U.S. patent application number 10/737059 was filed with the patent office on 2004-09-30 for reagents for oligonucleotide cleavage and deprotection.
This patent application is currently assigned to Applera Corporation. Invention is credited to Nelson, Jeffrey S..
Application Number | 20040191808 10/737059 |
Document ID | / |
Family ID | 23047660 |
Filed Date | 2004-09-30 |
United States Patent
Application |
20040191808 |
Kind Code |
A1 |
Nelson, Jeffrey S. |
September 30, 2004 |
Reagents for oligonucleotide cleavage and deprotection
Abstract
The present invention provides a process for the removal of
protecting groups, i.e. deprotection, from chemically synthesized
oligonucleotides. In one embodiment, the invention provides
reagents suitable for use in such a process, and kits incorporating
such reagents in a convenient, ready-to-use format. By use of the
process and reagents of the invention, side-reactions leading to
certain impurities that contaminate the synthesized
oligonucleotides can be minimized. Methods and reagents are
provided for deprotection of an oligonucleotide by reacting a
protected oligonucleotide with a deprotection reagent wherein the
deprotection reagent comprises an active methylene compound and an
amine reagent. The active methylene compound has the structure: 1
where substituent EWG is an electron-withdrawing group and R is
hydrogen, C.sub.1-C.sub.12 alkyl, C.sub.6-C.sub.20 aryl,
heterocycle or an electron-withdrawing group.
Inventors: |
Nelson, Jeffrey S.;
(Woodinville, WA) |
Correspondence
Address: |
MILA KASAN, PATENT DEPT.
APPLIED BIOSYSTEMS
850 LINCOLN CENTRE DRIVE
FOSTER CITY
CA
94404
US
|
Assignee: |
Applera Corporation
Foster City
CA
|
Family ID: |
23047660 |
Appl. No.: |
10/737059 |
Filed: |
December 16, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10737059 |
Dec 16, 2003 |
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10091231 |
Mar 4, 2002 |
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6664388 |
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60274309 |
Mar 8, 2001 |
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Current U.S.
Class: |
435/6.12 ;
536/25.3 |
Current CPC
Class: |
C07H 21/00 20130101;
C07H 21/04 20130101; Y02P 20/55 20151101 |
Class at
Publication: |
435/006 ;
536/025.3 |
International
Class: |
C12Q 001/68; C07H
021/04 |
Claims
We claim:
1. A method for deprotection of an oligonucleotide comprising the
step of reacting a protected oligonucleotide with a deprotection
reagent wherein the deprotection reagent comprises an active
methylene compound and an amine reagent, wherein the active
methylene compound has the structure: 13where EWG is an
electron-withdrawing group selected from nitro, ketone, ester,
carboxylic acid, nitrile, sulfone, sulfonate, sulfoxide, phosphate,
phosphonate, nitroxide, nitroso, trifluoromethyl and aryl groups
substituted with one or more nitro, ketone, ester, carboxylic acid,
nitrile, sulfone, sulfonate, sulfoxide, phosphate, phosphonate,
nitroxide, nitroso, and trifluoromethyl; and R is selected from
hydrogen, C.sub.1-C.sub.12 alkyl, C.sub.6-C.sub.20 aryl,
heterocycle and electron-withdrawing group; whereby protecting
groups are removed from the oligonucleotide.
2. The method of claim 1 wherein the protected oligonucleotide is
covalently attached to a solid support through a linkage.
3. The method of claim 2 further comprising the step of cleaving
the oligonucleotide from the solid support.
4. The method of claim 2 wherein the oligonucleotide remains
covalently attached to the solid support after reacting with the
deprotection reagent.
5. The method of claim 2 wherein the solid support comprises highly
cross-linked polystyrene.
6. The method of claim 2 wherein the solid support comprises
controlled-pore-glass.
7. The method of claim 2 wherein the solid support is a membrane
which allows the deprotection reagent to pass through.
8. The method of claim 2 wherein the solid support is a frit which
allows the deprotection reagent to pass through.
9. The method of claim 2 wherein the solid support is a planar,
non-porous material.
10. The method of claim 9 wherein the material is glass, quartz, or
diamond.
11. The method of claim 9 wherein the material is polystyrene,
polyethylene, polypropylene, nylon, graft of polystyrene and
polyethylene glycol, copolymer of ethylene and acrylate, or
copolymer of ethylene and methacrylate.
12. The method of claim 2 wherein the solid support is positioned
in a column having inlet and outlet openings whereby reagents may
flow through the column.
13. The method of claim 12 further comprising placing a plurality
of such columns in a holder and concurrently deprotecting a
plurality of oligonucleotides.
14. The method of claim 13 wherein the holder is a microtiter plate
having an array of such columns.
15. The method of claim 1 wherein the protected oligonucleotide
comprises at least one 2-cyanoethyl phosphate internucleotide
linkage.
16. The method of claim 1 wherein the protected oligonucleotide
comprises a nucleic acid analog.
17. The method of claim 16 wherein the nucleic acid analog is
LNA.
18. The method of claim 16 wherein the nucleic acid analog is
PNA.
19. The method of claim 16 wherein the nucleic acid analog is
2'-O-methyl RNA.
20. The method of claim 1 wherein the protected oligonucleotide is
covalently attached to a label.
21. The method of claim 20 wherein the label is selected from the
group consisting of a fluorescent dye, a quencher, biotin, a
mobility-modifier, a minor groove binder, and a linker selected
from C.sub.1-C.sub.6 alkylamine and C.sub.1-C.sub.6 alkylthiol.
22. The method of claim 21 wherein the minor groove binder is
CDPI-3.
23. The method of claim 21 wherein the fluorescent dye is a
fluorescein, a rhodamine, or a cyanine dye.
24. The method of claim 20 wherein the label is attached to the
5'-terminus of the polynucleotide.
25. The method of claim 20 wherein the label is attached to the
3'-terminus of the polynucleotide.
26. The method of claim 1 wherein the deprotection reagent further
comprises water.
27. The method of claim 1 wherein the deprotection reagent further
comprises an alcohol solvent.
28. The method of claim 27 wherein the alcohol solvent is
methanol.
29. The method of claim 27 wherein the alcohol solvent is
ethanol.
30. The method of claim 27 wherein the alcohol solvent is ethylene
glycol.
31. The method of claim 1 wherein the active methylene compound is
2,4-pentanedione.
32. The method of claim 1 wherein the active methylene compound is
1,3-cyclohexanedione.
33. The method of claim 1 wherein the active methylene compound is
ethyl acetoacetate.
34. The method of claim 1 wherein the active methylene compound is
malononitrile
35. The method of claim 1 wherein the active methylene compound is
malonic acid.
36. The method of claim 1 wherein the active methylene compound is
nitromethane.
37. The method of claim 1 wherein the active methylene compound is
malonamide.
38. The method of claim 1 wherein the active methylene compound is
a dialkylmalonate diester wherein the alkyl groups are
C.sub.1-C.sub.6 alkyl.
39. The method of claim 1 wherein the deprotection reagent
comprises a mixture of a dialkylmalonate diester wherein the alkyl
groups are C.sub.1-C.sub.6 alkyl, aqueous ammonium hydroxide, and
an alcohol solvent.
40. The method of claim 39 wherein the dialkylmalonate diester is
dimethylmalonate.
41. The method of claim 39 wherein the dialkylmalonate diester is
diethylmalonate.
42. The method of claim 39 wherein the dialkylmalonate diester is
di-n-propylmalonate.
