
eq) that is suspended in 4.0 ml of the same solvent. The mixture is
shaken for 1 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, dried over Na.sub.2SO.sub.4, the solvent
is evaporated and the pyridine is eliminated by coevaporation with
toluene. The isolated product is dried under vacuum. Yield
8-2%.
[0171] .sup.31P NMR (CD.sub.2Cl.sub.2) .delta. 10.23, 10.09, 9.70,
9.68, 9.52, 9.30, 9.24, 9.19 ppm.
[0172] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1421.06, m/z.sub.calc=1422.33.
[0173] The spectrophotometrical purity determined by HPLC is
82%.
EXAMPLE 26
Synthesis of 5'-O-DMTr-dA.sup.Bz-dA.sup.Bz-T-3'-O-Lev
H-phosphonate
Detritylation of 5'-O-DMTr-dA.sup.Bz-T-3'-O-Lev H-phosphonate
[0174] The H-phosphonate dimer 5'-O-DMTr-dA.sup.Bz-T-3'-O-Lev (105
mg, 0.100 mmol) is dissolved in 4.0 ml of CH.sub.2Cl.sub.2/MeOH
(7:3) and cooled in an ice bath. 1.0 ml of a solution of 10% BSA in
CH.sub.2Cl.sub.2/MeOH (7:3) is added drop wise under stirring and
the progress of the reaction is monitored by TLC. After 15 min the
mixture is quenched with a solution of NaHCO.sub.3. The organic
layer is washed with water to remove any trace of base, then it is
dried over Na.sub.2SO.sub.4 and the solvent is evaporated. The
product is purified by precipitation from CH.sub.2Cl.sub.2 in ether
and dried under vacuum. Yield 70%.
[0175] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=742.25, m/z.sub.calc=742.66.
[0176] The spectrophotometrical purity determined by HPLC is
92%.
Coupling
[0177] A solution of 5'-O-DMTr-dA.sup.Bz-H-phosphonate TEA salt
(69.8 mg, 0.084 mmol) and of 5'-OH-dA.sup.Bz-dT-3'-O-Lev
H-phosphonate (52.2 mg, 0.070 mmol) in 2.0 ml of
CH.sub.2Cl.sub.2/py (1:1) IS added to polystyrene-bound acid
chloride (311.0 mg, 2.1 mmol/g, 7.7 eq) that is suspended in 2.0 ml
of the same solvent. The mixture is shaken for 3 h at room
temperature until the disappearance of the monomers. The reaction
is monitored by reverse phase HPLC. The resin is filtered, washed
with CH.sub.2Cl.sub.2. The pyridinium salt present in solution is
removed by aqueous extraction and the aqueous phase is washed twice
with CH.sub.2Cl.sub.2. The organic fractions are collected, dried
over Na.sub.2SO.sub.4, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 75%.
[0178] .sup.31P NMR (CD.sub.2Cl.sub.2) .delta. 10.09, 9.39, 8.82,
8.76, 8.30, 7.56 ppm.
[0179] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1445.60, m/z.sub.calc=1447.40.
[0180] The spectrophotometrical purity determined by HPLC is
91.5%.
EXAMPLE 27
Synthesis of the dimer 5'-OH-T-dG.sup.IBu-3'-O-Lev cyanoethyl
phosphorothioate triester
[0181] Coupling procedure of
5'-O-DMTr-T-3'-cyanoethyl-phosphoramidite with
5'-OH-dG.sup.IBu-3'-O-Lev using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0182] 5'-OH-dG.sup.IBu-3'-O-Lev (201 mg, 0.46 mmol) and
5'-O-DMTr-T-3'-cyanoethyl-phosphoramidite (620 mg, 0.83 mmol, 1.8
eq) are dissolved in anhydrous dichloromethane (10 ml). The
solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (1.38 g, 4.6 mmol
tos.sup.-, 10 eq) and is shaken for 3 h. The resin is filtered off.
The reaction is followed by reverse phase HPLC and .sup.31P NMR.
The yield is determined by .sup.31P NMR. The desired T-dG phosphite
triester dimer is obtained with 100% of yield compared to the
5'-OH-dG.sup.IBu-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite triester
.sup.31P NMR (CDCl.sub.3) (d 140.76, 139.97; 60.7%) and
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d 8.10, 8.03;
39.3%).
[0183] Sulfurization: To a solution of
5'-O-DMTr-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite triester dimer
(0.46 mmol) in anhydrous dichloromethane is added AMBERLYST A26
tetrathionate form (1.28 g, 2.3 mmol S.sub.4O.sub.6.sup.2-, 5 eq.).
The reaction mixture is shaken for 2 h. The reaction is followed by
reverse phase HPLC and .sup.31P NMR. The yield is determined by
.sup.31P NMR. After filtration of the resin the desired T-dG
phosphorothioate triester dimer is obtained with 100% of yield
compared to the 5'-OH-dG.sup.IBu-3'-O-Lev. The crude is a mixture
of 5'-O-DMTr-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
.sup.31P NMR (CDCl.sub.3) (d 67.99, 67.71; 64.7%) and
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d 8.09, 8.02;
35.3%); MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M-DMTr].sup.+ m/z.sub.exp=809.00, m/z.sub.calc=809.77.
[0184] Detritytlation: To a solution of
5'-O-DMTr-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
triester (0.46 mmol) in 20 ml CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is
added 2 ml (1.2 mmol, 1.4 eq.) of a solution of benzene sulfonic
acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is
stirred 25 min at 0.degree. C. The reaction is is washed with 10 ml
of a saturated solution of NaHCO.sub.3, the organic layer is
separated, dried (MgSO.sub.4) and evaporated. The crude product is
dissolved in 3.5 mL dichloromethane and added to 50 mL diethylether
at 0.degree. C. to give a white precipitate. Yield: 370 mg, 0.46
mmol, 99%; .sup.31P NMR (CDCl.sub.3) d 67.77, 67.42; MALDI-TOF MS
(positive mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=910.42, m/z.sub.calc=909.77; HPLC HPLC (7.27 min;
Area=85%).
EXAMPLE 28
Synthesis of the dimer 5'-OH-dA.sup.Bz-dG.sup.IBu-3'-O-Lev
cyanoethyl phosphorothioate triester
[0185] Coupling procedure of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-dG.sup.IBu-3'-O-Lev using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0186] 5'-OH-dG.sup.IBu-3'-O-Lev (200 mg, 0.46 mmol) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite (713 mg, 0.83
mmol, 1.8 eq) are dissolved in anhydrous dichloromethane (10 ml).
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (1.38 g, 4.6 mmol
tos.sup.-, 10 eq) and is shaken for 2 h. The resin is filtered off.
The reaction is followed by reverse phase HPLC and .sup.31P NMR.
The yield is determined by HPLC. The desired dA.sup.Bz-dG phosphite
triester dimer (HPLC at 11.34 min; Area=61%) is obtained with 100%
of yield compared to the 5'-OH-dG.sup.IBu-3'-O-Lev (HPLC at 6.34
min; Area=0%). The crude is a mixture of
5'-O-DMTr-dA.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite
triester .sup.31P NMR (CDCl.sub.3) (d 140.82, 140.30),
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl phosphoramidite (d 149.90) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogeno-phosphonate (d 8.20,
8.03).
[0187] Sulfurization: To a solution of
5'-O-DMTr-dA.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite
triester dimer (0.46 mmol) in anhydrous dichloromethane is added
AMBERLYST A26 tetrathionate form (1.28 g, 2.3 mmol
S.sub.4O.sub.6.sup.2-, 5 eq.). The reaction mixture is shaken for 2
h. The reaction is followed by reverse phase HPLC and .sup.31P NMR.
The yield is determined by HPLC. After filtration of the resin the
desired dA.sup.Bz-dG phosphorothioate triester dimer (HPLC at 11.49
min; Area=61%) is obtained with 100% of yield compared to the
5'-OH-dG.sup.IBu-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-dA.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
.sup.31P NMR (CDCl.sub.3) (d 68.01, 67.93),
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl thiophosphoramidate (d 71.86,
71.54) and 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogenophosphonate
(d 8.20, 8.03); MALDI-TOF MS (positive mode, trihydroxyacetophenone
as matrix) [M-H].sup.+ m/z.sub.exp=1224.14,
m/z.sub.calc=1225.27.
[0188] Detritytlation: To a solution of
5'-O-DMTr-dA.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
triester (0.46 mmol) in 20 ml CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is
added 2 ml (1.2 mmol, 1.4 eq.) of a solution of benzene sulfonic
acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is
stirred 20 min at 0.degree. C. Another 1 ml (0.6 mmol, 0.7 eq.) of
a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added and the solution is
stirred for 40 min. The reaction is washed with 10 ml of a
saturated solution of NaHCO.sub.3, the organic layer is separated,
dried (MgSO.sub.4) and evaporated. The crude product is dissolved
in 4 mL dichloromethane and added to 50 mL diethylether at
0.degree. C. to give a white precipitate. Yield: 442 mg, 0.4 mmol,
87%; .sup.31P NMR (CDCl.sub.3) d 68.09, 67.78; MALDI-TOF MS
(positive mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=923.03, m/z.sub.calc=922.89; HPLC (8.08 min;
Area=85%).
EXAMPLE 29
Synthesis of the dimer 5'-OH-dC.sup.Bz-dG.sup.IBu-3'-O-Lev
cyanoethyl phosphorothioate triester
[0189] Coupling procedure of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'OH-dG.sup.IBu-3'-O-Lev using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0190] 5'-OH-dG.sup.IBu-3'-O-Lev (200 mg, 0.46 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite (694 mg, 0.83
mmol, 1.8 eq) are dissolved in anhydrous dichloromethane (10 ml),
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (1.38 g, 4.6 mmol
tos.sup.-, 10 eq) and is shaken for 3 h. The resin is filtered off.
The reaction is followed by reverse phase HPLC and .sup.31P NMR.
The yield is determined by HPLC. The desired dC-dG phosphite
triester dimer (HPLC at 12.01 min; Area=50%) is obtained with 100%
of yield compared to the 5'-OH-dG.sup.IBu-3'-O-Lev (HPLC at 6.34
min; Area=0%). The crude is a mixture of
5'-O-DMTr-dC.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite
triester .sup.31P NMR (CDCl.sub.3) (d 140.67, 140.59),
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl phosphoramidite (d 149.93) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogeno-phosphonate (d
8.08).
[0191] Sulfurization: To a solution of
5'-O-DMTr-dC.sup.Bz-dG.sup.IBu-O-Lev cyanoethyl phosphite triester
dimer (0.46 mmol) in anhydrous dichloromethane is added AMBERLYST
A26 tetrathionate form (1.37 g, 2.5 mmol S.sub.4O.sub.6.sup.2-, 5.4
eq.). The reaction mixture is shaken for 3 h. The reaction is
followed by reverse phase HPLC and .sup.31P NMR. The yield is
determined by HPLC. After filtration of the is resin the desired
dC-dG phosphorothioate triester dimer (HPLC at 12.26 min; Area=59%)
is obtained with 100% of yield compared to the
5'-OH-dG.sup.IBu-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-dC.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
.sup.31P NMR (CDCl.sub.3) (d 68.02, 67.55),
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl thiophosphoramidate (d 71.93,
71.62) and 5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogeno-phosphonate
(d 8.07).
