U.S. patent number 8,552,174 [Application Number 11/387,269] was granted by the patent office on 2013-10-08 for solutions, methods, and processes for deprotection of polynucleotides.
This patent grant is currently assigned to Agilent Technologies, Inc., The Regents of the University of Colorado. The grantee listed for this patent is Marvin H. Caruthers, Douglas J. Dellinger, Geraldine Dellinger, Joel Myerson, Agnieszka Sierzchala, Zoltan Timar. Invention is credited to Marvin H. Caruthers, Douglas J. Dellinger, Geraldine Dellinger, Joel Myerson, Agnieszka Sierzchala, Zoltan Timar.
United States Patent |
8,552,174 |
Dellinger , et al. |
October 8, 2013 |
**Please see images for:
( Certificate of Correction ) ** |
Solutions, methods, and processes for deprotection of
polynucleotides
Abstract
Methods of deprotecting polynucleotides are disclosed. One
aspect of the method of deprotecting polynucleotides, among others,
includes: providing a polynucleotide, wherein the polynucleotide
includes at least one nucleotide monomer that has at least one
protecting group selected from the following: a base having a
protecting group, a 2'-hydroxyl protecting group, and a combination
thereof, and deprotecting at least one of the protecting groups of
the polynucleotide by introducing the polynucleotide to a solution
including an .alpha.-effect nucleophile.
Inventors: |
Dellinger; Douglas J. (Boulder,
CO), Timar; Zoltan (Boulder, CO), Sierzchala;
Agnieszka (Boulder, CO), Dellinger; Geraldine (Boulder,
CO), Caruthers; Marvin H. (Boulder, CO), Myerson;
Joel (Berkeley, CA) |
Applicant: |
Name |
City |
State |
Country |
Type |
Dellinger; Douglas J.
Timar; Zoltan
Sierzchala; Agnieszka
Dellinger; Geraldine
Caruthers; Marvin H.
Myerson; Joel |
Boulder
Boulder
Boulder
Boulder
Boulder
Berkeley |
CO
CO
CO
CO
CO
CA |
US
US
US
US
US
US |
|
|
Assignee: |
Agilent Technologies, Inc.
(Santa Clara, CA)
The Regents of the University of Colorado (Denver,
CO)
|
Family
ID: |
37997368 |
Appl.
No.: |
11/387,269 |
Filed: |
March 23, 2006 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20070100137 A1 |
May 3, 2007 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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60731723 |
Oct 31, 2005 |
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Current U.S.
Class: |
536/25.31;
536/25.34 |
Current CPC
Class: |
C07H
21/04 (20130101); Y02P 20/55 (20151101) |
Current International
Class: |
C07H
21/00 (20060101) |
References Cited
[Referenced By]
U.S. Patent Documents
Other References
Kice et al., "Relative Nucleophilicity of Common Nucleophiles
toward Sulfonyl Sulfur. II. Comparison of the Relative Reactivity
of Twenty Different Nucleophiles toward Sulfonyl Sulfur vs.
Carbonyl Carbon," J. American Chemical Society, 95(12), 3912-3917
(Jun. 13, 1973): copy supplied by applicant. cited by examiner
.
Carey et al., part of Chapter 5 ("Nucleophilic Substitution"),
"Advanced Organic Chemistry, 3rd Edition," Plenum Press, New York,
NY, 1990, only p. 288 provided: copy supplied by applicant. cited
by examiner .
Edwards et al., "The Factors Determining Nucleophilic
Reactivities," J. American Chemical Society, 84(1), 16-24 (Jan. 5,
1962): copy supplied by applicant. cited by examiner .
Kirby et al., "Reactions of Alpha-Nucleophiles with a Model
Phosphate Diester," ARKIVOC, 2009(iii), 28-38: copy supplied by
applicant. cited by examiner .
Albert, et al., "Light-directed 5'-3' synthesis of complex
oligonucleotide microarrays", Nucleic Acids Research vol. 31 No. 7,
(2003),pp. 1-9. cited by applicant .
Bell, et al., "The catalyzed dehydration of acetaldehyde hydrate,
and the effect of structure on the velocity of proto lytic
reactions", Proceedings of the Royal Society of London. Series A,
Mathematical and Physical Sciences vol. 197 No. 1049,, (1949),pp.
141-159. cited by applicant .
Fujii, et al., "(Butylthio)carbonyl Group: A new Protecting Group
for the Guanine Residue in Oligoribonucleotide Synthesis",
Tetrahedron Letters vol. 28 No. 46,, (1987),pp. 5713-5716. cited by
applicant .
Jencks, et al., "Reactivity of Nucleophilic reagents toward
esters", J. Am. Chem. Soc. vol. 82 No. 7,, (1960),pp. 1778-1786.
cited by applicant .
Pitsch, et al., "Preparation of UNIT 2.9
2'-O-[(Triisopropylsilyl)oxy]methylprotected Ribonucleosides",
Current Protocols in Nucleic Acid Chemistry supplement 7 ,,
(2001),pp. 2.9.1-2.9.14. cited by applicant .
Scaringe, et al., "Preparation of 5'-Silyl-2'-Orthoester
Ribonucleosides for Use in Oligoribonucleotide Synthesis", Current
Protocols in Nucleic Acid Chemistry supplement 16,
(2004),2.10.1-2.10.16. cited by applicant .
Sekine, R et al., "Cyclic Orthoester Functions a New Protecting
Groups in Nucleosides", J. American Chemical Society 105(7),
(1983),2044-2049. cited by applicant .
Watkins, et al., "Synthesis of Benzyl and Benzyloxycarbonyl
Base-Blocked 2'-Deoxyribonucleosides", Journal of Organic Chemistry
(1982) vol. 47, (1982),pp. 4471-4477. cited by applicant .
PCT/US2007/064642, International Search Report and Written Opinion,
mailed Mar. 17, 2008, 10pgs. cited by applicant .
PCT/US2007/064644, International Search Report and Written Opinion,
mailed Aug. 22, 2008, 12pgs. cited by applicant.
|
Primary Examiner: Crane; Lawrence E
Parent Case Text
CROSS-REFERENCE TO RELATED APPLICATION
This application is related to U.S. provisional application
entitled, "METHODS FOR DEPROTECTING POLYNUCLEOTIDES," having Ser.
No. 60/731,723, filed Oct. 31, 2005, which is entirely incorporated
herein by reference.
This application is related to copending U.S. Utility patent
application entitled "MONOMER COMPOSITIONS FOR THE SYNTHESIS OF
RNA, METHODS OF SYNTHESIS, AND METHODS OF DEPROTECTION" filed on
Mar. 23, 2006 to Dellinger et al. and accorded Ser. No. 11/388,112,
which is entirely incorporated herein by reference.
This application is related to copending U.S. Utility patent
application entitled "MONOMER COMPOSITIONS FOR THE SYNTHESIS OF
POLYNUCLEOTIDES, METHODS OF SYNTHESIS, AND METHODS OF DEPROTECTION"
filed on Mar. 23, 2006 to Dellinger et al. and accorded Ser. No.
11/387,388, which is entirely incorporated herein by reference.
This application is related to copending U.S. Utility patent
application entitled "CLEAVABLE LINKERS FOR POLYNUCLEOTIDES" filed
on Mar. 23, 2006 to Dellinger et al. and accorded Ser. No.
11/389,388, which is entirely incorporated herein by reference.
This application is related to copending U.S. Utility patent
application entitled "THIOCARBONATE LINKERS FOR POLYNUCLEOTIDES"
filed on Mar. 23, 2006 to Dellinger et al. and accorded Ser. No.
11/389,326, which is entirely incorporated herein by reference.
This application is related to copending U.S. Utility patent
application entitled "PHOSPHORUS PROTECTING GROUPS" filed on Mar.
23, 2006 to Dellinger et al. and accorded Ser. No. 11/388,339,
which is entirely incorporated herein by reference.
Claims
What is claimed is:
1. A method of performing post-synthesis deprotection of a
synthetic precursor of a nucleic acid, comprising: providing a
synthetic precursor of a nucleic acid comprising at least one
protecting group selected from the group consisting of: a base
protecting group, a 2'-hydroxyl protecting group, and a combination
thereof, and deprotecting at least one of the protecting groups of
said synthetic precursor of a nucleic acid by contacting said
precursor with a solution comprising an .alpha.-effect nucleophile,
wherein the solution is at a pH of about 4 to 11, and wherein the
.alpha.-effect nucleophile has a pKa of about 4 to 13.
2. The method of claim 1, wherein the .alpha.-effect nucleophile is
a peroxyanion.
3. The method of claim 1, wherein the .alpha.-effect nucleophile is
selected from at least one of the following: hydrogen peroxide and
salts thereof, a peracid and salts thereof, a perboric acid and
salts thereof, an alkylperoxide and salts thereof, a hydroperoxide
and salts thereof, butylhydroperoxide and salts thereof,
benzylhydroperoxide and salts thereof, phenylhydroperoxide and
salts thereof, performic acid and salts thereof, peracetic acid and
salts thereof, perbenzoic acid and salts thereof, chloroperbenzoic
acid and salts thereof, and combinations thereof.
4. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises a hydroperoxide, wherein the solution is at a pH of about
7 to 10, and wherein the hydroperoxide has a pKa of about 8 to
13.
5. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises hydrogen peroxide, wherein the solution is at a pH of
about 8 to 10, and wherein the hydrogen peroxide has a pKa of about
11 to 13.
6. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises a peracid, wherein the solution is at a pH of about 7 to
10, and wherein the peracid has a pKa of about 6 to 11.
7. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises a perboric acid, wherein the solution is at a pH of about
8 to 10, and wherein the perboric acid has a pKa of about 9 to
12.
8. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises an alkylperoxide, wherein the solution is at a pH of
about 8 to 10, and wherein the alkylperoxide has a pKa of about 9
to 13.
9. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises a hydrogen peroxide salt, wherein the solution is at a pH
of about 8 to 10, and wherein the hydrogen peroxide salt has a pKa
of about 11 to 12.
10. The method of claim 1, wherein the .alpha.-effect nucleophile
comprises hydrogen peroxide and sodium formate, and wherein the
solution is at a pH of about 6 to 11.
11. The method of claim 1, wherein the solution is at a pH of about
7 to 10.
12. The method of claim 1, wherein the synthetic precursor of a
nucleic acid is attached to a solid support.
13. The method of claim 12, wherein the synthetic precursor of a
nucleic acid is attached to an array.
14. The method of claim 1, wherein the nucleic acid is a DNA.
15. The method of claim 1, wherein the nucleic acid is a RNA.
16. A method of performing post-synthesis deprotection of a
synthetic precursor of a nucleic acid, comprising: providing a
synthetic precursor of a nucleic acid comprising at least one
protecting group selected from the group consisting of: an
exocyclic amino protecting group, an imino protecting group, a
2'-hydroxyl protecting group, and combinations thereof; and
deprotecting at least one of the protecting groups of the synthetic
precursor of a nucleic acid by contacting said precursor with a
solution comprising an .alpha.-effect nucleophile, wherein the
solution is at a pH of about 4 to 10, and wherein the
.alpha.-effect nucleophile has a pKa of about 4 to 13.
17. The method of claim 16, wherein said synthetic precursor of a
nucleic acid is attached to a solid support.
18. The method of claim 17, wherein the said synthetic precursor of
a nucleic acid is attached to an array.
19. The method of claim 16, wherein the .alpha.-effect nucleophile
is a peroxyanion.
20. The method of claim 16, wherein the .alpha.-effect nucleophile
is selected from at least one of the following: hydrogen peroxide
and salts thereof, a peracid and salts thereof, a perboric acid and
salts thereof, an alkylperoxide and salts thereof, a hydroperoxide
and salts thereof, butylhydroperoxide and salts thereof,
benzylhydroperoxide and salts thereof, phenylhydroperoxide and
salts thereof, performic acid and salts thereof, peracetic acid and
salts thereof, perbenzoic acid and salts thereof, chloroperbenzoic
acid and salts thereof, and combinations thereof.
21. A method of performing post-synthesis deprotection of a
synthetic precursor of a nucleic acid, comprising: providing a
synthetic precursor of a nucleic acid comprising at least one
exocyclic amino protecting group and optionally comprising at least
one protecting group selected from the following: an imino
protecting group, a 2'-hydroxyl protecting group, and combinations
thereof; and deprotecting at least one of the exocyclic amino
protecting groups of said synthetic precursor of a nucleic acid by
contacting said precursor with a solution comprising an
.alpha.-effect nucleophile, wherein the solution is at a pH of
about 4 to 11, and wherein the .alpha.-effect nucleophile has a pKa
of about 4 to 13.
22. The method of claim 21, wherein said synthetic precursor of a
nucleic acid is attached to a solid support.
23. The method of claim 22, wherein said synthetic precursor of a
nucleic acid is attached to an array.
24. The method of claim 21, wherein the .alpha.-effect nucleophile
is a peroxyanion.
25. The method of claim 21, wherein the .alpha.-effect nucleophile
is selected from at least one of the following: hydrogen peroxide
and salts thereof, a peracid and salts thereof, a perboric acid and
salts thereof, an alkylperoxide and salts thereof, a hydroperoxide
and salts thereof, butylhydroperoxide and salts thereof,
benzylhydroperoxide and salts thereof, phenylhydroperoxide and
salts thereof, performic acid and salts thereof, peracetic acid and
salts thereof, perbenzoic acid and salts thereof, chloroperbenzoic
acid and salts thereof, and combinations thereof.
26. A method of performing post-synthesis deprotection of a
synthetic precursor of a nucleic acid, comprising: providing a
synthetic precursor of a nucleic acid comprising at least one
2'-hydroxyl protecting group and optionally comprising at least one
protecting group selected from the group consisting of: an
exocyclic amino protecting group, an imino protecting group, and
combinations thereof; and deprotecting the 2'-hydroxyl protecting
groups of said synthetic precursor of a nucleic acid by contacting
said precursor with a solution comprising an .alpha.-effect
nucleophile, wherein the solution is at a pH of about 4 to 10, and
wherein the .alpha.-effect nucleophile has a pKa of about 4 to
13.
27. The method of claim 26, wherein said synthetic precursor of a
nucleic acid is attached to a solid support.
28. The method of claim 27, wherein said synthetic precursor of a
nucleic acid is attached to an array.
29. The method of claim 26, wherein the .alpha.-effect nucleophile
is a peroxyanion.
30. The method of claim 26, wherein the .alpha.-effect nucleophile
is selected from at least one of the following: hydrogen peroxide
and salts thereof, a peracid and salts thereof, a perboric acid and
salts thereof, an alkylperoxide and salts thereof, a hydroperoxide
and salts thereof, butylhydroperoxide and salts thereof,
benzylhydroperoxide and salts thereof, phenylhydroperoxide and
salts thereof, performic acid and salts thereof, peracetic acid and
salts thereof, perbenzoic acid and salts thereof, chloroperbenzoic
acid and salts thereof, and combinations thereof.
31. A method of performing post-synthesis deprotection of a
synthetic precursor of a nucleic acid, comprising: providing a
synthetic precursor of a nucleic acid comprising at least one
exocyclic amino protecting group and at least one 2'-hydroxyl
group, and optionally comprising at least one imino protecting
group; and deprotecting the exocyclic amino protecting groups and
the 2'-hydroxyl groups of said synthetic precursor of a nucleic
acid by contacting said precursor with a solution comprising an
.alpha.-effect nucleophile, wherein the solution is at a pH of
about 4 to 10, and wherein the .alpha.-effect nucleophile has a pKa
of about 4 to 13.
32. The method of claim 31, wherein said synthetic precursor of a
nucleic acid is attached to a solid support.
33. The method of claim 32, wherein said synthetic precursor of a
nucleic acid is attached to an array.
34. The method of claim 31, wherein the .alpha.-effect nucleophile
is a peroxyanion.
35. The method of claim 31, wherein the .alpha.-effect nucleophile
is selected from hydrogen peroxide and salts thereof, a peracid and
salts thereof, a perboric acid and salts thereof, an alkylperoxide
and salts thereof, a hydroperoxide and salts thereof,
butylhydroperoxide and salts thereof, benzylhydroperoxide and salts
thereof, phenylhydroperoxide and salts thereof, performic acid and
salts thereof, peracetic acid and salts thereof, perbenzoic acid
and salts thereof, chloroperbenzoic acid and salts thereof, and
combinations thereof.
Description
BACKGROUND
Advances in the chemical synthesis of oligoribonucleotides have not
kept pace with the many advances in techniques developed for the
chemical synthesis of oligodeoxyribo-nucleotides. The synthesis of
RNA is actually a much more difficult task than the synthesis of
DNA. The internucleotide bond in native RNA is far less stable than
in the DNA series. The close proximity of a protected 2'-hydroxyl
to the internucleotide phosphate presents problems, both in terms
of the formation of the internucleotide linkage and in the removal
of the 2'-protecting group once the oligoribonucleotide has been
synthesized (See FIG. 1).
Only recently has there been a great demand for small synthetic
RNA. The discoveries of the RNAi pathway and small RNAs, such as
siRNA, miRNAs and ntcRNAs associated with the RNA interference
pathway is primarily responsible for this increased demand. Most
recent attempts at the chemical synthesis of oligoribonucleotides
have followed the synthetic strategy for the chemical synthesis of
oligodeoxyribonucleotides: the standard phosphoramidite approach
[Matteucci, M. D., Caruthers, M. H. J. Am. Chem. Soc. 1981, 103,
3186-3191]. Such methods proceed by the step-wise addition of
protected ribonucleoside phosphoramidite monomers to a growing RNA
chain connected to a solid phase support. However, efficient solid
phase synthesis of oligoribonucleotides still poorly compared to
the efficiency of oligodeoxyribonucleotides synthesis.
Until recently, the typical approach to RNA synthesis utilized
monomers whereby the 5'-hydroxyl of the ribonucleoside was
protected by the acid-labile dimethoxytrityl (DMT) protecting
group. Various protecting groups have been placed on the
2'-hydroxyl to prevent isomerization and cleavage of the
internucleotide bond during the acid deprotection step. By using
this as a starting point for RNA synthesis, researchers have
focused on finding an ideal 2'-protecting group compatible with
acid deprotection. Research directed toward the discovery of this
ideal 2'-protecting group has taken two primary courses: the use of
acid-stable 2'-protecting groups and the use of acid-labile
2'-protecting groups. The use of acid-stable 2'-protecting groups
has been quite limiting from a chemical perspective, since there
are not many options available when the base lability of RNA is
considered. Acid-stable protecting groups are typically base-labile
or nucleophile-labile (e.g., removed by a strong base or a strong
nucleophile). General base-labile protecting groups are removed by
elimination or fragmentation subsequent to proton abstraction by a
strong base. An example of this type of protecting group is a
propionitrile-containing protecting group, which is removed by
beta-elimination to form acrylonitrile after a proton is abstracted
from the methylene carbon adjacent to the nitrile group. It is
difficult to use these types of protecting groups on the
2'-hydroxyl of RNA since subsequent proton abstraction from the
ensuing 2'-hydroxyl results in cleavage of the internucleotide bond
via formation of a 2'-3' cyclic phosphate and destruction of the
RNA.
##STR00001##
This approach is therefore only viable if the pH conditions used
for proton abstraction from the protecting group are below pH 11,
the pH at which proton abstraction from the 2'-hydroxyl begins to
give rapid cleavage of the internucleotide bond. The approach of
using a general base-labile protecting group for the 2'-hydroxyl
has been further stymied by the necessary use of weak bases during
the oxidation and capping reactions that occur in the standard
phosphoramidite oligonucleotide synthesis process.
Protecting groups that are removed by the weakly basic conditions
below pH 11 (such that the 2'-hydroxyl is not appreciably
deprotonated) are typically unstable to the conditions used for
capping and oxidation. As a result, the approach of using general
base-labile protecting groups for 2'-hydroxyl protection has rarely
been pursued, and never enabled.
Alternatively, there have been many attempts at the use of
nucleophile-labile protecting groups for the protection of the
2'-hydroxyl. The difficulty associated with the use of
nucleophile-labile protecting groups is that most typical
nucleophiles are governed by the Bronsted-type plot of
nucleophilicity as a function of basicity: the stronger the
nucleophilicity, the stronger the basicity. As a result, strong
nucleophiles are usually also strong bases and therefore the use of
strong nucleophiles for deprotection of the 2'-hydroxyl typically
results in the destruction of the desired RNA product by a
subsequent proton abstraction from the 2'-hydroxyl. The use of
nucleophile-labile 2'-hydroxyl protecting groups for RNA synthesis
has only been enabled by the use of fluoride ion, a
silicon-specific nucleophile that is reactive with silanes and
siloxanes at a wide variety of pH conditions.
The most popular of these acid-stable protecting groups seem to be
the t-butyl-dimethylsilyl group known as TBDMS [Ogilvie et al.,
Can. J. Chem., Vol 57, pp. 2230-2238 (1979)]. Widely practiced in
the research community, the use of TBDMS as 2'-protecting group,
dominated the previously small market for chemical synthesis of RNA
for a very long time [Usman et al. J. Am. Chem. Soc. 109 (1987)
7845], [Ogilvie et al. Proc. Natl. Acad. Sci. USA 85 (1988) 5764].
The oligoribonucleotide syntheses carried out therewith are,
however, by no means satisfactory and typically produces poor
quality RNA products.
Several publications have reported the migration of the alkylsilyl
group under a variety of conditions [Scaringe et al, Nucleic Acids
Res 18, (18) 1990 5433-5441; Hogrefe et al. Nucleic Acids Research,
1993, 21 (20), 4739-4741]. Also, the loss of the 2'-silyl group
that occurs during the removal of exocyclic amine protecting groups
has been widely described in the literature [Stawinski et. al.
Nucleic Acids Res. 1988, 16 (19), 9285-9298]. Methods that use less
stable exocyclic amine protecting groups such as phenoxyacetyl or
methoxyacetyl were subsequently developed to circumvent this
problem [Schulhof et al. Nucleic Acids Res. 1987 15(2) 397-416].
However, the synthesis of the
5'-O-dimethoxytrityl-2'-O-tert-butyldimethylsilyl-ribo-3'-O-(.beta.-cyano-
ethyl, N-diisopropyl)phosphoramidite monomers is still challenging
and costly due to the non-regioselective introduction of the
2'-silyl group and the added chemical requirements to prevent
migration of the silyl group during the phosphoramidite production.
It is also well known in the art that the coupling efficiency of
these monomers is greatly decreased due to the steric hindrance of
the 2'-TBDMS protecting group, thereby affecting the yield and
purity of the full-length product, and also limiting the length of
the oligoribonucleotide that can be achieved by this chemical
synthesis.
The most recent acid-stable 2'-hydroxyl protection approach for RNA
synthesis was developed by Pitsch et al. [U.S. Pat. No. 5,986,084]
to try to circumvent the problems encountered with the previous
2'-silyl protecting groups. This approach also relies on the use of
2'-O-acetals groups further protected by an alkylsilane, which is
removed by the silicon-specific nucleophile fluoride ion. Although
somewhat less acid stable than TBDMS, it is used in combination
with acid-labile 5'-protecting groups such as DMT or the
5'-9-phenylxanthen-9-yl (Pix) group shown below.
##STR00002##
Because of the presence of the methylene group, this 2'-protecting
group is less bulky than the TBDMS, allowing higher coupling
efficiency. Since the protecting group is an acetal moiety, there
is no significant problem of isomerization. The commercial
protecting group typically used in this approach is the
tri-isopropyloxymnethyl derivative known by the abbreviation TOM.