43. The method of claim 39 wherein the dialkylmalonate diester is
diisopropylmalonate.
44. The method of claim 1 wherein the amine reagent is aqueous
ammonium hydroxide.
45. The method of claim 1 wherein the amine reagent is aqueous
methylamine.
46. The method of claim 1 wherein the amine reagent is
ethylamine.
47. The method of claim 1 wherein the amine reagent is
isopropylamine.
48. The method of claim 1 wherein the amine reagent is
n-propylamine.
49. The method of claim 1 wherein the amine reagent is
n-butylamine.
50. The method of claim 1 wherein the amine reagent is
1,2-ethylenediamine.
51. The method of claim 1 wherein the amine reagent is
1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) or
1,5-diazabicyclo[4.3.0]non-5-- ene (DBN).
52. The method of claim 2 wherein said reacting step is effected
by: wetting the protected oligonucleotide covalently attached to
the solid support with an active methylene compound and a solvent,
and then treating the protected oligonucleotide with an amine
reagent.
53. The method of claim 52 wherein the solid support is confined in
a column having inlet and outlet openings whereby reagents may flow
through the column.
54. The method of claim 53 wherein a plurality of columns are
configured in a holder whereby a plurality of oligonucleotides are
deprotected concurrently.
55. The method of claim 55 wherein the holder is in a microtiter
well configuration of equally spaced columns.
56. The method of claim 52 further comprising the step wherein the
protected oligonucleotide and the amine reagent are placed in a
sealable vessel whereby the oligonucleotide is deprotected.
57. The method of claim 52 wherein the amine reagent is aqueous
ammonium hydroxide.
58. The method of claim 52 wherein the amine reagent is ammonia
gas.
59. The method of claim 52 wherein the amine reagent is a
C.sub.1-C.sub.6 alkylamine.
60. The method of claim 52 wherein the solvent is an alcohol, an
ether, an amide, acetonitrile, dichloromethane, or
dimethylsulfoxide.
61. The method of claim 60 wherein the alcohol is methanol,
ethanol, n-propanol, isopropanol, or 1,2-ethylene glycol.
62. The method of claim 60 wherein the ether is diethyl ether,
tetrahydrofuran, 1,4-dioxane, or 1,2-dimethoxyethane.
63. The method of claim 60 wherein the amide is acetamide,
formamide, benzamide, or dimethylformamide.
64. An oligonucleotide deprotection reagent comprising an active
methylene compound and an amine reagent wherein the active
methylene compound has the structure 14where EWG is an
electron-withdrawing group selected from nitro, ketone, ester,
carboxylic acid, nitrile, sulfone, sulfonate, sulfoxide, phosphate,
phosphonate, nitroxide, nitroso, trifluoromethyl and aryl groups
substituted with one or more nitro, ketone, ester, carboxylic acid,
nitrile, sulfone, sulfonate, sulfoxide, phosphate, phosphonate,
nitroxide, nitroso, and trifluoromethyl; and R is hydrogen,
C.sub.1-C.sub.12 alkyl, C.sub.6-C.sub.20 aryl, heterocycle or
electron-withdrawing group.
65. The oligonucleotide deprotection reagent of claim 64 wherein
the active methylene compound is a dialkylmalonate diester and the
amine reagent is aqueous ammonium hydroxide.
66. The oligonucleotide deprotection reagent of claim 65 wherein
the dialkylmalonate diester is dimethylmalonate.
67. The oligonucleotide deprotection reagent of claim 65 wherein
the dialkylmalonate diester is diethylmalonate.
68. The oligonucleotide deprotection reagent of claim 65 wherein
the dialkylmalonate diester is di-n-propylmalonate.
69. The oligonucleotide deprotection reagent of claim 65 wherein
the dialkylmalonate diester is diisopropylmalonate.
70. The oligonucleotide deprotection reagent of claim 65 wherein
the active methylene compound is 1 to 10% by volume of the
reagent.
71. The oligonucleotide deprotection reagent of claim 65 further
comprising an alcohol solvent.
72. The oligonucleotide deprotection reagent of claim 71 wherein
the alcohol solvent is 1 to 30% by volume of the reagent.
73. A deprotected oligonucleotide deprotected by the deprotection
reagent of claim 64.
74. The deprotected oligonucleotide of claim 73 wherein the
deprotected oligonucleotide comprises a nucleic acid analog.
75. The deprotected oligonucleotide of claim 74 wherein the nucleic
acid analog is LNA.
76. The deprotected oligonucleotide of claim 74 wherein the nucleic
acid analog is PNA.
77. The deprotected oligonucleotide of claim 74 wherein the nucleic
acid analog is 2'-O-methyl RNA.
78. The deprotected oligonucleotide of claim 73 wherein the
deprotected oligonucleotide is covalently attached to a label.
79. The deprotected oligonucleotide of claim 78 wherein the label
is selected from a fluorescent dye, a quencher, biotin, a
mobility-modifier, a minor groove binder, and a linker selected
from C.sub.1-C.sub.6 alkylamine and C.sub.1-C.sub.6 alkylthiol.
80. The deprotected oligonucleotide of claim 79 wherein the minor
groove binder is CDPI-3.
81. The deprotected oligonucleotide of claim 79 wherein the
fluorescent dye is a fluorescein, a rhodamine, or a cyanine
dye.
82. The deprotected oligonucleotide of claim 78 wherein the label
is attached to the 5'-terminus of the polynucleotide.
83. The deprotected oligonucleotide of claim 78 wherein the label
is attached to the 3'-terminus of the polynucleotide.
Description
I. CROSS REFERENCE TO RELATED APPLICATIONS
[0001] The present application is a continuation of U.S.
application Ser. No. 10/091,231 filed on Mar. 4, 2002, which claims
the benefit under 35 USC .sctn.119(e) of provisional U.S.
application No. 60/274,309, filed Mar. 8, 2001, which are all
incorporated herein by reference.
II. FIELD OF THE INVENTION
[0002] This invention relates generally to synthetic
oligonucleotide compounds. More specifically, this invention
relates to cleavage of oligonucleotides from solid supports and
deprotection of oligonucleotides.
III. BACKGROUND OF THE INVENTION
[0003] Oligonucleotides are essential reagents in many important
molecular biology experiments, assays and information gathering
operations, such as the polymerase chain reaction (PCR), diagnostic
probes, single nucleotide polymorphism (SNP) detection, and genomic
sequencing. The benefits of conducting the synthesis of
oligonucleotides by the sequential addition and covalent attachment
of monomeric units onto a solid support is well appreciated. In
particular, the method of Caruthers is highly optimized and almost
universally adopted (U.S. Pat. Nos. 4,458,066 and 4,973,679). The
vast majority of the millions of oligonucleotides consumed each
year are prepared by automated synthesis with phosphoramidite
nucleoside monomers (Beaucage (1992) Tetrahedron Lett. 22:1859-62,
U.S. Pat. No. 4,415,732).
[0004] Conducting chemical reactions on solid supports has several
practical advantages: (i) excess reagents and soluble by-products
can be easily removed and separated by simple washing and
filtration steps, (ii) dispensing, manipulating, organizing the
parallel production of many oligonucleotides is facilitated, and
(iii) reactions can be scaled up or down for economy and ease of
handling.
[0005] Many applications utilize oligonucleotides with a covalently
attached label. Labels may impart some function, e.g. affinity,
detection, or other physical property. Oligonucleotide labels often
have reactive functionality, which may preferably be protected to
minimize side reactions and modifications.