[0192] Detritytlation: To a solution of
5'-O-DMTr-dC.sup.Bz-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
triester (0.46 mmol) in 20 ml CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is
added 2 ml (1.2 mmol, 1.4 eq.) of a solution of benzene sulfonic
acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is
stirred 20 min at 0.degree. C. Another 1 ml (0.6 mmol, 0.7 eq.) of
a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added and the solution is
stirred for 10 min. The reaction is washed with 10 ml of a
saturated solution of NaHCO.sub.3, the organic layer is separated,
dried (MgSO.sub.4) and evaporated. The crude product is dissolved
in 7 mL dichloromethane and added to 50 mL diethylether at
0.degree. C. to give a white precipitate. Yield: 493 mg, 0.33 mmol,
71%; .sup.31P NMR (CDCl.sub.3) d 67.38, 66.77; MALDI-TOF MS
(positive mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=898.84, m/z.sub.calc=898.86; HPLC (8.34 min;
Area=60%).
EXAMPLE 30
Synthesis of the dimer 5'-OH-dG.sup.IBu-dG.sup.IBu-3'-O-Lev
cyanoethyl phosphorothioate triester
[0193] Coupling procedure of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite with
5'-OH-dG.sup.IBu-3'-O-Lev using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0194] 5'-OH-dG.sup.IBu-3'-O-Lev (200 mg, 0.46 mmol) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite (698 mg, 0.84
mmol, 1.8 eq) are dissolved in anhydrous dichloromethane (10 ml).
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (1.38 g, 4.6 mmol
tos.sup.-, 10 eq) and is shaken for 1 h 15 min. The resin is
filtered off. The reaction is followed by reverse phase HPLC and
.sup.31P NMR. The yield is determined by HPLC. The desired dG-dG
phosphite triester dimer (HPLC at 11.01 min; Area=65%) is obtained
with 100% of yield compared to the 5'-OH-dG.sup.IBu-3'-O-Lev (HPLC
at 6.34 min; Area=0%). The crude is a mixture of
5'-O-DMTr-dG.sup.IBu-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite
triester .sup.31P NMR (CDCl.sub.3) (d 141.91, 140.29) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 8.80,
8.06).
[0195] Sulfurization: To a solution of
5'-O-DMTr-dG.sup.IBu-dG.sup.IBu-3'-O-Lev cyanoethyl phosphite
triester dimer (0.46 mmol) in anhydrous dichloromethane is added
AMBERLYST A26 tetrathionate form (1.28 g, 2.3 mmol
S.sub.4O.sub.6.sup.2-, 5 eq.). The reaction mixture is shaken for 1
h 20 min. The reaction is followed by reverse phase HPLC and
.sup.31P NMR. The yield is determined by HPLC. After filtration of
the resin the desired dG-dG phosphorothioate triester dimer (HPLC
at 11.52 min; Area=75%) is obtained with 100% of yield compared to
the 5'-OH-dG.sup.IBu-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-dG.sup.IBu-dG.sup.IBu-3'-O-Lev cyanoethyl
phosphorothioate .sup.31P NMR (CDCl.sub.3) (d 68.61, 67.64) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 8.07);
MALDI-TOF MS (positive mode, trihydroxyacetophenone as matrix)
[M-DMTr].sup.+ m/z.sub.exp=904.14, m/z.sub.calc=904.87.
[0196] Detritytlation: To a solution of
5'-O-DMTr-dG.sup.IBu-dG.sup.IBu-3'-O-Lev cyanoethyl
phosphorothioate triester (0.46 mmol) in 20 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 2 ml (1.2 mmol, 1.4 eq.)
of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 25 min
at 0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(MgSO.sub.4) and evaporated. The crude product is dissolved in 7.5
mL dichloromethane and added to 50 mL diethylether at 0.degree. C.
to give a white precipitate. Yield: 450 mg, 0.41 mmol, 88; .sup.31P
NMR (CDCl.sub.3) d 67.85, 67.66; MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-H].sup.+ m/z.sub.exp=905.45,
m/z.sub.calc=904.87; HPLC (7.95 min; Area=82%).
EXAMPLE 31
Synthesis of the trimer 5'-OH-dA.sup.Bz-T-dG.sup.IBu-3'-O-Lev
cyanoethyl phosphorothioate triester
[0197] Coupling procedure of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate triester
using the poly(4-vinylpyridinum p-toluenesulfonate) (Aldrich):
[0198] 5'-OH-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate
triester (362 mg, 0.4 mmol) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphoramidite (623 mg, 0.73
mmol, 1.8 eq) are dissolved in anhydrous dichloromethane (15 ml).
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (1.2 g, 4.0 mmol
tos.sup.-, 10 eq) and is shaken for 6 h 20 min. Water (50 mL) is
added to hydrolyze the remaining phosphoramidite. After 1 h the
resin is filtered off. The reaction is followed by reverse phase
HPLC and .sup.31P NMR. The yield is determined by HPLC. The desired
dA-T-dG is phosphite triester trimer (HPLC at 11.32 min; Area=66%)
is obtained with 100% of yield compared to the
5'-OH-T-dG.sup.IBu-3'-O-Lev cyanoethyl phosphorothioate triester
(HPLC at 7.27 min; Area=0%). The crude is a mixture of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphite-T-3'-cyanoethylthionophosphot-
riester-dG.sup.IBu-T-O-Lev trimer .sup.31P NMR (CDCl.sub.3) (d
140.97, 140.79, 140.40, 139.90, 67.89, 67.87, 67.83) and
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d 8.12,
8.03).
[0199] Sulfurization: To a solution of
5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl-phosphite-T-3'-cyanoethyl-thionophospho-
triester-dG.sup.IBu-3'-O-Lev (0.4 mmol) in anhydrous
dichloromethane is added AMBERLYST A26 tetrathionate form (1.12 g,
2.0 mmol S.sub.4O.sub.6.sup.2-, 5 eq.). The reaction mixture is
shaken for 14 h. The reaction is followed by reverse phase HPLC and
.sup.31P NMR. The yield is determined by HPLC. After filtration of
the resin the desired dA-T-dG phosphorothioate triester trimer
(HPLC at 11.63 min; Area=64%) is obtained with 100% of yield
compared to the 5'-OH-T-dG.sup.IBu-3'-O-Lev cyanoethyl
phosphorothioate triester. The crude is a mixture of
5'-O-DMTr-dA.sup.Bz-T-dG.sup.IBu-3'-O-Lev cyanoethyl
phosphorothioate triester .sup.31P NMR (CDCl.sub.3) (d 68.05,
67.92, 67.84, 67.68) and 5'-O-DMTr-dA.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (d 8.16, 7.98); MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-DMTr].sup.+
m/z.sub.exp=1583.16, m/z.sub.calc=1582.53.
[0200] Detritytlation: To a solution of
5'O-DMTr-dA.sup.Bz-T-dG.sup.IBu-3'-O-Lev cyanoethyl
phosphorothioate triester (0.4 mmol) in 60 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 4 ml (2.5 mmol, 6.3 eq.)
of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 30 min
at 0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(MgSO.sub.4) and evaporated. The crude product is dissolved in 10
mL dichloromethane and added to 50 mL diethylether at 0.degree. C.
to give a white precipitate. Yield: 543 mg, 0.32 mmol, 80%;
.sup.31P NMR (CDCl.sub.3) d 67.94, 67.79, 67.72, 67, 66, 67.58,
67.28, 67.14; MALDI-TOF MS (positive mode, trihydroxyacetophenone
as matrix) [M-H].sup.- m/z.sub.exp=1296.07, m/z.sub.calc=1296.22;
HPLC (9.39 min; Area=77%).
EXAMPLE 32
Synthesis of the tetramer 5'-OH-dC.sup.Bz-dG.sup.IBu-T-T-3'-O-Lev
cyanoethyl phosphorothioate triester
[0201] 1.sup.st Coupling procedure of
5'-O-DMTr-T-3'-cyanoethyl-phosphoramidite with 5'-OH-T-3'-O-Lev
using the poly(4-vinylpyridinum p-toluenesulfonate) (Aldrich)
providing the 5'O-DMTr-T-T-3'-O-Lev cyanoethyl phosphite triester
dimer:
[0202] 5'-OH-T-3'-O-Lev (340 mg, 1.0 mmol) and
5'-O-DMTr-T-3'-cyanoethyl-phosphoramidite (1266 mg, 1.7 mmol, 1.7
eq) are dissolved in anhydrous dichloromethane (10 ml). The
solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (3.0 g, 10 mmol
tos.sup.-, 10 eq) and is shaken for 5 h 15 min. Water (50 mL) is
added to hydrolyze the remaining phosphoramidite. After 1 h 15 min
the resin is filtered off. The reaction is followed by reverse
phase HPLC and .sup.31P NMR. The yield is determined by HPLC. The
desired T-T phosphite triester dimer (HPLC at 11.14 min; Area 71%)
is obtained with 100% of yield compared to the 5'-OH-T-3'-O-Lev
(HPLC at 5.49 min; Area=0%). The crude is a mixture of
5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphite triester .sup.31P NMR
(CDCl.sub.3) (d 140.58, 140.31) and 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (d 8.10, 8.04).
[0203] 1.sup.st Sulfurization: To a solution of
5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphite triester dimer (1.0
mmol) in anhydrous dichloromethane is added AMBERLYST A26
tetrathionate form (3.89 g, 7.0 mmol S.sub.4O.sub.6.sup.2-, 7 eq.).
The reaction mixture is shaken for 20 h. The reaction is followed
by reverse phase HPLC and .sup.31P NMR. The yield is determined by
HPLC. After filtration of the resin the desired T-T
phosphorothioate triester dimer (HPLC at 11.44 min; Area=75%) is
obtained with 100% of yield compared to the 5'-OH-T-3'-O-Lev. The
crude is a mixture of 5'-O-DMTr-T-T-3'-O-Lev cyanoethyl
phosphorothioate .sup.31P NMR (CDCl.sub.3) (d 68.20, 68.14) and
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d 8.11, 8.05).
[0204] 1.sup.st Detritytlation: To a solution of
5'O-DMTr-T-T-3'-O-Lev cyanoethyl phosphorothioate triester (1.0
mmol) in 70 ml CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 4 ml (2.5
mmol, 2.5 eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 40 min
at 0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(MgSO.sub.4) and evaporated. The crude product is dissolved in 8 mL
dichloromethane and added to 50 mL diethylether at 0.degree. C. to
give a white precipitate. Yield: 764 mg, 0.99 mmol, 99%; .sup.31P
NMR (CDCl.sub.3) d 67.87, 67.60; MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-H].sup.+ m/z.sub.exp=713.95,
m/z.sub.calc=714.66; HPLC (7.70 min; Area=88%).