Although this protecting group scheme solves many of the problems
encountered by the TBDMS chemistry, it suffers from other
significant difficulties. The synthesis of the TOM-protected
monomers is extremely difficult and low yielding. The protecting
group itself requires a low yield multi-step synthesis prior to its
placement on the nucleoside. The attachment to the nucleoside is
performed through a nucleophillic displacement reaction by a 2'-3'
alkoxide generated from a dialkyl tin reagent that produces a
mixture of non-regioselective products that have to be separated
and isolated by chromatography. In the case of the guano sine
nucleoside, the tin reagents can preferentially react with the
heterobase rather than the 2'-,3'-hydroxyl moieties. In many cases,
the overall yield of desired products from these reactions can be
significantly less than 10%, rendering the monomer synthons and
subsequent RNA products very expensive to produce.
Alternatively, many researchers have pursued the use of acid-labile
groups for the protection of the 2'-hydroxyl moiety. The classic
acid-labile protecting group is the 2'-acetal moiety, which was
initially developed by Reese [Reese, C. B., Org. Biomol. Chem.
2005, 3(21), 3851-68], such as tetrahydropyran (THP) or
4-methoxy-tetrahydropyran (MTHP), 1-(2-chloroethoxy)ethyl (Cee) [O.
Sakatsume et al. Tetrahedron 47 (1991) 8717-8728],
1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) [M. Vaman Rao et
al., J. Chem. Soc. Perkin Trans., Paper 2:43-55 (1993), Daniel C.
Capaldi et al., Nucleic Acids Research, 22(12):2209-2216
(1994)].
One of the advantages of acetal protecting groups compared with
silyl ethers protecting groups is that they can be introduced
regioselectively into the 2' position through the use of the
Markiewicz protecting group: tetraisopropyldisiloxane-1,3-diyl.
This protecting group, also known as TIPS, simultaneously blocks
the 5'- and 3'-hydroxyls to allow complete regioselective upon
introduction of the acetal group on to the 2'-hydroxyl [Markiewicz
W. T., J. Chem Research (S) 1979 24-25)]. Another advantage is that
the phosphoramidite coupling with 2'-acetal protected monomers is
typically more efficient than with trialkyl silanes. The problems
encountered when using the combination of 5'-O-DMT and 2'-O-acetals
groups reside in the difficulty to find suitable 2'-O acetal groups
that are both completely stable to the anhydrous acidic conditions
used to remove the 5'O-DMT group and completely labile to the mild
aqueous acid conditions used to remove this 2'-acetal protecting
group, while not cleaving the internucleotide bond of the RNA. The
removal of acetals that are stable under DMT deprotection
conditions typically requires prolonged exposure to acidic
conditions that degrade the RNA. To inhibit the loss of the 2'
protecting group, the 5'-9-phenylxanthen-9-yl (Pix) group was
applied, which is more labile than the DMT protecting group.
Even considering all of these innovations, the inability to find a
viable combination of 2'-acetal and 5'-acid labile protecting
groups that fits into the standard phosphoramidite synthesis cycle
has resulted in these chemical schemes that were never effectively
commercialized. Conversely, acetals used in combination with 5'
protecting groups such as leuvinyl and 9-fluorenylmethyloxycarbonyl
(FMOC) that are deprotected under non-acidic conditions like
hydrazinolysis have not met significant success. One of the
overriding reasons that 2'-acetals have not achieved wide
acceptance is that they tend to be too stable under the required
acid deprotection conditions once the monomers are incorporated
onto an oligonucleotide, due to the close proximity of the
protected 2'-hydroxyl to the internucleotide phosphate. There is a
significant change in the stability of the protecting group once
the oligonucleotide is produced. Conditions that can effectively
remove an acetal group from a protected nucleoside monomer tend to
be ineffective to remove the same group from the
oligonucleotide.
To address this issue, Dellinger et al. developed 2'-orthoester
protecting groups whose labiality on the oligonucleotide is less
affected by close proximity to the internucleotide phosphate
allowing effective removal under aqueous acid conditions that do
not degrade the desired RNA product. The use of 2'-cyclic
orthoesters was evaluated using a regioselective coupling procedure
as well as a set of 5'-nucleophile labile carbonates [Marvin H.
Caruthers, Tadeusz K. Wyrzkiewicz, and Douglas J. Dellinger.
"Synthesis of Oligonucleotides and Oligonucleotide Analogs on
Polymer Supports" In Innovation and Perspectives in Solid Phase
Synthesis: Peptides, Proteins and Nucleic Acids (R. Epton, ed.)
Mayflower Worldwide Limited, Birmingham, 39-44 (1994)].
Subsequently, Scaringe et. al. developed a set of 5'- and
2'-protecting groups that overcome the problems associated with use
of 5'-DMT. This method uses a 5'-silyloxy protecting group [U.S.
Pat. No. 5,889,136, U.S. Pat. No. 6,111,086, and U.S. Pat. No.
6,590,093] which require silicon-specific fluoride ion nucleophiles
to be removed, in conjugation with the use of optimized
2'-orthoesters protecting groups (ACE). Although the coupling
efficiency is greatly increased with the use of the ACE
2'-orthoester protecting group, and the final deprotection facile
under pH conditions at which RNA is stable, the use of fluoride
anions to deprotect the 5'-protecting groups prior each
condensation cycle carries some disadvantages for routine synthesis
of RNA and is even more problematic for large-scale synthesis of
RNA. Because this chemistry requires atypical nucleoside protecting
groups and custom synthesized monomers, namely on the 5'OH, it is
difficult and time consuming to build RNA sequences that contain
other commercially available phosphoramidite monomers, such as
modified nucleotides, fluorescent labels, or anchors.
In order to incorporate a wide variety of alternative monomers and
modifications using this chemistry, it is necessary to have each of
them custom-synthesized with the appropriate 5'-silyloxy protecting
group, thus significantly limiting the commercial applications for
this chemistry. The ACE chemistry has the ability to produce very
high quality RNA, but the reactions conditions are tricky and the
synthesis not robust enough to routinely produce long sequences of
RNAs. As a result, there is still clearly a need for the
development of a chemical synthesis method for RNA that is simple
and robust and produces high quality RNA products, while fitting
into the standard phosphoramidite oligonucleotide synthesis
approach. The commercial success of the ACE chemistry clearly
illustrates the need to develop a RNA synthesis method that is
founded upon mild and simple final deprotection conditions that
will not affect the integrity of the final RNA product.
While protected, the RNA molecule has similar stability to the DNA
molecule. Consequently, the final deprotection conditions to treat
a synthetic RNA molecule are typically the same as the conditions
to treat a synthetic DNA molecule prior to the removal of the
2'-hydroxyl protecting group. As a result, the current methods of
RNA synthesis perform the final deprotection of the synthetic RNA
in a 4-, 3-, or a 2-step fashion. 1. Deprotection of the protected
phosphotriester, most commonly the cyanoethyl group (CNE), which is
performed by brief exposure to ammonia (1/2 hr at room temperature)
or in the case of the methyl group, by treatment with thiophenol
for 1/2 hr at room temperature. 2. Cleavage of the
oligoribonucleotides from the support performed under basic
conditions, usually by exposure to ammonium hydroxide, anhydrous
ammonia in an alcohol, methylamine, other alkyl amines, basic
non-amine solutions such as potassium carbonate solutions, or
non-nucleophillic bases such as 1,8-diazabicyclo[5.4.0]undec-7-ene
(DBU) in organic solvents. 3. Deprotection of the nucleobases,
which one most commonly protected on the exocyclic amine with
protecting groups such as phenoxyacetyl (PAC), acetyl (Ac),
isobutyryl (iBu) or benzoyl (Bz) and which are typically also
removed under basic conditions. Most of the time, steps 2 and 3 are
performed simultaneously. 4. Usually, the 2'-deprotection is
performed post-cleavage of the oligonucleotide from the support. In
the case of TBDMS and TOM chemistry, the oligoribonucleotide is
exposed to fluoride anions to deblock the 2' hydroxyl groups after
cleavage of the oligoribonucleotide from the support. In the case
of the ACE chemistry, the 2'-O-orthoester group can be removed with
acidic conditions after cleavage of the oligoribonucleotide from
the support, but also can be kept and deprotected during shipment
to the customers or after shipment by the customers (this procedure
allows keeping the oligoribonucleotide intact longer, since RNA is
very sensitive to nuclease RNase degradation). Steps 1-3 can be
performed simultaneously, when appropriate, making it a 2-step
deprotection process, or step 1 can be performed independently, and
steps 2-3 combined, making it a 3-step final deprotection
process.
The removal of the 2'-hydroxyl protecting group is problematic for
both the 3- and 2-step processes. In the 3-step process, the
phosphorus protecting group is typically removed first, while the
oligoribonucleotide is still attached to a solid support. In the
second step, the heterobase protecting groups are removed using a
nucleophillic base like ammonia or methyl amine, also which usually
result in the cleavage of the oligoribonucleotide from the
support.
Finally, a fluoride ion-based solution under neutral, mildly
acidic, or mildly basic conditions (TBDMS, TOM) [Pitsch, et. al.
Helv. Chim. Acta, 2001, 84, 3773-3795] or a weak acidic solution is
used to remove the ACE 2'-hydroxyl protecting group [Scaringe et
al, Nucleic Acids Res 18, (18) 5433-5441 (1990); Scaringe et al, J.
Am. Chem. Soc., 120, 11820-11821 (1998)]. This process requires
that the 2'-hydroxyl protecting group is orthogonally stable to the
deblock conditions utilized to remove the protecting group for the
3'- or 5'-hydroxyl functional during the chemical synthesis
process, and stable to the conditions utilized for deprotection of
the phosphorus protecting groups and the heterobase protecting
groups. Most often it is seen that a loss of the 2'-protecting
group occurs to some extent during one of these previous deblock or
deprotection processes. The result is modification of the desired
RNA strand or cleavage of the desired RNA product.
Modification and cleavage decreases the yield and quality of the
desired RNA products and can often prevent synthesis and isolation
of oligonucleotide sequences significantly longer than 15 or 20
nucleotides in length. In the case of the use of a fluoride ion
solution for deprotection of the 2'-hydroxy group, removal of
residual fluoride ions requires additional steps and can be quite
difficult and time consuming.
In the 3-step process, removal of the phosphorus protecting groups
is accomplished simultaneously with the removal of the heterobase
protecting groups. This is usually accomplished using a
nucleophillic base like ammonia or methylamine. Most often the
phosphorus-protecting group is removed using a beta-elimination
reaction such as the formation of acrylonitrile from a
3-hydroxypropionitrile ester. However, the use of this system for
the protection of the internucleotide phosphodiester linkage,
followed by simultaneous deprotection during cleavage of the
heterobase protecting groups, results in a number of notable side
reactions that affect the yield and purity of the final product.
The use of protecting groups that are susceptible to cleavage by
proton abstraction followed by beta-elimination generally decreases
the reactivity of the active phosphorus intermediate due to their
electron withdrawing nature, and this effect lowers the per-cycle
coupling efficiency. In addition, the elimination products such as
acrylonitrile are reactive toward the heterobases and often form
base adducts that result in undesired modifications.
SUMMARY
Methods of deprotecting polynucleotides are disclosed. An
embodiment of the method of deprotecting polynucleotides, among
others, includes: providing a polynucleotide, wherein the
polynucleotide includes at least one nucleotide monomer that has at
least one protecting group selected from the following: a base
having a protecting group, a 2'-hydroxyl protecting group, and a
combination thereof, and deprotecting at least one of the
protecting groups of the polynucleotide by introducing the
polynucleotide to a solution including an .alpha.-effect
nucleophile, wherein the solution is at a pH of about 4 to 11,
wherein the .alpha.-effect nucleophile has a pKa of about 4 to
13.
An embodiment of the method of deprotecting polynucleotides, among
others, includes: providing a polynucleotide, wherein the
polynucleotide includes at least one nucleotide monomer that has at
least one protecting group selected from the following: an
exocyclic amino protecting group, an imino protecting group, a
2'-hydroxyl protecting group, and a combination thereof, and
deprotecting at least one of the protecting groups of the
polynucleotide by introducing the polynucleotide to a solution
including an .alpha.-effect nucleophile, wherein the solution is at
a pH of about 4 to 10, and wherein the .alpha.-effect nucleophile
has a pKa of about 4 to 13.
An embodiment of the method of deprotecting polynucleotides, among
others, includes: providing a polynucleotide, wherein the
polynucleotide includes at least one nucleotide monomer that has at
least one protecting group selected from the following: an
exocyclic amino protecting group, an imino protecting group, a
2'-hydroxyl protecting group, and a combination thereof; and
deprotecting at least one of the exocyclic amino protecting groups
of the polynucleotide by introducing the polynucleotide to a
solution including an .alpha.-effect nucleophile, wherein the
solution is at a pH of about 4 to 10, and wherein the
.alpha.-effect nucleophile has a pKa of about 4 to 13.
An embodiment of the method of deprotecting polynucleotides, among
others, includes: providing a polynucleotide, wherein the
polynucleotide includes at least one nucleotide monomer that has at
least one protecting group selected from the following: an
exocyclic amino protecting group, an imino protecting group, a
2'-hydroxyl protecting group, and a combination thereof; and
deprotecting the 2'-hydroxyl protecting groups of the
polynucleotide by introducing the polynucleotide to a solution
including an .alpha.-effect nucleophile, wherein the solution is at
a pH of about 4 to 10, and wherein the .alpha.-effect nucleophile
has a pKa of about 4 to 13.
An embodiment of the method of deprotecting polynucleotides, among
others, includes: providing a polynucleotide, wherein the
polynucleotide includes at least one nucleotide monomer that has at
least one protecting group selected from the following: an
exocyclic amino protecting group, an imino protecting group, a
2'-hydroxyl protecting group, and a combination thereof, and
deprotecting the exocyclic amino protecting groups and the
2'-hydroxyl groups of the polynucleotide by introducing the
polynucleotide to a solution including an .alpha.-effect
nucleophile, wherein the solution is at a pH of about 4 to 10, and
wherein the .alpha.-effect nucleophile has a pKa of about 4 to
13.
Additional objects, advantages, and novel features of this
disclosure shall be set forth in part in the descriptions and
examples that follow and in part will become apparent to those
skilled in the art upon examination of the following specifications
or may be learned by the practice of the disclosure. The objects
and advantages of the disclosure may be realized and attained by
means of the instruments, combinations, compositions, and methods
particularly pointed out in the appended claims.
BRIEF DESCRIPTION OF THE DRAWINGS
Reference is now made to the following drawings. Note that the
components in the drawings are not necessarily to scale.
FIG. 1 schematically illustrates a prior art multi-step RNA
synthesis method.
FIGS. 2A through 2E illustrate chromatograph of a synthetic RNA and
a solution of 5% hydrogen peroxide in a solution having a pH of
about 9 at various times (FIG. 2A (time.sub.RNA=0), FIG. 2B
(time.sub.HP=0), FIG. 2C (time=3 hours), FIG. 2D (time=12 hours),
and FIG. 2E (time=24 hours)).
FIG. 3 illustrates the transient protection of hydroxyl moieties
("Jones Procedure").
FIG. 4 illustrates the transient protection of hydroxyl moieties
("Markiewicz Procedure").
FIG. 5 illustrates the selective protection of exocyclic amine with
chloroformate reagents.
FIG. 6 illustrates the selective protection of 2'-hydroxyl with
chloroformate reagents.
FIG. 7 illustrates the preparation of
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)ribonucleosides.
FIG. 8 illustrates the simultaneous protection of
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)ribonucleosides using
chloroformates or pyrocarbonates.
FIG. 9 illustrates the selective protection of exocyclic amine with
pyrocarbonate reagents.
FIG. 10 illustrates the selective protection of 2'-hydroxyl with
pyrocarbonate reagents.
FIG. 11 illustrates the selective protection of exocyclic amine
with hemimethylthioacetal chloroformate reagents.
FIG. 12 illustrates the synthesis of
O-trimethylsilylhemimethylthioacetal as an intermediate in the
preparation of the corresponding chloroformate.
FIG. 13 illustrates the O-trimethylsilylhemimethylthioketals as
intermediate in the preparation of the corresponding
pyrocarbonate.
FIG. 14 illustrates the selective protection of exocyclic amine
with hemimethylthioketal pyrocarbonate reagents.
FIG. 15 illustrates the selective protection of 2'-hydroxyl with
hemimethylthioketal pyrocarbonate reagents.
FIG. 16 illustrates the 2'-hydroxyl protective groups.
FIG. 17 illustrates the Michael addition at the C-6 carbon of the
heterobase followed by nucleophillic acyl substitution at the C-4
carbon resulting in formation of a urea.
FIG. 18 illustrates that O-4 protection prevents initial Michael
addition at C-6.
FIG. 19 illustrates the formation of C-4 triazolide.
FIG. 20 illustrates the regiospecific synthesis of a 2'-protected
nucleoside with O-4 protection.
FIG. 21 illustrates HPLC Chromatograms of RNA synthesized by the
present disclosure.
FIG. 22 illustrates HPLC Chromatograms of RNA synthesized by the
present disclosure.
FIG. 23 illustrates HPLC Chromatograms of RNA synthesized by the
present disclosure.
DETAILED DESCRIPTION
Embodiments of the present disclosure employ, unless otherwise
indicated, conventional techniques of synthetic organic chemistry,
biochemistry, molecular biology, and the like, which are within the
skill of one in the art. Such techniques are explained fully in the
literature.
The following examples are put forth so as to provide those of
ordinary skill in the art with a complete disclosure and
description of how to perform the methods and use the compositions
disclosed and claimed herein. Efforts have been made to ensure
accuracy with respect to numbers (e.g., amounts, temperature,
etc.), but some errors and deviations should be accounted for in
the specification. Unless indicated otherwise, parts are parts by
weight, temperature is in .degree. C., and pressure is at or near
atmospheric. Standard temperature and pressure are defined as
20.degree. C. and 1 atmosphere.
Before the embodiments of the present disclosure are described in
detail, it is to be understood that unless otherwise indicated, the
present disclosure is not limited to particular materials,
reagents, reaction materials, manufacturing processes, or the like,
as such may vary. It is also to be understood that the terminology
used herein is for purposes of describing particular embodiments
only, and is not intended to be limiting. It is also possible in
the present disclosure that steps may be executed in different
sequence where this is logically possible.
It must be noted that, as used in the specification and the
appended claims, the singular forms "a," "an" and "the" include
plural referents unless the context clearly dictates otherwise.
Thus, for example, reference to "a support" includes a plurality of
supports. In this specification and in the claims that follow,
reference will be made to a number of terms that shall be defined
to have the following meanings, unless a contrary intention is
apparent.
As used herein, polynucleotides include single or multiple stranded
configurations, where one or more of the strands may or may not be
completely aligned with another. The terms "polynucleotide" and
"oligonucleotide" shall be generic to polydeoxynucleotides
(containing 2-deoxy-D-ribose), to polyribonucleotides (containing
D-ribose), to any other type of polynucleotide which is an
N-glycoside of a purine or pyrimidine base, and to other polymers
in which the conventional backbone has been replaced with a
non-naturally occurring or synthetic backbone or in which one or
more of the conventional bases has been replaced with a
non-naturally occurring or synthetic base.
A "nucleotide" and a "nucleotide moiety" refer to a sub-unit of a
nucleic acid (whether DNA or RNA or an analogue thereof) which may
include, but is not limited to, a phosphate group, a sugar group
and a nitrogen containing base, as well as analogs of such
sub-units. Other groups (e.g., protecting groups) can be attached
to the sugar group and nitrogen containing base group.
A "nucleoside" references a nucleic acid subunit including a sugar
group and a nitrogen containing base. It should be noted that the
term "nucleotide" is used herein to describe embodiments of the
disclosure, but that one skilled in the art would understand that
the term "nucleoside" and "nucleotide" are interchangable in most
instances. One skilled in the art would have the understanding that
additional modification to the nucleoside may be necessary, and one
skilled in the art has such knowledge.
A "nucleotide monomer" refers to a molecule which is not
incorporated in a larger oligo- or poly-nucleotide chain and which
corresponds to a single nucleotide sub-unit; nucleotide monomers
may also have activating or protecting groups, if such groups are
necessary for the intended use of the nucleotide monomer.
A "polynucleotide intermediate" references a molecule occurring
between steps in chemical synthesis of a polynucleotide, where the
polynucleotide intermediate is subjected to further reactions to
get the intended final product (e.g., a phosphite intermediate,
which is oxidized to a phosphate in a later step in the synthesis),
or a protected polynucleotide, which is then deprotected.
An "oligonucleotide" generally refers to a nucleotide multimer of
about 2 to 100 nucleotides in length, while a "polynucleotide"
includes a nucleotide multimer having any number of nucleotides
greater than 1. The terms "oligonucleotide" and "polynucleotide"
are often used interchangeably, consistent with the context of the
sentence and paragraph in which they are used in.
It will be appreciated that, as used herein, the terms "nucleoside"
and "nucleotide" will include those moieties which contain not only
the naturally occurring purine and pyrimidine bases, e.g., adenine
(A), thymine (T), cytosine (C), guanine (G), or uracil (U), but
also modified purine and pyrimidine bases and other heterocyclic
bases which have been modified (these moieties are sometimes
referred to herein, collectively, as "purine and pyrimidine bases
and analogs thereof"). Such modifications include, e.g.,
diaminopurine and its deravitives, inosine and its deravitives,
alkylated purines or pyrimidines, acylated purines or pyrimidines
thiolated purines or pyrimidines, and the like, or the addition of
a protecting group such as acetyl, difluoroacetyl, trifluoroacetyl,
isobutyryl, benzoyl, 9-fluorenylmethoxycarbonyl, phenoxyacetyl,
dimethylformamidine, N,N-diphenyl carbamate, or the like. The
purine or pyrimidine base may also be an analog of the foregoing;
suitable analogs will be known to those skilled in the art and are
described in the pertinent texts and literature. Common analogs
include, but are not limited to, 1-methyladenine, 2-methyladenine,
N6-methyladenine, N6-isopentyladenine,
2-methylthio-N6-isopentyladenine, N,N-dimethyladenine,
8-bromoadenine, 2-thiocytosine, 3-methylcytosine, 5-methylcytosine,
5-ethylcytosine, 4-acetylcytosine, 1-methylguanine,
2-methylguanine, 7-methylguanine, 2,2-dimethylguanine,
8-bromoguanine, 8-chloroguanine, 8-aminoguanine, 8-methylguanine,
8-thioguanine, 5-fluorouracil, 5-bromouracil, 5-chlorouracil,
5-iodouracil, 5-ethyluracil, 5-propyluracil, 5-methoxyuracil,
5-hydroxymethyluracil, 5-(carboxyhydroxymethyl)uracil,
5-(methylaminomethyl)uracil, 5-(carboxymethylaminomethyl)-uracil,
2-thiouracil, 5-methyl-2-thiouracil, 5-(2-bromovinyl)uracil,
uracil-5-oxyacetic acid, uracil-5-oxyacetic acid methyl ester,
pseudouracil, 1-methylpseudouracil, queosine, inosine,
1-methylinosine, hypoxanthine, xanthine, 2-aminopurine,
6-hydroxyaminopurine, 6-thiopurine, and 2,6-diaminopurine.
An "internucleotide bond" refers to a chemical linkage between two
nucleoside moieties, such as a phosphodiester linkage in nucleic
acids found in nature, or such as linkages well known from the art
of synthesis of nucleic acids and nucleic acid analogues. An
internucleotide bond may include a phospho or phosphite group, and
may include linkages where one or more oxygen atoms of the phospho
or phosphite group are either modified with a substituent or
replaced with another atom, e.g., a sulfur atom, or the nitrogen
atom of a mono- or di-alkyl amino group.