[0006] Upon completion of synthesis, the solid support-bound
oligonucleotide is removed from the support by chemical cleavage of
the covalent linkage between the oligonucleotide and the solid
support, and deprotected to remove all remaining protecting groups
from the oligonucleotide. The steps of cleavage and deprotection
may be concurrent and conducted with the same reagent.
Alternatively, cleavage and deprotection may be conducted at
different temperatures and with different reagents.
[0007] Typically, cleavage of the oligonucleotide (20 .mu.mole to 1
nmole) from the solid support is performed in the synthesis column
at room temperature using about 1 to 3 ml concentrated ammonium
hydroxide NH.sub.4OH (about 28-30% NH.sub.3 in water). Cleavage of
the typical ester linkage at the 3' terminus of the oligonucleotide
is complete in about one hour under these conditions. While the
linkage between the oligonucleotide and the solid support is
cleaving, ammonium hydroxide is also removing the 2-cyanoethyl
groups from the internucleotide phosphates and the nucleobase
protecting groups. Depending on the nucleobase and the type of
protecting groups, deprotection (removal of protecting groups) of
the oligonucleotide requires approximately 1 to 8 hours at
55.degree. C. treatment with concentrated ammonium hydroxide.
[0008] Alternatively, cleavage and deprotection may be conducted
with anhydrous amines (U.S. Pat. No. 5,750,672), methylamine (U.S.
Pat. Nos. 5,348,868 and 5,518,651), hydrazine and ethanolamine
(Polushin (1991) Nucleic Acids Res. Symposium Series No. 24, p.
49-50; Polushin (1994) Nucleic Acids Res. 22:639-45)
[0009] A typical post-synthesis, cleavage/deprotection routine on
automated DNA synthesizers (e.g. Models 392, 394, 3948, Applied
Biosystems, Foster City, Calif.) delivers concentrated ammonium
hydroxide through the synthesis column after completion of
oligonucleotide synthesis and allows it to stand in the column for
about one hour, with periodic deliveries of more ammonium hydroxide
and collection of the eluant in a vessel. The vessel containing the
cleaved and partially deprotected oligonucleotide can then be
transferred to a heating device to complete deprotection.
Alternatively, the nucleobase protecting groups may be sufficiently
labile to not require further heating to yield a fully deprotected
oligonucleotide. The ammonium hydroxide is removed under vacuum or
in a stream of air or inert gas. The crude oligonucleotide may be
purified by various methods, including hydrophobic cartridge
purification, reverse-phase HPLC, polyacrylamide gel
electrophoresis, and precipitation. For some applications, the
crude oligonucleotide may be pure enough to perform adequately.
[0010] After completion of cleavage of the oligonucleotides from
the support, the remaining protecting groups are removed by
incubation in the ammonium hydroxide solution at either room
temperature or with heating, e.g. 55.degree. C. for 6-24 hours.
Alternatively, oligonucleotides can be cleaved and/or deprotected
with ammonia, or other amines, in the gas phase whereby the reagent
gas comes into contact with the oligonucleotide while attached to,
or in proximity to, the solid support (U.S. Pat. Nos. 5,514,789;
5,738,829).
[0011] The particular cleavage and deprotection protocol used in
any situation is largely determined by protecting groups employed
on the nucleobases, the internucleotide phosphorus, the sugars, 3'
or 5' terminus, and any covalently attached label. The first
generation set of nucleobase protecting groups utilized in the
phosphodiester method of synthesis includes benzoyl (bz) and
isobutyryl (ibu) protecting groups, utilized as adenosine A.sup.bz,
cytosine C.sup.bz and guanosine G.sup.ibu (Schaller (1963) J. Amer.
Chem. Soc. 85, 3821-3827 and Buchi (1972) J. Mol. Biol. 72:251).
Generally, thymidine T is not protected.
[0012] It is known that certain side-reactions occur during the
cleavage and deprotection reactions. Modifications of the
nucleobases, internucleotide phosphate groups, and pendant amino
groups have been characterized (Chang (1999) Nucleosides &
Nucleotides 18:1205-1206; Manoharan (1999) Nucleosides &
Nucleotides 18:1199-1201). Acrylonitrile, released from
deprotection of the internucleotide phosphate groups, may form
adducts on the nucleobases, labels, or other sites (EP 1028124; WO
0046231; Eritja (1 992) Tetrahedron 48:4171-82; Wilk (1999) J. Org.
Chem. 64:7515-22). Other impurities are uncharacterized, but known
to detract from the purity of oligonucleotides and cause loss of
performance. Where deprotection of protecting groups is incomplete,
oligonucleotides may hybridize with lower specificity or affinity,
leading to mispriming or mutagenicity.
[0013] New reagents and methods for cleavage and deprotection of
oligonucleotides are desirable. Certain protecting groups may not
be compatible with deprotection reagents or automated synthesizers
and protocols, leading to modifications. Certain labels, e.g. those
with extended conjugation or reactive functionality, may lead to
modifications of the labels or the oligonucleotide during the
cleavage and deprotection steps. Reagents and methods which
minimize or eliminate side reactions and modifications are
desirable.
IV. SUMMARY
[0014] The present invention provides a process for the removal of
protecting groups, i.e. deprotection, from chemically synthesized
oligonucleotides. In one embodiment, the invention provides
reagents suitable for use in such a process, and kits incorporating
such reagents in a convenient, ready-to-use format. By use of the
process and reagents of the invention, side-reactions leading to
certain impurities that contaminate the synthesized
oligonucleotides can be minimized.
[0015] In a first aspect, the invention provides a method for
deprotection of an oligonucleotide by reacting a protected
oligonucleotide with a deprotection reagent wherein the
deprotection reagent comprises an active methylene compound and an
amine reagent. The active methylene compound has the structure:
2
[0016] The substituent EWG is an electron-withdrawing group
selected from nitro, ketone, ester, carboxylic acid, nitrile,
sulfone, sulfonate, sulfoxide, phosphate, phosphonate, nitroxide,
nitroso, trifluoromethyl and aryl groups substituted with one or
more nitro, ketone, ester, carboxylic acid, nitrile, sulfone,
sulfonate, sulfoxide, phosphate, phosphonate, nitroxide, nitroso,
and trifluoromethyl. The substituent R is selected from hydrogen,
C.sub.1-C.sub.12 alkyl, C.sub.6-C.sub.20 aryl, heterocycle and
electron-withdrawing group. The amine reagent may be aqueous
ammonium hydroxide, aqueous methylamine, or anhydrous
C.sub.1-C.sub.6 alkylamine. In addition to an active methylene
compound and an amine reagent, the deprotection reagent of the
invention may include water or an alcohol solvent. Protecting
groups are removed from the oligonucleotide by treatment with the
deprotection reagent.
[0017] The oligonucleotide may be covalently attached to a solid
support through a linkage. The oligonucleotide may be cleaved from
the solid support either before, during, or after the protecting
groups are removed. The solid support may be an organic polymer or
inorganic. The solid support may be a membrane or frit which allows
the deprotection reagent to pass through.
[0018] The solid support may be confined in a column or other
enclosure which has inlet and outlet openings for the deprotection
reagents to pass or flow through. The columns may be configured in
a variety of formats, including holders of many columns, e.g. 96-
or 384-well microtitre plate formats. A plurality of
oligonucleotides in a holder may be deprotected concurrently or
separately through discriminate or indiscriminate delivery or
exposure to the deprotection reagents.