[0205] 2.sup.nd Coupling procedure of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite with
5'-OH-T-T-3'-O-Lev cyanoethyl phosphorothioate dimer using the
poly(4-vinylpyridinum p-toluenesulfonate) (Aldrich) providing the
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphite-T-3'-cyanoethyl-thionophosph-
otriester-T-3'-O-Lev trimer:
[0206] 5'-OH-T-T-3'-O-Lev cyanoethyl phosphorothioate (764 mg, 0.99
mmol) and 5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite (1400
mg, 1.7 mmol, 1.7 eq) are dissolved in anhydrous dichloromethane
(20 ml). The solution is transferred under argon in a flask
containing the poly(4-vinylpyridinum p-toluenesulfonate) (3.0 g, 10
mmol tos.sup.-, 10 eq) and is shaken for 2 h 50 min. Water (50 mL)
is added to hydrolyze the remaining phosphoramidite. After 1 h 20
min the resin is filtered off. The reaction is followed by reverse
phase HPLC and .sup.31P NMR. The yield is determined by HPLC. The
desired
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphite-T-3'-cyanoethyl-thionophosph-
otriester-T-3'-O-Lev trimer (HPLC at 11.65 min; Area=72%) is
obtained with 100% of yield compared to the 5'-OH-T-T-3'-O-Lev
cyanoethyl phosphorothioate (HPLC at 7.70 min; Area 0%). The crude
is a mixture of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphite-T-3'-cyanoethyl-thionophosph-
otriester-T-3'-O-Lev trimer .sup.31P NMR (CDCl.sub.3) (d 142.78,
142.67, 141.54, 141.50, 68.47, 68.39, 68.16, 67.93) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 8.59,
8.05).
[0207] 2.sup.nd Sulfurization: To a solution of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphite-T-3'-cyanoethyl-thionophosph-
otriester-T-3'-O-Lev trimer (0.99 mmol) in anhydrous
dichloromethane is added AMBERLYST A26 tetrathionate form (2.78 g,
5.0 mmol S.sub.4O.sub.6.sup.2-, 5 eq.). The reaction mixture is
shaken for 18 h 45 min. The reaction is followed by reverse phase
HPLC and .sup.31P NMR. The yield is determined by HPLC. After
filtration of the resin the desired dG-T-T phosphorothloate
triester trimer (HPLC at 11.66 min; Area=58%) is obtained with 100%
of yield compared to the 5'-OH-T-T-3'-O-Lev cyanoethyl
phosphorothloate. The crude is a mixture of
5'-DMTr-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl phosphorothioate
triester trimer .sup.31P NMR (CDCl.sub.3) (d 68.94, 68.43, 68.09,
67.93, 67.69, 67.34); MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-H].sup.+ m/z.sub.exp=1484.81,
m/z.sub.calc=1485.47 and 5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl
hydrogenophosphonate (d 8.59, 8.52).
[0208] 2.sup.nd Detritytlation: To a solution of
5'-DMTr-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl phosphorothioate
triester trimer (0.99 mmol) in 75 ml CH.sub.2Cl.sub.2/CH.sub.3OH
(7/3) is added 4 ml (2.5 mmol, 2.5 eq.) of a solution of benzene
sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 40 min at 0.degree. C. The reaction is washed
with 10 ml of a saturated solution of NaHCO.sub.3, the organic
layer is separated, dried (MgSO.sub.4) and evaporated. The crude
product is dissolved in 8 mL dichloromethane and added to 50 mL
diethylether at 0.degree. C. to give a white precipitate. Yield:
1257 mg, 0.78 mmol, 79%; .sup.31P NMR (CDCl.sub.3) d 68.32, 68.07,
68.01, 67.95, 67, 86, 67.51, 67.25; MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-H].sup.- m/z.sub.exp=1182.12,
m/z.sub.calc=1183.09; HPLC (8.94 min; Area=79%).
[0209] 3.sup.rd Coupling procedure of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'OH-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl phosphorothioate triester
trimer using the poly(4-vinylpyridinum p-toluenesulfonate)
(Aldrich) providing the
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphite-dG.sup.IBu-cyanoethyl-thi-
onophosphotriester-T-3'-cyanoethyl-thionophosphotriester-T-3'-O-Lev
tetramer:
[0210] 5'-OH-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl phosphorothioate
triester trimer (1257 mg, 0.78 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite (1420 mg, 1.7
mmol, 2.2 eq) are dissolved in anhydrous dichloromethane (20 ml).
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (3.0 g, 10 mmol
tos.sup.-, 12.8 eq) and is shaken for 4 h 50 min. Water (100 mL) is
added to hydrolyze the remaining phosphoramidite. After 20 min the
resin is filtered off. The reaction is followed by reverse phase
HPLC and .sup.31P NMR. The yield is determined by HPLC. The desired
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphite-dG.sup.IBu-3'-cyanoethyl-thio-
nophosphotriester-T-3'-cyanoethyl-thionophosphotriester-T-3'-O-Lev
tetramer (HPLC at 12.04 min; Area=79%) is obtained with 100% of
yield compared to the 5'-OH-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl
phosphorothioate triester trimer (HPLC at 8.94 min; Area=0%). The
crude is a mixture of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphite-dG.sup.IBu-3'-cyanoethyl-thio-
nophosphotriester-T-3'-cyanoethyl-thionophosphotriester-T-3'-O-Lev
tetramer .sup.31P NMR (CDCl.sub.3) (d 141.01, 140.93, 140.05,
139.90, 68.50, 68.09, 68.04, 67.95) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d
8.15).
[0211] 3.sup.rd Sulfurization: To a solution of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphite-dG.sup.IBu-3'-cyanoethyl-thio-
nophosphotriester-T-3'-cyanoethylthionophosphotriester-T-3'-O-Lev
trimer (0.78 mmol) in anhydrous dichloromethane is added AMBERLYST
A26 tetrathionate form (2.78 g, 5.0 mmol S.sub.4O.sub.6.sup.2-, 6.4
eq.). The reaction mixture is shaken for 3 h. The reaction is
followed by reverse phase HPLC and .sup.31P NMR. The yield is
determined by HPLC. After filtration of the resin the desired
dC-dG-T-T phosphorothioate triester tetramer (HPLC at 121.18 min;
Area=73%) is obtained with 100% of yield compared to the
5'-OH-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl phosphorothioate triester
trimer. The crude is a mixture of
5'-DMTr-dC.sup.Bz-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl
phosphorothioate triester tetramer .sup.31P NMR (CDCl.sub.3) (d
68.51, 68.45, 68.22, 68.18, 68.10, 68.09, 67.70, 67.65); MALDI-TOF
MS (positive mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=1947.90, m/z.sub.calc=1947.89 and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d
8.09).
[0212] 3.sup.rd Detritytlation: To a solution of
5'-DMTr-dC.sup.Bz-dG.sup.IBu-T-T-3'-O-Lev cyanoethyl
phosphorothioate triester tetramer (0.78 mmol) in 80 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 7 ml (4.4 mmol, 5.6 eq.)
of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 50 min
at 0.degree. C. The reaction is washed with 10 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(MgSO.sub.4) and evaporated. The crude product is dissolved in 12
mL CH.sub.2Cl.sub.2/CH.sub.3OH (2/1) and added to 100 mL
diethylether at 0.degree. C. to give a white precipitate. Yield:
1334 mg, 0.53 mmol, 68%; .sup.31P NMR (CDCl.sub.3) d 68.50, 68.41,
67.93, 67.86, 67.81, 67.74, 67.71, 67.64, 67.57, 67.51; MALDI-TOF
MS (positive mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=1645.24, m/z.sub.calc=1645.52; HPLC (9.95 min;
Area=68%).
EXAMPLE 33
Synthesis of the dimer 5'-OH-dC.sup.Bz-dC.sup.Bz-3'-O-TBDMS
cyanoethyl phosphorothioate triester
[0213] Coupling procedure of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-dC.sup.Bz-3'-O-TBDMS using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0214] 5'-OH-dC.sup.Bz-3'-O-TBDMS (100 mg, 0.22 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite (384 mg, 0.46
mmol, 2.1 eq) are dissolved in anhydrous acetonitrile (15 ml). The
solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (690 mg, 2.3 mmol
tos.sup.-, 10.3 eq) and is shaken for 6 h. The resin is filtered
off. The reaction is followed by .sup.31P NMR. The yield is
determined by .sup.31P NMR. The desired dc-dc phosphite triester
dimer is obtained with 100% of yield compared to the
5'-OH-dG.sup.IBu-3'-O-TBDMS. The crude is a mixture of
5'-O-DMTr-dC.sup.Bz-dC.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester .sup.31P NMR (CDCl.sub.3) (d 141.06, 140.93) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d
8.67).
[0215] Sulfurization: To a solution of
5'-O-DMTr-dC.sup.Bz-dC.sup.Bz-3'-O-TBDMS cyanoethyl phosphite
triester dimer (0.22 mmol) in anhydrous acetonitrile is added
AMBERLYST A26 tetrathionate form (620 mg, 1.2 mmol
S.sub.4O.sub.6.sup.2-, 5.4 eq.). The reaction mixture is shaken for
65 h. The reaction is followed by .sup.31P NMR. The yield is
determined by .sup.31P NMR. After filtration of the resin the
desired dC-dC phosphorothioate triester dimer is obtained with 100%
of yield compared to the 5'-OH-dC.sup.Bz-3'-O-TBDMS. The crude is a
mixture of 5'-O-DMTr-dC.sup.Bz-dC.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate .sup.31P NMR (CDCl.sub.3) (d 68.24, 68.19) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d
8.57).
[0216] Detritytlation: To a solution of
5'-O-DMTr-dC.sup.Bz-dC.sup.Bz-3'-O-TBDMS cyanoethyl
phosphorothioate triester (0.22 mmol) in 20 ml
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added 0.5 ml (0.3 mmol, 1.3
eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred 30 min
at 0.degree. C. Another 0.5 ml (0.3 mmol, 1.3 eq.) of a solution of
benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is
added and the solution is stirred for 30 min. Another 0.7 ml (0.4
mmol, 1.8 eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added and the solution is
stirred for 30 min. The reaction is washed with 5 ml of a saturated
solution of NaHCO.sub.3, the organic layer is separated, dried
(NaSO.sub.4), evaporated and purified on a silica gel column. The
desired dimer dC-dC is eluted with CH.sub.2Cl.sub.2/CH.sub.3OH
(33/1). Yield: 106 mg, 0.1 mmol, 52%; .sup.31P NMR (CDCl.sub.3) d
67.92, 67.78; MALDI-TOF MS (positive mode, trihydroxyacetophenone
as matrix) [M-H].sup.+ m/z.sub.exp=908.47, m/z.sub.calc=909.02;
HPLC (12.73 min; Area=85%).
EXAMPLE 34
Synthesis of the dimer 5'-OH-dG.sup.IBu-dA.sup.Bz-3'-O-Lev
cyanoethyl phosphorothioate triester
[0217] Coupling procedure of
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-Lev using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0218] 5'-OH-dA.sup.Bz-3'-O-Lev (2.235 g, 4.93 mmol) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl-phosphoramidite (6.13 g, 7.43
mmol, 1.5 eq) are dissolved in anhydrous dip chloromethane (100
ml). The solution is transferred under argon in a flask containing
the poly(4-vinylpyridinum p-toluenesulfonate) (14.76 g, 49.3 mmol
tos.sup.-, 10 eq) and is shaken for 2 h 45 min. Water (0.2 ml) is
added and the mixture is shaken for 1 h 25 min. The resin is
filtered off. The reaction is followed by reverse phase HPLC and
.sup.31P NMR. The yield is determined by HPLC. The desired dG-dA
phosphite triester dimer (HPLC at 11.69 min; Area=65%) is obtained
with 100% of yield compared to the 5'-OH-dA.sup.Bz-3'-O-Lev (HPLC
at 7.20 min; Area=0%). The crude is a mixture of
5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-Lev cyanoethyl phosphite
triester .sup.31P NMR (CDCl.sub.3) (d 140.52, 140.20) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 8.59,
8.09).