A "group" includes both substituted and unsubstituted forms.
Typical substituents include one or more lower alkyl, amino, imino,
amido, alkylamino, arylamino, alkoxy, aryloxy, thio, alkylthio,
arylthio,or aryl, or alkyl; aryl, alkoxy, thioalkyl, hydroxyl,
amino, amido, sulfonyl, thio, mercapto, imino, halo, cyano, nitro,
nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl,
silyl, silyloxy, and boronyl, or optionally substituted on one or
more available carbon atoms with a nonhydrocarbyl substituent such
as cyano, nitro, halogen, hydroxyl, sulfonic acid, sulfate,
phosphonic acid, phosphate, phosphonate, or the like. Any
substituents are typically chosen so as not to substantially
adversely affect reaction yield (for example, not lower it by more
than 20% (or 10%, or 5%, or 1%) of the yield otherwise obtained
without a particular substituent or substituent combination). An
"acetic acid" includes substituted acetic acids such as
di-chloroacetic acid (DCA) or tri-chloroacetic acid (TCA).
A "phospho" group includes a phosphodiester, phosphotriester, and
H-phosphonate groups. In the case of either a phospho or phosphite
group, a chemical moiety other than a substituted 5-membered furyl
ring may be attached to O of the phospho or phosphite group which
links between the furyl ring and the P atom.
A "protecting group" is used in the conventional chemical sense to
reference a group, which reversibly renders unreactive a functional
group under specified conditions of a desired reaction, as taught,
for example, in Greene, et al., "Protective Groups in Organic
Synthesis," John Wiley and Sons, Second Edition, 1991, which is
incorporated herein by reference. After the desired reaction,
protecting groups may be removed to deprotect the protected
functional group. All protecting groups should be removable (and
hence, labile) under conditions which do not degrade a substantial
proportion of the molecules being synthesized. In contrast to a
protecting group, a "capping group" permanently binds to a segment
of a molecule to prevent any further chemical transformation of
that segment. It should be noted that the functionality protected
by the protecting group may or may not be a part of what is
referred to as the protecting group.
A "hydroxyl protecting group" or "O-protecting group" refers to a
protecting group where the protected group is a hydroxyl. A
"reactive-site hydroxyl" is the terminal 5'-hydroxyl during 3'-5'
polynucleotide synthesis and is the 3'-hydroxyl during 5'-3'
polynucleotide synthesis. An "acid-labile protected hydroxyl" is a
hydroxyl group protected by a protecting group that can be removed
by acidic conditions. Similarly, an "acid-labile protecting group"
is a protecting group that can be removed by acidic conditions.
A "linking moiety" is a group known in the art to connect
nucleotide moieties in a polynucleotide or oligonucleotide
compound.
The term "alkyl" is art-recognized, and includes saturated
aliphatic groups, including straight-chain alkyl groups,
branched-chain alkyl groups, cycloalkyl (alicyclic) groups, alkyl
substituted cycloalkyl groups, and cycloalkyl substituted alkyl
groups. In certain embodiments, a straight chain or branched chain
alkyl has about 30 or fewer carbon atoms in its backbone (e.g.,
C.sub.1-C.sub.30 for straight chain, C.sub.3-C.sub.30 for branched
chain), and alternatively, about 20 or fewer. For example the term
"alkyl" can refer to straight or branched chain hydrocarbon groups,
such as methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl,
t-butyl, pentyl, hexyl, heptyl, octyl, and the like. Likewise,
cycloalkyls have from about 3 to about 10 carbon atoms in their
ring structure, and alternatively about 5, 6 or 7 carbons in the
ring structure. The term "alkyl" is also defined to include
halosubstituted alkyls and heteroatom substituted alkyls.
Moreover, the term "alkyl" (or "lower alkyl") includes "substituted
alkyls", which refers to alkyl moieties having substituents
replacing a hydrogen on one or more carbons of the hydrocarbon
backbone. Such substituents may include, for example, a hydroxyl, a
carbonyl (such as a carboxyl, an alkoxycarbonyl, a formyl, or an
acyl), a thiocarbonyl (such as a thioester, a thioacetate, or a
thioformate), an alkoxyl, a phosphoryl, a phosphonate, a
phosphonate, an amino, an amido, an amidine, an imine, a cyano, a
nitro, an azido, a sulfhydryl, an alkylthio, a sulfate, a
sulfonate, a sulfamoyl, a sulfonamido, a sulfonyl, a heterocyclic,
an aralkyl, or an aromatic or heteroaromatic moiety. It will be
understood by those skilled in the art that the moieties
substituted on the hydrocarbon chain may themselves be substituted,
if appropriate. For instance, the substituents of a substituted
alkyl may include substituted and unsubstituted forms of amino,
azido, imino, amido, phosphoryl (including phosphonate and
phosphonate), sulfonyl (including sulfate, sulfonamido, sulfamoyl
and sulfonate), and silyl groups, as well as ethers, alkylthios,
carbonyls (including ketones, aldehydes, carboxylates, and esters),
--CN, and the like. Cycloalkyls may be further substituted with
alkyls, alkenyls, alkoxys, alkylthios, aminoalkyls,
carbonyl-substituted alkyls, --CN, and the like.
The term "alkoxy" means an alkyl group linked to oxygen thus:
R--O--. In this function, R represents the alkyl group. An example
would be the methoxy group CH.sub.3O--.
The term "aryl" refers to 5-, 6-, and 7-membered single-ring
aromatic groups that may include from zero to four heteroatoms, for
example, benzene, pyrrole, furan, thiophene, imidazole, oxazole,
thiazole, triazole, pyrazole, pyridine, pyrazine, pyridazine and
pyrimidine, and the like. Those aryl groups having heteroatoms in
the ring structure may also be referred to as "aryl heterocycles"
or "heteroaromatics."
The aromatic ring may be substituted at one or more ring positions
with such substituents as described above, for example, halogen,
azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl,
alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate,
phosphonate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl,
sulfonamido, ketone, aldehyde, ester, heterocyclic, aromatic or
heteroaromatic moieties, --CF.sub.3, --CN, or the like.
The term "aryl" also includes polycyclic ring systems having two or
more cyclic rings in which two or more carbons are common to two
adjoining rings (the rings are "fused rings") wherein at least one
of the rings is aromatic (e.g., the other cyclic rings may be
cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, and/or
heterocyclyls).
The terms "halogen" and "halo" refer to fluorine, chlorine,
bromine, and iodine.
The terms "heterocycle", "heterocyclic", "heterocyclic group" or
"heterocyclo" refer to fully saturated or partially or completely
unsaturated, including aromatic ("heteroaryl") or nonaromatic
cyclic groups (for example, 3 to 13 member monocyclic, 7 to 17
member bicyclic, or 10 to 20 member tricyclic ring systems) which
have at least one heteroatom in at least one carbon atom-containing
ring. Each ring of the heterocyclic group containing a heteroatom
may have 1, 2, 3, or 4 heteroatoms selected from nitrogen atoms,
oxygen atoms and/or sulfur atoms, where the nitrogen and sulfur
heteroatoms may optionally be oxidized and the nitrogen heteroatoms
may optionally be quaternized. The heterocyclic group may be
attached at any heteroatom or carbon atom of the ring or ring
system. The rings of multi-ring heterocycles may be either fused,
bridged and/or joined through one or more spiro unions.
The terms "substituted heterocycle", "substituted heterocyclic",
"substituted heterocyclic group" and "substituted heterocyclo"
refer to heterocycle, heterocyclic, and heterocyclo groups
substituted with one or more groups preferably selected from alkyl,
substituted alkyl, alkenyl, oxo, aryl, substituted aryl,
heterocyclo, substituted heterocyclo, carbocyclo (optionally
substituted), halo, hydroxy, alkoxy (optionally substituted),
aryloxy (optionally substituted), alkanoyl (optionally
substituted), aroyl (optionally substituted), alkylester
(optionally substituted), arylester (optionally substituted),
cyano, nitro, amido, amino, substituted amino, lactam, urea,
urethane, sulfonyl, and the like, where optionally one or more pair
of substituents together with the atoms to which they are bonded
form a 3 to 7 member ring.
When used herein, the terms "hemiacetal", "thiohemiacetal",
"acetal", and "thioacetal", are recognized in the art, and refer to
a chemical moiety in which a single carbon atom is geminally
disubstituted with either two oxygen atoms or a combination of an
oxygen atom and a sulfur atom. In addition, when using the terms,
it is understood that the carbon atom may actually be geminally
disubstituted by two carbon atoms, forming ketal, rather than
acetal, compounds.
The term "electron-withdrawing group" is art-recognized, and refers
to the tendency of a substituent to attract valence electrons from
neighboring atoms (i.e., the substituent is electronegative with
respect to neighboring atoms). A quantification of the level of
electron-withdrawing capability is given by the Hammett sigma
constant. This well known constant is described in many references,
for instance, March, Advanced Organic Chemistry 251-59, McGraw Hill
Book Company, New York, (1977). Exemplary electron-withdrawing
groups include nitro, acyl, formyl, sulfonyl, trifluoromethyl,
cyano, chloride, and the like.
The term "electron-donating group" is art-recognized, and refers to
the tendency of a substituent to repel valence electrons from
neighboring atoms (i.e., the substituent is less electronegative
with respect to neighboring atoms). Exemplary electron-donating
groups include amino, methoxy, alkyl (including C.sub.1-6 alkyl
that can have a linear or branched structure), C.sub.4-9
cycloalkyl, and the like.
The term "deprotecting simultaneously" refers to a process which
aims at removing different protecting groups in the same process
and performed substantially concurrently or concurrently. However,
as used herein, this term does not imply that the deprotection of
the different protecting groups occur at the same time or with the
same rate or same kinetics.
As used herein, "dissociation constant" (e.g., an acid dissociation
constant) has its conventional definition as used in the chemical
arts and references a characteristic property of a molecule having
a tendency to lose a hydrogen ion. The value of a dissociation
constant mentioned herein is typically expressed as a negative log
value (i.e., a pKd).
Discussion
The present disclosure includes nucleotide structures such as
nucleotide monomers and oligonucleotide or polynucleotide compounds
(e.g., synthetic ribonucleic acid (RNA)) having nucleotide
moieties. The nucleotide monomers and the nucleotide moieties
include various types of protecting groups that can be used in
conjunction with methods, processes, and/or compositions of the
present disclosure for the deprotection of polynucleotides.
Embodiments of the present disclosure enable quasi-quantitative or
quantitative and rapid synthesis of the desired deprotected,
full-length polynucleotide product. Embodiments of the present
disclosure also include methods, processes, compositions, and
nucleotide structures that enable the synthesis of RNA with greater
efficiency and lower cost compared to previous methods.
Embodiments of the present disclosure provide for methods,
processes, compositions, and nucleotide structures that overcome at
least some of the degradation problems of the polynucleotides
(e.g., RNA), which occur during the deprotection procedure due to
the use of strongly basic conditions, by the use of peroxyanions in
mildly basic solutions and the protecting groups described herein
(e.g., 2'-hydroxyl protecting groups, base protecting groups, and
phosphorus protecting groups). Embodiments of the present
disclosure can be used in conjunction with other methods,
processes, compositions, and nucleotide structures.
An advantage of embodiments of the present disclosure is that
deprotection of the bases can be performed even after removal of
the 2'-hydroxyl protecting groups, as opposed to prior methods.
Another advantage of embodiments of the present disclosure is that
the deprotection can also be used to cleave the protecting groups
of the bases in polynucleotide synthesis where, for example, the
oligodeoxynucleotide includes a nucleotide, a modified nucleoside,
or a non-nucleoside moiety that is sensitive to strong bases such
as fluorescent labels.
Exemplary methods of deprotecting polynucleotides, among others,
include: providing a synthetically made ribonucleic acid (RNA)
(e.g., synthesized on a solid support (e.g., bead, CPG, polymeric
support, an array)), wherein the RNA, optionally, has at least one
2'-hydroxyl protecting group (e.g., a silyl protecting group, a
silyloxy protecting group, an ester protecting group, a carbonate
protecting group, a thiocarbonate protecting group, a carbamate
protecting group, an acetal protecting group, an acetaloxycarbonyl
protecting group, an orthoester protecting group, an orthothioester
protecting group, an orthoesteroxycarbonyl protecting group,
orthothioesteroxycarbonyl protecting group, orthoesterthiocarbonyl
protecting group, orthothioesterthiocarbonyl protecting group, a
thioacetal protecting group, a thioacetaloxycarbonyl protecting
group, and combinations thereof), wherein the RNA, optionally, has
at least one protected exocyclic amine on a heterocyclic base
protected by a base protecting group (e.g., an acyl protecting
group, an oxycarbonyl protecting group, a thiocarbonyl protecting
group, an alkyloxymethylcarbonyl protecting group (optionally
substituted), an alkylthiomethylcarbonyl protecting group
(optionally substituted), an aryloxymethylcarbonyl protecting group
(optionally substituted), an arylthiomethylcarbonyl protecting
group (optionally substituted), an dialkylformamidine protecting
group (optionally substituted), a dialkylamidine protecting group
(optionally substituted), and combinations thereof), wherein the
RNA, optionally, has at least one protected imine on a heterocyclic
base by a base protecting group (e.g., an acyl protecting group
(optionally substituted), an alkyloxylcarbonyl protecting group
(optionally substituted), an aryloxycarbonyl protecting group
(optionally substituted), an alkylthiocarbonyl protecting group
(optionally substituted), an arylthiocarbonyl protecting group
(optionally substituted), and combinations thereof), wherein,
optionally, the RNA has at least one phosphorus protecting group
(e.g., substituted and unsubstituted: alkyl, benzyl, alkylbenzyl,
dialkylbenzyl, trialkylbenzyl, thioalkylbenzyl, phenylthiobenzyl,
dithioalkylbenzyl, trithioalkylbenzyl, thioalkylhalobenzyl,
alkyloxybenzyl, dialkyloxybenzyl, halobenzyl, dihalobenzyl,
trihalobenzyl, esterified salicyl, and alkylnitrile protecting
groups, as well as other protecting groups described herein);
deprotecting (e.g., deprotecting, simultaneously or independently,
one or more of the 2'-hydroxyl protecting group, the base
protecting group, and/or the phosphorus protecting group) the RNA
in a solution including an .alpha.-effect nucleophile (e.g.,
hydrogen peroxide, peracids, perboric acids, alkylperoxides,
hydrogen peroxide salts, hydroperoxides, butylhydroperoxide,
benzylhydroperoxide, phenylhydroperoxide, performic acid, peracetic
acid, perbenzoic acid, chloroperbenzoic acid, mixtures with other
compounds (e.g., sodium formate) and combinations thereof), wherein
the solution is at a pH of about 4 to 11 (e.g, a pH of about 6 to
11 and a pH of about 8 to 11), wherein the .alpha.-effect
nucleophile has a pKa of about 4 to 13; (prior to or after
deprotecting) optionally, cleaving (e.g., simultaneously or
independently) the RNA from the support; and optionally,
precipitating the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing on a solid support a ribonucleic acid (RNA), wherein
the RNA has at least one 2'-hydroxyl protecting group and at least
one protected exocyclic amine on a heterocyclic base; wherein said
2'-hydroxyl group is protected with an orthoester protecting group;
introducing the RNA to a solution including an .alpha.-effect
nucleophile, wherein the solution is at a pH of about 6 to 11 and
wherein the .alpha.-effect nucleophile has a pKa of about 4 to 13;
deprotecting said 2'-orthoester protecting group under acidic
conditions; (prior to or after) optionally, simultaneously or
independently cleaving the RNA from the support; and optionally,
precipitating the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing on a solid support a ribonucleic acid (RNA), wherein
the RNA has at least one 2'-hydroxyl protecting group and at least
one protected exocyclic amine on a heterocyclic base; wherein said
2'-hydroxyl protecting group includes an acetal protecting group;
introducing the RNA to a solution including an .alpha.-effect
nucleophile, wherein the solution is at a pH of about 6 to 11 and
wherein the .alpha.-effect nucleophile has a pKa of about 4 to 13,
deprotecting said 2'-acetal protecting group under acidic
conditions; (prior to or after) optionally, simultaneously or
independently cleaving the RNA from the support; and optionally,
precipitating the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing on a solid support a ribonucleic acid (RNA), wherein
the RNA has at least one 2'-hydroxyl protecting group and at least
one protected exocyclic amine on a heterocyclic base; wherein said
2'-hydroxyl protecting group is triisopropyloxymethyl (TOM) group;
introducing the RNA to a solution including an .alpha.-effect
nucleophile, wherein the solution is at a pH of about 6 to 11 and
wherein the .alpha.-effect nucleophile has a pKa of about 4 to 13;
subsequently, deprotecting said 2'-triisopropyloxyrnethyl
protecting group under fluoride anions conditions; optionally,
cleaving the RNA from the support; and optionally, precipitating
the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing on a solid support a ribonucleic acid (RNA), wherein
the RNA has at least one 2'-hydroxyl protecting group and at least
one protected exocyclic amine on a heterocyclic base; wherein said
2'-hydroxyl protecting group includes a tert-butyldimethylsilyl
(TBDMS) protecting group; introducing the RNA to a solution
including an .alpha.-effect nucleophile, and wherein the solution
is at a pH of about 6 to 11 wherein the .alpha.-effect nucleophile
has a pKa of about 4 to 13; deprotecting said 2'-TBDMS protecting
group with fluoride anions; (prior to or after) optionally,
simultaneously or independently cleaving the RNA from the support;
and optionally, precipitating the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing on a polystyrene solid support a ribonucleic acid
(RNA), wherein the RNA has at least one phosphorus protecting
group, at least one 2'-hydroxyl protecting group and at least one
protected exocyclic amine on a heterocyclic base; wherein said
phosphorus protecting group is a methyl and said 2'-hydroxyl
protecting group is a trisiopropyloxymethyl (TOM) group;
deprotecting said methyl group with thiophenol or derivative of
thiophenol; then deprotecting said 2'-trisiopropyloxymethyl
protecting group under fluoride anions conditions; subsequently,
introducing the RNA to a solution including an .alpha.-effect
nucleophile, and wherein the solution is at a pH of about 6 to 11
and wherein the .alpha.-effect nucleophile has a pKa of about 4 to
13; deprotecting the excocyclic amine protecting group; optionally,
simultaneously or independently cleaving the RNA from the support;
and optionally precipitating the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing on polystyrene solid support a ribonucleic acid (RNA),
wherein the RNA has at least one phosphorus protecting group, at
least one 2'-hydroxyl protecting group and at least one protected
exocyclic amine on a heterocyclic base; wherein said phosphorus
protecting group is a methyl and said 2'-hydroxyl protecting group
is a tert-butyldimethylsilyl (TBDMS) protecting group; deprotecting
said methyl group with thiophenol or derivative of thiophenol; then
deprotecting said 2'-TBDMS protecting group under fluoride anions
conditions; subsequently, introducing the RNA to a solution
including an .alpha.-effect nucleophile, and wherein the solution
is at a pH of about 6 to 11 and wherein the .alpha.-effect
nucleophile has a pKa of about 4 to 13; deprotecting said exocyclic
amine protecting group; optionally, simultalneously or
independently cleaving the RNA from the support; and optionally
precipitating the RNA out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing optionally on a solid support a polynucleotide wherein
the polynucleotide has at least one protected exocyclic amine on a
heterocyclic base; deprotecting the exocyclic amino groups by
introducing the polynucleotide to a solution including an
.alpha.-effect nucleophile, and wherein the solution is at a pH of
about 6 to 11 and wherein the .alpha.-effect nucleophile has a pKa
of about 4 to 13, optionally, simultaneously or independently
cleaving the polynucleotide from the support; and optionally,
precipitating the polynucleotide out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing optionally on a solid support a polynucleotide wherein
the polynucleotide has at least one protected exocyclic amine on a
heterocyclic base and at least one protected imine on a
heterocyclic base; deprotecting the exocyclic amino groups by
introducing the polynucleotide to a solution including an
(.alpha.-effect nucleophile, wherein the solution is at a pH of
about 6 to 11 and wherein the .alpha.-effect nucleophile has a pKa
of about 4 to 13, optionally, simultaneously or independently
cleaving the polynucleotide from the support; and optionally,
precipitating the polynucleotide out of the solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing optionally on a solid support a polynucleotide wherein
the polynucleotide has at least one protected exocyclic amine on a
heterocyclic base, at least one protected imine on a heterocyclic
base and at least one 2'-hydroxyl protecting group; deprotecting
the exocyclic amino groups by introducing the polynucleotide to a
solution including an .alpha.-effect nucleophile, and wherein the
solution is at a pH of about 6 to 11 and wherein the .alpha.-effect
nucleophile has a pKa of about 4 to 13, optionally, simultaneously
or independently cleaving the polynucleotide from the support; and
optionally, precipitating the polynucleotide out of the
solution.
In another embodiment of the present disclosure, exemplary methods
of deprotecting polynucleotides, among others, include:
synthesizing optionally on a solid support a polynucleotide wherein
the polynucleotide has at least one protected exocyclic amine on a
heterocyclic base, at least one protected imine on a heterocyclic
base and at least one 2'-hydroxyl protecting group; deprotecting
the exocyclic amino groups and the 2'-hydroxyl protecting groups by
introducing the polynucleotide to a solution including an
.alpha.-effect nucleophile, wherein the solution is at a pH of
about 6 to 11 and wherein the .alpha.-effect nucleophile has a pKa
of about 4 to 13, optionally, simultaneously or independently
cleaving the polynucleotide from the support; and optionally,
precipitating the polynucleotide out of the solution.
Deprotecting
As mentioned above, embodiments of the present disclosure include
methods for deprotecting a polynucleotide (e.g., an RNA molecule)
such as those described herein. In particular, the method includes
deprotecting an RNA molecule in a solution of an .alpha.-effect
nucleophile (e.g., a peroxyanion solution), where the
.alpha.-effect nucleophile has a pKa of about 4 to 13. In addition,
the solution is at a pH of about 6 to 11.
One advantage of using a mildly basic solution including an
.alpha.-effect nucleophile is that the method substantially avoids
isomerization and cleavage of the internucleotide bonds of the RNA
that is catalyzed by the general-base removal of the proton from
the 2'-hydroxyl. In addition, the solution including an
.alpha.-effect nucleophile is compatible with standard
phosphoramidite methods for polynucleotide synthesis. Further, the
deprotected RNA molecules are stable and show little or no
degradation for an extended period of time when stored in the
solution including the .alpha.-effect nucleophile. An additional
advantage of using the solution including an .alpha.-effect
nucleophile is that the disadvantages associated with the 3- and
2-step processes typically used for RNA deprotecting are not
present, and the embodiments of the present disclosure can be used
to deprotect in a single step.
It should be noted that embodiments of the present disclosure
include methods that are multi-step methods, and use of the
.alpha.-effect nucleophile (e.g., for deprotection of the one or
more 2'-hydroxyl protecting groups, one or more base protecting
groups, and/or one or more phosphorus protecting groups) may be one
of a number of steps used in the synthesis and/or deprotection of
the polynucleotide. For example, one step of the method may use the
.alpha.-effect nucleophile to deprotect one or more protecting
groups, while one or more other steps may include other solutions
(e.g., TBDMS, TOM, ACE, and like chemistries) used to deprotect one
or more of the protecting groups.
In general, the methods involve forming and/or providing a
synthetic RNA molecule, where the RNA molecule has at least one of
the following: a base having a protecting group, a 2'-hydroxyl
protecting group, a phosphorus protecting group, and combinations
thereof. Then, the RNA molecule is introduced and mixed with a
solution including a least one type of an .alpha.-effect
nucleophile, where the solution is at a pH of about 4 to 11. In
addition, the .alpha.-effect nucleophile has a pKa of about 4 to
12. One or more of the protecting groups can be deprotected through
interaction with the .alpha.-effect nucleophile.