[0019] Oligonucleotides which may be deprotected by the
deprotection reagents of the invention include nucleic acid
analogs. Oligonucleotides may bear one or more covalently attached
labels such as a fluorescent dye, a quencher, biotin, a
mobility-modifier, and a minor groove binder.
[0020] In a second aspect, the invention provides a method for
deprotection of an oligonucleotide by first wetting the protected
oligonucleotide covalently attached to the solid support with an
active methylene compound and a solvent, and then reacting the
protected oligonucleotide with an amine reagent. The amine reagent
may be in liquid or gas phase; aqueous or anhydrous, e.g. aqueous
ammonium hydroxide, ammonia gas or a C.sub.1-C.sub.6
alkylamine.
[0021] In a third aspect, the invention includes an oligonucleotide
deprotection reagent wherein the deprotection reagent comprises an
active methylene compound and an amine reagent. The active
methylene compound has the structure: 3
[0022] The substituent EWG is an electron-withdrawing group
selected from nitro, ketone, ester, carboxylic acid, nitrile,
sulfone, sulfonate, sulfoxide, phosphate, phosphonate, nitroxide,
nitroso, trifluoromethyl and aryl groups substituted with one or
more nitro, ketone, ester, carboxylic acid, nitrile, sulfone,
sulfonate, sulfoxide, phosphate, phosphonate, nitroxide, nitroso,
and trifluoromethyl. The substituent R is selected from hydrogen,
C.sub.1-C.sub.12 alkyl, C.sub.6-C.sub.20 aryl, heterocycle and
electron-withdrawing group. The active methylene compound may be 1
to 10% by volume of the deprotection reagent. The deprotection
reagent may further include an alcohol solvent which is 1 to 30% by
volume of the reagent.
[0023] In a fourth aspect, the invention includes deprotected
oligonucleotides deprotected by the deprotection reagents of the
invention.
V. BRIEF DESCRIPTION OF THE FIGURES
[0024] FIGS. 1a-1b show reverse-phase HPLC chromatograms of
T.sub.15-Q-CDPI.sub.3, cleaved and deprotected with 15%
ethanol:NH.sub.4OH only (FIG. 1a) and with 3% diethylmalonate (DEM)
in 15% ethanol:NH.sub.4OH (FIG. 1b).
[0025] FIGS. 2a-2d show reverse-phase HPLC chromatograms of 5'
F-CAG TCG CCC TGC C-Q-CDPI.sub.3 3' (SEQ ID. NO 3) cleaved and
deprotected with 15% ethanol:NH4OH and either 0% DEM (FIG. 2a),
0.1% DEM (FIG. 2b), 1% DEM (FIG. 2c), or 3% DEM (FIG. 2d).
[0026] FIGS. 3a-3d show reverse-phase HPLC chromatograms of 5'
F-CTT CTT GCT AAT TCC-Q-CDPI.sub.3 3' (SEQ ID. NO 4) cleaved and
deprotected with 15% ethanol:NH4OH and either 0% DEM (FIG. 3a),
0.1% DEM (FIG. 3b), 1% DEM (FIG. 3c), or 3% DEM (FIG. 3d).
[0027] FIGS. 4a-4b show reverse-phase HPLC chromatograms of
5.degree. F-CCA TGC GTT AGC C-Q-CDPI.sub.3 3' (SEQ ID. NO. 5)
cleaved and deprotected with 15% ethanol:NH.sub.4OH only (FIG. 4a)
and with 3% diethylmalonate (DEM) in 15% ethanol:NH.sub.4OH (FIG.
4b).
[0028] FIGS. 5a-5b show reverse-phase HPLC chromatograms of 5'
H.sub.2N-(PEO).sub.2-AAA ATC AAG AAC TAC AAG ACC GCC C 3' (SEQ ID.
NO. 6) cleaved and deprotected with concentrated NH4OH only (FIG.
5a) and with 1% diethylmalonate (DEM) in 15% ethanol:NH.sub.4OH
(FIG. 5b).
VI. DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS
[0029] Reference will now be made in detail to certain embodiments
of the invention, examples of which are illustrated in the
accompanying drawings. While the invention will be described in
conjunction with the illustrated embodiments, it will be understood
that they are not intended to limit the invention to those
embodiments. On the contrary, the invention is intended to cover
all alternatives, modifications, and equivalents, which may be
included within the invention as defined by the appended
claims.
[0030] VI.1 Definitions
[0031] Unless stated otherwise, the following terms and phrases as
used herein are intended to have the following meanings:
[0032] "Nucleobase" means a nitrogen-containing heterocyclic moiety
capable of forming Watson-Crick hydrogen bonds in pairing with a
complementary nucleobase or nucleobase analog, e.g. a purine, a
7-deazapurine, or a pyrimidine. Typical nucleobases are the
naturally occurring nucleobases adenine, guanine, cytosine, uracil,
thymine, and analogs of the naturally occurring nucleobases, e.g.
7-deazaadenine, 7-deazaguanine, 7-deaza-8-azaguanine,
7-deaza-8-azaadenine (U.S. Pat. No. 5,912,340), inosine,
nebularine, nitropyrrole, nitroindole, 2-aminopurine,
2,6-diaminopurine, hypoxanthine, pseudouridine, pseudocytosine,
pseudoisocytosine, 5-propynylcytosine, isoguanine,
2-thiopyrimidine, 6-thioguanine, 4-thiothymine, 4-thiouracil,
O.sup.6-methylguanine, N.sup.6-methyladenine,
O.sup.4-methylthymine, 5,6-dihydrothymine, 5,6-dihydrouracil,
4-methyl-indole, phenoxazine, 7-deazapurine, pseudo-isocytidine,
isoguanosine, 4(3H)-pyrimidone, hypoxanthine, 8-oxopurines,
pyrazolo[3,4-D]pyrimidines (U.S. Pat. Nos. 6,143,877 and 6,127,121)
and ethenoadenine (Fasman (1989) Practical Handbook of Biochemistry
and Molecular Biology, pp. 385-394, CRC Press, Boca Raton,
Fla.).
[0033] "Nucleoside" means a compound consisting of a nucleobase
linked to the C-1' carbon of a ribose sugar. The ribose may be
substituted or unsubstituted. Substituted ribose sugars include,
but are not limited to, those riboses in which one or more of the
carbon atoms, e.g., the 2'-carbon atom, is substituted with one or
more of the same or different --R, --OR, --NRR or halogen groups,
where each R is independently hydrogen, C.sub.1-C.sub.6 alkyl or
C.sub.5-C.sub.14 aryl. Sugars include ribose, 2'-deoxyribose,
2',3'-dideoxyribose, 2'-haloribose, 2'-fluororibose,
2'-chlororibose, 2'-C-alkyl, 2'-alkylribose, e.g. 2'-O-methyl,
4'-.alpha.-anomeric nucleotides, 1'-.alpha.-anomeric nucleotides,
2'-4'- and 3'-4'-linked and other "locked", bicyclic sugar
modifications (WO 98/22489; WO 98/39352; WO 99/14226).
Modifications at the 2'- or 3'-position include hydrogen, hydroxy,
methoxy, ethoxy, allyloxy, isopropoxy, butoxy, isobutoxy,
methoxyethyl, alkoxy, phenoxy, azido, amino, alkylamino, fluoro,
chloro and bromo. When the nucleobase is purine, e.g. A or G, the
ribose sugar is attached to the N.sup.9-position of the nucleobase.