[0219] Sulfurization: To a solution of
5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-Lev cyanoethyl phosphite
triester dimer (4.93 mmol) in anhydrous dichloromethane is added
AMBERLYST A26 tetrathionate form (19.7 g, 24.63 mmol
S.sub.4O.sub.6.sup.2-, 5 eq.). The reaction mixture is shaken for 3
h 10 min. The reaction is followed by reverse phase HPLC and
.sup.31P NMR. The yield is determined by .sup.31P NMR. After
filtration of the resin the desired dG-dA phosphorothioate triester
dimer is obtained with 100% of yield compared to the
5'-OH-dA.sup.Bz-3'-O-Lev. The crude is a mixture of
5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-Lev cyanoethyl phosphorothioate
.sup.31P NMR (CDCl.sub.3) (d 68.45, 67.73) and
5'-O-DMTr-dG.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 8.60,
8.04).
[0220] Detritytlation: To a solution of
5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-Lev cyanoethyl phosphorothioate
triester (4.93 mmol) in 200 ml dichloromethane is added 50 ml
methanol and 20 ml (12.6 mmol, 2.6 eq.) of a solution of benzene
sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 40 min at 0.degree. C. Another 6 ml (3.8 mmol,
0.8 eq.) of a solution of benzene sulfonic acid 10% in
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) is added and the solution is
stirred for 15 min. Another 4 ml (2.5 mmol, 0.5 eq.) of a solution
of benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3)
is added and the solution is stirred for 15 min. The reaction is
washed with 70 ml of a saturated solution of NaHCO.sub.3, the
organic layer is separated, dried (MgSO.sub.4) and evaporated. The
crude product is dissolved in 16 mL dichloromethane and added to
100 ml diethylether at 0.degree. C. to give a white precipitate.
Yield: 4.28 mg, 3.8 mmol, 77%; .sup.31P NMR (CDCl.sub.3) d 68.07,
67.80; MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M-H].sup.+ m/z.sub.exp=923.08, m/z.sub.calc=922.89; HPLC
(8.90 min and 9.07 min; Area=70%). After complete deprotection with
ammonia solution (28% NH.sub.3 in water, 14 h) MALDI-TOF MS
(positive mode, trihydroxyacetophenone as matrix) [M-H].sup.+
m/z.sub.exp=597.57, m/z.sub.calc=596.51; HPLC (8.45 min and 8.77
min; Area=82%).
EXAMPLE 35
Synthesis of the dimer 5'-DMTr-O-dC.sup.Bz-dA.sup.Bz-3'-OH
cyanoethyl phosphorothioate triester
[0221] Coupling procedure of
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite with
5'-OH-dA.sup.Bz-3'-O-Lev using the poly(4-vinylpyridinum
p-toluenesulfonate) (Aldrich):
[0222] 5'OH-dA.sup.Bz-3'-O-Lev (200 mg, 0.44 mmol) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl-phosphoramidite (626 mg, 0.75
mmol, 1.7 eq) are dissolved in anhydrous dichloromethane (10 ml).
The solution is transferred under argon in a flask containing the
poly(4-vinylpyridinum p-toluenesulfonate) (1.3 g, 3 mmol tos.sup.-,
6.8 eq) and is shaken for 8 h. The resin is filtered off. The
reaction is followed by reverse phase HPLC and .sup.31P NMR. The
yield is determined by HPLC. The desired dC-dA phosphite triester
dimer (HPLC at 13.13 min; Area=63%) is obtained with 100% of yield
compared to the 5'-OH-dA.sup.Bz-3'-O-Lev (HPLC at 7.39 min;
Area=0%). The crude is a mixture of
5'-O-DMTr-dG.sup.Bz-dA.sup.Bz-3'-O-Lev cyanoethyl phosphite
triester .sup.31P NMR (CDCl.sub.3) (d 140.68, 140.58) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d 8.04,
8.02).
[0223] Sulfurization: To a solution of
5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-Lev cyanoethyl phosphite
triester dimer (0.44 mmol) in anhydrous dichloromethane is added
AMBERLYST A26 tetrathionate form (2.5 g, 4.38 mmol
S.sub.4O.sub.6.sup.2-, 9.9 eq.). The reaction mixture is shaken for
10 h. The reaction is followed by reverse phase HPLC and .sup.31P
NMR. The yield is determined by .sup.31P NMR. After filtration of
the resin the desired dC-dA phosphorothioate triester dimer is
obtained with 100% of yield compared to the
5'-OH-dA.sup.Bz-3'-O-Lev. The Solvent is removed under reduced
pressure. The crude is a mixture of
5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-Lev cyanoethyl phosphorothioate
.sup.31P NMR (CDCl.sub.3) (d 68.33, 68.30) and
5'-O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d 8.04,
8.02).
[0224] Deprotection of the levulinyl group: The
5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-Lev cyanoethyl phosphorothioate
triester (0.44 mmol) is dissolved in 16 ml pyridine and 4 ml acetic
acid. AMBERLYST 15 hydrazine form (1 g, 3.91 mmol
N.sub.2H.sub.5.sup.-, 8.7 eq.) is added and the solution is shaken
for 1 h 30 min. The reaction is followed by reverse phase HPLC. The
yield is determined by reverse phase HPLC. After filtration of the
resin the desired dC-dA phosphorothioate triester dimer is obtained
with 100% of yield compared to the 5'-OH-dA.sup.Bz-3'-O-Lev. The
Solvent is removed under reduced pressure. The crude is a mixture
of 5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-OH cyanoethyl phosphorothioate
HPLC (12.24 min and 12.45 min; Area=66%) and
5'O-DMTr-dC.sup.Bz-3'-cyanoethyl hydrogenophosphonate HPLC (10.71
min and 10.82 min; Area 34%). MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M-H].sup.+ m/z.sub.exp=1120.23,
m/z.sub.calc=1121.16.
Synthesis of Resins
EXAMPLE 36
Synthesis of AMBERLYST A26 Periodate Form
[0225] 10 g commercial Amberlyst A26 hydroxide form (Rohm &
Haas) is washed twice with 20 ml methanol and twice with 20 ml
dichloromethane and dried in is vacuum. Potassium tetrathionate (10
g, 47 mmol, 1.4 eq.) is dissolved in 300 ml deionized water. The
solution is added to the resin and shaken for 17 hours. The
solution is filtered off. Another time Potassium tetrathionate (10
g, 47 mmol, 1.4 eq.) is dissolved in 200 ml deionized water. The
solution is added to the resin and shaken for 6 hours. The solution
is filtered off. The resin is washed with 1 l deionized water,
twice with 30 ml methanol and twice with 30 ml dichloromethane and
dried under reduced pressure for 3 hours to give 8.2 g of
solid-supported periodate. The reagents loading was determined by
elemental analysis, giving a value of 27.16% for iodine (3.40% for
nitrogen and 40.20% for carbon. Loading: 2.14 mmol IO.sub.4.sup.-
per gram of resin. The resin can be recycled applying the same
protocol. Comparable resins are commercially available.
EXAMPLE 37
Synthesis of AMBERLYST 15 Hydrazine Form
[0226] 5 g commercial Amberlyst 15 H.sup.+ form (Aldrich) is washed
successively with 20 ml hydrochloric acid and with 500 ml deionized
water. Hydrazine (4.38 g, 87.5 mmol, 3.8 eq.) is dissolved in 100
ml deionized water. The solution is added to the resin and shaken
for 16 hours. The solution is filtered off. The resin is washed
successively with 500 ml deionized water, 50 ml methanol and with
50 ml dichloromethane and dried under reduced pressure for 3 hours
to give 5.2 g of solid-supported hydrazine. The reagents loading
was determined by elemental analysis, giving a value of 10.94% for
nitrogen (12.37% for sulfur and 44.19% for carbon. Loading: 191
mmol N.sub.2H.sub.5.sup.+ per gram of resin.
EXAMPLE 38
Recycling of poly(4-vinylpyridinum p-toluenesulfonate)
[0227] Used poly(4-vinylpyridinum p-toluenesulfonate) (20 g) is
washed successively for one hour each with acetonitrile (100 ml),
dichloromethane (100 ml) and methanol (100 ml). Then the resin is
added to a solution of p-toluene sulfonic acid (40 g, 0.23 mol) in
methanol (400 ml) and shaken for 21 h. The solution is filtered off
and the resin is washed with methanol (150 ml) and dichloromethane
(150 ml) and dried at 80.degree. C. under vacuum over
P.sub.2O.sub.5 for 8 h. The reagents loading was determined by
elemental analysis, giving a value of 10.73% for sulfur and 4.90%
for nitrogen. Loading: 3.35 mmol tos.sup.- per gram of resin.
Synthesis of Phosphodiester Oligomers
Formation of the Phosphate Triester Bridge
[0228] In this part, we focus on the formation of natural
phosphodiester oligomers. The coupling of the phosphoramidite
nucleotide and of the 5'-OH nucleoside was performed with the resin
polyvinyl pyridinium p-toluene sulfonate (PVP) commercially
available from ALDRICH. The oxidation of the phosphite triester
linkage was achieved with the resin
polystyrylmethyltrimethylamonium metaperiodate
(PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-) commercially available
from NOVABIOCHEM. Then, the detritylation step was performed in
solution with BSA. The purification was an extraction in
dichloromethane followed by a precipitation in ether.
EXAMPLE 39
Synthesis of the dimer 5'-OH-T-T-3'-O-Lev cyanoethyl phosphate
triester
[0229] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phosphoramidite with 5'-OH-T-3'-O-Lev using the PVP resin.
[0230] A solution of 5'-OH-T-3'-O-Lev (170 mg, 0.5 mmol) and
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (745 mg, 1 mmol, 2 eq) In
anhydrous acetonitrile (15 ml) is added to PVP resin (1.5 g, 5 mmol
pyrH.sup.+, 10 eq). The reaction is followed by reverse phase HPLC.
After 5 h the reaction is complete. The desired dimer
5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphite triester is
characterized by .sup.31P NMR. The crude is a mixture of
5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphite triester (d 140.62,
140.48) and of 5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d
8.81, 8.76).
[0231] Oxidation: The PVP resin is filtered off and the resulting
solution is added to PS--N(CH.sub.3).sub.3.sup.+IO.sub.4 (1 g, 2.5
mmol IO.sub.4.sup.-, 5 eq.). The reaction is followed by .sup.31P
NMR and by reverse phase HPLC. The reaction is complete after 45
min. The desired dimer 5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphate
triester is characterized by .sup.31P NMR. The crude is a mixture
of 5'-O-DMTr-T-3'-cyanoethyl phosphate diester (d -2.80),
5'-O-DMTr-T-T-3'-O-Lev cyanoethyl phosphate triester (d -1.48,
-1.63), 5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d 8.69,
8.64).