In general, these solutions including the .alpha.-effect
nucleophiles can be predominately buffered aqueous solutions or
buffered aqueous/organic solutions. Under these conditions, it is
convenient and cost effective to remove the deprotecting solutions
by simple precipitation of the desired RNA oligonucleotides
directly from the deprotecting mixture by addition of ethanol to
the solution. Under these conditions, the RNA is pelleted to the
bottom of a centrifuge tube, and the deprotecting mixture
containing the .alpha.-effect nucleophile is removed by simply
pouring off the supernatant and rinsing the pellet with fresh
ethanol. The desired RNA is then isolated by resuspending in a
typical buffer for chromatographic purification or direct usage in
the biological experiment of interest. Because of the nature of
most .alpha.-effect nucleophiles, removal from the desired RNA
products is significantly less tedious and time consuming; this is
especially true in comparison the use of a fluoride-ion solution
for final deprotection of the RNA molecule.
One significant advantage for post-synthetic deprotection applied
to any method of RNA synthesis is that the .alpha.-effect
nucleophile solution can be exploited to remove a variety of
commonly used protecting groups the protecting groups described
herein, and/or linkers under pH conditions that do not catalyze
rapid degradation of RNA by the general-base removal of the proton
from the 2'-hydroxyl moiety. Unlike the commonly applied use of
strong bases and/or typical nucleophiles for post synthetic
deprotection of RNA, partial loss of the 2'-protecting group, prior
to or during exposure to the .alpha.-effect nucleophiles, does not
result in cleavage of the internucleotide bond. Therefore, the use
of the .alpha.-effect nucleophile solutions simply for the
deprotection of heterobase blocking groups has significant
advantages over current methods, even if coupled with the use of
routine protecting groups. These advantages become even more
significant if they are used with the protecting groups described
herein that are specifically optimized for rapid removal under the
oxidative, nucleophillic conditions at neutral to mildly basic
pH.
The solution containing the .alpha.-effect nucleophiles has a pH of
about 4 to 11, about 5 to 11, about 6 to 11, about 7 to 11, about 8
to 11, about 4 to 10, about 5 to 10, about 6 to 10, about 7 to 10,
and about 8 to 10. In particular, the solution has a pH of about 7
to 10. It should also be noted that the pH is dependent, at least
in part, upon the .alpha.-effect nucleophile in the solution and
the protecting groups of the RNA. Appropriate adjustments to the pH
can be made to the solution to accommodate the .alpha.-effect
nucleophile.
The .alpha.-effect nucleophiles can include, but are not limited
to, peroxyanions, hydroxylamine derivatives, hydroximic acid and
derivatives thererof, hydroxamic acid and derivatives thereof,
hydrazine and derivatives thereof, carbazide and derivatives
thereof, semicarbazides and derivatives thereof, and combinations
thereof. The peroxyanion .alpha.-effect nucleophiles can include
compounds such as, but not limited to, hydrogen peroxide and salts
thereof, peracids and salts thereof, perboric acids and salts
thereof, alkylperoxides and salts thereof, hydroperoxides and salts
thereof, butylhydroperoxide and salts thereof, benzylhydroperoxide
and salts thereof, phenylhydroperoxide and salts thereof, perfornic
acid and salts thereof, peracetic acid and salts thereof,
perbenzoic acid and salts thereof, chloroperbenzoic acid and salts
thereof, benzoic acids and salts thereof, substituted perbenzoic
acids and salts thereof, cumene hydroperoxide and salts thereof,
perbutric acid and salts thereof, tertriarylbutylperoxybenzoic acid
and salts thereof, decanediperoxoic acid and salts thereof, and
combinations thereof.
Hydrogen peroxide, salts of hydrogen peroxide, and mixtures of
hydrogen peroxide and performic acid are especially useful.
Hydrogen peroxide, which has a pKa of around 11, is particularly
useful for deprotecting solutions above pH 9.0. Below pH 9.0, there
is not generally a sufficient concentration of peroxyanion to work
as an effective nucleophile. Below pH 9.0 it is especially useful
to use mixtures of hydrogen peroxide and peracids. These peracids
can be preformed and added to the solution, or they can be formed
in situ by the reaction of hydrogen peroxide and the carboxylic
acid or carboxylic acid salt. For example, an equal molar mixture
of hydrogen peroxide and sodium formate can be used at pH
conditions below 9.0 as an effective peroxyanion deprotecting
solution, where hydrogen peroxide alone is not an effective
deprotecting mixture. The utility of peracids tends to be dependent
upon the pKa of the acid and size of molecule. The higher the pKa
of the acid, the more useful as a peroxyanion solution; the larger
the size of the molecule, the less useful. However, it is important
that the pKa of the peracid be lower than the pH of the desired
peroxyanion solution.
The .alpha.-effect nucleophiles typically used in these reactions
are typically strong oxidants; therefore, one should limit the
concentration of the reagent in the deprotecting solution in order
to avoid oxidative side products where undesired. The
.alpha.-effect nucleophiles are typically less than 30% weight/vol
of the solution, more typically between 0.1% and 10% weight/vol of
the solution, and most typically 3% to 7% weight/vol of the
solution. The typical 3% solution of hydrogen peroxide is about 1
molar hydrogen peroxide. A solution of between 1 molar and 2 molar
hydrogen peroxide is especially useful. A typical solution of
hydrogen peroxide and performic acid is an equal molar mixture of
hydrogen peroxide and performic acid, both in the range of 1 to 2
molar. An example of an in situ prepared solution of performic acid
is 2 molar hydrogen peroxide and 2 molar sodium formate buffered at
pH 8.5.
The pKa of the .alpha.-effect nucleophile can be from about 4 to
13, about 4 to 12, about 4 to 11, about 5 to 13, about 5 to 12,
about 5 to 11, about 6 to 13, about 6 to 11, about 7 to 13, about 7
to 12, and about 7 to 11.
It should also be noted that the pKa is a physical constant that is
characteristic of the specific .alpha.-effect nucleophile. Chemical
substitution and solvolysis conditions can be used to raise or
lower the pKa and therefore specifically optimize the conditions of
deprotecting. Appropriate selection of the .alpha.-effect
nucleophile should be made considering the other conditions of the
method and the protecting groups of the RNA. In addition, mixtures
of peroxides and hydroperoxides can be used with molecules to form
peroxyanions in situ.
As an example, a solution of hydrogen peroxide can be used with a
solution of formic acid at pH conditions below 9.0. At pH
conditions less than 9.0, hydrogen peroxide is not significantly
ionized due to its ionization constant of around 11. At pH 7.0
only, about 0.01% of the hydrogen peroxide is in the ionized form
of the .alpha.-effect nucleophile. However, the hydrogen peroxide
can react in situ with the formic acid to form performic acid in a
stable equilibrium. At pH 7.0, the performic acid is significantly
in the ionized form and is an active .alpha.-effect nucleophile.
The advantage of such an approach is that solutions of performic
acid tend to degrade rapidly, and stabilizers need to be added. The
equilibrium that is formed between the hydrogen peroxide solutions
and the formic acid helps stabilize the performic acid such that it
can be used to completely deprotect the RNA prior to degrading.
Performic acid is especially useful in a buffered mixture of
hydrogen peroxide at pH 8.5 because the pKa of performic acid is
approximately 7.1. Peracetic acid is useful at pH 8.5 but less
useful than performic acid because the pKa of peracetic acid is
approximately 8.2. At pH 8.5, peracetic acid is only about 50%
anionic, whereas at pH 8.5, performic acid is more than 90%
anionic.
In general, the pKa for the hydroperoxides is about 8 to 13. The
pKa for hydrogen peroxide is quoted to be about 10 to 12, depending
upon the method of analysis and solvent conditions. The pKa for the
alkylperoxides is about 8 to 14. The pKa for the peracids is about
3 to 9. In embodiments where the peroxyanion is hydroperoxide, the
solution is at pH of about 9 to 11. In embodiments where the
peroxyanion is hydrogen peroxide, the solution is at pH of about 9
to 10.
In embodiments where the peroxyanion is an alkylperoxide, the
solution is at pH of about 8 to 11. In embodiments where the
peroxyanion is a peracid, the solution is at pH of about 6 to 9. In
addition, the peracid has a pKa of about 4 to 10.
In addition, the aqueous buffer solution includes a buffer such as,
but not limited to, tris(hydroxymethyl)aminomethane,
aminomethylpropanol, citric acid, N,N'-bis(2-hydroxyethyl)glycine,
2-[bis(2-hydroxyethyl)amino]-2-(hydroxy-methyl)-1,3-propanediol,
2-(cyclohexylamino)ethane-2-sulfonic acid,
N-2-Hydroxyethyl)piperazine-N'-2-ethane sulfonic acid,
N-(2-hydroxyethyl)piperazine-N'-3-propane sulfonic acid,
morpholinoethane sulfonic acid, morpholinopropane sulfonic acid,
piperazine-N,N'-bis(2-ethane sulfonic acid),
N-tris(hydroxymethyl)methyl-3-aminopropane sulfonic acid,
N-Tris(hydroxymethyl)methyl-2-aminoethane sulfonic acid,
N-tris(hydroxymethyl)methylglycine, and combinations thereof.
2'-Hydroxyl Protecting Groups and Deprotection
Embodiments of the disclosure include nucleotide monomers and
polynucleotide compounds including at least one nucleotide moiety
unit, where the nucleotide monomer and the nucleotide moiety each
include a 2'-hydroxyl protecting group. The nucleotide monomer and
the nucleotide moiety are different, in at least one way, in that
the nucleotide moiety is part of a polynucleotide compound, while
the nucleotide monomer is not part of a polynucleotide compound.
The nucleotide moiety includes a linking moiety that links a
plurality of nucleotide moieties together (and/or to a substrate),
while the nucleotide monomer does not include such a linking
moiety. For the following discussion the structures will be
referred to as "nucleotide monomer", but it is to be understood
that the structures can be nucleotide moieties if a linking group
is included in the structure to interconnect nucleotide moieties in
a polynucleotide compound.
As mentioned above, embodiments of the disclosure can include
nucleotide monomers having a 2'-hydroxyl protecting group. A
variety of 2'-hydroxyl protecting groups have been used for RNA
synthesis. The 2'-hydroxyl protecting groups can be used in
conjunction with other protecting groups (e.g., base protecting
groups and/or phosphorus protecting groups). In an embodiment of
the present disclosure, the 2'-hydroxyl protecting groups can
include, but are not limited to, groups that can be removed with
peroxyanions as well as groups that have been specifically
developed and optimized to be removed by peroxyanions. In addition,
the 2'-hydroxyl protecting groups can include, but are not limited
to, the structures (e.g., structure I) described in further detail
below.
Exemplary 2'-hydroxyl protecting groups include, but are not
limited to: acid-labile protecting groups, nucleophile-labile
protecting groups, fluoride-labile protecting groups and
oxidative-labile protecting groups. These groups are attached to
the 2'-oxygen through a variety of functionalities that include,
but are not limited to, esters, carbonates, thiocarbonates,
carbamates, acetals, thioacetals, carbonates of hemiacetals,
carbonates of thiohemiacetals, orthoesters, thioorthoesters,
carbonates of orthoesters, carbonates of thioorthoesters, silyl,
siloxanes, carbonates and thiocarbonates of silanes, carbonates and
thiocarbonates of siloxanes, silyl protected hemiacetals,
carbonates and thiocarbonates of silyl protected hemiacetals,
carbonates and thiocarbonates of hemiacetals, carbonates and
thiocarbonate of thiohemiacetals, and a variety of substituted
derivatives of any of the previously described functionalities.
The nucleotide monomer can include, but is not limited to, a
structure such as structures I. The following structure illustrates
embodiments that include 2'-hydroxyl protecting groups.
##STR00003##
B can include, but is not limited to, a base and a base including a
protection group.
In addition, the nucleotide monomer can include, but is not limited
to, a structure such as structures II. The following structure
illustrates embodiments that include 2'-hydroxyl protecting
groups.
##STR00004##
For structure I and II, R.sub.1 and R.sub.2 are each independently
selected from a group such as, but not limited to, H, a protecting
group, and
##STR00005## wherein only one of R.sub.1 and R.sub.2 is
##STR00006##
In an embodiment, R.sub.1 and/or R.sub.2 can include a linking
moiety that interconnects the nucleotide moieties in a
polynucleotide or connects to a substrate.
R.sub.3 is a group such as, but not limited to, an alkyl group, an
aryl group, a substituted alkyl, and a substituted aryl group. In
an embodiment, R3 can include a linking moiety that interconnects
the nucleotide moieties in a polynucleotide or connects to a
substrate.
R.sub.4 and R.sub.5 are each independently selected from a group
such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl, and a substituted aryl group. In addition,
R.sub.4 and R.sub.5 can be, optionally, cyclically connected to
each other. In an embodiment, R.sub.4 and/or R.sub.5 can include a
linking moiety that interconnects the nucleotide moieties in a
polynucleotide.
In an embodiment, R1 and R2 may each individually be selected from
one of the following: H, a protecting group, and:
##STR00007##
but where both R1 and R2 are not
##STR00008##
R.sub.3 can include, but is not limited to, an alkyl group, a
substituted alkyl group, an aryl group, and a substituted aryl
group. In an embodiment, R.sub.3 is optionally a linking moiety
that links to another nucleotide moiety of a polynucleotide or
connects to a substrate. Nuc is a nucleotide or polynucleotide.
In another embodiment, R1 and R2 can have the following
structure:
##STR00009##
R' and R'' are each individually a group such as, but not limited
to, H, an alkyl group, an aryl group, a substituted alkyl, a
substituted aryl group. In an embodiment, R' and/or R'' can include
a linking moiety that interconnects the nucleotide moieties in a
polynucleotide or connects to a substrate.
R.sub.3 is a group such as, but not limited to, an alkyl group, an
aryl group, a substituted alkyl, and a substituted aryl group. In
an embodiment, R3 can include a linking moiety that interconnects
the nucleotide moieties in a polynucleotide or connects to a
substrate.
R.sub.4 and R.sub.5 are each independently selected from a group
such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl, and a substituted aryl group. In addition,
R.sub.4 and R.sub.5 can be, optionally, cyclically connected to
each other. In an embodiment, R.sub.4 and/or R.sub.5 can include a
linking moiety that interconnects the nucleotide moieties in a
polynucleotide or connects to a substrate.
2HPG is a 2'-hydroxyl protecting group such as, but not limited to,
one of the groups listed below I, II, III, IVa, IVb, V, VI, VIIa,
VIIb, and VIII:
Group I:
##STR00010## R.sub.6, R.sub.7, and R.sub.8 are each independently
selected from a group such as, but not limited to, an alkyl group,
a substituted alkyl, a substituted alkyl with an
electron-withdrawing group, a substituted aryl group with an
electron-withdrawing group, a group that is converted into an
electron withdrawing group by oxidation (e.g., via peroxyanions),
an aryl group, a substituted aryl group, where R.sub.6, R.sub.7,
and R.sub.8 are not each a methyl group, where R.sub.6, R.sub.7,
and R.sub.8 are not each an unsubstituted alkyl, and where R.sub.6,
R.sub.7, and R.sub.8 are optionally cyclically connected to each
other.
Group II:
##STR00011## R.sub.6, R.sub.7, and R.sub.8 are each independently
selected from a group such as, but not limited to, an alkyl group,
an aryl group, a substituted alkyl group, and a substituted aryl
group, and R.sub.6, R.sub.7, and R.sub.8 are optionally cyclically
connected to each other.
Group III:
##STR00012## R.sub.9 is a group such as, but not limited to, an
alkyl group, an aryl group, a substituted alkyl with an
electron-withdrawing group, and a substituted aryl group with an
electron-withdrawing group, where R.sub.10 and R'.sub.10 are each
independently selected from a group such as, but not limited to, H,
an alkyl group, and a substituted alkyl with an
electron-withdrawing group.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
SG can include one or more groups, where each group is attached to
one of the carbons in the carbon ring. SG is a group such as, but
not limited to, H, an alkyl group, an aryl group, a substituted
alkyl with an electron-donating group, and a substituted aryl group
with an electron-donating group.
Group IVa and IVb:
##STR00013## R.sub.6 and R.sub.7 are independently selected from a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group, R.sub.6
and R.sub.7 are optionally cyclically connected to each other or to
the phenol and where R.sub.11 is a group such as, but not limited
to, an ester protecting group and silyl protecting group.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
R.sub.12 can include one or more groups, where each group is
attached to one of the carbons in the carbon ring. R.sub.12 is a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group.
Group V:
##STR00014## R.sub.6 and R.sub.7 are independently selected from a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group, where
R.sub.6 and R.sub.7 are optionally cyclically connected to each
other and where R.sub.13 is an amide-protecting group.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
R.sub.12 can include one or more groups, where each group is
attached to one of the carbons in the carbon ring. R.sub.12 is a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group.
Group VI:
##STR00015## R.sub.6 and R.sub.7 are independently selected from a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group, and
R.sub.6 and R.sub.7 are optionally cyclically connected to each
other.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
SG and SR.sub.14 can each include one or more groups, where each
group is attached to one of the carbons in the carbon ring.
SR.sub.14 is one or more thioether independently selected from a
thioalkyl group, a thioaryl group, a substituted thioalkyl group,
and a substituted thioaryl group. In an embodiment, R.sub.14
includes, but is not limited to, an alkyl group, an aryl group, a
substituted alkyl group, and a substituted aryl group. SG is a
group such as, but not limited to, H, an alkyl group, an aryl
group, a substituted alkyl with an electron-donating group, a
substituted aryl group with an electron-donating group, and an
electron-donating group in the ortho or para position to the
thioether SR.sub.14.
Groups VIIa and VIIb:
##STR00016## R.sub.6 and R.sub.7 are independently selected from a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group, where
R.sub.6 and R.sub.7 are optionally cyclically connected to each
other or to the phenol and where R.sub.11 is a group such as, but
not limited to, an ester protecting group and silyl protecting
group.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
R.sub.12 can include one or more groups, where each group is
attached to one of the carbons in the carbon ring. R.sub.12 is a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group.
Group VIII:
##STR00017## R.sub.6 and R.sub.7 are independently selected from a
group such as, but not limited to, an alkyl group, an aryl group, a
substituted alkyl with an electron-withdrawing group, and a
substituted aryl group with an electron-withdrawing group, where
and R.sub.6 and R.sub.7 are optionally cyclically connected to each
other.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
SG and SR.sub.14 can each include one or more groups, where each
group is attached to one of the carbons in the carbon ring.
SR.sub.14 is one or more thioethers independently selected from a
thioalkyl group, a thioaryl group, a substituted thioalkyl group,
and a substituted thioaryl group. In an embodiment R.sub.14 can
include, but is not limited to, an alkyl group, an aryl group, a
substituted alkyl group, and a substituted aryl group. SG is a
group such as, but not limited to, H, an alkyl group, an aryl
group, a substituted alkyl with an electron-donating group, a
substituted aryl group with an electron-donating group, and an
electron-donating group in the ortho or para position to the
thioether SR.sub.14.
It should be noted that some properties may be considered when
selecting a 2'-hydroxyl protecting group and these include, but are
not limited to, whether the groups has specificity for introduction
on the 2'-hydroxyl (regioselectivity), whether the group does not
lead to isomerisation products, whether the group does not
compromise coupling yield, and whether the group can be easily
removed remove without degrading the RNA.
Regioselective Introduction
The 2'-hydroxyl protecting groups can be placed on the molecule in
either a regioselective manner, a non-regioselective manner, or a
regiospecific manner. In a regioselective manner, the protecting
group is setup by various conditions and circumstances in the
chemical reaction to react only with the hydroxyl region that is
desired, in this case the 2'-hydroxyl.
An example of a regioselective protecting group is the
dimethoxytrityl protecting group [Schaller, H.; Weimann, G.; Lorch,
B.; Khorana, H. G., J. Am. Chem. Soc. 1963, 85, 3821-3827, which is
incorporated herein by reference]. The dimethoxytrityl protecting
groups will regioselectively react with only the 5'-hydroxyl. This
protecting group is regioselective because the rate of reaction of
dimethoxytrityl chloride with the 5'-hydroxyl is at least 100 times
faster than with either the 2' or 3' hydroxyls. The 2'-hydroxyl can
then be regioselectively or non-regioselectively reacted with the
desired 2'-protective group. In a regioselective manner, the
desired 2'-hydroxyl protecting group is typically reacted with
5'-protected nucleosides using various asymmetric Lewis Acid
catalysts. Although it is possible to find conditions and reagents
that give some level of regioselectivity, complete regioselectivity
is difficult to achieve using this method, and this approach tends
to produce a mixture of structural isomers. The desired
2'-protected nucleoside must then be separated from the undesired
3'-protected nucleoside or the bis-2',3'-protected nucleoside
chromatographically. Typically this approach is used to enrich the
amount of the desired 2'-protected nucleoside produced in order to
decrease the cost of obtaining the correct 2'-protected nucleoside.
Rarely has it been demonstrated that this approach achieves
complete regioselectivity. Often differential regioselectivity is
demonstrated for the different heterobase containing nucleosides.
Complete regioselectivity may be obtained with one or more
nucleosides, but usually one or more of the nucleosides show little
or no regioselectivity resulting, in low synthetic yield of the
desired monomer.
##STR00018##
It is therefore most often preferable to utilize a regiospecific
approach to protection of the 2'-hydroxyl. In a regiospecific
manner a nucleoside, that can contain a heterobase protecting
group, is typically then reacted on the 5' and 3' hydroxyls with an
additional blocking group that transiently protects both positions
simultaneously. An example of such a blocking group is the
1,3-tetraisopropyl disiloxane [Markiewicz W. T., J. Chem Research
(S) 1979 24-25)]. The desired 2'-hydroxyl protecting group is then
reacted specifically with the 2'-hydroxyl.
##STR00019## This is usually the most preferred method of
protecting of the 2'-hydroxyl. However, there are several examples
whereby the desired 2'-hydroxyl protecting group is incompatible
with the blocking groups needed to transiently protect the 3' and
5' hydroxyls. As an example, the 1,3-tetraisopropyl disiloxane is a
transient blocking group that is used to block the 5' and 3'
hydroxyls simultaneously, allowing the 2'-hydroxyl to then be
regioselectively reacted. The 1,3-tetraisopropyl disiloxane group
is subsequently removed using a solution of fluoride ions. Due to
the required deprotection conditions of the 1,3-tetraisopropyl
disiloxane group, 2'-protecting groups that contain silyl or
silicon atoms are not compatible with this regioselective approach
[Beigelman, L, and Serebryany, V, Nucleosides, Nucleotides, and
Nucleic Acids, 2003, Vol 22, 1007-1009, which is incorporated
herein by reference]. Isomerization
Additionally, the stability of the 2'-hydroxyl protecting group to
migration is an important factor that limits the scope and the
usefulness of a variety of protecting group classes or species
within a class of protecting group. Because the 2'-hydroxyl moiety
is "cis" to the 3'-hydroxyl it can promote the isomerization of
many classes of protecting groups from the 2'-hydroxyl to the
3'-hydroxyl and vise versa. Often this isomerization reaction is
catalyzed by the addition of weak acids or weak bases. This becomes
problematic for silica gel purification, since silica gel is weakly
acidic and therefore protecting groups that are susceptible to acid
catalyzed isomerization are difficult to purify by column
chromatography. A similar reaction can occur during formation of
the 3'-phosphoramidite. There are two basic methods for the
formation of phosphoramidites. The first is through the use of a
chlorophosphine [Beaucage, S. L.; Caruthers, M. H. Tetrahedron
Lett. 1981, 22, 1859-1862, which is incorporated herein by
reference]. The use of a chlorophosphine reagent requires exposure
of the nucleoside to a weak base like triethyl amine or
diusopropylethyl amine. Protecting groups that are susceptible to
base catalyzed isomerization are difficult to phosphitylate by this
method as shown below.