When the nucleobase is pyrimidine, e.g. C, T or U, the pentose
sugar is attached to the N.sup.1-position of the nucleobase
(Kornberg and Baker, (1992) DNA Replication, 2.sup.nd Ed., Freeman,
San Francisco, Calif.).
[0034] "Nucleotide" means a phosphate ester of a nucleoside, as a
monomer unit or within a nucleic acid. Nucleotides are sometimes
denoted as "NTP", or "dNTP" and "ddNTP" to particularly point out
the structural features of the ribose sugar. "Nucleotide
5'-triphosphate" refers to a nucleotide with a triphosphate ester
group at the 5' position. The triphosphate ester group may include
sulfur substitutions for the various oxygens, e.g.
.alpha.-thio-nucleotide 5'-triphosphates.
[0035] As used herein, the terms "oligonucleotide" and
"polynucleotide" are used interchangeably and mean single-stranded
and double-stranded polymers of nucleotide monomers, including
2'-deoxyribonucleotides (DNA) and ribonucleotides (RNA) linked by
internucleotide phosphodiester bond linkages, or internucleotide
analogs, and associated counter ions, e.g., H.sup.+,
NH.sub.4.sup.+, trialkylammonium, Mg.sup.2+, Na.sup.+and the like.
A polynucleotide may be composed entirely of deoxyribonucleotides,
entirely of ribonucleotides, or chimeric mixtures thereof.
Polynucleotides may be comprised of internucleotide, nucleobase and
sugar analogs. Polynucleotides typically range in size from a few
monomeric units, e.g. 5-40, when they are frequently referred to as
oligonucleotides, to several thousand monomeric nucleotide units.
Unless denoted otherwise, whenever a polynucleotide sequence is
represented, it will be understood that the nucleotides are in 5'
to 3' order from left to right and that "A" denotes deoxyadenosine,
"C" denotes deoxycytidine, "G" denotes deoxyguanosine, and "T"
denotes thymidine, unless otherwise noted.
[0036] "Protected oligonucleotide" means any oligonucleotide or
polynucleotide prepared by synthesis means, e.g. phosphoramidite
nucleoside method of automated synthesis on solid support, which
includes one or more protecting groups on functional groups such as
the exocyclic amine of a nucleobase, the internucleotide phosphate
linkage, or 5' terminus hydroxyl or amine. Protecting group
terminology follows the general strategies taught by Greene, T. and
Wuts, P. "Protective Groups in Organic Synthesis", Third Edition,
John Wiley & Sons, Inc., New York, N.Y. (1999).
[0037] The term "nucleic acid analogs" refers to analogs of nucleic
acids comprising one or more nucleotide analog units, and
possessing some of the qualities and properties associated with
nucleic acids, e.g. Watson/Crick, wobble, and Hoogsteen base
pairing, and other sequence recognition effects. Nucleic acid
analogs may have modified nucleobase moieties, modified sugar
moieties, and/or modified internucleotide linkages (Englisch (1991)
Angew. Chem. Int. Ed. Engl. 30:613-29). Modifications include
labels. One class of nucleic acid analogs is where the
internucleotide moiety is modified to be neutral and uncharged at
or near neutral pH, such as phosphoramidate, phosphotriester, and
methyl phosphonate oligonucleotides where one of the non-bridging
oxygen atoms is replaced by a neutral substituent, e.g. --NR.sub.2,
--OR, --R. Another class of nucleic acid analogs is where the sugar
and internucleotide moieties have been replaced with an uncharged,
neutral amide backbone, such as morpholino-carbamate and peptide
nucleic acids (PNA). A form of PNA is a N-(2-aminoethyl)-glycine
amide backbone polymer (Nielsen, 1991). Whenever a PNA sequence is
represented, it is understood that the amino terminus is at the
left side and the carboxyl terminus is at the right side.
[0038] "Deprotection reagent" means any reagent or formulation in a
liquid or gaseous state which removes a protecting group from a
protected oligonucleotide by chemical reaction, or cleaves an
oligonucleotide from a solid support.
[0039] "Solid support" means any particle, bead, or surface upon
which synthesis of an oligonucleotide occurs.
[0040] "Active methylene compound" means any organic reagent which
bears an acidic proton bound to carbon and capable of removal under
basic conditions, typically with a pKa of about 6 to 20.
[0041] The terms "cleaving" or "cleavage" refer to breaking a
covalent bond that attaches an oligonucleotide to a solid
support.
[0042] The term "label", as used herein, means any moiety which can
be attached to an oligonucleotide and that functions to: (i)
provide a detectable signal; (ii) interact with a second label to
modify the detectable signal provided by the first or second label,
e.g. FRET; (iii) stabilize hybridization, i.e. duplex formation;
(iv) affect mobility, e.g. electrophoretic mobility or
cell-permeability, by charge, hydrophobicity, shape, or other
physical parameters, or (v) provide a capture moiety, e.g.,
affinity, antibody/antigen, or ionic complexation.
[0043] The terms "linker", "LINKER", and "linkage" are used
interchangeably and mean a chemical moiety comprising a covalent
bond or a chain of atoms that covalently attaches, or is attached
to, a label to a polynucleotide, one label to another, or a solid
support to a polynucleotide or nucleotide.
[0044] "Linking moiety" means a chemically reactive group,
substituent or moiety, e.g. a nucleophile or electrophile, capable
of reacting with another molecule to form a covalent bond, or
linkage.
[0045] "Substituted" as used herein refers to a molecule wherein
one or more hydrogen atoms are replaced with one or more
non-hydrogen atoms, functional groups or moieties. For example, an
unsubstituted nitrogen is --NH.sub.2, while a substituted nitrogen
is --NHCH.sub.3. Exemplary substituents include but are not limited
to halo, e.g., fluorine and chlorine, (C.sub.1-C.sub.8) alkyl,
sulfate, sulfonate, sulfone, amino, ammonium, amido, nitrile, lower
alkoxy, phenoxy, aromatic, phenyl, polycyclic aromatic,
heterocycle, water-solubilizing group, and linking moiety. "Alkyl"
means a saturated or unsaturated, branched, straight-chain,
branched, or cyclic hydrocarbon radical derived by the removal of
one hydrogen atom from a single carbon atom of a parent alkane,
alkene, or alkyne. Typical alkyl groups consist of 1-12 saturated
and/or unsaturated carbons, including, but not limited to, methyl,
ethyl, propyl, butyl, and the like.
[0046] "Alkoxy" means --OR where R is (C.sub.1-C.sub.6) alkyl.
[0047] "Alkyldiyl" means a saturated or unsaturated, branched,
straight chain or cyclic hydrocarbon radical of 1-20 carbon atoms,
and having two monovalent radical centers derived by the removal of
two hydrogen atoms from the same or two different carbon atoms of a
parent alkane, alkene or alkyne. Typical alkyldiyl radicals
include, but are not limited to, 1,2-ethyldiyl, 1,3-propyldiyl,
1,4-butyldiyl, and the like.
[0048] "Aryl" means a monovalent aromatic hydrocarbon radical of
6-20 carbon atoms derived by the removal of one hydrogen atom from
a single carbon atom of a parent aromatic ring system. Typical aryl
groups include, but are not limited to, radicals derived from
benzene, substituted benzene, naphthalene, anthracene, biphenyl,
and the like.
[0049] "Aryldiyl" means an unsaturated cyclic or polycyclic
hydrocarbon radical of 6-20 carbon atoms having a conjugated
resonance electron system and at least two monovalent radical
centers derived by the removal of two hydrogen atoms from two
different carbon atoms of a parent aryl compound.