[0232] Detritylation: The PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
is filtered off and the solvent are evaporated. The crude is
dissolved in 8 ml of CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled
in an ice bath. To this solution is added 2 ml of a solution of
benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 45 min at 0.degree. C. The reaction is stopped
with 20 ml of a saturated solution of NaHCO.sub.3. The aqueous
phase is extracted three times with dichloromethane. The organic
layer is separated, dried (Na.sub.2SO.sub.4) and evaporated under
reduce pressure. The residue is dissolved in 5 ml of
CH.sub.2Cl.sub.2/MeOH (4/1) and added to 50 ml of cooled diethyl
ether drop by drop with a strong stirring. The mixture is
centrifuged for 45 min and the supernatant is eliminated. The
desired 5'-OH-T-T-3'-O-Lev cyanoethyl phosphate triester dimer is
obtained with a yield of 75.4% (calculated: 91% per step) compared
to the 5'-OH-T-3'-O-Lev. .sup.31P NMR (CD.sub.3CN) d -1.67, -1.72.
MALDI-TOF MS (positive mode, trihydroxyacetophenone as matrix)
[M+H].sup.+ m/z.sub.exp=700.42, m/z.sub.calc=698.60. The
spectrophotometric purity (91%) is determined by HPLC at 260
nm.
EXAMPLE 40
Synthesis of the trimer 5'-OH-G.sup.IBu-T-T-3'-O-Lev cyanoethyl
phosphate triester
[0233] Coupling procedure of 5'-O-DMTr-G.sup.IBu-3'-cyanoethyl
phosphoramidite with 5'-OH-T-T-3'-O-Lev dimer using the PVP
resin.
[0234] A solution of 5'-OH-T-T-3'-O-Lev (263 mg, 377 mmol) and
5'-O-DMTr-G.sup.IBu-3'-cyanoethyl phosphoramidite (623 mg, 754
mmol, 2 eq) in anhydrous acetonitrile (15 ml) is added to PVP resin
(1.1 g, 3.8 mmol pyrH.sup.+, 10 eq). The reaction is followed by
reverse phase HPLC. After 3 h 30 min the reaction is complete. The
desired trimer 5'-O-DMTr-G.sup.IBu-T-T-3'-O-Lev is characterized by
.sup.31P NMR. The crude is a mixture of
5'-O-DMTr-G.sup.IBu-T-T-3'-O-Lev trimer (phosphite triester linkage
d 141.56, 141.50, 141.44, 141.39, 141.13, 141.05; phosphate
triester linkage d -1.35; -1.44, -132, -1.57) and of
5'-O-DMTr-G.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 9.03,
8.84).
[0235] Oxidation: The PVP resin is filtered off and the resulting
solution is added to PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
(0.75 g, 1.9 mmol IO.sub.4.sup.-, 5 eq.). The reaction is followed
by .sup.31P NMR and by reverse phase HPLC. The reaction is complete
after 45 min. The desired dimer 5'-O-DMTr-G.sup.IBu-T-T-3'-O-Lev
cyanoethyl phosphate triester is characterized by .sup.31P NMR. The
crude is a mixture of 5'-O-DMTr-G.sup.IBu-3'-cyanoethyl phosphate
diester (d -2.52), 5'-O-DMTr-G.sup.IBu-T-T-3'-O-Lev cyanoethyl
phosphate triester (d -1.23, -1.35, -1.43, -1.50, -1.55),
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d 9.09, 8.90).
[0236] Detritylation: The PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
is filtered off and the solvent are evaporated. The crude is
dissolved in 8 ml of CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled
in an ice bath. To this solution is added 2 ml of a solution of
benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 45 min at 0.degree. C. The reaction is stopped
with 20 ml of a saturated solution of NaHCO.sub.3. The aqueous
phase is extracted three times with dichloromethane. The organic
layer is separated, dried (Na.sub.2SO.sub.4) and evaporated under
reduce pressure. The residue is dissolved in 5 ml of
CH.sub.2Cl.sub.2/MeOH (4/1) and added to 50 ml of cooled diethyl
ether drop by drop with a strong stirring. The mixture is
centrifuged for 45 min and the supernatant is eliminated. The
desired 5'-OH-G.sup.IBu-T-T-3'-O-Lev cyanoethyl phosphate triester
trimer is obtained with a yield of 37% (calculated: 72% per step)
compared to the 5'-OH-T-T-3'-O-Lev. .sup.31P NMR (CD.sub.3CN) d
-1.59, -1.68, -1.71, -1.75. MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M+H].sup.+ m/z.sub.exp=1149.60,
m/z.sub.calc=1150.96. The spectrophotometric purity (87%) is
determined by HPLC at 260 nm.
[0237] This low yield is due to the low solubility of the
detritylated trimer in dichloromethane, acetonitrile. The trimer is
soluble in methanol, and DMF.
EXAMPLE 41
Synthesis of the dimer 5'-OH-T-A.sup.Bz-3'-O-Lev cyanoethyl
phosphate triester
[0238] Coupling procedure of 5'-O-DMTr-T-3'-cyanoethyl
phosphoramidite with 5'-OH-A.sup.Bz-3'-O-Lev using the PVP
resin.
[0239] A solution of 5'-OH-A.sup.Bz-3'-O-Lev (453 mg, 1 mmol) and
5'-O-DMTr-T-3'-cyanoethyl phosphoramidite (1.49 g, 2 mmol, 2 eq) in
anhydrous acetonitrile (20 ml) is added to PVP resin (3 g, 10 mmol
pyrH.sup.+, 10 eq). The reaction is followed by reverse phase HPLC.
After 5 h the reaction is complete. The desired dimer
5'-O-DMTr-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphite triester is
characterized by .sup.31P NMR. The crude is a mixture of
5'-O-DMTr-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphite triester (d
140.48, 140.30) and of 5'-O-DMTr-T-3'-cyanoethyl
hydrogenophosphonate (d 8.76, 8.71).
[0240] Oxidation: The PVP resin is filtered off and the resulting
solution is added to PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.- (2
g, 5 mmol IO.sub.4.sup.-, 5 eq.). The reaction is followed by
.sup.31P NMR and by reverse phase HPLC. The reaction is complete
after 15 min. The desired dimer 5'-O-DMTr-T-A.sup.Bz-3'-O-Lev
cyanoethyl phosphate triester is characterized by .sup.31P NMR. The
crude is a mixture of 5'-O-DMTr-T-3'-cyanoethyl phosphate diester
(.sup.31P NMR (CD.sub.3CN) d -3.01), 5'-O-DMTr-T-A.sup.Bz-3'-O-Lev
cyanoethyl phosphate triester (d -1.58, -1.80),
5'-O-DMTr-T-3'-cyanoethyl hydrogenophosphonate (d 8.76, 8.71).
[0241] Detritylation: The PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
is filtered off and the solvent are evaporated. The crude is
dissolved in 16 ml of CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled
in an ice bath. To this solution is added 4 ml of a solution of
benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 45 min at 0.degree. C. The reaction is stopped
with 30 ml of a saturated solution of NaHCO.sub.3. The aqueous
phase is extracted three times with dichloromethane. The organic
layer is separated, dried (Na.sub.2SO.sub.4) and evaporated under
reduce pressure. The residue is dissolved in 10 ml of
CH.sub.2Cl.sub.2/MeOH (4/1) and added to 100 ml of cooled diethyl
ether drop by drop with a strong stirring. The mixture is
centrifuged for 45 min and the supernatant is eliminated. The
desired 5'-OH-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphate triester
dimer is obtained with a yield of 73% (calculated: 90% per step)
compared to the 5'-OH-T-3'-O-Lev. .sup.31P NMR (CD.sub.3CN) d
-1.77. MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=811.72, m/z.sub.calc=810.45. The
spectrophotometric purity (96%) is determined by HPLC at 260
nm.
EXAMPLE 42
Synthesis of the trimer 5'-OH-C.sup.Bz-T-A.sup.Bz-3'-O-Lev
cyanoethyl phosphate triester
[0242] Coupling procedure of 5'-O-DMTr-C.sup.Bz-3'-cyanoethyl
phosphoramidite with 5'-OH-T-A.sup.Bz-3'-O-Lev using the PVP
resin.
[0243] A solution of 5'OH-T-A.sup.Bz-3'-O-Lev (618 mg, 0.76 mmol)
and 5'-O-DMTr-C.sup.Bz-3'-cyanoethyl phosphoramidite (1.27 g, 1.52
mmol, 2 eq) in anhydrous acetonitrile (25 ml) and anhydrous DMF
(2.5 ml) is added to PVP resin (2.3 g, 7.6 mmol pyrH.sup.+, 10 eq).
The reaction is followed by reverse phase HPLC. After 2 h 30 the
reaction is complete. The desired trimer
5'-O-DMTr-C.sup.Bz-A.sup.Bz-T-3'-O-Lev cyanoethyl phosphite
triester is characterized by .sup.31P NMR. The crude is a mixture
of 5'-O-DMTr-C.sup.Bz-A.sup.Bz-T-3'-O-Lev trimer (phosphite
triester linkage d 140.76, 140.65, 140.09, 140.03; phosphate
triester linkage d -1.53, -1.57) and of
5'-O-DMTr-C.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d 8.73).
[0244] Oxidation: The PVP resin is filtered off and the resulting
solution is added to PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
(1.52 g, 3.8 mmol IO.sub.4.sup.-, 5 eq.). The reaction is followed
by .sup.31P NMR and by reverse phase HPLC. The reaction is complete
after 15 min. The desired trimer
5'-O-DMTr-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphate
triester is characterized by .sup.31P NMR. The crude is a mixture
of 5'-O-DMTr-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphate
triester (d -1.54, -1.59, -162, -1.72),
5'-O-DMTr-C.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d 8.74).
[0245] Detritylation: The PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
is filtered off and the solvent are evaporated. The crude is
dissolved in 32 ml of CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled
in an ice bath. To this solution is added 8 ml of a solution of
benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 1 h at 0.degree. C. The reaction is stopped
with 40 ml of a saturated solution of NaHCO.sub.3. The aqueous
phase is extracted three times with dichloromethane. The organic
layer is washed with an aqueous solution of Na.sub.2S.sub.2O.sub.3
0.2 M. The organic layer is separated, dried (Na.sub.2SO.sub.4) and
evaporated under reduce pressure. The residue is dissolved in 10 ml
of CH.sub.2Cl.sub.2 and added to 100 ml of cooled diethyl ether
drop by drop with a strong stirring. The mixture is centrifuged for
45 min and the supernatant is eliminated. The desired
5'-OH-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphate triester
trimer is obtained with a yield of 90% (calculated: 96% per step)
compared to the dimer 5'OH-T-A.sup.Bz-3'-O-Lev. .sup.31P NMR
(CD.sub.3CN) d -1.75, -1.79, -1.87, -1.91. MALDI-TOF MS (positive
mode, trihydroxyacetophenone as matrix) [M+H].sup.+
m/z.sub.exp=1257.53, m/z.sub.calc=1258.08. The spectrophotometric
purity (89%) is determined by HPLC at 260 nm.
EXAMPLE 43
Synthesis of the tetramer
5'-OH-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphate
triester
[0246] Coupling procedure of 5'-O-DMTr-G.sup.IBu-3'-cyanoethyl
phosphoramidite with 5'-OH-C.sup.Bz-T-A.sup.Bz-3'-O-Lev using the
PVP resin.
[0247] A solution of 5'-OH--C.sup.Bz-T-A.sup.Bz-3'-O-Lev (866 mg,
0.69 mmol) and 5'-O-DMTr-G.sup.IBu-3'-cyanoethyl phosphoramidite
(1.14 g, 1.38 mmol, 2 eq) in anhydrous acetonitrile (25 ml) and
anhydrous DMF (2.5 ml) is added to PVP resin (2.1 g, 6.9 mmol
pyH.sup.+, 10 eq). The reaction is followed by reverse phase HPLC.