##STR00020##
Alternatively, phosphoramidites can be prepared by the
"bis-dialkylaminophosphine" method [Barone A D, Tang J Y, Caruthers
M H, Nucleic Acids Res., 1984, 12(10), 4051-61, which is
incorporated herein by reference]. This method uses a weak acid
such as tetrazole of the amine salt of tetrazole to catalyze the
reaction of the bis-dialkylaminophosphine with the 3'-hydroxyl.
##STR00021##
Protecting groups that undergo isomerization under these conditions
can be difficult to phosphitylate forming the 3'-phosphoramidite.
It is therefore preferable to utilize protecting group classes or
species within a protecting group that are not susceptible to
isomerization under either weak acid or weak base conditions. A
clear example of a protecting group that can isomerize under weak
acid and weak base conditions is the silyl TBDMS. Although
unidentified by the authors, the original method published for the
use of this protecting group for the 2'-hydroxyl [Usman N, Ogilvie
K K, Jiang M Y, Cedergren R J, J. Am. Chem. Soc., 1987, 109(25),
7845-7854] gave only isomerized mixtures of the phosphoramidite
monomers and as a result it was necessary to develop highly
specialized techniques for preparation and purification to limit
the amount of isomerized products in the phosphoramidite monomers.
Another protecting group class that is particularly susceptible to
isomerize is the ester class. The isomerization of esters can be
inhibited by the use of large bulky alkyl or aryl groups. Therefore
large bulky esters are particularly preferred as 2'-protecting
groups over smaller groups like acetyl.
Carbonates and Thiocarbonates:
Carbonates and thiocarbonates do not undergo isomerization from the
2'hydroxyl to the 3' hydroxyl and vice versa. The chemical
transition that would lead to isomerization always results in the
formation of 2',3'-cyclic carbonates, which are the
thermodynamically favored product. The formation of 2',3'-cyclic
carbonates under acidic or basic conditions can be quite facile and
lead to low yields of the desired 2'-protected product.
##STR00022##
However, tertiary carbonates as shown by Losse and tertiary
thiocarbonates as discovered in the present disclosure are
resistant to formation of 2'-3' cyclic carbonates and are
particularly useful as 2'-protection [Losse G, Suptitz G, Krusche,
K, Journal fur Praktische Chemie, 1992, 334(6), 531-532, which is
incorporated herein by reference].
##STR00023## Carbonates are particularly useful since, even if the
cyclic carbonate is formed at some percentage during the synthesis
of the monomers, the cyclic carbonate does not produce a reactive
monomer (3'-isomer) with the protecting group on the 3'-hydroxyl.
This is especially important to ensure only formation of
5'-3'-linked RNA molecules. However, all tertiary carbonates are
not useful for the synthesis of RNA molecules. Tertiary
alkylcarbonates can be quite stable to nucleophiles and resistant
to cleavage by peroxyanions. The tertiary butyloxycarbonyl group
was previously described for the protection of the 2'-hydroxyl for
solid-phase RNA synthesis. The resistance of this group to removal
by a variety of mild pH conditions demonstrated the unsuitability
of this group for RNA synthesis [Losse G, Naumann, W, Winkler, A,
Suptitz G, Journal fur Praktische Chemie, 1994, 336(3), 233-236,
which is incorporated herein by reference]. In order to remove this
protecting group the authors needed to employ a high concentration
(4 molar) of hydrochloric acid in dioxane. It has also been
demonstrated that this protecting group was quite stable to the
mildly basic but highly nucleophillic conditions of peroxyanion
cleavage using 2 molar hydrogen peroxide at pH 9.5. Therefore, it
was found that the carbonate moiety should be modified to make the
group more labile to nucleophiles and specifically to peroxyanion
nucleophiles. This can be accomplished in at least two methods. The
first is the addition of electron withdrawing groups to the alkyl
or aryl substituents that can then affect the stability of the
cleavage products formed as shown below.
##STR00024##
An example of adding an electron-withdrawing group to a tertiary
carbonate includes the example of using one or more trifluoromethyl
groups to replace one or more of the methyl groups on the tertiary
butyloxycarbonyl group as shown below.
##STR00025##
A particularly useful method of adding an electron-withdrawing
group to a tertiary carbonate (see below) is to replace one or more
of the methyl groups on the tertiary butyloxycarbonyl group with a
substituted benzene ring and to have the benzene ring substituted
with one or more electron withdrawing groups.
##STR00026##
Electron-withdrawing groups can either exist as part of the
protecting group prior to cleavage by peroxyanions, or be created
by the deprotection reaction. A particularly useful approach
illustrated below is to use substituents on the alkyl or aryl
groups that are electron-donating and to have those substituents
chemically converted to electron-withdrawing groups in the solution
of peroxyanion. The electron donating effect helps stabilize the
protecting group during the oligomerization process, and then this
effect is reversed during cleavage of the protecting group to
produce an electron-withdrawing group that stabilizes the products
from the cleavage reaction and then aids the facile removal under
mild pH conditions.
##STR00027##
An example of adding an electron-withdrawing group to a tertiary
carbonate is the example of using one or more thiomethyl ethers to
replace one or more of the methyl groups on the tertiary
butyloxycarbonyl group. Thiomethylethers are typically stable to
oxidation in the presence of the dilute iodine solutions that are
used for oxidation of the phosphite triester to phosphate triester
during the routine phosphoramidite DNA or RNA synthesis cycle.
However, in the presence of dilute solutions of hydroperoxides,
peracids, or combinations of hydroperoxides and peracids, the
thiomethylether is rapidly oxidized to the corresponding sulfone
(as shown below). The methyl sulfone is a strongly
electron-withdrawing group that stabilizes the products from the
cleavage reaction and then aids the facile removal of the under
mild pH conditions.
##STR00028##
A particularly convenient method of adding a moiety to a tertiary
carbonate that can then be chemically converted to an
electron-withdrawing group by peroxyanions is the direct
substitution of a sulfur atom for an oxygen atom in the bridging
position to form a thiocarbonate (see below).
##STR00029##
From data on the cleavage and oxidation of thiocarbonates, it
appears that the sulfur is not oxidized prior to the cleavage.
Tertiary butylthiocarbonyl protected nucleosides exposed to 1 to 2
molar solutions of hydrogen peroxide at pH 6.0 do not generate
sulfur oxidation products or cleavage of the thiocarbonate group,
even after a 24-hour exposure. However, if the pH is raised to 9.5,
the cleavage of the thiocarbonate is group is complete in
approximately 10 minutes. The data suggests that once the cleavage
reaction occurs, using a nucleophillic solution of hydrogen
peroxide, the resulting mercaptan is rapidly oxidized to the
sulfonate, making the reaction rapid and irreversible.
The second method for making the group more labile to nucleophiles,
and specifically to peroxyanion nucleophiles, is to incorporate a
moiety or moieties that enhances removal of the protecting group by
a fragmentation process that creates thermodynamically stabile
fragments illustrated below. This stabilizes the products of the
cleavage reaction promoting facile removal of protecting groups
under mild pH conditions.
##STR00030##
Examples of such protecting groups are the tertiary carbonates of
thiohemiacetals. Shown below is an example of 2'-hydroxyl
protection using 2-thiomethylpropane-2-oxycarbonyl. Upon cleavage
by peroxyanion nucleophiles the protecting group is fragmented into
the highly thermodynamically stable products of acetone and
methanesulfonate.
##STR00031##
Oxidizable 2'-Hydorxyl Protecting Groups
Another embodiment includes nucleotide monomers and polynucleotides
that include nucleotide moieties, where each of the nucleotide
monomers and the nucleotide moieties include, but are not limited
to, a protecting group (e.g., group I, group II, group VI, group
VIIa, group VIIb, group VIII,) that can undergo oxidative
transformations to enhance the lability of the protecting group
towards the nucleophilic removal. The oxidative transformation can
occur prior to the cleavage, typically generating an electron
withdrawing species on the protecting group that did not exist
prior to the oxidation reaction or after the cleavage reaction to
generate a species that cannot participate in an equilibrium
reaction to reform the protecting group. An example of a species
that undergoes an oxidative transformation to produce an electron
withdrawing species that makes the protecting group more labile is
the 2-methylthiobenzoyl group. The 2-methylthiobenzoyl group has
similar stability to benzoyl or 2-methylbenzoyl. However, upon
exposure to a buffered 6% hydrogen peroxide solution at pH 9.5, the
2-methylthio moiety is oxidized to a methylsulfone, and the
methylsulfone derivative is significantly more labile to
nucleophiles than benzoyl or 2-methylbenzoyl. The resulting
2-methylsulfonbenzoyl is cleaved rapidly by the hydroperoxide
anion. An example of an oxidative transformation that occurs after
the cleavage of the protecting group is the t-butylthiocarbonate.
The sulfur atom on the t-butylthiocarbonate is not oxidized when
exposed to 6% hydrogen peroxide at pH 5.0, and its lability towards
nucleophile is similar to t-butylcarbonate. However, using 6%
hydrogen peroxide at pH 9.5, rapidly generates the t-butylsulfonic
acid and the removal of the protecting group is quite facile. This
is in stark contrast to the use of t-butyl carbonate as a
2'-hydroxyl protecting group, which was shown to be convenient to
introduce onto the 2'-hydroxyl of a nucleoside and resistant to the
formation of the 2'-3'-cyclic carbonate. However difficult, if not
impossible, to remove this protecting group without destroying the
desired RNA products. The t-butyl carbonate was shown to be very
resistant to nucleophiles and was removed using 5 molar solutions
of hydrochloric acid.
Heterocyclic Base Protecting Groups
Embodiments of the disclosure include nucleotide monomers and
polynucleotide compounds including at least one nucleotide moiety
unit, where the nucleotide monomer and the nucleotide moiety each
include a heterocyclic base protecting group. The nucleotide
monomer and the nucleotide moiety are different, in at least one
way, in that the nucleotide moiety is part of a polynucleotide
compound, while the nucleotide monomer is not part of a
polynucleotide compound. The nucleotide moiety includes a linking
moiety that links a plurality of nucleotide moieties, while the
nucleotide monomer does not include such a linking moiety. For the
following discussion the structures may be referred to as
"nucleotide monomer", but it is to be understood that the
structures can be nucleotide moieties if a linking group is
included in the structure to interconnect nucleotide moieties in a
polynucleotide compound.
Exocyclic amines of the aglycone need to be protected during
polynucleotide synthesis. Typically, the following exocyclic amines
N-4 of cytidine, N-6 of adenosine, and N-2 of guanosine require,
protection during RNA synthesis. Sometimes, the imino group can
require additional protection. In the case of imino protection, the
N-3 or O-4 of uridine and the N-1 or O-6 of guanosine can require a
protecting group. In most cases, the protecting groups utilized for
exocyclic amines can also be applied to the protection of the imino
group through a screening process.
Embodiments of the disclosure can include nucleotide monomers and
polynucleotide compounds (e.g., ribonucleotide compounds) including
nucleotide monomers and moieties having 2'-hydroxyl protecting
groups as described herein as well as heterocyclic base protecting
groups. The polynucleotide can include nucleotide monomers and
moieties having structures XX through XXII. Embodiments of the
position of the base protecting groups (APG) are shown on
structures XX through XXIII:
##STR00032##
The APGs can include, but are not limited to, base protecting
groups that are removed under a same set of conditions as the 2HPG
(e.g., in peroxyanions solutions). For example, the APG and the
2HPG can be removed in a single step when exposed to a peroxyanion
solution. For example, APG can be acetyl, chloroacetyl,
dicholoracetyl, trichloroacetyl, fluoroacetyl, difluoroacetyl,
trifluoroacetyl, nitroacetyl, propionyl, n-butyryl, i-butyryl,
n-pentanoyl, i-pentanoyl, t-pentanoyl, phenoxyacteyl,
2-chlorophenoxyacetyl, t-butyl-phenoxyacetyl, methylthioacetyl,
phenylthioacetyl, 2-chlorophenylthioacetyl,
3-chlorophenylthioacetyl, 4-chlorophenylthioacetyl,
t-butyl-phenylthioacetyl, benzoyl, 2-nitrobenzoyl, 3-nitrobenzoyl,
4-nitrobenzoyl, 2-chlorobenzoyl, 3-chlorobenzoyl, 4-chlorobenzoyl,
2,4-di-chlorobenzoyl, 2-fluorobenzoyl, 3-fluorobenzoyl,
4-fluorobenzoyl, 2-trifluoromethylbenzoyl,
3-trifluoromethylbenzoyl, 4-trifluoromethylbenzoyl,
benzyloxycarbonyl, and the like.
The APGs can include, but are not limited to, base protecting
groups that are removed under a different set of conditions as the
2HPG. These groups that can not be removed by peroxyanion depend
strongly on the base (A, G, or C) they are protecting. Most of the
amidine protecting groups such as dirnethylformamidine,
dibutylformamidine, dimethylacetamidine, diethylacetamidine are
stable to peroxyanions.
R1 and R2 are each individually selected from one of the following:
H, a protecting group, and
##STR00033## but R1 and R2 are both not:
##STR00034##
R1 and R2 can also be a linking moiety that interconnects a
plurality of nucleotide moieties in a polynucleotide or connects to
a substrate.
R.sub.3 can include, but is not limited to, an alkyl group, a
substituted alkyl group, an aryl group, and a substituted aryl
group. R.sub.3 can optionally be a linking moiety that links to
another nucleotide moiety of a polynucleotide or connects to a
substrate. R.sub.4 and R.sub.5 can each independently include, but
are not limited to, an alkyl group, a substituted alkyl group, an
aryl group, a substituted aryl group, a cyclic alkyl, a substituted
cyclic alkyl, a heterocycle, a substituted heterocycle, an aryl
group, and a substituted aryl group. In an embodiment, R.sub.3 can
include a linking moiety that links to another nucleotide moiety of
the polynucleotide or connects to a substrate.
X can include, but is not limited to, H, OH, halogen, an alkoxy
group, a substituted alkoxy group, an aryloxy group, a substituted
aryloxy group, an amino group, a substituted amino group, a cyano
group, an azido group, a sulfonic acid group, a protecting group,
and an O-protecting group.
The APGs can include, but are not limited to, exocyclic amino
protecting groups. In addition, the APG can include, but are not
limited to, base protecting groups that are removed under a same
set of conditions as the 2'-hydroxyl protecting groups (e.g., in
peroxyanions solutions). For example, the APG and the 2'-hydroxyl
protecting groups can be removed in a single step when exposed to a
peroxyanion solution.
In an embodiment, the APG is a moiety that can undergo oxidative
transformations in peroxyanion solutions (as discussed in more
detail below) to enhance the lability of the protecting group
towards nucleophillic removal. These oxidative transformations can
occur prior to the cleavage, typically generating an electron
withdrawing species on the protecting group that did not exist
prior to the oxidation reaction or after the cleavage reaction to
generate a species that cannot participate in an equilibrium
reaction to reform the protecting group.
The 2-methylthiobenzoyl group is an example of a species that
undergoes an oxidative transformation to produce and electron
withdrawing species that makes the protecting group more labile.
The 2-methylthiobenzoyl group has similar stability than benzoyl or
2-methylbenzoyl. However, upon exposure to a buffered 6% hydrogen
peroxide solution at about pH 9.5, the 2-methylthio moiety is
oxidized to a methylsulfone, and the methylsulfone derivative is
significantly more labile to nucleophiles than benzoyl or
2-methylbenzoyl. The resulting 2-methylsulfonbenzoyl is cleaved
rapidly by the hydroperoxide anion.
The t-butylthiocarbamaie group is an example of an oxidative
transformation that occurs after the cleavage of the protecting
group. The sulfur atom on the t-butylthiocarbamate is not oxidized
when exposed to 6% hydrogen peroxide at pH 5.0, and the lability to
nucleophile is similar to t-butylcarbamate. However, using 6%
hydrogen peroxide at about pH 9.5 rapidly renders the
t-butylsulfonic acid, and the removal of the protecting group quite
facile.
It should also be noted that as for the protection of heterobase
protecting groups, a particularly useful set of the 2'-hydroxyl
protecting group includes a moiety that can undergo oxidative
transformations in peroxyanion solutions to enhance the lability of
the protecting group towards nucleophillic removal, or a moiety
that can be cleaved in peroxyanion solutions thus be deprotected
simultaneoulsy with the heterobase protecting groups in one single
step (one pot reaction). These 2'-hydroxyl protecting groups
include, but are not limited to, an ester protecting group, a
carbonate protecting group, a thiocarbonate protecting group, and a
carbamate protecting group.
The APGs can include, but are not limited to, base protecting
groups such as those having the following structures:
##STR00035## ##STR00036##
It should be noted that Q is an atom such as, but not limited to,
sulfur (S) and oxygen (O), and that R is a group such as, but not
limited to, an alkyl group, a substituted alkyl group, an aryl
group, and a substituted aryl group. R' and R'' are each
independently selected from a group such as, but not limited to, a
halogen, an alkyl group, a substituted alkyl group, an aryl group,
and a substituted aryl group. R.sub.15 is a group such as, but not
limited to, an alkyl group, an aryl group, a substituted alkyl, and
a substituted aryl group.
It should be noted that bonds (e.g., indicated by lines) that are
directed into the center of a ring structure (e.g., benzene ring)
mean that the bond can be to any one of the carbons of the ring
that are only bonded to a hydrogen and another carbon of the ring.
R.sub.16 can include one or more groups, where each group is
attached to one of the carbons in the carbon ring. Each R.sub.16 is
independently a group such as, but not limited to, H, a halogen, a
hydroxyl group, an alkoxy group, a substituted alkoxy group, an
aryloxy group, a substituted aryloxy group, an amino group, a
substituted amino group, a nitro group, a nitrile group, an alkyl
group, an aryl group, a substituted alkyl, and a substituted aryl
group. In an embodiment, when there is more than one R.sub.16
(e.g., multiple R.sub.16's bonded to different carbons on the
carbon ring), then two or more of R.sub.16 are optionally
cyclically connected to each other. R.sub.17, R.sub.18, and
R.sub.19, are each independently a group such as, but not limited
to, H, an alkyl group, an aryl group, a substituted alkyl, and a
substituted aryl group. In an embodiment, two or three of R.sub.17,
R.sub.18, and R.sub.19 can be cyclically connected to each
other.
In another embodiment, the nucleotide polymer can include, but is
not limited to, a nucleotide polymer that includes at least one
structure such as those shown in structures I through III above.
Embodiments of the position of the base protecting groups (APG) on
the bases are shown on structures XX through XXII above.
In an embodiment, it should be noted that R1 and R2 may each
individually be selected from one of the following: H, a protecting
group, and:
##STR00037##
but where both R1 and R2 are not
##STR00038##
R.sub.3 can include, but is not limited to, an alkyl group, a
substituted alkyl group, an aryl group, and a substituted aryl
group. R.sub.3 can be a linking moiety that links to another
nucleotide moiety of a polynucleotide. Nuc is a nucleotide or
polynucleotide.
The APGs can include, but are not limited to, base protecting
groups that are removed under a different set of conditions than
the 2'-hydroxyl protecting groups, for example wherein the
2'-hydroxyl protecting groups include, but are not limited to,
TBDMS, TOM, ACE, acetals such as THP, and derivatives of acetals
(Ctmp and the like).
In addition, the APGs can include, but are not limited to, base
protecting groups such as acetyl, chloroacetyl, dicholoracetyl,
trichloroacetyl, fluoroacetyl, difluoroacetyl, trifluoroacetyl,
nitroacetyl, propionyl, n-butyryl, i-butyryl, n-pentanoyl,
i-pentanoyl, t-pentanoyl, phenoxyacteyl, 2-chlorophenoxyacetyl,
t-butyl-phenoxyacetyl, methylthioacetyl, phenylthioacetyl,
2-chlorophenylthioacetyl, 3-chlorophenylthioacetyl,
4-chlorophenylthioacetyl, t-butyl-phenylthioacetyl,
benzyloxycarbonyl, (9-fluoroenyl)-methoxycarbonyl (Fmoc),
2-nitrophenylsulfenyl, 4-nitrophenylethylcarbonyl,
4-nitrophenylethoxycarbonyl, diphenylcarbamoyl,
morpholinocarbamoyl, dialkylformamidines, succinyl, phthaloyl,
benzoyl, 4-trifluoromethylbenzoyl, 2-methylbenzoyl,
3-methylbenzoyl, 4-methylbenzoyl, 2,4-dimethylbenzoyl,
2,6-dimethylbenzoyl, 2,4,6-trimethylbenzoyl, 2-methoxybenzoyl,
3-methoxybenzoyl, 4-methoxybenzoyl, 2,4-dimethoxybenzoyl,
2,6-dimethoxybenzoyl, 2,4,6-trimethoxybenzoyl, 2-methylthiobenzoyl,
3-methylthiobenzoyl, 4-methylthiobenzoyl, 2,4-dimethylthiobenzoyl,
2,6-dimethylthiobenzoyl, 2,4,6-trimethylthiobenzoyl,
2-chlorobenzoyl, 3-chlorobenzoyl, 4-chlorobenzoyl,
2,4-dichlorobenzoyl, 2,6-dicholorbenzoyl, 2-fluorobenzoyl,
3-fluorobenzoyl, 4-fluorobenzoyl, 2,4-difluorobenzoyl,
2,6-difluorobenzoyl, 2,5-difluorobenzoyl, 3,5-difluorobenzoyl,
2-trifluoromethylbenzoyl, 3-trifluoromethylbenzoyl,
2,4-trifluoromethylbenzoyl, 2,6-trifluoromethylbenzoyl,
2,5-trifluoromethylbenzoyl, 3,5-trifluoromethylbenzoyl,
2-nitrobenzoyl, 3-nitrobenzoyl, 4-nitrobenzoyl, (3-methoxy
4-phenoxy)benzoyl, (triphenyl)silylethyleneoxycarbonyl,
(diphenylmethyl)silylethyleneoxycarbonyl,
(phenyldimethyl)silylethyleneoxycarbonyl,
(trimethyl)silylethyleneoxycarbonyl,
(triphenyl)silyl(2,2-dimethyl)ethyleneoxycarbonyl,
(diphenylmethyl)silyl[(2,2-dimethyl)ethylene]oxycarbonyl,
phenyldimethylsilyl[(2,2-dimethyl)ethylene]oxycarbonyl,
trimethylsilyl[(2,2-dimethyl)ethylene]oxycarbonyl,
methyloxycarbonyl, ethyloxycarbonyl, propyloxycarbonyl,
isopropyloxycarbonyl, butyloxycarbonyl, isobutyloxycarbonyl,
t-butyloxycarbonyl, phenyloxycarbonyl, benzyloxycarbonyl,
methylthiocarbonyl, ethylthiocarbonyl, propylthiocarbonyl,
isopropylthiocarbonyl, butylthiocarbonyl, isobutylthiocarbonyl,
t-butylthiocarbonyl, phenylthiocarbonyl, benzylthiocarbonyl,
methyloxymethyleneoxycarbonyl, methylthiomethylene-oxycarbonyl,
phenyloxymethylene-oxycarbonyl, phenylthiomethyleneoxycarbonyl,
methyloxy(methyl)methyleneoxycarbonyl,
methylthio(methyl)methyleneoxycarbonyl,
methyloxy(dimethyl)methyleneoxycarbonyl,
methylthio(dimethyl)methyleneoxycarbonyl,
phenyloxy(methyl)methyleneoxycarbonyl,
phenylthio(methyl)methyleneoxycarbonyl,
phenyloxy(dimethyl)methyleneoxycarbonyl,
phenylthio(dimethyl)methyleneoxycarbonyl, and substituted
derivatives of any of these previously described groups.