[0050] "Heterocycle" means any ring system having at least one
non-carbon atom in a ring.
[0051] "Substituted alkyl", "substituted alkyldiyl", "substituted
aryl" and "substituted aryldiyl" mean alkyl, alkyldiyl, aryl and
aryldiyl respectively, in which one or more hydrogen atoms are each
independently replaced with another substituent. Typical
substituents include, but are not limited to, --X, --R, --OH, --OR,
--SR, --SH, --NH.sub.2, --NHR, --NR.sub.2, --.sup.+NR.sub.3,
--N.dbd.NR.sub.2, --CX.sub.3, --CN, --OCN, --SCN, --NCO, --NCS,
--NO, --NO.sub.2, --N.sub.2.sup.+, --N.sub.3, --NHC(O)R, --C(O)R,
--C(O)NR.sub.2--S(O).sub.2O.sup.-, --S(O).sub.2R, --OS(O).sub.2OR,
--S(O).sub.2NR, --S(O)R, --OP(O)(OR).sub.2, --P(O)(OR).sub.2,
--P(O)(O.sup.-).sub.2, --P(O)(OH).sub.2, --C(O)R, --C(O)X, --C(S)R,
--C(O)OR, --CO.sub.2.sup.+, --C(S)OR, --C(O)SR, --C(S)SR,
--C(O)NR.sub.2, --C(S)NR.sub.2, --C(NR)NR.sub.2, where each X is
independently a halogen and each R is independently --H,
C.sub.1-C.sub.6 alkyl, C.sub.5-C.sub.14 aryl, heterocycle, or
linking group.
[0052] "Intemucleotide analog" means a phosphate ester analog of an
oligonucleotide such as: (i) alkylphosphonate, e.g. C.sub.1-C.sub.4
alkylphosphonate, especially methylphosphonate; (ii)
phosphoramidate; (iii) alkylphosphotriester, e.g. C.sub.1-C.sub.4
alkylphosphotriester; (iv) phosphorothioate; and (v)
phosphorodithioate. Internucleotide analogs also include
non-phosphate analogs wherein the sugar/phosphate subunit is
replaced by an a non-phosphate containing backbone structure. One
type of non-phosphate oligonucleotide analogs has an amide linkage,
such as a 2-aminoethylglycine unit, commonly referred to as PNA
(Nielsen (1991) "Sequence-selective recognition of DNA by strand
displacement with a thymidine-substituted polyamide", Science
254:1497-1500).
[0053] "Water solubilizing group" means a substituent which
increases the solubility of the compounds of the invention in
aqueous solution. Exemplary water-solubilizing groups include but
are not limited to quaternary amine, sulfate, sulfonate,
carboxylate, phosphonate, phosphate, polyether, polyhydroxyl, and
boronate.
[0054] "Array" means a predetermined spatial arrangement of
oligonucleotides present on a solid support or in an arrangement of
vessels.
[0055] VI.2 Oligonucleotide Synthesis
[0056] Oligonucleotides which are cleaved and deprotected by the
reagents and methods of the invention may be synthesized on solid
supports by the phosphoramidite method (U.S. Pat. Nos. 4,415,732
and 4,973,679; Beaucage, S. and Iyer, R. (1992) Tetrahedron
48:2223-2311) using: (1) 3' phosphoramidite nucleosides, I (2)
supports e.g. silica, controlled-pore-glass (U.S. Pat. No.
4,458,066) and polystyrene (U.S. Pat. Nos. 5,047,524 and
5,262,530), and (3) automated synthesizers (Models 392, 394, 3948,
3900 DNA/RNA Synthesizers, Applied Biosystems). Other support
materials include polyacrylate, hydroxethylmethacrylate, polyamide,
polyethylene, polyethyleneoxy, or copolymers and grafts of
such.
[0057] Generally, the phosphoramidite method of synthesis is
preferred because of efficient and rapid coupling and the stability
of the starting nucleoside monomers. The method entails cyclical
addition of monomers, e.g. structure I, to an oligonucleotide chain
growing on a solid-support, most commonly in the 3' to 5' direction
in which the 3' terminus nucleoside is attached to the
solid-support at the beginning of synthesis through a linkage. The
linkage typically includes base-labile functionality, such as a
succinate, diglycolate, oxalate, or hydroquinone-diacetate (Pon
(1997) Nucleic Acids Res. 25:3629-35) and is cleavable by ammonia,
amines, carbonate, hydroxide, and other basic reagents. The 3'
phosphoramidite nucleoside monomer units are commercially available
and share the general structure I: 4
[0058] where, R.sub.1 is a protecting group or substituent, e.g.
2-cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl,
and substituted aryl; R.sub.2 and R.sub.3 are amine substituents,
e.g. isopropyl, morpholino, methyl, ethyl, lower alkyl, cycloalkyl,
and aryl; R.sub.4 is an exocyclic nitrogen protecting group such as
benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl,
phthaloyl (U.S. Pat. No. 5,936,077), 2-(4-nitro-phenyl)ethyl,
pent-4-enoyl, dimethylformamidine (dmf), dialkylformamidine, and
dialkylacetamidine; and R.sub.5 is an acid-labile protecting group
such as 4, 4'-dimethoxytrityl (DMT), 4-methoxytrityl (MMT), pixyl,
trityl, and trialkylsilyl. Alternatively, oligonucleotides can be
synthesized in the 5' to 3' direction with 5' phosphoramidite
nucleoside monomers, e.g. the 5' bears a phosphoramidite group and
the 3' bears an acid-labile protecting group (Wagner (1997)
Nucleosides & Nucleotides, 16:1657-60).
[0059] Cleavage and deprotection with the reagents and methods of
the invention may be conducted on oligonucleotides with more labile
linkages to a solid support and more labile protecting groups. More
labile nucleobase protecting groups are commercially available,
e.g., phenoxyacetyl type: Expedite.TM. (Sinha (1993) Biochimie
75:13-23; available from Applied Biosystems, Foster City, Calif.)
and PAC.TM. phosphoramidites (U.S. Pat. No. 4,980,460; Schulhof
(1987) Nucleic Acids Res. 15:397-416; Schulhof (1988) Nucleic Acids
Res. 16:319; available from Amersham Pharmacia), and formamidines
and acetamidines (McBride (1986) J. Amer. Chem. Soc. 108:2040-48;
Froehler (1983) Nucleic Acids Res. 11:8031-36; Theisen (1993)
Nucleosides & Nucleotides 12:1033-46). These labile protecting
groups are deprotected significantly faster than the first
generation set. For example, the set A.sup.bz, C.sup.bz, G.sup.dmf,
T (Fastphoramidite.TM., Applied Biosystems, Foster City, Calif.)
requires only one hour at 65.degree. C. in concentrated ammonium
hydroxide for complete deprotection.
[0060] The invention may be practiced on oligonucleotides which are
covalently attached to any solid support through a linkage. The
solid support may be any material, in any configuration, dimension,
or scale upon which the oligonucleotide may be attached or
synthesized. Typical solid supports include beads or particles of
highly cross-linked polystyrene (U.S. Pat. Nos. 5,047,524;
5,262,530) or controlled-pore-glass. Dimensionally, solid supports
may be approximately 1 to 100 .mu.m average diameter and
monodisperse or widely variant in size and shape. The beads or
particles may be enclosed in a column having inlet and outlet
openings. Reagents for conducting the phosphoramidite method of
synthesis may be made to flow through a column mounted on the
automated synthesizer. Alternatively, the solid support may be a
porous membrane, filter, frit, or other flow-through device or
configuration which conducts similar reagent flow.