After 3 h the reaction is complete. The desired tetramer
5'-O-DMTr-G.sup.IBu-C.sup.Bz-A.sup.Bz-T-3'-O-Lev O-Lev is
characterized by .sup.31P NMR. The crude is a mixture of
5'-O-DMTr-G.sup.IBu-C.sup.Bz-A.sup.Bz-T-3'-O-Lev tetramer
(phosphite triester linkage d 141.86, 141.82, 141.76, 141.61,
140.69, 140.66, 140.61; phosphate triester linkage d -1.53, -1.58,
-1.61, -1.64, -1.71, -1.82) and of
5'-O-DMTr-G.sup.IBu-3'-cyanoethyl hydrogenophosphonate (d 9.01,
8.84).
[0248] Oxidation: The PVP resin is filtered off and the resulting
solution is added to PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
(1.38 g, 3.45 mmol IO.sub.4.sup.-, 5 eq.). The reaction is followed
by .sup.31P NMR and by reverse phase HPLC. The reaction is complete
after 45 min. The desired tetramer
5'-O-DMTr-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl
phosphate triester is characterized by .sup.31P NMR. The crude is a
mixture of 5'-O-DMTr-G.sup.IBu-3'-cyanoethyl phosphate diester
(.sup.31P NMR (CD.sub.3CN) d -2.69),
5'-O-DMTr-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl
phosphate triester (d -1.38, -1.43, -1.53, -1.60, -1.64),
5'-O-DMTr-C.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d 9.02,
8.38).
[0249] Detritylation: The PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
is filtered off and the solvent are evaporated. The crude is
dissolved in 32 ml of CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled
in an ice bath. To this solution is added 8 ml of a solution of
benzene sulfonic acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The
solution is stirred 1 h 15 at 0.degree. C. The reaction is stopped
with 40 ml of a saturated solution of NaHCO.sub.3. The aqueous
phase is extracted three times with dichloromethane. The organic
layer is washed with an aqueous solution of Na.sub.2S.sub.2O.sub.3
0.2 M. The organic layer is separated, dried (Na.sub.2SO.sub.4) and
evaporated under reduce pressure. The residue is dissolved in 4 ml
of CH.sub.2Cl.sub.2 and added to 100 ml of cooled diethyl ether
drop by drop with a strong stirring. The mixture is centrifuged for
45 min and the supernatant is eliminated. The desired
5'-OH-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl phosphate
triester tetramer is obtained with a yield of 83% (calculated: 94%
per step) compared to the trimer
5'-OH-C.sup.Bz-T-A.sup.Bz-3'-O-Lev. .sup.31P NMR (CD.sub.3CN) d
-1.59, -1.69, -1.81. MALDI-TOF MS (positive mode,
trihydroxyacetophenone as matrix) [M+H].sup.+ m/z.sub.exp=1708.44,
m/z.sub.calc=1710.45. The spectrophotometric purity (80%) is
determined by HPLC at 260 nm.
EXAMPLE 44
Synthesis of the pentamer
5'-OH-A.sup.Bz-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl
phosphate triester
[0250] Coupling procedure of 5'-O-DMTr-A.sup.Bz-3'-cyanoethyl
phosphoramidite with 5'-OH-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev
using the PVP resin.
[0251] A solution of 5'-OH-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev
(982 mg, 0.57 mmol) and 5'-O-DMTr-A.sup.Bz-3'-cyanoethyl
phosphoramidite (1.15 g, 1.15 mmol, 2 eq) in anhydrous acetonitrile
(20 ml) and anhydrous DMF (2.5 ml) is added to PVP resin (1.7 g,
5.7 mmol pyrH.sup.+, 10 eq). The reaction is followed by reverse
phase HPLC. After 3 h the reaction is complete. The desired
pentamer 5'-O-DMTr-A.sup.BzG.sup.IBu-C.sup.Bz-A.sup.Bz-T-3'-O-Lev
is characterized by .sup.31P NMR. The crude is a mixture of
5'-O-DMTr-A.sup.Bz-G.sup.IBu-C.sup.Bz-A.sup.Bz-T-3'-O-Lev pentamer
(phosphite triester linkage d 141.00, 140.78, 140.68, 140.16,
139.94; phosphate triester linkage d -1.36, -1.42, -1.46, -1.52,
-1.57, -1.67, -1.70, -1.82) and of 5'-O-DMTr-A.sup.Bz-3'-cyanoethyl
hydrogenophosphonate (d 8.76, 8.71).
[0252] Oxidation: The PVP resin is filtered off and the resulting
solution is added to PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.- (1.2
g, 2.87 mmol IO.sub.4.sup.-, 5 eq.). The reaction is followed by
.sup.31P NMR and by reverse phase HPLC. The reaction is complete
after 45 min. The desired pentamer
5'-O-DMTr-A.sup.Bz-G.sup.IBu-C.sup.Bz-A.sup.Bz-3'-O-Lev cyanoethyl
phosphate triester is characterized by .sup.31P NMR. The crude is a
mixture of 5'-O-DMTr-A.sup.Bz-3'-cyanoethyl phosphate diester
(.sup.31P NMR (CD.sub.3CN) d -2.67),
5'-O-DMTr-A.sup.Bz-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev
cyanoethyl phosphate triester (d -1.24, -1.39, -1.54, -1.66,
-1.71), 5'-O-DMTr-A.sup.Bz-3'-cyanoethyl hydrogenophosphonate (d
8.82).
[0253] Detritylation: The PS--N(CH.sub.3).sub.3.sup.+IO.sub.4.sup.-
is filtered off and the solvent are evaporated. The crude is
dissolved in 50 ml of CH.sub.2Cl.sub.2, the solution is washed with
50 ml of an aqueous solution of Na.sub.2S.sub.2O.sub.3 0.2 M. The
organic layer is separated, dried (Na.sub.2SO.sub.4) and evaporated
under reduce pressure. The crude is dissolved in 16 ml of
CH.sub.2Cl.sub.2/CH.sub.3OH (7/3) and cooled in an ice bath. To
this solution is added 4 ml of a solution of benzene sulfonic acid
10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is stirred
45 min at 0.degree. C. 70 ml of CH.sub.2Cl.sub.2 and 10 ml of
pyridine are added to the solution. The reaction is stopped with 70
ml of a saturated solution of NaHCO.sub.3. The aqueous phase is
extracted three times with 30 ml of CH.sub.2Cl.sub.2 and 5 ml of
pyridine. The organic layer is separated, dried (Na.sub.2SO.sub.4)
and evaporated under reduce pressure. The residue is dissolved in 5
ml of CH.sub.2Cl.sub.2/MeOH (4/1) and added to 100 ml of cooled
diethyl ether drop by drop with a strong stirring. The mixture is
centrifuged for 45 min and the supernatant is eliminated. The
desired 5'-OH-A.sup.Bz-G.sup.IBu-C.sup.Bz-T-O-3'-O-Lev cyanoethyl
phosphate triester pentamer is obtained with a yield of 85%
(calculated: 95% per step) compared to the tetramer
5'OH-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev. .sup.31P NMR
(CD.sub.3CN) d -1.35, -1.42, -1.55, -1.63. MALDI-TOF MS (positive
mode, trihydroxyacetophenone as matrix) [M+H].sup.+
m/z.sub.exp=2179.40, m/z.sub.calc=2180.83. The spectrophotometric
purity (84%) is determined by HPLC at 260 nm.
Final Deprotection of the Pentamere
[0254] 20 mg (9 mmol) of the
5'-OH-A.sup.Bz-G.sup.IBu-C.sup.Bz-T-A.sup.Bz-3'-O-Lev cyanoethyl
phosphate triester pentamer is dissolved in 5 ml of aqueous ammonia
solution (30%). After 16 h at 55.degree. C., the ammonia is
evaporated. .sup.31P NMR (D.sub.2O) d 0.26, 0.04, -0.03, -0.09.
MALDI-TOF MS (negative mode, trihydroxyacetophenone as matrix)
[M+H].sup.- m/z.sub.exp=1486.29, m/z.sub.calc=1486.03. The
spectrophotometric purity (74%) is determined by HPLC at 260
nm.
H-Phosphonate Synthesis
EXAMPLE 45
Synthesis of the dimer 5'-O-DMTr-dG.sup.IBu-T-3'-O-Lev
H-phosphonate
[0255] A solution of 5'-OH-T-3'-O-Lev (42.5 mg, 0.125 mmol) and of
5'-O-DMTr-dG.sup.IBu-H-phosphonate TEA salt (120.7 mg, 0.150 mmol,
1.2 eq) in 2.0 ml of CH.sub.2Cl.sub.2/py (1:1) is added to
polystyrene-bound acid chloride (430.0 mg, 2.1 mmol/g, 6.6 eq) that
is suspended in 3.0 ml of the same solvent. The mixture is shaken
for 1 h 30 min at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 70%.
[0256] .sup.31P NMR (CD.sub.2Cl.sub.2) a 10.20, 8.99 ppm.
[0257] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1025.72, m/z.sub.calc=1027.02.
[0258] The spectrophotometrical purity determined by HPLC is
98%.
EXAMPLE 46
Synthesis of the dimer 5'-O-DMTr-O-dG.sup.IBu-dC.sup.Bz-3'-O-Lev
H-phosphonate
[0259] A solution of 5'-OH-dC.sup.Bz-3'-O-Lev (53.7 mg, 0.125 mmol)
and of 5'-O-DMTr-dG.sup.IBu-H-phosphonate TEA salt (120.7 mg, 0.150
mmol, 1.2 eq) in 2.0 ml of CH.sub.2Cl.sub.2/PY (1:1) is added to
polystyrene-bound acid chloride (430.0 mg, 2.1 mmol/g, 6.6 eq) that
is suspended in 3.0 ml of the same solvent. The mixture is shaken
for 1 h 30 min at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 72%.
[0260] .sup.31P NMR (CD.sub.2Cl.sub.2) a 9.78, 9.16 ppm.
[0261] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1113.16, m/z.sub.calc=1116.11.
[0262] The spectrophotometrical purity determined by HPLC is
99%.
EXAMPLE 47
Synthesis of the dimer 5'-O-DMTr-dC.sup.Bz-T-3'-O-Lev
H-phosphonate
[0263] A solution of 5'-OH-T-3'-O-Lev (142.0 mg, 0.417 mmol) and of
5'-O-DMTr-dC.sup.Bz-H-phosphonate TEA salt (120.0 mg, 0.500 mmol,
1.2 eq) in 4.0 ml of CH.sub.2Cl.sub.2/py (1:1) is added to
polystyrene-bound acid chloride (830.0 mg, 2.1 mmol/g, 4.2 eq) that
is suspended in 4.0 ml of the same solvent. The mixture is shaken
for 1 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 100%.
[0264] .sup.31P NMR (CD.sub.2Cl.sub.2) a 10.16, 8.72 ppm.
[0265] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1020.21, m/z.sub.calc=1021.01.
[0266] The spectrophotometrical purity determined by HPLC is
99%.