It should also be noted that as for the protection of the
2'-hydroxyl group, a particularly useful set of heterobase
protecting groups is a moiety that can undergo oxidative
transformations in peroxyanion solutions (as discussed in more
detail below) to enhance the lability of the protecting group
towards nucleophilic removal. These oxidative transformations can
occur prior to the cleavage, typically generating an electron
withdrawing species on the protecting group that did not exist
prior to the oxidation reaction or after the cleavage reaction to
generate a species that cannot participate in an equilibrium
reaction to reform the protecting group. An example of a species
that undergoes an oxidative transformation to produce an electron
withdrawing species that makes the protecting group more labile is
the 2-methylthiobenzoyl group. The 2-methylthiobenzoyl group has
similar stability to benzoyl or 2-methylbenzoyl. However, upon
exposure to a buffered 6% hydrogen peroxide solution at pH 9.5, the
2-methylthio moiety is oxidized to a methylsulfone, and the
methylsulfone derivative is significantly more labile to
nucleophiles than benzoyl or 2-methylbenzoyl. The resulting
2-methylsulfonbenzoyl is cleaved rapidly by the hydroperoxide
anion. An example of an oxidative transformation that occurs after
the cleavage of the protecting group is the t-butylthiocarbamate.
The sulfur atom on the t-butylthiocarbamate is not oxidized when
exposed to 6% hydrogen peroxide at pH 5.0, and the lability to
nucleophiles is similar to t-butylcarbamate. However using 6%
hydrogen peroxide at pH 9.5, rapidly generates the t-butylsulfonic
acid and the removal of the protecting group is quite facile.
In an embodiment, the APGs can include, but are not limited to,
base protecting groups that are removed under a same set of
conditions as the 2HPG (e.g., in peroxyanions solutions). For
example, the APG and the 2HPG can be removed in a single step when
exposed to a peroxyanion solution. For example, APG can be acetyl,
chloroacetyl, dicholoracetyl, trichloroacetyl, fluoroacetyl,
difluoroacetyl, trifluoroacetyl, nitroacetyl, propionyl, n-butyryl,
i-butyryl, n-pentanoyl, i-pentanoyl, t-pentanoyl, phenoxyacteyl,
2-chlorophenoxyacetyl, t-butyl-phenoxyacetyl, methylthioacetyl,
phenylthioacetyl, 2-chlorophenylthioacetyl,
3-chlorophenylthioacetyl, 4-chlorophenylthioacetyl,
t-butyl-phenylthioacetyl, benzoyl, 2-nitrobenzoyl, 3-nitrobenzoyl,
4-nitrobenzoyl, 2-chlorobenzoyl, 3-chlorobenzoyl, 4-chlorobenzoyl,
2,4-di-chlorobenzoyl, 2-fluorobenzoyl, 3-fluorobenzoyl,
4-fluorobenzoyl, 2-trifluoromethylbenzoyl,
3-trifluoromethylbenzoyl, 4-trifluoromethylbenzoyl,
benzyloxycarbonyl and the like.
In an embodiment, the APGs can include, but are not limited to,
base protecting groups that are removed under a different set of
conditions as the 2HPG. These groups that can not be removed by
peroxyanion depend strongly on the base (A, G or C) they are
protecting. Most of the amidine protecting groups such as
dimethylformamidine, dibutylformamidine, dimethylacetamidine,
diethylacetamidine are stable to peroxyanions.
Substrates for Solid Phase Synthesis
The polynucleotides (one or more units) can be attached to suitable
substrates that may have a variety of forms and compositions. The
substrates may derive from naturally occurring materials, naturally
occurring materials that have been synthetically modified, or
synthetic materials. Examples of suitable support materials
include, but are not limited to, nitrocellulose, glasses, silicas,
teflons, and metals (e.g., gold, platinum, and the like). Suitable
materials also include polymeric materials, including plastics (for
example, polytetrafluoroethylene, polypropylene, polystyrene,
polycarbonate, and blends thereof, and the like), polysaccharides
such as agarose (e.g., that available commercially as
Sepharose.RTM., from Pharmacia) and dextran (e.g., those available
commercially under the tradenames Sephadex.RTM. and Sephacyl.RTM.,
also from Pharmacia), polyacrylamides, polystyrenes, polyvinyl
alcohols, copolymers of hydroxyethyl methacrylate and methyl
methacrylate, and the like.
One advantage of using .alpha.-effect nucleophiles is that unlike
methods using fluoride-based solutions for the final deprotection
of RNA, the .alpha.-effect nucleophiles are compatible with either
polymeric or silica substrates. In this regard, silica substrates
can be used since they are less expensive than polymeric
substrates.
In contrast, fluoride ion final deprotection conditions attack the
silica substrate in a similar manner as attacks the silicon
protecting groups it is attempting to remove. As a result, the
silica substrate can be dissolved or partially dissolved, giving a
significant amount of fluorosilicate impurities that are difficult
to remove. Also, the attack on the substrate decreases the
effective concentration of the fluoride reagent used for
deprotection, requiring longer deprotection times and higher
concentrations of fluoride reagent. As a result, the use of
fluoride ion final deprotection is often limited to the use of
polymeric supports or multiple step final deprotections.
While the foregoing embodiments have been set forth in considerable
detail for the purpose of making a complete disclosure, it will be
apparent to those of skill in the art that numerous changes may be
made to such details without departing from the spirit and the
principles of the disclosure. Accordingly, the disclosure should be
limited only by the following claims.
All patents, patent applications, and publications mentioned herein
are hereby incorporated by reference in their entireties.
EXAMPLES
FIGS. 2A through 2E illustrate chromatographs of a synthetic RNA
(SEQ. ID NO. 1,5' GUCACCAGCCCACUUGAG 3') and a solution of 5%
hydrogen peroxide in a solution having a pH of about 8 at various
times (FIG. 2A (time.sub.RNA=0), FIG. 2B (time.sub.HP=0), FIG. 2C
(time=3 hours), FIG. 2D (time=12 hours), and FIG. 2E (time=24
hours)).
The synthetic RNA showed little or no degradation in a solution of
5% hydrogen peroxide in a solution having a pH of about 8 for up to
24 hours.
General Examples
Transient Protection of Hydroxyl Moieties
The chemical protection of the exocyclic amino groups on the
heterobases of DNA and RNA are typically accomplished using the
"Jones procedures" (FIG. 3) that were initially described by Ti et.
al. J. Am. Chem Soc 1982, 104, 1316-1319, which was incorporated
herein by reference. In this procedure a nucleoside was transiently
protected using excess trimethylsilyl chloride in pyridine. The
trimethylsilyl groups react with all available hydroxyls and amines
on the molecule. The trimethylsilyl group blocks the reaction of
the hydroxyls with any further protecting groups, but the exocyclic
amine remains reactive even though they can contain trimethylsilyl
groups. This procedure can be adapted and optimized by anyone
skilled in the art to a variety of substrates. For example, a
larger excess of trimethylsilyl chloride was useful for obtaining
higher yields on guanosine nucleosides (Fan et. al., Org. Lett. Vol
6. No. 15, 2004). If the nucleoside substrate already contains
protective groups on one or more of the hydroxyl residues, the
excess of trimethylsilyl chloride was scaled back. This procedure
can also be used for protection of the imino groups on guanosine,
thymidine and uridine.
Once the nucleoside has been transiently protected with
trimethylsilyl groups, the exocyclic amine groups can be reacted
with any number of amino reactive protecting groups. Examples of
these, for illustration not exclusion, are acid chlorides, active
esters such as p-nitrophenyl ester, chloroformates,
thiochloroformates, acid anhydrides, pyrocarbonates,
dithiopyrocarbonates, and the like.
Transient Protection of 5' and 3' Hydroxyl Moieties For
Regioselective Protection of the 2'-Hydroxyl
The chemical protection of the 5' and 3' hydroxyl moiety of a
nucleoside was typically accomplished using a disiloxane deravitive
known as tetraisopropyldisiloxane dichloride (TIPS). This
protecting group simultaneously blocks the 5' and 3' hydroxyls to
allow for complete regioselective introduction of a protective
group on to the 2'-hydroxyl (FIG. 4) [Markiewicz, W. T., J. Chem
Research (S) 1979 24-25) which was incorporated herein by
reference].
Preparation of Novel Chloroformates as Amino and Hydroxyl Reactive
Protecting Groups
The preparation chloroformates includes using solutions of
phosgene. Alcohols and mercaptans are typically reacted with excess
phosgene at dry ice temperatures. It was often important to add one
equivalent of a non-nucleophillic base, like pyridine or triethyl
amine, to both catalyze the reaction and neutralize the HCl formed.
The order of addition should be considered since, during the
reaction, it was significant that the phosgene was generally in
high concentration relative to the alcohol or mercaptan; this
prevents the formation of carbonates or thiocarbonates. The
phosgene solution (6 molar equivalents) was typically cooled on a
dry ice/ethanol bath, and an alcohol or mercaptan solution in
toluene/pyridine was added dropwise. The solution was allowed to
warm to room temperature and was filtered under a blanket of dry
argon gas. The resulting clear solution was evaporated to an oil
using a rotary evaporator attached to a Teflon head diaphragm pump.
The excess phosgene can be removed by evaporation, since phosgene
was a gas at room temperature. The evaporation process removes the
solvent and excess phosgene. The exhaust from the pump was bubbled
through an aqueous solution of KOH to neutralize the excess
phosgene. The temperature was controlled during the evaporation
since some chloroformates can have low boiling points. Tertiary
chloroformates are typically made using metal salts of alcohols and
mercaptans. In this case, the metal salt, such as sodium salt, was
formed on the alcohol or mercaptan prior to reacting with phosgene,
and typically a non-nucleophilic base was not required.
FIG. 5 illustrates the selective protection of exocyclic amine with
chloroformate reagents. FIG. 6 illustrates the selective protection
of 2'-hydroxyl with chloroformate reagents.
Simultaneous Protection of Amino and Hydroxyl Moieties with Novel
Protecting Groups
Nucleosides can be protected using the Markiewicz procedure to give
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleosides. Those
monomers can then be reacted with either chloroformates or
pyrocarbonates to produce ribonucleosides simultaneously protected
with the same protecting group. This procedure has the specific
advantage of streamlining the synthesis of nucleoside monomers for
RNA synthesis and thus reducing the cost and complexity of
synthesis. The ability to utilize the same protecting group on both
the heterobase and 2'-hydroxyl was specifically enabled through the
use of peroxyanions for the final deprotection. Peroxyanion
nucleophillic cleavage at mildly basic pH allows for the
deprotection of both groups under pH conditions that does not give
rise to cyclization and cleavage of the internucleotide bond. If
typical nucleophiles were used to simultaneously remove the
protective groups from the exocyclic amine and 2'-hydroxyl it would
require that the reactions occur under strongly basic conditions.
Under the strongly basic conditions of typical nucleophiles,
removal of the 2'-hydroxyl protective group would immediately
result in cyclization and cleavage of the internucleotide bond.
FIG. 7 illustrates the preparation of
5',3'-O-(tTetraisopropyldisiloxane-1,3-diyl)ribonucleosides. FIG. 8
illustrates the simultaneous protection of
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)ribonucleosides using
chloroformates or pyrocarbonates.
Preparation of Pyrocarbonates as Amino and Hydroxyl Reactive
Protecting Groups
Many tertiary chloroformates are only stable at low temperatures.
However, most tertiary thiochloroformates are stable at room
temperature. The instability of tertiary chloroformates at room
temperature makes it difficult to isolate and use these reagents.
As a result, pyrocarbonates were selected for use in the
preparation of nucleoside N-carbonyloxy compounds that have a
tertiary carbon attached to the oxygen. These pyrocarbonates are
significantly more stable at room temperature than the
corresponding chlorofornates. Pyrocarbonates are typically made
using the metal salt or trimethylsilyl derivatives of tertiary
alcohols. The metal salt of the alcohol was reacted in a non-polar
solvent, such as hexanes with carbon dioxide, to form the
corresponding carbonic acid. One half of one equivalent of methane
sulfonyl chloride was added to the reaction to form the
pyrocarbonate. The reaction was then quenched with a 5% aqueous
solution of sulfuric acid and the pyrocarbonate isolated by
evaporation of the hexanes layer.
FIG. 9 illustrates the selective protection of exocyclic amine with
pyrocarbonate reagents. FIG. 10 illustrates the selective
protection of 2'-hydroxyl with pyrocarbonate reagents.
General Procedure for the Synthesis of
O-Trimethylsilylhemimethylthioacetals as Intermediate in the
Preparation of Chloroformate Amino Reactive Protecting Groups
(Group IV)
##STR00039## Preparation of KCN-18-Crown-6 Complex
The potassium cyanide-18-crown-6 complex was prepared by the
dissolution of 1 equivalent of potassium cyanide in anhydrous
methanol of 1 equivalent of 18-crown-6 (Aldrich). The solvent was
removed at 65.degree. C. using a Teflon head diaphragm pump,
followed by drying under high vacuum at room temperature for 15 to
20 min.
A dry, round bottom flask was charged with 1 equivalent of the
aldehyde and 1.1 equivalent of an alkyl or arylthiotrimethylsilane.
Upon addition of 5.times.10.sup.-4 equivalents of the solid
potassium cyanide-18-crown-6 complex, the reaction was initiated.
Often the reaction becomes exothermic and requires cooling with an
ice bath. Upon completion of the reaction, the
O-trimethylsilylhemimethylthioacetal products were typically
isolated by direct distillation from the crude mixture.
FIG. 11 illustrates the selective protection of exocyclic amine
with hemimethylthioacetal chloroformate reagents. FIG. 12
illustrates the synthesis of O-trimethylsilylhemimethylthioacetals
as intermediates in the preparation of the corresponding
chloroformate.
General Procedure for the Synthesis of
O-Trimethylsilylhemimethylthioketals as Intermediates in the
Preparation of Pyrocarbonates for the Synthesis of Group V Amino
Reactive Protecting Groups
To a dry 25-mL flask was added 10 mg (0.03 mmol)) of anhydrous zinc
iodine, 10 mg (0.15 mmol) of imidazole, and 10 mmol of the aldehyde
or ketone in 5 mL of anhydrous ether. To this stirred solution was
added 22 mmol of the appropriate thiosilane. General reaction time
of 1 hr at 25.degree. C. was observed. Typically, the products were
isolated by distillation after dilution with ether, followed by
extraction with water. The ether layer was typically evaporated,
and the residual distilled at reduced pressure.
FIG. 13 illustrates O-trimethylsilylhemimethylthioketals as
intermediate in the preparation of the corresponding pyrocarbonate.
FIG. 14 illustrates the selective protection of exocyclic amine
with hemimethylthioketal pyrocarbonate reagents. FIG. 15
illustrates the selective protection of 2'-hydroxyl with
hemimethylthioketal pyrocarbonate reagents.
Exocyclic Amino Protecting Group Examples
Group I
Synthesis of N-(methylthiomethyloxycarbonyl)ribonucleosides
Acetic acid methylthiomethyl ester (50 mmol) was purchased from TCI
America (Portland, Oreg.) and dissolved in 200 mL of ether, and 100
mL of a 1.0 M solution of KOH in water was added. The reaction was
allowed to stir overnight and the ether solution separated and
evaporated to an oil. The resulting methylthiomethyl hemiacetal was
dissolved in anhydrous toluene with an equal molar amount of
anhydrous pyridine. A phosgene solution (6 molar equivalents) was
cooled on a dry ice/ethanol bath, and the hemiacetal solution added
dropwise. The solution was allowed to warm to room temperature and
filtered under a blanket of dry argon gas. The resulting clear
solution was evaporated to an oil using a rotary evaporator
attached to a Teflon head diaphragm pump to produce
methylthiomethylchloroformate. The evaporation process removed the
solvent and excess phosgene. The exhaust from the pump was bubbled
through an aqueous solution of KOH to neutralize the excess
phosgene. A ribonucleoside (10 mmole) was coevaporated 3 times with
pyridine and then dried on vacuum pump for 2 hours. Anhydrous
pyridine (50 mL) and trimethylsilyl chloride (8.8 ml, 70 mmole)
were added, and the mixture was stirred at room temperature for 2
hours. Methylthiomethylchloroformate (20 mmole) was then added, and
stirring continued for another 12 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was evaporated
to remove the excess pyridine, and 200 mL of DCM was added with 5%
aqueous solution of NaHCO.sub.3. The precipitated product was dried
and utilized in the next reactions.
Group II
Synthesis of N-(methylthiocarbamate)ribonucleosides
Methylthiochloroformate was purchased from Aldrich. A
ribonucleoside (10 mmole) was coevaporated 3 times with pyridine,
and then dried on a vacuum pump for 2 hours. Anhydrous pyridine (50
mL) and trimethylsilyl chloride (8.8 ml, 70 mmole) were added, and
the mixture was stirred at room temperature for 2 hours.
Methylthiochloroformate (20 mmole) was then added, and stirring
continued for another 12 hours. Water (10 mL) was added to quench
the reaction and hydrolyze trimethylsilyl groups. The reaction
mixture was left overnight. Crude product was evaporated to remove
the excess pyridine, and 200 mL of DCM was added with 5% aqueous
solution of NaHCO.sub.3. The precipitated product was dried and
utilized in the next reactions.
Group III
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)N-thiomethylacetyl
riboguanosine
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)riboguanosine (20 mmole)
was coevaporated 3 times with pyridine and then dried on vacuum
pump for 2 hours. Anhydrous pyridine (100 mL) and trimethylsilyl
chloride (12.8 ml, 100 mmole) were added, and the mixture was
stirred at room temperature for 2 hours. Thiomethyacetyl chloride
(24 mmole) was then added, and stirring continued for another 12
hours. Water (100 mL) was added to quench the reaction and
hydrolyze trimethylsilyl groups. The reaction mixture was left for
1 hour. Crude product was extracted with DCM, washed with 5%
aqueous solution of NaHCO.sub.3, and purified by column
chromatography using CHCl.sub.3 with a gradient of methanol (0-3%).
The yield was about 69%.
Group IV
Synthesis of
N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane)ribonucleosides
A dry, round bottom flask was charged with 5 mL (55.1 mmol) of
isobutyraldehyde and 10.4 g (57 mmol) of phenylthiosilane. Upon
addition of 10 mg of the solid potassium cyanide-18-crown-6
complex, the reaction was initiated. The reaction became exothermic
and required cooling with an ice bath. Upon completion of the
reaction, the O-trimethylsilyl-1-phethylthiomethyl-1-H-isobutane,
11.3 grams (81% yield), was isolated by direct distillation from
the crude mixture at 71.degree. C. at 0.05 mm Hg.
The resulting O-trimethylsilyl-1-phethylthiomethyl-1-H-isobutane
was dissolved in anhydrous toluene with an equal molar amount of
anhydrous pyridine. A phosgene solution (6 molar equivalents) was
cooled on a dry ice/ethanol bath, and the
O-trimethylsilyl-1-phethylthiomethyl-1-H-isobutane solution added
dropwise. The solution was allowed to warm to room temperature and
filtered under a blanket of dry argon gas. The resulting clear
solution was evaporated to an oil using a rotary evaporator
attached to a Teflon head diaphragm pump to produce
phethylthiomethyl-1-H-isobutryloxy chloroformate. A ribonucleoside
(10 mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 2 hours. Anhydrous pyridine (50 mL) and
trimethylsilyl chloride (8.8 ml, 70 mmole) were added, and the
mixture stirred at room temperature for 2 hours.
Phethylthiomethyl-1-H-isobutryloxy chloroformate (20 mmole) was
then added, and stirring continued for another 12 hours. Water (10
mL) was added to quench the reaction and hydrolyze trimethylsilyl
groups. The reaction mixture was left overnight. Crude product was
evaporated to remove the excess pyridine, and 200 mL of DCM was
added with 5% aqueous solution of NaHCO.sub.3. The precipitated
product can be dried and utilized in the next reactions.
Group V
Synthesis of
N-(carbonyloxy-1-methylthiomethylcyclohexane)ribonucleosides
To a dry 100-mL flask was added 30 mg (0.09 mmol) of anhydrous zinc
iodine, 30 mg (0.45 mmol) of imidazole, and 5.89 grams of
cyclohexanone (60 mmol) of in 15 mL of anhydrous ether. To this
stirred solution was added 8.1 grams (66 mmol) of methylthiosilane.
The reaction was allowed to stir at room temperature for 1 hour and
then diluted with 50 mL of ether. The ether was extracted with
water and dried over sodium sulfate. The ether was evaporated, and
the product distilled at 45.degree. C. at 0.01 mm Hg, giving 10.2
grams of 1-trimethylsilyloxy-1-methylthiomethylcyclohexane at about
84% yield.
A 250 mL four-necked flask equipped with a stirrer, a thermometer,
a gas-inlet tube, and a dropping funnel was filled with nitrogen,
1-trimethylsilyloxy-1-methylthiomethylcyclo-hexane (10.2 g, 50
mmol), and hexane (100 mL). Through the mixture in the flask,
carbon dioxide gas (1.4 liters, 60 mmol) was bubbled at 0.degree.
C. using a gas dispersion tube over one hour while stirring. Then,
to the resulting slurry type mixture, pyridine (80 mg, 1 mmol) was
added at 0.degree. C., and then methanesulfonyl chloride (2.87 g,
25 mmol) was dropwise added at the same temperature, followed by
stirring at the same temperature for 2.5 hours. After the reaction,
5% sulfuric acid (25 ml) was added to the reaction mixture, and the
mixture was stirred for 30 minutes and then kept standing to
separate. The resulting organic layer was washed with a 5% aqueous
solution of sodium bicarbonate and water successively and
concentrated under reduced pressure at 35 to 40.degree. C. to
obtain colorless liquid
bis-(1-methylthiomethylcyclohexane)pyrocarbonate (16.1 g). The
yield was 89%. This product was analyzed by gas chromatography. The
purity was about 98.6% by GC/MS.
A ribonucleoside (10 mmole) was coevaporated 3 times with pyridine,
and then dried on a vacuum pump for 2 hours. Anhydrous pyridine (50
mL) and trimethylsilyl chloride (8.8 ml, 70 mmole) were added, and
the mixture was stirred at room temperature for 2 hours.
bis-(1-Methylthiomethylcyclohexane)pyrocarbonate 7.24 grams (20
mmole) was then added, and stirring continued for another 12 hours.
Water (10 mL) was added to quench the reaction and hydrolyze
trimethylsilyl groups. The reaction mixture was left overnight.
Crude product was evaporated to remove the excess pyridine, and 200
mL of DCM was added with 5% aqueous solution of NaHCO.sub.3. The
precipitated product was dried and utilized in the next
reactions.
Group VI
Synthesis of N-(4-thiomethylbenzoyl)ribonucleosides
4-(Methylthio)benzoic acid (50 mmol) was purchased from Aldrich and
dissolved in anhydrous hexanes. A large excess of oxalyl chloride
(Aldrich) was added to the hexanes solution, and the mixture fitted
with a reflux condenser. The reaction was refluxed overnight, and
the acid chloride isolated by evaporation.