[0061] Alternatively, the solid support may be an impermeable,
rigid organic polymer, such as polyvinylchloride, polyethylene,
polystyrene, polyacrylate, polycarbonate and copolymers thereof.
Yet another solid support may be a non-porous, planar material such
as glass, quartz, or diamond (EP 1063286). Suitable materials also
include metals, e.g. aluminum, gold, platinum, silver, copper, and
the like, or alloys thereof. The metals may be solid blocks, or
surfaces, including layers. The materials may have at least one
substantially planar surface in a slide, sheet, plate, or disc
configuration (WO 01/01142). In one embodiment, a block material
such as glass is coated with a metallic layer or thin film such as
gold, silver, copper or platinum. Deposition of metal films may be
conducted by methods such as electron beam evaporation. The
metallic layer is derivatized with reactive functionality to which
is attached an oligonucleotide. For example, a gold layer may be
derivatized with a disulfide linkage to the 3' or 5' terminus of an
oligonucleotide.
[0062] Inorganic solid supports such as glass,
controlled-pore-glass, silica gel are typically derivatized with
silane reagents such as aminoalkyl-trialkoxysilanes or
mercaptoalkyl-trialkoxysilanes, which yield amino and thiol
functional groups, respectively. Oligonucleotides, the initial
nucleoside for oligonucleotide synthesis, or universal support
reagents may then be covalently attached to the amino or thiol
derivatized solid supports.
[0063] An array of solid support surfaces upon which
oligonucleotides may be synthesized or attached may be made to
undergo cleavage or deprotection with the reagents, and by the
methods of the invention, in a parallel or sequential fashion. One
or a subset of the protected oligonucleotides on an array may be
selectively cleaved and deprotected by masking, targeted delivery
of reagents, or other means of directing exposure to the reagents
(Fodor, U.S. Pat. No. 5,445,934).
[0064] VI.3 Methods of Oligonucleotide Cleavage and
Deprotection
[0065] Upon completion of synthesis, the solid support-bound
oligonucleotide is removed from the support by chemical cleavage of
the covalent linkage between the oligonucleotide and the solid
support, and deprotected to remove all remaining protecting groups
from the oligonucleotide, including P from nucleobases and
cyanoethyl from the internucleotide linkages. The steps of cleavage
and deprotection may be coincidental and conducted with the same
reagent, e.g. concentrated ammonium hydroxide when P is an amide
type protecting group and LINKER is an ester, structure II.
Alternatively, the steps of cleavage and deprotection can be
conducted separately with "orthogonal" reagents. For example, when
LINKER is disulfide, the nucleobase P and phosphate protecting
groups may be removed from a protected oligonucleotide with
ammonium hydroxide and the deprotected oligonucleotide will remain
attached to the solid support. Conversely, the same protected
oligonucleotide may be cleaved from the solid support with its
protecting groups intact with a disulfide-selective cleaving
reagent, such as dithiothreitol. The net result of cleavage and
deprotection is exemplified by the structures of a protected
oligonucleotide II and a cleaved and deprotected oligonucleotide
III: 5
[0066] In one embodiment of the invention, the 3' terminus of a
protected oligonucleotide is represented by structure II, showing 2
nucleotides of 5 to about 100 nucleotides. The nucleobases are
protected with base-labile protecting groups, P. An exemplary set
is A.sup.bz, G.sup.ibu, C.sup.bz, and T. The internucleotide
phosphate groups may be protected by 2-cyanoethyl, methyl, or some
other protecting group. The 3' terminus is attached through a
linkage, LINKER, to a solid support, S, in structure II. The
linkage includes base-labile functionality such as ester,
carbamate, or phosphate (EP 839 829). Typically the 3' ester is
succinate, diglycolate, oxalate, or hydroquinone-diacetate. After
synthesis, the protected oligonucleotide is reacted with a
deprotection reagent of the invention to effect removal of
nucleobase protecting groups, P, and internucleotide phosphate
protecting groups, 2-cyanoethyl. Concurrently or separately, the 3'
terminus linkage is cleaved to separate the oligonucleotide from
the solid support to ultimately yield the cleaved and deprotected
oligonucleotide shown by structure III.
[0067] In another embodiment, the linkage is chosen to be
non-cleaving, i.e. resistant to cleavage during synthesis and
deprotection steps. A non-cleaving linkage may contain inert types
of functionality such as amide, alkyl, phosphate, or ether
functionality. An oligonucleotide synthesized with a non-cleaving
linkage may be deprotected by the reagents and methods of the
invention and utilized in a solid-phase format, e.g. a biochip, DNA
chip, or array, where a plurality of deprotected oligonucleotides
are immobilized on a solid substrate. A grid or matrix of
solid-support bound oligonucleotides may be thus arrayed in known
locations and addressable by complementary nucleic acids or other
reagents, light, a laser, current, or detection apparatus.
[0068] In another embodiment, the linkage to a solid support is
chosen to be selectively cleavable, i.e. resistant to cleavage
during synthesis and deprotection steps but cleavable with other
reagents or conditions. A linkage to a solid support may be
selectively cleavable when it contains a C--Si or an O--Si bond and
cleavage is conducted with a fluoride anion reagent, e.g.
tetra-butylammonium fluoride or triethylammonium hydrogen fluoride.
A linkage may be selectively cleavable when it contains disulfide,
--S--S--, functionality and is cleaved by dithiothreitol or other
disulfide cleaving reagents. A linkage may be selectively cleavable
when it contains an ortho-nitrobenzyl group and is cleaved under
photolysis conditions.
[0069] A surprising and unexpected aspect of the invention is that
a deprotection reagent including an active methylene compound and
an amine reagent is effective and efficient at cleavage and
deprotection of oligonucleotides. The novel deprotection reagents
and methods of the invention may minimize undesired side reactions
leading to impurities or modifications of oligonucleotides,
including their covalently attached labels. The amine reagent
serves as a nucleophile to displace the protecting groups and the
active methylene compound serves to react with or render inert
certain intermediates which may further react to modify the
oligonucleotide or any label on the oligonucleotide. Other
mechanisms may occur and other benefits may accrue from use of the
deprotection reagent of the invention.
[0070] In one embodiment, the amine reagent and active methylene
compound are mixed together to provide a deprotection reagent that
can be applied to a protected oligonucleotide to remove protecting
groups (Examples 1-3). The reaction may be conducted at room
temperature or at an elevated temperature. When the protected
oligonucleotide is covalently attached to a solid support through a
linkage, the process of removing protecting groups may be
concurrent with cleaving the oligonucleotide from the solid
support. After cleavage, the cleaved oligonucleotide may be
separated from the solid support by filtration through a frit or
membrane, or by decantation. The cleaved oligonucleotide may be
further deprotected under an elevated temperature or with addition
of other reagents to assist in the removal of protecting groups.
When deprotection is complete, the deprotected oligonucleotide may
be separated from the deprotection reagents by conventional,
well-known means such as evaporation, precipitation,
electrophoresis, chromatography, or hydrophobic cartridge
procedures. One or more of the compounds in the deprotection
reagent may be sufficiently volatile to be removed by evaporation
under a stream of gas or under vacuum.
[0071] The amine reagent may be used in a liquid formulation or in
a gaseous state (Boal (1996) Nucleic Acids Res. 24:3115-17).