EXAMPLE 48
Synthesis of the dimer 5'-O-DMTr-dG.sup.IBu-dA.sup.Bz-3'-O-Lev
H-phosphonate
[0267] A solution of 5'-OH-dA.sup.Bz-3'-O-Lev (189.0 mg, 0.417
mmol) and of 5'-O-DMTr-dG.sup.IBu-H-phosphonate TEA salt (402.0 mg,
0.500 mmol, 1.2 eq) in 4.0 ml of CH.sub.2Cl.sub.2/Py (1:1) is added
to polystyrene-bound acid chloride (830.0 mg, 2.1 mmol/g, 4.2 eq)
that is suspended in 4.0 ml of the same solvent. The mixture is
shaken for 1 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 83%.
[0268] .sup.31P NMR (CD.sub.2Cl.sub.2) a 6.80, 670 ppm.
[0269] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1140.30, m/z.sub.calc=1140.14.
[0270] The spectrophotometrical purity determined by HPLC is
85%.
EXAMPLE 49
Synthesis of the dimer 5'-O-DMTr-T-T-3'-O-Lev H-phosphonate
[0271] A solution of 5'-OH-T-3'-O-Lev (142.0 mg, 0.417 mmol) and of
5'-O-DMTr-T-H-phosphonate TEA salt (354.8 mg, 0.500 mmol, 1.2 eq)
in 4.0 ml of CH.sub.2Cl.sub.2/py (1:1) is added to
polystyrene-bound acid chloride (830.0 mg, 2.1 mmol/g, 4.2 eq) that
is suspended in 4.0 ml of the same solvent. The mixture is shaken
for 1 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 98%.
[0272] .sup.31P NMR (CD.sub.2Cl.sub.2) a 9.99, 8.55 ppm.
[0273] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) no result
[0274] The spectrophotometrical purity determined by HPLC is
99%.
EXAMPLE 50
Synthesis of the trimer 5'-O-DMTr-dG.sup.IBu-T-T-3'-O-Lev
H-phosphonate
[0275] Detritylation of 5'-O-DMTr-T-T-3'-O-Lev H-phosphonate
[0276] The H-phosphonate dimer 5'-O-DMTr-T-T-3'-O-Lev (115 mg,
0.123 mmol) is dissolved in 4.0 ml of CH.sub.2Cl.sub.2/MeOH (7:3)
and cooled in an ice bath. To this solution 1.0 ml of a solution of
10% BSA (benzene sulfonic acid) in CH.sub.2Cl.sub.2/MeOH (7:3) is
added drop wise under stirring and the progress of the reaction is
monitored by TLC. After 15 min the solution is diluted with 20 ml
of CH.sub.2Cl.sub.2 and then 0.4 g of poly(4-vinyl-pyridine) are
added. The mixture is shaken 5 minutes and the resin is filtered
off and washed with CH.sub.2Cl.sub.2. The product is purified by
precipitation from CH.sub.2Cl.sub.2 with ether and dried under
vacuum. Yield 94%.
[0277] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) no result The spectrophotometrical purity determined by
HPLC is 99%.
Coupling
[0278] A solution of 5'-OH-T-T-3'-O-Lev (712 mg, 0.116 mmol) and of
5'-O-DMTr-dG.sup.IBu-H-phosphonate TEA salt (140.5 mg, 0.174 mmol,
1.5 eq) in 2.0 ml of CH.sub.2Cl.sub.2/Py (1:1) is added to
polystyrene-bound acid chloride (660.0 mg, 2.1 mmol/g, 12 eq) that
is suspended in 4.0 ml of the same solvent. The mixture is shaken
for 4 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, dried over Na.sub.2SO.sub.4, the solvent
is evaporated and the pyridine is eliminated by coevaporation with
toluene. The isolated product is dried under vacuum. Yield 55%.
[0279] .sup.31P NMR (CD.sub.2Cl.sub.2) a 10.22, 10.07, 9.73, 9.00,
8.84, 8.75, 8.59 ppm.
[0280] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1312.50, m/z.sub.calc=1315.21.
[0281] The spectrophotometrical purity determined by HPLC is
93%.
EXAMPLE 51
Synthesis of the tetramer
5'-O-DMTr-dC.sup.Bz-dG.sup.IBu-T-T-3'-O-Lev H-phosphonate
Detritylation of 5'-O-DMTr-dG.sup.IBu-T-T-3'-O-Lev
H-phosphonate
[0282] The H-phosphonate trimer 5'-O-DMTr-dG.sup.IBu-T-T-3'-O-Lev
(84 mg, 0.064 mmol) is dissolved in 4.0 ml of CH.sub.2Cl.sub.2/MeOH
(7:3) and cooled in an ice bath. To this solution 1.0 ml of a
solution of 10% BSA (benzene sulfonic acid) in
CH.sub.2Cl.sub.2/MeOH (7:3) is added drop wise under stirring and
the progress of the reaction is monitored by TLC. After 15 min the
solution is diluted with 20 ml of CH.sub.2Cl.sub.2 and then 0.4 g
of poly(4-vinyl-pyridine) are added. The mixture is shaken 5
minutes and the resin is filtered off and washed with
CH.sub.2Cl.sub.2. The product is purified by precipitation from
CH.sub.2Cl.sub.2 with ether and dried under vacuum. Yield 71%.
[0283] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1012.07, m/z.sub.calc=1012.84.
[0284] The spectrophotometrical purity determined by HPLC is
83%.
Coupling
[0285] A solution of 5'-OH-dG.sup.IBu-T-T-3'-O-Lev H-phosphonate
(45.9 mg, 0.045 mmol) and of 5'-O-DMTr-dC.sup.Bz-H-phosphonate TEA
salt (54.3 mg, 0.068 mmol, 1.5 eq) in 1.0 ml of CH.sub.2Cl.sub.2/py
(1:1) is added to polystyrene-bound acid chloride (260.0 mg, 2.1
mmol/g, 12 eq) that is suspended in 1.5 ml of the same solvent. The
mixture is shaken for 3 h and 30 minutes at room temperature until
the disappearance of the monomers. The reaction is monitored by
reverse phase HPLC. The resin is filtered, washed with
CH.sub.2Cl.sub.2. The pyridinium salt present in solution is
removed by aqueous extraction and the aqueous phase is washed twice
with CH.sub.2Cl.sub.2. The organic fractions are collected, dried
over Na.sub.2SO.sub.4, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 75%. .sup.31P NMR (CD.sub.2Cl.sub.2) a
11.58, 11.11, 10.52, 10.32, 10.14, 9.66, 9.40, 9.14, 8.99, 8.35,
7.40, 7.17, 6.99 ppm.
[0286] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1690.10, m/z.sub.calc=1692.51.
[0287] The spectrophotometrical purity determined by HPLC is
92%.
EXAMPLE 52
Synthesis of the dimer 5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-Lev
H-phosphonate
[0288] A solution of 5'-OH-dA.sup.Bz-3'-Lev (197.3 mg, 0.435 mmol)
and of 5'-O-DMTr-dC.sup.Bz-H-phosphonate TEA salt (400.0 mg, 0.500
mmol) in 4.0 ml of CH.sub.2Cl.sub.2/Py (1:1) is added to
polystyrene-bound acid chloride (830.0 mg, 2.1 mmol/g, 4.2 eq) that
is suspended in 4.0 ml of the same solvent. The mixture is shaken
for 1 h at room temperature until the disappearance of the
monomers. The reaction is monitored by reverse phase HPLC. The
resin is filtered, washed with CH.sub.2Cl.sub.2. The pyridinium
salt present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The organic
fractions are collected, the solvent is evaporated and the pyridine
is eliminated by coevaporation with toluene. The isolated product
is dried under vacuum. Yield 95%.
[0289] .sup.31P NMR (CD.sub.2Cl.sub.2) a 9.94, 8.94 ppm.
[0290] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1132.14, m/z.sub.calc=1134.13.
[0291] The spectrophotometrical purity determined by HPLC is
96%.
EXAMPLE 53
Synthesis of the trimer
5'--O-DMTr-dG.sup.IBu-dC.sup.Bz-dA.sup.Bz-3'-O-Lev
H-phosphonate
Detritylation of 5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-Lev
H-phosphonate
[0292] The H-phosphonate dimer
5'-O-DMTr-dC.sup.Bz-dA.sup.Bz-3'-O-Lev (180 mg, 0.158 mmol) is
dissolved in 4.0 ml of CH.sub.2Cl.sub.2/MeOH (7:3) and cooled in an
ice bath. To this solution 1.0 ml of a solution of 10% BSA (benzene
sulfonic acid) in CH.sub.2Cl.sub.2/MeOH (7:3) is added drop wise
under stirring and the progress of the reaction is monitored by
TLC. After 15 min the solution is diluted with 20 ml of
CH.sub.2Cl.sub.2 and then 0.4 g of poly(4-vinyl-pyridine) are
added. The mixture is shaken 5 minutes and the resin is filtered
off and washed with CH.sub.2Cl.sub.2. The product is purified by
precipitation from CH.sub.2Cl.sub.2 with ether and dried under
vacuum. Yield 83%.
[0293] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=831.91, m/z.sub.calc=831.75.
[0294] The spectrophotometrical purity determined by HPLC is
74%.
Coupling
[0295] A solution of 5'-OH-dC.sup.Bz-dA.sup.Bz-3'-O-Lev (109 mg,
0.131 mmol) and of 5'-O-DMTr-dG.sup.IBu-H-phosphonate TEA salt
(126.5 mg, 0.157 mmol, 1.2 eq) in 2.0 ml of CH.sub.2Cl.sub.2/py
(1:1) is added to polystyrene-bound acid chloride (660.0 mg, 2.1
mmol/g, 6 eq) that is suspended in 3.5 ml of the same solvent. The
mixture is shaken for 4 h at room temperature until the
disappearance of the monomers. The reaction is monitored by reverse
phase HPLC. The resin is filtered, washed with CH.sub.2Cl.sub.2.
The pyridinium salt present in solution is removed by aqueous
extraction and the aqueous phase is washed twice with
CH.sub.2Cl.sub.2. The organic fractions are collected, dried over
Na.sub.2SO.sub.4, the solvent is evaporated and the pyridine is
eliminated by coevaporation with toluene. The isolated product is
dried under vacuum. Yield 50%.
[0296] .sup.31P NMR (CD.sub.2Cl.sub.2) a 10.24, 10.06, 9.96, 9.88,
9.44, 9.38, 9.33, 9.28 ppm.
[0297] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1516.14, m/z.sub.calc=1517.43.
[0298] The spectrophotometrical purity determined by HPLC is
74%.
EXAMPLE 54
Synthesis of dimer 5'-O-DMTr-T-dG.sup.IBu-3'-O-lev
H-phosphonate
[0299] A solution of 5'-OH-dG.sup.IBu-3'-O-Lev (435 mg, 1.0 mmol)
and of 5'-O-DMTr-dT-H-phosphonate TEA salt (850 mg, 1.2 mmol) in
7.0 ml of CH.sub.2Cl.sub.2/py (1:1, v/v) is added to
polystyrene-bound acid chloride (1.5 g, 2.4 mmol/g, 3 eq) that is
suspended in 7.0 ml of the same solvent. The mixture is shaken for
2 h 15 at room temperature until the disappearance of the monomers.
The reaction is monitored by reverse phase HPLC. The resin is
filtered, washed with CH.sub.2Cl.sub.2. The pyridinium salt present
in solution is removed by aqueous extraction and the aqueous phase
is washed twice with CH.sub.2Cl.sub.2. The organic fractions are
collected, the solvent is evaporated and the pyridine is eliminated
by coevaporation with toluene. The isolated product is dried under
vacuum. 914 mg Yield 89%.