Ribonucleoside (10 mmole) was coevaporated 3 times with pyridine
and then dried on vacuum pump for 2 hours. Anhydrous pyridine (50
mL) and trimethylsilyl chloride (6.3 ml, 50 mmole) were added, and
the mixture was stirred at room temperature for 2 hours.
4-thiomethylbenzoyl chloride (11 mmole) was then added, and
stirring continued for another 48 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was extracted
with DCM, washed with 5% aqueous solution of NaHCO.sub.3, and
purified by column chromatography, using CHCl.sub.3 with a gradient
of methanol (0-5%). The yields were: A 46%; C 56%; and G 8%.
Group VII
Synthesis of N-(2-thiomethylbenzoyl)ribonucleosides
2-(Methylthio)benzoic acid (50 mmol) was purchased from Aldrich and
dissolved in anhydrous hexanes. A large excess of oxalyl chloride
(Aldrich) was added to the hexanes solution, and the mixture fitted
with a reflux condenser. The reaction was refluxed overnight, and
the 2-thiomethylbenzoyl chloride isolated by evaporation.
Ribonucleoside (10 mmole) was coevaporated 3 times with pyridine
and then dried on vacuum pump for 2 hours. Anhydrous pyridine (50
mL) and trimethylsilyl chloride (6.3 ml, 50 mmole) were added, and
the mixture was stirred at room temperature for 2 hours.
2-Thiomethylbenzoyl chloride (11 mmole) was then added, and
stirring continued for another 48 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was extracted
with DCM, washed with 5% aqueous solution of NaHCO3, and purified.
The yields were: A 44%; C 62%;and G 31%.
Group VIII
Synthesis of N-(2-thiomethylphenoxycarbonyl)ribonucleosides
2-Thiomethylphenyl chloroformate was made in situ by the reaction
of 2-(methyl-mercapto)phenol (Aldrich) with a 20% phosgene solution
in toluene (Fluka). The phenol was dissolved in anhydrous toluene
with an equal molar amount of anhydrous pyridine. The phosgene
solution (6 molar equivalents) was cooled on a dry ice/ethanol
bath, and the phenol solution added dropwise. The solution was
allowed to warm to room temperature and filtered under a blanket of
dry argon gas. The resulting clear solution was evaporated to an
oil using a rotary evaporator attached to a Teflon head diaphragm
pump. The evaporation process removed the solvent and excess
phosgene. The exhaust from the pump was bubbled through an aqueous
solution of KOH to neutralize the excess phosgene. A ribonucleoside
(10 mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 2 hours. Anhydrous pyridine (50 mL) and
trimethylsilyl chloride (8.8 ml, 70 mmole) were added, and the
mixture was stirred at room temperature for 2 hours.
2-Thiomethylphenyl chloroformate (20 mmole) was then added, and
stirring continued for another 12 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was evaporated
to remove the excess pyridine, and 200 mL of DCM was added with 5%
aqueous solution of NaHCO.sub.3. The precipitated product was dried
and utilized in the next reactions.
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)N-(2-thiomethylphenoxycarbonyl-
)ribonucleosides
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (10
mmole) was coevaporated 3 times with pyridine, and then dried on
vacuum pump for 2 hours. Anhydrous pyridine (50 mL) and
trimethylsilyl chloride (6.3 ml, 50 mmole) were added, and the
mixture was stirred at room temperature for 2 hours.
2-thiomethylphenyl chloroformate (20 mmole) was then added, and
stirring continued for another 12 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was extracted
with DCM, washed with 5% aqueous solution of NaHCO.sub.3, and
purified by column chromatography using CHCl.sub.3 with a gradient
of methanol (0-4%).
Group IX
Synthesis of N-(4-thiomethylphenoxycarbonyl)ribonucleosides
4-Thiomethylphenyl chloroformate was made in situ by the reaction
of 4-(methyl-mercapto)phenol (Aldrich) with a 20% phosgene solution
in toluene (Fluka). The phenol was dissolved in anhydrous toluene
with an equal molar amount of anhydrous pyridine. The phosgene
solution (6 molar equivalents) was cooled on a dry ice/ethanol
bath, and the phenol solution added dropwise. The solution was
allowed to warm to room temperature and filtered under a blanket of
dry argon gas. The resulting clear solution was evaporated to an
oil using a rotary evaporator attached to a Teflon head diaphragm
pump. The evaporation process removed the solvent and excess
phosgene. The exhaust from the pump was bubbled through an aqueous
solution of KOH to neutralize the excess phosgene. A ribonucleoside
(10 mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 2 hours. Anhydrous pyridine (50 mL) and
trimethylsilyl chloride (8.8 ml, 70 mmole) were added, and the
mixture was stirred at room temperature for 2 hours.
4-Thiomethylphenyl chloroformate (20 mmole) was then added, and
stirring continued for another 12 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was evaporated
to remove the excess pyridine, and 200 mL of DCM was added with 5%
aqueous solution of NaHCO.sub.3. The precipitated product was dried
and utilized in the next reactions.
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)N-(4-thiomethylphenoxy-carbony-
l)ribonucleosides
4-Thiomethylphenyl chloroformate was made in situ by the reaction
of 4-(methyl-mercapto)phenol (Aldrich) with a 20% phosgene solution
in toluene (Fluka). The phenol was dissolved in anhydrous toluene
with an equal molar amount of anhydrous pyridine. The phosgene
solution (6 molar equivalents) was cooled on a dry ice/ethanol
bath, and the phenol solution added dropwise. The solution was
allowed to warm to room temperature and filtered under a blanket of
dry argon gas. The resulting clear solution was evaporated to an
oil using a rotary evaporator attached to a Teflon head diaphragm
pump. The evaporation process removed the solvent and excess
phosgene. The exhaust from the pump was bubbled through an aqueous
solution of KOH to neutralize the excess phosgene.
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (10
mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 2 hours. Anhydrous pyridine (50 mL) and
trimethylsilyl chloride (6.3 ml, 50 mmole) were added, and the
mixture was stirred at room temperature for 2 hours.
4-Thiomethylphenyl chloroformate (20 mmole) was then added, and
stirring continued for another 12 hours. Water (10 mL) was added to
quench the reaction and hydrolyze trimethylsilyl groups. The
reaction mixture was left overnight. Crude product was extracted
with DCM, washed with 5% aqueous solution of NaHCO.sub.3, and
purified by column chromatography using CHCl.sub.3 with a gradient
of methanol (0-3%).
Group X
Synthesis of N-(t-butylthiocarbamate)ribonucleosides
t-Butylthiochloroformate was made in situ by the reaction of sodium
2-methyl-2-propanethiolate (Aldrich) with a 20% phosgene solution
in toluene (Fluka). The sodium 2-methyl-2-propanethiolate was
suspended in anhydrous toluene. The phosgene solution (6 molar
equivalents) was cooled on a dry ice/ethanol bath, and the sodium
2-methyl-2-propanethiolate solution added dropwise. The solution
was allowed to warm to room temperature and filtered under a
blanket of dry argon gas. The resulting clear solution was
evaporated to an oil using a rotary evaporator attached to a Teflon
head diaphragm pump. Due to the low boiling point of the resulting
chloroformate, the water bath on the rotary evaporator was kept to
20.degree. C. The evaporation process removed the solvent and
excess phosgene. The exhaust from the pump was bubbled through an
aqueous solution of KOH to neutralize the excess phosgene. A
ribonucleoside (10 mmole) was coevaporated 3 times with pyridine
and then dried on vacuum pump for 2 hours. Anhydrous pyridine (50
mL) and trimethylsilyl chloride (8.8 ml, 70 mmole) were added, and
the mixture was stirred at room temperature for 2 hours.
t-Butylthiochloroformate (20 mmole) was then added, and stirring
continued for another 12 hours. Water (10 mL) was added to quench
the reaction and hydrolyze trimethylsilyl groups. The reaction
mixture was left overnight. Crude product was evaporated to remove
the excess pyridine, and 200 mL of DCM was added with 5% aqueous
solution of NaHCO.sub.3. The precipitated product was dried and
utilized in the next reactions.
TABLE-US-00001 TABLE 1 Deprotection Time of various APG exocyclic
amino Protecting groups in a solution of 5% Hydrogen Peroxide in
AMP buffer pH~9/methanol (50/50, v/v). N4-APG- N6-APG- N2-APG- APG-
Cytidine Adenosine Guanosine Phenoxyacetyl <1 min <30 min
<8 hrs 4-t-butylphenoxyacetyl <1 min <30 min <8 hrs
Acetyl <1 min <30 min <8 hrs Chloroacetyl- <1 min
<30 min <8 hrs dichloroacetyl <1 min <30 min <8 hrs
trichloroacetyl <1 min <30 min <8 hrs Fluoroacetyl <1
min <30 min <8 hrs Difluoroacetyl <1 min <30 min <8
hrs Trifluoroacetyl <1 min <30 min <8 hrs Nitroacetyl
<1 min <30 min <8 hrs n-propionyl <30 min <2 hrs
stable n-butyryl <30 min <2 hrs stable i-butyryl <30 min
<2 hrs stable n-pentanoyl <30 min <2 hrs stable
i-pentanoyl <30 min <2 hrs stable t-pentanoyl <30 min
<2 hrs stable MeSCH2CO <60 min <6 hrs >24 hrs PhSCH2CO
<60 min <6 hrs >24 hrs 2-Cl--PhSCH2CO <60 min <6 hrs
>24 hrs 3-Cl--PhSCH2CO <60 min <6 hrs >24 hrs
4-Cl--PhSCH2CO <60 min <6 hrs >24 hrs 2-NO2-Benzoyl <60
min <6 hrs >24 hrs 3-NO2-Benzoyl <60 min <6 hrs >24
hrs 4-NO2-Benzoyl <60 min <6 hrs >24 hrs 2-Cl-Benzoyl
<60 min <6 hrs >24 hrs 3-Cl-Benzoyl <60 min <6 hrs
>24 hrs 4-Cl-Benzoyl <60 min <6 hrs >24 hrs
2,4-di-Cl-Benzoyl <60 min <6 hrs >24 hrs 2-F-Benzoyl
<60 min <6 hrs stable 3-F-Benzoyl <60 min <6 hrs stable
4-F-Benzoyl <60 min <6 hrs stable 2-CF3-Benzoyl <60 min
<6 hrs >24 hrs 3-CF3-Benzoyl <60 min <6 hrs >24 hrs
4-CF3-Benzoyl <60 min <6 hrs >24 hrs Benzoyl <60 min
<6 hrs stable 2-MeO-Benzoyl <2 hrs <24 hrs stable
3-MeO-Benzoyl <2 hrs <24 hrs stable 4-MeO-Benzoyl <2 hrs
<24 hrs stable 2-Me-Benzoyl <2 hrs <24 hrs stable
3-Me-Benzoyl <2 hrs <24 hrs stable 4-Me-Benzoyl <2 hrs
>24 hrs stable 2,4-di-Me-Benzoyl <6 hrs >24 hrs stable
2,4,6-tri-Me-Benzoyl <6 hrs >24 hrs stable t-Butyl-SCO <24
hrs <24 hrs <24 hrs Methyl-SCO <24 hrs <24 hrs <24
hrs Ethyl-SCO <24 hrs <24 hrs <24 hrs Propyl-SCO <24
hrs <24 hrs <24 hrs i-propyl-SCO <24 hrs <24 hrs <24
hrs Phenyl-SCO <24 hrs <24 hrs <24 hrs 2-Cl--PhSCO <24
hrs <24 hrs <24 hrs 3-Cl--PhSCO <24 hrs <24 hrs <24
hrs 4-Cl--PhSCO <24 hrs <24 hrs <24 hrs 2-F--PhSCO <24
hrs <24 hrs <24 hrs 3-F--PhSCO <24 hrs <24 hrs <24
hrs 4-F--PhSCO <24 hrs <24 hrs <24 hrs 2-CF3--PhSCO <24
hrs <24 hrs <24 hrs 3-CF3--PhSCO <24 hrs <24 hrs <24
hrs 4-CF3--PhSCO <24 hrs <24 hrs <24 hrs 2-NO2--PhSCO
<24 hrs <24 hrs <24 hrs 3-NO2--PhSCO <24 hrs <24 hrs
<24 hrs 4-NO2--PhSCO <24 hrs <24 hrs <24 hrs
2-OMe--PhSCO <24 hrs <24 hrs <24 hrs 3-OMe--PhSCO <24
hrs <24 hrs <24 hrs 4-OMe--PhSCO <24 hrs <24 hrs <24
hrs
2'-Hydroxyl Protecting Group Examples
FIG. 16 illustrates exemplary 2'-hydroxyl protective groups.
General procedure for the synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-tert-butyl
thiocarbonate-N-tert-butyl thiocarbonate protected
ribonucleosides
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (20
mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 12 hours. Anhydrous pyridine (200 mL) and
appropriate chloroformate (120 mmole) were added, and the mixture
was stirred at room temperature for 12 hours. The product was
purified by column chromatography using hexanes with a gradient of
ethyl acetate (0-60%).
Group I
Example 1
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-(2-(1-oxy-1-methylethyl)-
1,3-dithiane) protected ribonucleosides
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (10
mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 12 hours. Anhydrous pyridine (100 mL),
p-nitrophenyl chloroformate (3.02 g, 15 mmole), and DMAP (488 mg, 4
mmole) were added, and the mixture was stirred at room temperature
for 12 hours. The 2'-O-(4-nitrophenyl carbonate) derivate was
isolated by flash chromatography, using hexanes with a gradient of
ethyl acetate (0-100%) and then dried on vacuum pump for 12
hours.
1,3-Dithiane (4.08 g, 34.00 mmol) in THF (80 mL) was added to
n-butyl lithium (37.40 mmol) at -78.degree. C. The mixture was
allowed to warm to 0.degree. C. on an ice/water bath and then
stirred for 30 min. The mixture was once again cooled to
-78.degree. C., and a solution of freshly distilled acetone (3.74
mL, 50.94 mmol) in anhydrous THF (50 mL) was added drop-wise with
stirring. The mixture was allowed to warm to room temperature and
stirred to keep the lithium salt of
2-(1-hydroxy-1-methylethyl)1,3-dithiane suspended.
The 5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)2'-O-(4-nitrophenyl
carbonate)ribonucleoside was redissolved in anhydrous pyridine (75
mL), and the THF solution of
2-(1-hydroxy-1-methylethyl)1,3-dithiane was added. The mixture was
stirred at room temperature for 12 hours. The final product was
purified by flash chromatography using hexanes with a gradient of
ethyl acetate (0-30%). The yield was about 74%.
Example 2
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-(1,1,1,3,3,3-hexafluoro--
2-oxy-2-methyl-2-propane) protected ribonucleosides
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (10
mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 12 hours. Anhydrous pyridine (100 mL),
p-nitrophenyl chloroformate (3.02 g, 15 mmole), and DMAP (488 mg, 4
mmole) were added, and the mixture was stirred at room temperature
for 12 hours. The 2'-O-(4-nitrophenyl carbonate) derivate was
isolated by flash chromatography using hexanes with a gradient of
ethyl acetate (0-100%) and then dried on vacuum pump for 12 hours.
Anhydrous pyridine (75 mL) and sodium
1,1,1,3,3,3-hexafluoro-2-methyl-2-propanolate (1.68 g, 15 mmole)
were added, and the mixture was stirred at room temperature for 12
hours. The final product was purified by flash chromatography using
hexanes with a gradient of ethyl acetate (0-30%). The yield was
about 22%.
Group II
Example 3
General procedure for the synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)2'-O-(tert-butyl
thiocarbonate) protected ribonucleosides (two-step procedure)
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (10
mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 12 hours. Anhydrous pyridine (100 mL),
p-nitrophenyl chloroformate (3.02 g, 15 mmole), and DMAP (488 mg, 4
mmole) were added, and the mixture was stirred at room temperature
for 12 hours. The 2'-O-(4-nitrophenyl carbonate) derivate was
isolated by flash chromatography using hexanes with a gradient of
ethyl acetate (0-100%) and then dried on vacuum pump for 12 hours.
Anhydrous pyridine (75 mL) and sodium 2-methyl-2-propanethiolate
(1.68 g, 15 mmole) were added, and the mixture was stirred at room
temperature for 12 hours. The final product was purified by flash
chromatography using hexanes with a gradient of ethyl acetate
(0-30%). The yields were about 76% for tert-Butyl thiocarbonate U
analog, about 63% for tert-Butyl thiocarbonate rA-iBu analog, and
18% for tert-Butyl thiocarbonate rG-AcSMe analog.
General procedure for the synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)2'-O-carbonate/thiocarbonate
protected ribonucleosides (one-step procedure)
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)ribonucleoside (20
mmole) was coevaporated 3 times with pyridine and then dried on
vacuum pump for 12 hours. Anhydrous pyridine (200 mL) and an
appropriate chloroformnate (120 mmole) were added, and the mixture
was stirred at room temperature for 12 hours. The product was
purified by column chromatography using hexanes with a gradient of
ethyl acetate (0-60%). The yields were about 76% for tert-Butyl
thiocarbonate U analog and 61% for tert-Butyl thiocarbonate rC-Ac
analog.
Group III
Example 5
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-(2-thiomethylacetamide)p-
henylcarbamat protected ribonucleosides
2-Nitrophenylaniline (6.9 gm 50 mmol) was dissolved in 100 mL of
anhydrous pyridine. Thiomethyacetyl chloride (55 mmole) was then
added, and the reaction stirred for 12 hours. The excess
thiomethyacetyl chloride was neutralized by the addition of 10 mL
of methanol, and the reaction evaporated to dryness. The product,
2-nitro-1-thiomethyl-phenylacetamide, was purified by silica gel
flash chromatography in methylene chloride with a gradient of
methanol (0-5%). The product was converted to the aniline
deravitive using a Raney nickel alloy with ammonium chloride in
water as described by Bhumik and Akamanchi, (Can. J. Chem. Vol 81,
2003 197-198), which was incorporated herein by reference. The
aniline derivative (10 mmol) was converted to the isocyanate in
situ by dissolving in toluene (50 mL) with 10% pyridine. A 20%
solution of phosgene (10 mL) in toluene (Fluka) was placed in a 100
mL round bottom flask and cooled to -78.degree. C. The aniline
solution was added dropwise, and the reaction allowed to warm to
0.degree. C. and stirred overnight. The solution was allowed to
warm to room temperature and filtered under a blanket of dry argon
gas. The resulting clear solution was evaporated to an oil using a
rotary evaporator attached to a Teflon head diaphragm pump. The
excess phosgene and HCl was removed by evaporation. The exhaust
from the pump was bubbled through an aqueous solution of KOH to
neutralize the excess phosgene. The resulting crude isocyanate,
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)uridine (3 mmole), was
coevaporated 3 times with pyridine and then dried on vacuum pump
for 2 hours. Anhydrous pyridine (2 mL) and isocyanate (6 mmole)
were added, and the mixture was stirred at room temperature for 3
hours. The product was purified by column chromatography using
CHCl.sub.3 with a gradient of methanol (0-3%). The yields were
about 64% for uridine
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-(2-thiomethylacetamide)p-
henylcarbamate.
Group IV
Example 6
Synthesis of
5'-Dimethoxytrityl-2'-O-(2-triisopropylsilyloxy)dimethylphenylmethyl-carb-
onate protected ribonucleosides
2-Hydroxylacetophenone (15 g, 110 mmol) was dissolved in anhydrous
dichloromethane (150 mL) with triethyl amine (250 mmol).
Triisopropylsilyl chloride (130 mmol) was dissolved in anhydrous
dicholonnethane (50 mL) and added to the stirring solution of the
acetophenone. The reaction was allowed to stir at room temperature
overnight and was quenched by the addition of water (200 mL). The
dichloromethane layer was separated and dried over sodium sulfate.
The silylated acetophenone was purified by flash chromatography in
hexanes with an ethyl acetate gradient (0 to 30%). The purified
silylated acetophenone (30 mmol) was redissolved in ether and
cooled to 0.degree. C. on an ice/water bath. Methyl magnesium
bromide (33 mmol) in ether (1.0 M, Aldrich) was added dropwise to
the stirring solution, and the reaction allowed to react for 30
minutes at 0.degree. C. This solution was added directly to a
solution of phosgene (30mmol) at -20.degree. C. The phosgene
reaction was allowed to stir at -20.degree. C. for 30 min and then
added to a pyridine solution of 5'-dimethoxytrityl uridine
(ChemGenes, Waltham, Mass). The reaction was allowed to stir
overnight and warm to room temperature. The reaction was
neutralized by the addition of 10 mL of water and evaporated to an
oil. The crude reaction was purified directly on silica gel
chromatography using methylene chloride with a methanol gradient
(1-4%). Two main products were isolated, including of the 2' and 3'
protected isomers. The yields were about 19% for
uridine-5'-DMT-2'-O-(2-triisopropylsilyloxy)dimethylphenylmethylcarbonate-
.
Group V
Example 7
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-2-(o-thiomethyl-phenylac-
etamide)-2-propane carbonate Uridine
2'-Nitroacetophenone was (30 mmol) dissolved in ether and cooled to
0.degree. C. on an ice/water bath. Methyl magnesium bromide (33
mmol) in ether (1.0 M, Aldrich) was added dropwise to the stirring
solution, and the reaction allowed to react for 30 minutes at
0.degree. C. A cold aqueous solution of ammonium chloride was added
to the mixture to quench the unreacted methyl magnesium bromide and
to protonate the alcohol producing the
2-(o-nitrophenyl)-2-propanol. The nitrophenyl group was reduced to
the 2-(o-anisyl)-2-propanol by the method described by Bhumik and
Akamanchi, (Can. J. Chem. Vol 81, 2003 197-198). The
2-(o-anisyl)-2-propanol was purified by silica gel chromatography
using dichloromethane and a methanol gradient. The
2-(o-anisyl)-2-propanol (15 mmol) was dissolved in 50 mL of
anhydrous pyridine. Thiomethyacetyl chloride (15 mmole) was then
added, and the reaction stirred for 12 hours. The excess
thiomethyacetyl chloride was neutralized by the addition of 5 mL of
methanol and the reaction evaporated to dryness. The product,
2-(o-thiomethyl-phenylacetamide)-2-propanol was purified by silica
gel flash chromatography in methylene chloride with a gradient of
methanol (0-5%). The 2-(o-thiomethylphenylacetamide)-2-propanol (10
mmol) was dissolved in THF 30 mL and converted to the sodium salt
using sodium metal. This solution was added directly to a solution
of phosgene (10mmol) at -20.degree. C. The phosgene reaction was
allowed to stir at -20.degree. C. for 30 min and then added to a
pyridine solution of
5',3'-O-(Tetraisopropyl-disiloxane-1,3-diyl)uridine (Monomer
Sciences, New Market, Ala.). The reaction was allowed to stir
overnight and warm to room temperature. The reaction was
neutralized by the addition of 10 mL of water and evaporated to an
oil. The crude reaction was purified directly on silica gel
chromatography using methylene chloride with a methanol gradient
(1-4%).
Group VI
Example 8
Synthesis of
5'-Dimethoxytrityl-2'-O-(2-triisopropylsilyloxy)dimethylphenylmethyl-thio-
carbonate protected ribonucleosides
2-Hydroxylacetophenone (15 g, 110 mmol) was dissolved in anhydrous
dichloromethane (150 mL) with triethyl amine (250 mmol).
Triisopropylsilyl chloride (130 mmol) was dissolved in anhydrous
dicholormethane (50 mL) and added to the stirring solution of the
acetophenone. The reaction was allowed to stir at room temperature
overnight and was quenched by the addition of water (200 mL). The
dichloromethane layer was separated and dried over sodium sulfate.
The silylated acetophenone was purified by flash chromatography in
hexanes with an ethyl acetate gradient (0 to 30%). The purified
silylated acetophenone (30 mmol) was redissolved in ether and
cooled to 0.degree. C. on an ice/water bath. Methyl magnesium
bromide (33 mmol) in ether (1.0 M, Aldrich) was added dropwise to
the stirring solution, and the reaction allowed to react for 30
minutes at 0.degree. C. A cold aqueous solution of ammonium
chloride was added to the mixture to quench the unreacted methyl
magnesium bromide and to protonate the alcohol producing the
2-(o-triisopropylsilyl-oxyphenyl)-2-propanol. The tertiary alcohol
was then converted to a thiol by the method described by Nishio (J.
Chem. Soc., Chem. Commun., 1989, 4, 205-206), which was
incorporated herein by reference. The sodium thiolate was formed
using sodium metal in THF and the resulting solution was added
directly to a solution of phosgene (30 mmol) at -20.degree. C. The
phosgene reaction was allowed to stir at -20.degree. C. for 30 min
and then added to a pyridine solution of 5'-dimethoxytrityl uridine
(ChemGenes, Waltham, Mass.). The reaction was allowed to stir
overnight and warm to room temperature. The reaction was
neutralized by the addition of 10 mL of water and evaporated to an
oil. The crude reaction was purified directly on silica gel
chromatography using methylene chloride with a methanol gradient
(1-4%). Two main products were isolated consisting of the 2' and 3'
protected isomers.
Group VII
Example 9
Synthesis of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl)-2'-O-dimethylphenyl-methylthi-
ocarbonate protected ribonucleosides
Sodium 2-phenyl-2-propanethiolate was synthesized from
2-phenyl-2-nitropropane by the method described by Komblum and
Widmer (J. Am. Chem. Soc., 1987, 100:22, 7086-7088), which was
incorporated herein by reference.
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)uridine (10 mmole) was
coevaporated 3 times with pyridine and then dried on vacuum pump
for 12 hours. Anhydrous pyridine (100 mL), p-nitrophenyl
chloroformate (3.02 g, 15 mmole) and DMAP (488 mg, 4 mmole) were
added, and the mixture was stirred at room temperature for 12
hours. 2'-O-(4-nitrophenyl carbonate) derivate was isolated by
flash chromatography using hexanes with a gradient of ethyl acetate
(0-100%) and then dried on vacuum pump for 12 hours. Anhydrous
pyridine (75 mL) and Sodium 2-phenyl-2-propanethiolate (15 mmole)
were added, and the mixture was stirred at room temperature for 12
hours. The final product was purified by flash chromatography using
hexanes with a gradient of ethyl acetate (0-30%). The yield was
about 55% for
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)-2'-O-dimethylphenyl-methylthi-
ocarbonate uridine.
General procedure for the removal of
5',3'-O-(Tetraisopropyldisiloxane-1,3-diyl) protecting group with
hydrogen fluoride pyridine complex
Anhydrous hydrogen fluoride-pyridine (3.5 mL) was carefully added
to an ice-cold solution. of pyridine (4 mL) in MeCN (24 mL). The
mixture was stirred for about 5 minutes and then transferred via
cannula to
5',3'-O-(tetraisopropyldisiloxane-1,3-diyl)2'-O-thiocarbonate
protected ribonucleoside (10 mmole). The reaction was left with
stirring at room temperature for 2-3 hours. Crude reaction mixture
(without concentration) was applied to the silica gel, and the
product was purified by column chromatography using hexanes
followed by ethyl acetate with a gradient of acetone (0-5%).
General procedure for the synthesis of
5'-O-(4,4'-dimethoxy-trityl)-2'-O-(tert-butyl
thiocarbonate)-N-(tert-butyl thiocarbonate) protected
ribonucleosides
The 2'-O-(tert-butyl thiocarbonate)-N-(tert-butyl thiocarbonate)
protected ribonucleoside (10 mmole) was coevaporated 3 times with
pyridine and then dried on vacuum pump for 12 hours. Anhydrous
pyridine (100 mL) and dimethoxytrityl chloride (4.1 g, 12 mmole)
were added, and the mixture was stirred at room temperature for 12
hours. The 5'-O-(4,4'-dimethoxy-trityl)-2'-O-(tert-butyl
thiocarbonate)-N-(tert-butyl thiocarbonate) derivate was isolated
by flash chromatography using hexanes with a gradient of ethyl
acetate (0-100%) and then dried on vacuum pump for 12 hours.
General procedure for the synthesis of
5'-O-Dimethoxytrityl-2'-O-thiocarbonate ribonucleoside
3'-N,N-diisopropyl(methyl)phosphoramidites
5'-O-Dimethoxytrityl-2'-O-thiocarbonate ribonucleoside (1 mmole)
was dried on a vacuum pump for 12 hours. Anhydrous THF (3 mL),
2,4,6-collidine (0.993 mL, 7.5 mmole) and N-methylimidazole (0.04
mL, 0.5 mmole) were added. N,N-diisopropylmethyl phosphonamidic
chloride (0.486 mL, 2.5 mmole) was then added dropwise over 10
minutes at RT, and the reaction mixture was left with stirring for
.about.3 hours. Crude mixture (without concentration) was applied
on the silica gel, and the product was purified by column
chromatography using benzene with a gradient of ethyl acetate
(0-40%).
Synthesis of Oligodeoxyribonucleotides and Oligoribonucleotides
The solid phase synthesis of oligodeoxyribonucleotides and
oligoribonucleotides was accomplished using an ABI model 394
automated DNA synthesizer from Applied Biosystems (Foster City,
Calif.). The synthesis cycle was adapted from a standard
one-micromolar 2-cyanoethyl-phosphoramidite RNA or DNA synthesis
cycle. For the ACE chemistry, a separate synthesizer was specially
adapted with Teflon tubing and fittings to handle the fluoride ion
deblock conditions. The ACE chemistry was performed as described by
Scaringe et. al. J. Am. Chem. Soc., 1998, 120(45) 11820-11821,
which was incorporated herein by reference. The TOM chemistry was
performed as described by Pitsch, et. al. in U.S. Pat. No.
5,986,084, which was incorporated herein by reference. RNA was
synthesized using the 2'-TBDMS method as described by Wincott et.
al., Nucleic Acids Research, 1995, 23, 2677-2684, which was
incorporated herein by reference.
Deprotection with Hydrogen Peroxide Solution of Chemically
Synthesized RNA with Commercially available Amino Protecting
Groups
Example 1
RNA synthesized with 2'-ACE monomers. Cytidine was protected with
acetyl, adenosine was protected with isobutyryl, and guanosine was
protected with t-butylphenoxyacetyl (Sinha, et. al., Biochimie,
1993, 75, 13-23). The solid support was polystyrene containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution, deprotected
the exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE
groups were then cleaved using a buffered aqueous formic acid
solution at pH 3.8 overnight.
Example 2
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with t-butylphenoxyacetyl. The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 3
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with t-butylphenoxyacetyl. The solid support was the
polystyrene based Rapp Polymere containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines. The RNA was then directly precipitated by adding
5 volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 4
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with t-butylphenoxyacetyl. The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution, and deprotected
the exocyclic amines. The RNA containing the 2'-TBDMS protecting
groups were then precipitated from the hydrogen peroxide solution
and exposed to a solution of HF/tetraethylene diamine (20% TEMED,
10% HF(aq) in acetonitrile at pH 8.6) for 6 hours at room
temperature. The reaction mixture was diluted with water and
purified by ion-exchange chromatography.
Example 5
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with t-butylphenoxyacetyl. The solid support was the
polystyrene-based Rapp Polymere containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines. The RNA was then directly precipitated by adding
5 volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Deprotection of New Amino Protecting Groups (I-X) on Chemically
Synthesized RNA with hydrogen Peroxide Solution
Example 6
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(methylthiomethyloxy-carbonyl). The solid
support was the polystyrene based Rapp Polymer containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution, deprotected
the exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE
groups were then cleaved using a buffered aqueous formic acid
solution at pH 3.8 overnight.
Example 7
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(methylthiocarbamate). The solid support was
the polystyrene based Rapp Polymer containing a peroxide oxidizable
safety catch linker. The capping step using acetic anhydride was
removed from the synthesis cycle. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution, deprotected the
exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE groups
were then cleaved using a buffered aqueous formic acid solution at
pH 3.8 overnight.
Example 8
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-thiomethylacetyl. The solid support was the
polystyrene based Rapp Polymer containing a peroxide oxidizable
safety catch linker. The capping step using acetic anhydride was
removed from the synthesis cycle. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution, deprotected the
exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE groups
were then cleaved using a buffered aqueous formnic acid solution at
pH 3.8 overnight.
Example 9
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane), adenosine
was protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was the polystyrene based
Rapp Polymer containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution, deprotected the
exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE groups
were then cleaved using a buffered aqueous formic acid solution at
pH 3.8 overnight.
Example 10
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with N-(carbonyloxy-1-methylthiomethylcyclohexane), adenosine was
protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was the polystyrene based
Rapp Polymer containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution, deprotected the
exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE groups
were then cleaved using a buffered aqueous formic acid solution at
pH 3.8 overnight.
Example 11
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(4-thiomethylbenzoyl),
and guanosine was protected with t-butylphenoxyacetyl. The solid
support was the polystyrene based Rapp Polymer containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution, deprotected
the exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE
groups were then cleaved using a buffered aqueous formic acid
solution at pH 3.8 overnight.
Example 12
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(2-thiomethylbenzoyl),
and guanosine was protected with t-butylphenoxyacetyl. The solid
support was the polystyrene based Rapp Polymer containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution, deprotected
the exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE
groups were then cleaved using a buffered aqueous formic acid
solution at pH 3.8 overnight.
Example 13
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with N-(2-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymer containing
a peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution, deprotected
the exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE
groups were then cleaved using a buffered aqueous formic acid
solution at pH 3.8 overnight.
Example 14
RNA was synthesized with 2'-ACE monomers. Cytidine was protected
with N-(4-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymer containing
a peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution, deprotected
the exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE
groups were then cleaved using a buffered aqueous formic acid
solution at pH 3.8 overnight.
Example 15
RNA synthesized with 2'-ACE monomers. Cytidine was protected with
acetyl, adenosine was protected with isobutyryl, and guanosine was
protected with N-(t-butylthiocarbamate). The solid support was the
polystyrene based Rapp Polymer containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
released the RNA oligonucleotides into solution, deprotected the
exocyclic amines, and modified the 2'-ACE groups. The 2'-ACE groups
were then cleaved using a buffered aqueous formic acid solution at
pH 3.8 overnight.
Example 16
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(methylthiomethyloxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was controlled pore glass containing a peroxide
oxidizable safety catch linker. The acetic anhydride capping step
was removed from the synthesis cycle. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This released the RNA oligonucleotides into solution and deprotects
the exocyclic amines. The RNA containing the 2'-TOM protecting
groups was then precipitated from the hydrogen peroxide solution
and exposed to a solution of HF/tetraethylene diamine (20% TEMED,
10% HF(aq) in acetonitrile at pH 8.6) for 6 hours at room
temperature. The reaction mixture was diluted with water and
purified by ion-exchange chromatography.
Example 17
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(methylthiomethyloxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymere
containing a peroxide oxidizable safety catch linker. The acetic
anhydride capping step was removed from the synthesis cycle.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifuigation.
Example 18
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(methylthiocarbamate). The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. The acetic anhydride capping step was removed from the
synthesis cycle. Following synthesis, the methyl protecting groups
on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 19
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(methylthiocarbamate). The solid support was
the polystyrene based Rapp Polymere containing a peroxide
oxidizable safety catch linker. The acetic anhydride capping step
was removed from the synthesis cycle. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 20
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-thiomethylacetyl. The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. The acetic anhydride capping step was removed from the
synthesis cycle. Following synthesis, the methyl protecting groups
on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 21
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-thiomethylacetyl. The solid support was the
polystyrene based Rapp Polymere containing a peroxide oxidizable
safety catch linker. The acetic anhydride capping step was removed
from the synthesis cycle. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 22
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane), adenosine
was protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was controlled pore glass
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 23
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane), adenosine
was protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was the polystyrene based
Rapp Polymere containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 24
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(carbonyloxy-1-methylthiomethylcyclohexane), adenosine was
protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was controlled pore glass
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 25
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(carbonyloxy-1-methylthiomethylcyclohexane), adenosine was
protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was the polystyrene based
Rapp Polymere containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 26
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(4-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was controlled pore glass containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 27
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(4-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was the polystyrene based Rapp Polymere containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 28
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(2-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was controlled pore glass containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 29
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(2-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was the polystyrene based Rapp Polymere containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 30
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(2-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was controlled pore glass containing a peroxide
oxidizable safety catch linker. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 31
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(2-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymere
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 32
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(4-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was controlled pore glass containing a peroxide
oxidizable safety catch linker. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 33
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with N-(4-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymere
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 34
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(t-butylthiocarbamate). The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TOM protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 35
RNA was synthesized using 2'-TOM monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(t-butylthiocarbamate). The solid support was
the polystyrene based Rapp Polymere containing a peroxide
oxidizable safety catch linker. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 36
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(methylthiomethyloxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was controlled pore glass containing a peroxide
oxidizable safety catch linker. The Acetic Anhydride capping step
was removed from the synthesis cycle. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a 6% hydrogen peroxide solution buffered at
pH 9.4 using aminomethylpropanol buffer in 50/50 methanol/water.
This releases the RNA oligonucleotides into solution and deprotects
the exocyclic amines. The RNA containing the 2'-TBDMS protecting
groups was then precipitated from the hydrogen peroxide solution
and exposed to a solution of HF/tetraethylene diamine (20% TEMED,
10% HF(aq) in acetonitrile at pH 8.6) for 6 hours at room
temperature. The reaction mixture was diluted with water and
purified by ion-exchange chromatography.
Example 37
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(methylthiomethyloxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymere
containing a peroxide oxidizable safety catch linker. The acetic
anhydride capping step was removed from the synthesis cycle.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 38
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(methylthiocarbamate). The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. The acetic anhydride capping step was removed from the
synthesis cycle. Following synthesis, the methyl protecting groups
on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 39
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(methylthiocarbamate). The solid support was
the polystyrene based Rapp Polymere containing a peroxide
oxidizable safety catch linker. The acetic anhydride capping step
was removed from the synthesis cycle. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 40
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-thiomethylacetyl. The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. The acetic anhydride capping step was removed from the
synthesis cycle. Following synthesis, the methyl protecting groups
on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 41
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-thiomethylacetyl. The solid support was the
polystyrene based Rapp Polymere containing a peroxide oxidizable
safety catch linker. The acetic anhydride capping step was removed
from the synthesis cycle. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was then directly precipitated by adding
5 volumes of anhydrous ethanol, cooling on dry ice then isolating
by centrifugation.
Example 42
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane), adenosine
was protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was controlled pore glass
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 43
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane), adenosine
was protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was the polystyrene based
Rapp Polymere containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 44
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(carbonyloxy-1-methylthiomethylcyclohexane), adenosine was
protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was controlled pore glass
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 45
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(carbonyloxy-1-methylthiomethylcyclohexane), adenosine was
protected with isobutyryl, and guanosine was protected with
t-butylphenoxyacetyl. The solid support was the polystyrene based
Rapp Polymere containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 46
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(4-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was controlled pore glass containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF (aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 47
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(4-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was the polystyrene based Rapp Polymere containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 48
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(2-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was controlled pore glass containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 49
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with N-(2-thiomethylbenzoyl),
guanosine was protected with t-butylphenoxyacetyl. The solid
support was the polystyrene based Rapp Polymere containing a
peroxide oxidizable safety catch linker. Following synthesis, the
methyl protecting groups on the phosphodiesters were cleaved using
1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate
in DMF for 30 minutes. The deprotection solution was washed from
the solid support bound oligonucleotide using water. The support
was then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 50
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(2-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was controlled pore glass containing a peroxide
oxidizable safety catch linker. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 51
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(2-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymere
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 52
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(4-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was controlled pore glass containing a peroxide
oxidizable safety catch linker. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 53
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with N-(4-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with t-butylphenoxyacetyl.
The solid support was the polystyrene based Rapp Polymere
containing a peroxide oxidizable safety catch linker. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Example 54
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(t-butylthiocarbamate). The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 50/50 methanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA containing the 2'-TBDMS protecting groups
was then precipitated from the hydrogen peroxide solution and
exposed to a solution of HF/tetraethylene diamine (20% TEMED, 10%
HF(aq) in acetonitrile at pH 8.6) for 6 hours at room temperature.
The reaction mixture was diluted with water and purified by
ion-exchange chromatography.
Example 55
RNA was synthesized using 2'-TBDMS monomers. Cytidine was protected
with acetyl, adenosine was protected with isobutyryl, and guanosine
was protected with N-(t-butylthiocarbamate). The solid support was
the polystyrene based Rapp Polymere containing a peroxide
oxidizable safety catch linker. Following synthesis, the methyl
protecting groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a solution of HF/tetraethylene diamine (20%
TEMED, 10% HF(aq) in acetonitrile at pH 8.6) for 2 hours at room
temperature. The fluoride ion solution was washed from the support
using acetonitrile followed by water. The support was then treated
with a 6% hydrogen peroxide solution buffered at pH 9.4 using
aminomethylpropanol buffer in 10/90 ethanol/water for 4 hours. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines. The RNA was directly precipitated by adding 5
volumes of anhydrous ethanol, cooling on dry ice, and then
isolating by centrifugation.
Deprotection with Hydrogen Peroxide Solution of Chemically
Synthesized RNA on Peroxyanion Cleavable Linker with Commercially
Available Exocyclic Amino Protecting Groups and Novel 2' Hydroxyl
Protecting Groups
Example 56
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
tert-butylphenoxyacetyl. The solid support was controlled pore
glass containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution, and deprotected
the exocyclic amines and the 2'-BSC groups. The RNA was then
directly precipitated by adding 5 volumes of anhydrous ethanol,
cooling on dry ice, and then isolating by centrifugation.
Example 57
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
N-(methylthiomethyloxycarbonyl). The solid support was controlled
pore glass containing a peroxide oxidizable safety catch linker.
Acetic anhydride capping was removed from the synthesis cycle.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 58
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
N-(methylthiocarbamate). The solid support was controlled pore
glass containing a peroxide oxidizable safety catch linker. Acetic
anhydride capping was removed from the synthesis cycle. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 59
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
N-thiomethylacetyl. The solid support was controlled pore glass
containing a peroxide oxidizable safety catch linker. Acetic
anhydride capping was removed from the synthesis cycle. Following
synthesis, the methyl protecting groups on the phosphodiesters were
cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 60
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
N-(carbonyloxy-1-phethylthiomethyl-1-H-isobutane). The solid
support was controlled pore glass containing a peroxide oxidizable
safety catch linker. Following synthesis, the methyl protecting
groups on the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 61
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
N-(carbonyloxy-1-methylthiomethylcyclohexane). The solid support
was controlled pore glass containing a peroxide oxidizable safety
catch linker. Following synthesis, the methyl protecting groups on
the phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
releases the RNA oligonucleotides into solution and deprotects the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 62
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with N-(4-thiomethyl-benzoyl), guanosine was
protected with tert-butylphenoxyacetyl. The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 63
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with N-(2-thiomethyl-benzoyl), guanosine was
protected with tert-butylphenoxyacetyl. The solid support was
controlled pore glass containing a peroxide oxidizable safety catch
linker. Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 64
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with
N-(2-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with
tert-butylphenoxyacetyl. The solid support was controlled pore
glass containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centriftigation.
Example 65
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with
N-(4-thiomethylphenoxycarbonyl), adenosine was protected with
isobutyryl, and guanosine was protected with
tert-butylphenoxyacetyl. The solid support was controlled pore
glass containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
Example 66
RNA was synthesized using 2'-tert-butylthiocarbonate (BSC)
protected monomers. cytidine was protected with acetyl, adenosine
was protected with isobutyryl, and guanosine was protected with
N-(tert-butylthiocarbamate). The solid support was controlled pore
glass containing a peroxide oxidizable safety catch linker.
Following synthesis, the methyl protecting groups on the
phosphodiesters were cleaved using 1 M
disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate in
DMF for 30 minutes. The deprotection solution was washed from the
solid support bound oligonucleotide using water. The support was
then treated with a 6% hydrogen peroxide solution buffered at pH
9.4 using aminomethylpropanol buffer in 10/90 ethanol/water. This
released the RNA oligonucleotides into solution and deprotected the
exocyclic amines and the 2'-BSC groups. The RNA was then directly
precipitated by adding 5 volumes of anhydrous ethanol, cooling on
dry ice, and then isolating by centrifugation.
O-4 Protection on Uridine
When a carbonyl protective group was present on the 2'-hydroxyl
that contains a strong electron withdrawing group, a molecular ion
minus 52 Dalton (M-52) side product has been observed in the mass
spectroscopy analysis of such RNA products and only associated with
the incorporation of uridine. Although not intending to be bound by
theory, the product may be the result of Michael addition at the
C-6 carbon of the heterobase followed by nucleophillic acyl
substitution at the C-4 carbon, resulting in formation of a
urea.
FIG. 17 illustrates a Michael addition at the C-6 carbon of the
heterobase followed by nucleophillic acyl substitution at the C-4
carbon, resulting in formation of a urea. However, this mechanism
can be avoided by employing O-4 protection as described below.
FIG. 18 illustrates that an O-4 protection prevents initial Michael
addition at C-6.
O-4 Protecting on Uridine can be Quite Convenient and High Yielding
by Employing the Formation of a Triazole Deravitive as Described by
(Reference)
FIG. 19 illustrates the formation of C-4 triazolide. Because the
triazolide intermediate was quite stable to isolate, it can easily
fit into a regioselective scheme for monomer synthesis.
FIG. 20 illustrates the regiospecific synthesis of 2'-Protected
Nucleoside with O-4 protection.
HPLC Chromatograms of RNA Synthesized by the Present Disclosure
CPG-Q-T-(U.sup.2'Bsc).sub.20 was synthesized by regular 4-step DMT
chemistry on CPG-Q-T using DMTrU.sup.2'BscOMe phosphoramidite, and
then the product was treated with MeCN/TEMED/HF (4/1/0.5) (40 min),
neutralized (TRIS pH 7.4), and filtered on Sephadex column. FIG. 21
illustrates fraction 3 on RP HPLC.
CPG-Q-T-rC-rA was synthesized by regular 4-step DMT chemistry with
DMTrC.sup.Ac.sub.2'BscOMe phosphoramidite and
DMTrA.sup.ibu.sub.2'BscOMe phosphoramidite. The product was cleaved
(off the CPG, the Bsc and Ac from C, and ibu from A) by 5%
H.sub.2O.sub.2 (pH 9.4, 50 mM alkaline buffer, 10% MeOH), and the
crude cleavage mixture was analysed by HPLC (regular) (FIG. 22,
upper panel) and LC-MS (capillary HPLC) (FIG. 22, on middle panel).
FIG. 22 illustrates the TIC (on the lower panel).
CPG-Q-T-rCrArCrA was synthesized by regular 4-step DMT chemistry
with DMTrC.sup.Ac.sub.2'BscOMe phosphoramidite and
DMTrA.sup.ibu.sub.2'BscOMe phosphoramidite. Analysis was similar to
dTrCrA (FIG. 23).
SEQUENCE LISTINGS
1
1118RNAArtificial SequenceChemically Synthesized 1gucaccagcc
cacuugag 18
* * * * *