[0300] .sup.31P NMR (CD.sub.2Cl.sub.2) a 12.63, 8.92 ppm.
[0301] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1026.6, m/z.sub.calc=1027.0. The
spectrophotometrical purity determined by HPLC is 96%.
EXAMPLE 55
Synthesis of the trimer 5'-O-DMTr-C.sup.bz-T-dG.sup.ibu-3'-O-Lev
H-phosphonate
Detritylation of 5'-O-DMTr-T-dG.sup.ibu-3'-O-lev H-phosphonate
[0302] The H-phosphonate dimer 5'-O-DMTr-T-dG.sup.ibu-3'-O-Lev (430
mg, 0.420 mmol) is dissolved in M ml of CH.sub.2Cl.sub.2/MeOH (7:3,
v/v) and cooled in an ice bath. To this solution 2.0 ml of a
solution of 10% BSA (benzene sulfonic acid) in
CH.sub.2Cl.sub.2/MeOH (7:3, v/v) is added drop wise under stirring
and the progress of the reaction is monitored by TLC. After 20 min
the solution is diluted with 50 ml of CH.sub.2Cl.sub.2 and then 0.8
g of poly(4-vinyl-pyridine) are added. The mixture is shaken 5
minutes and the resin is filtered off and washed with
CH.sub.2Cl.sub.2. The product is purified by precipitation from
CH.sub.2Cl.sub.2 with ether and dried under vacuum. 320 mg Yield
100%. The spectrophotometrical purity determined by HPLC is
98%.
[0303] Coupling
[0304] A solution of 5'-OH-T-dGibu-3'-O-Lev (320 mg, 0.43 mmol) and
of 5'-O-DMTr-dG.sup.IBu-H-phosphonate TEA salt (413 mg, 0.52 mmol,
1.2 eq) in 4.5 ml of CH.sub.2Cl.sub.2/py (1:1, v/v) is added to
polystyrene-bound acid chloride (1050 mg, 2.4 mmol/g, 5 eq) that is
suspended in 4.5 ml of the same solvent. The mixture is shaken for
4 h at room temperature until the disappearance of the monomers.
The reaction is monitored by reverse phase HPLC. The resin is
filtered, washed with CH.sub.2Cl.sub.2. The pyridinium salt present
in solution is removed by aqueous extraction and the aqueous phase
is washed twice with CH.sub.2Cl.sub.2. The organic fractions are
collected, dried over Na.sub.2SO.sub.4, the solvent is evaporated
and the pyridine is eliminated by coevaporation with toluene. The
product is purified by precipitation from CH.sub.2Cl.sub.2 with
ether and dried under vacuum. 538 mg Yield 89%.
[0305] .sup.31P NMR (CD.sub.2Cl.sub.2) a 12.68, 12.46, 10.27, 9.46,
9.40, 9.11, 8.96, 8.92. ppm.
[0306] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1404.0, m/z.sub.calc=1404.3. The
spectrophotometrical purity determined by HPLC is 94%.
EXAMPLE 56
Synthesis of the trimer 5'-O-DMTr-C.sup.bz-T-dG.sup.ibu-3'-O-lev
S-phenyl phosphotriester
[0307] To a solution of 5'-O-DMTr-C.sup.bz-T-dG.sup.ibu-3'-O-lev
H-phosphonate (110 mg, 0.078 mmol) in 2 ml of CH.sub.2Cl.sub.2/py
(1:1), N-(phenylsulfanyl)phthalimide (80 mg, 0.314 mmol, 4 eq) and
Triethylamine (200 mL, 10 eq) were added. The reaction is stirred
for 3 h at room temperature. The solvent is evaporated. The product
is purified by precipitation from CH.sub.2Cl.sub.2 with ether and
dried under vacuum. 117 mg Yield 92%
[0308] .sup.31P NMR signals between 24.09 and 25.76 ppm
[0309] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1621.8, m/z.sub.calc=1620.6. The
spectrophotometrical purity determined by HPLC is 87%.
EXAMPLE 57
Synthesis of the trimer 5'-O-DMTr-C.sup.bz-T-dG.sup.ibu-3'-O-lev
S-cyanoethyl phosphotriester
[0310] The trimer 5'-O-DMTr-C.sup.bz-T-dG.sup.ibu-3'-O-lev
H-phosphonate (118 mg, 0.084 mmol) is coevaporated twice with dry
pyridine (2.times.2 ml) and dissolved in 2 ml of
CH.sub.2Cl.sub.2/Py (1:1). To this solution is added successively
triethylamine (6 mL, 0.5 eq), trimethylsilyl chloride (100 mL, 0.84
mmol, 10 eq) and N-[(2-cyanoethyl)thio]phthalimide (78 mg, 0.336
mmol, 10 eq).
[0311] After 1 h 30 the reaction is complete. The pyridinium salt
present in solution is removed by aqueous extraction and the
aqueous phase is washed twice with CH.sub.2Cl.sub.2. The solvent is
evaporated. The product is purified by precipitation from
CH.sub.2Cl.sub.2 with ether and dried under vacuum. 106 mg Yield
80%
[0312] .sup.31P NMR signals between 26.86 and 28.75 ppm.
[0313] MALDI-TOF MS (positive mode, trihydroxyacetophenone as
matrix) [M+H].sup.+ m/z.sub.exp=1574.6, m/z.sub.calc=1574.6. The
spectrophotometrical purity determined by HPLC is 84%.
EXAMPLE 58
GENERAL PROCEDURE FOR THE SYNTHESIS OF 5'-OH-3'-O-Lev CYANOETHYL
PHOSPHOROTHIONOTRIESTER BASE PROTECTED DIMERS USING THE
PHOSPHORAMIDITE METHOD ON 10 MMOL SCALE
[0314] Coupling procedure of
5'-O-DMTr-3'-cyanoethyl-phosphoramidite base protected nucleotide
with 5'-OH-3'-O-Lev base protected nucleoside using the
poly(4-vinylpyridinum p-toluenesulfonate) (Aldrich):
[0315] 5'-OH-3'-O-Lev base protected nucleoside (10 mmol) and
5'-O-DMTr-3'-cyanoethyl-phosphoramidite base protected nucleotide
(15 mmol, 1.5 eq) are dissolved in anhydrous dichloromethane (100
ml). The solution is transferred under argon in a flask containing
the poly(4-vinylpyridinum p-toluenesulfonate) (100 mmol PyrH.sup.+,
10 eq.) and shaken. The reaction is followed by reverse phase HPLC
and is usually complete between 1 h 30 and 2 h 30. The desired
5'-O-DMTr-3'-O-Lev cyanoethyl phosphite triester base protected
dimer is characterized by .sup.31P NMR. The crude is a mixture of
5'-O-DMTr-3'-O-Lev cyanoethyl phosphite triester base protected
dimer and of 5'-O-DMTr-3'-cyanoethyl H-phosphonate base protected
nucleotide. The poly(4-vinylpyridinum p-toluenesulfonate) is
filtered off, washed 3 times with 50 ml of CH.sub.2Cl.sub.2 and the
solution is concentrated to 100 ml.
[0316] Sulfurization: To the resulting solution is added AMBERLYST
A26 tetrathionate form (50 mmol S.sub.4O.sub.6.sup.2-, 5 eq.), and
the reaction mixture is shaken. The reaction is followed by reverse
phase HPLC and .sup.31P NMR and is usually complete between 1 h 30
and 2 h 30. The crude is a mixture of 5'-O-DMTr-3'-O-Lev cyanoethyl
phosphorothionotriester base protected dimer and
5'-O-DMTr-3'-cyanoethyl diester H-phosphonate base protected
nucleotide. The resin AMBERLYST A26 tetrathionate form is filtered
off and washed 3 times with 50 ml of CH.sub.2Cl.sub.2.
TABLE-US-00001 dimers phosphite triester phosphorothionotriester
5'-O-DMTr-Nu-Nu-3'-O-Lev RT (min) .sup.31P NMR d RT (min) .sup.31P
NMR d A.sup.Bz-A.sup.Bz 17.81 140.64; 140.46 18.23 68.30; 68.24
C.sup.Bz-A.sup.Bz 19.09 140.48; 140.39 19.35, 19.61* 68.31; 68.26
G.sup.IBu-T 15.95; 16.14* 143.50; 141.71 16.73; 17.01* 68.65; 68.19
G.sup.IBu-A.sup.Bz 16.86 140.34; 140.02 17.30; 17.56* 67.57; 67.41
*mixture of Sp and Rp diastereoisomeres
[0317] Detritytlation: To the previous solution is added 100 ml of
MeOH so that the CH.sub.2Cl.sub.2/MeOH ratio is about 7/3. The
mixture is cooled at 0.degree. C. To the resulting solution is
added 90 ml (56 mmol, 5.6 eq.) of a solution of benzene sulfonic
acid 10% in CH.sub.2Cl.sub.2/CH.sub.3OH (7/3). The solution is
stirred at 0.degree. C. The detritylation is monitored by TLC and
reverse phase HPLC. The reaction time is between 30 min and 1 h.
When the reaction is complete, 100 ml of H.sub.2O is added to the
mixture, the solution is shaken for 10 min at 0.degree. C. Then,
the reaction is stopped by stirring at 0.degree. C. for 10 min with
100 ml of a saturated solution of NaHCO.sub.3. The solution is
diluted with 300 ml of CH.sub.1Cl.sub.2. The organic layer is then
washed up to 4 times with H.sub.2O/saturated solution of
NaHCO.sub.3 in water (1/1), dried with Na.sub.2SO.sub.4, (50 g) and
evaporated. The crude product is dissolved in 50 ml
CH.sub.2Cl.sub.2 and added dropwise to 1 l of diethylether at
0.degree. C. to give a is white precipitate of the pure desired
5'-OH-3'-O-lev cyanoethyl phosphorothionotriester base protected
dimer. The solid is filtered off, washed with 500 ml diethylether
and dried under vacuum. The dimer is characterized by .sup.31P NMR
and by MALDI-TOF. The spectrophotometric purity is determined by
reverse phase HPLC at 260 nm,
TABLE-US-00002 Dimers performed Dimers MW following this procedure
5'-OH-Nu-Nu-3'-O-Lev (g/mol) .sup.31P-NMR RT (min) Yield
HPLC-Purity A.sup.Bz-A.sup.Bz 939.91 68.11; 68.06* 10.85 91% (9.5
g) 91% C.sup.Bz-A.sup.Bz 915.88 68.03; 67.80* 11.32; 11.46* 94%
(8.7 g) 91% G.sup.IBu-T 808.77 68.48; 68.09* 9.72 91% (7.4 g) 91%
G.sup.IBu-A.sup.Bz 921.89 68.02; 67,80* 10.32; 10.68* 98% (10.3 g)
92% *mixture of Sp and Rp diastereoisomeres HPLC-Gradient [column:
Macherey- Nagel Nucleosil 100-5 C18]: 0 to 5 min --> 10% of
CH.sub.3CN to 40% of CH.sub.3CN (in TEAAc 50 mM) 5 to 20 min -->
40% of CH.sub.3CN to 80% of CH.sub.3CN (in TEAAc 50 mM) 20 to 25
min --> 80% of CH.sub.3CN to 100% of CH.sub.3CN (in TEAAc 50
mM)
* * * * *