Certain amines are gases at room temperature and pressure, such as
ammonia (bp=-33.degree. C.) and are effective at removing
oligonucleotide protecting groups and conducting cleavage (Kempe,
U.S. Pat. No. 5,514,789). The protected oligonucleotide may be
contacted by ammonia gas in an enclosed, pressurized space,
container, or bomb. The ammonia may be delivered through a conduit
from a pressurized vessel as a gas (Kempe, U.S. Pat. No.
5,738,829), or generated from aqueous ammonium hydroxide within an
enclosed space that also includes the protected oligonucleotide. In
the latter embodiment, ammonia gas or a vapor of ammonia and water
may be created by enclosure in an enclosed space of an open
container, e.g. a pan or flask, of ammonium hydroxide solution. The
gaseous state of the reagent increases in concentration by raising
the temperature in the enclosed space (Example 6).
[0072] In another embodiment, the active methylene compound may
contact the protected oligonucleotide prior to the amine reagent,
or in a mixture including the amine reagent. In one embodiment, the
active methylene compound and a solvent are mixed and used to wet a
solid support to which a protected oligonucleotide is covalently
attached. A sufficient volume of the mixture is delivered to cover
the solid support or wet the surface, e.g. in a flow-through vessel
such as a column (Example 6). The amine reagent is delivered next
to the solid support, ensuring that a sufficient amount of the
active methylene reagent is retained. The side-reaction suppression
benefits of the active methylene reagent is thus realized by a
sequential delivery of reagents.
[0073] VI.4 Reagents For Oligonucleotide Cleavage and
Deprotection
[0074] Oligonucleotides may be cleaved and/or deprotected by novel
reagents of the invention which include an active methylene
compound and an amine reagent. Active methylene compounds include
organic reagents which bear an acidic proton bound to carbon
capable of removal under basic conditions, typically with a pKa of
about 6 to 20. The active methylene compound may constitute 1 to
10% by volume of the deprotection reagent. Active methylene
compounds are represented by the structure: 6
[0075] where the acidity of the carbon group is increased by an
electron-withdrawing group (EWG). Other substituents (R) on the
acidic carbon may be a second or third electron-withdrawing group,
hydrogen, alkyl, aryl, or any functional group which renders the
proton acidic in the range of about pKa=6-20. Electron-withdrawing
groups include nitro, ketone, ester, carboxylic acid, nitrile,
sulfone, sulfonate, sulfoxide, phosphate, phosphonate, nitroxide,
nitroso, and trifluoromethyl. Electron-withdrawing groups also
include aryl groups substituted with one or more nitro, ketone,
ester, carboxylic acid, nitrile, sulfone, sulfonate, sulfoxide,
phosphate, phosphonate, nitroxide, nitroso, and trifluoromethyl
groups. Useful classes of active methylene compounds include: (i)
1,3 keto-esters, e.g. ethylacetoacetate; (ii) 1,3 diketones, e.g.
2,4-pentanedione and cyclohexanedione, (iii) malonate derivatives,
e.g. malononitrile, malonic acid, malonamide, and dialkylmalonate
diesters. Dialkylmalonate diesters include dimethylmalonate,
diethylmalonate (DEM), di-n-propylmalonate, and
diisopropylmalonate.
[0076] The effects of the concentration of an active methylene
compound were investigated with four ethanolic ammonia (15%
ethanol:conc. NH.sub.4OH) reagents containing 0%, 0.1%, 1%, and 3%
of diethylmalonate (FIGS. 2a-2d). Each of the four reagents was
used to cleave and deprotect a portion of an oligonucleotide
labelled with a fluorescent dye, a quencher moiety, and a minor
groove binder (Example 3). Analysis by reverse phase HPLC showed
significant contaminating impurities in the reagent without an
active methylene compound (0% DEM). The presence of 0.1% DEM
eliminated most of the impurities. The presence of 1% and 3%
essentially eliminated all late eluting impurities.
[0077] In an embodiment where the active methylene compound is
dissolved in a solvent and used to wet the solid support to which a
protected oligonucleotide is covalently attached, prior to
treatment with the amine reagent, the solvent may be selected from
an alcohol, an ether, an amide, acetonitrile, dichloromethane, or
dimethylsulfoxide. Alcohol solvents include methanol, ethanol,
n-propanol, isopropanol, or 1,2-ethylene glycol. Ether solvents
include diethyl ether, tetrahydrofuran, 1,4-dioxane, or
1,2-dimethoxyethane. Amide solvents include acetamide, formamide,
benzamide, or dimethylformamide
[0078] The amine reagent may be used in the gaseous state or
dissolved in water, as a solution to treat the oligonucleotide on
the solid support. The composition of the amine reagent includes
any reagent with a primary, secondary, or tertiary amino group
which reacts with a protected oligonucleotide to effect removal of
the protecting groups. Amine reagents thus include: (i) ammonia
(NH.sub.3) gas; (ii) ammonia dissolved as ammonium hydroxide
(NH.sub.4OH) in water or mixtures of water and alcohol solvents;
(iii) alkylamines, R.sub.2NH and RNH.sub.2 where R is
C.sub.1-C.sub.6 alkyl; (iv) alkyl and aryldiamines,
H.sub.2N--R--NH.sub.2, where R is C.sub.1-C.sub.20 alkyldiyl or
C.sub.6-C.sub.20 aryldiyl; and (v) formamidines such as
1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) and
1,5-diazabicyclo[4.3.0]non-5- -ene (DBN).
[0079] Alcohol solvents include methanol, ethanol, ethylene glycol,
isopropanol, and other hydroxyl containing reagents which assist in
solubilizing the reagents, wetting the solid support, increasing
reaction rates, or minimizing side-reactions. The alcohol solvent
may constitute 1 to 30% by volume of the deprotection reagent.
[0080] The amine reagent may contact the oligonucleotide in the
gaseous state, generated from a solution in a closed system or
environment with the oligonucleotide. For example, the protected
oligonucleotide bound to a solid support may be enclosed in a
container which further contains an open vessel of ammonium
hydroxide solution. The container may be sealed, or open to the
atmosphere. When sealed, the container may be heated, in the manner
of a bomb apparatus. The ammonia vapors may thus contact the
oligonucleotide and remove protecting groups. Alternatively, the
amine reagent may be passed through, or delivered to, a column or
vessel containing the oligonucleotide. For example, the amine
reagent may be installed on an automated synthesizer and delivered
to a column, as part of the programmed delivery of reagents which
may flow through the inlet and outlet openings of the column. The
active methylene reagent may be delivered to the vessel containing
the oligonucleotide prior to the amine reagent, or as a mixture
with the amine reagent.
[0081] One or more columns in which the oligonucleotides are
synthesized may be placed in, or transferred to, a holder
apparatus, e.g. microtitre well tray, in which the method of
deprotection of the invention may be conducted. The holder may be
enclosed in a sealable vessel in which deprotection reagents are
also placed or delivered. For example, a holder containing
protected oligonucleotides on solid supports in columns can be
sealed in a stainless steel pressure vessel. A deprotection reagent
can either be placed in the vessel before sealing, or delivered
through a conduit into the vessel. In this general manner, a
plurality, e.g. several or hundreds, of oligonucleotides may be
simultaneously cleaved and deprotected. Alternatively, more than
one holder of columns may be sealed in the vessel. Also, the
holders may be introduced and processed serially, by manual
intervention, or programmed robotic means.
[0082] VI.5 Labelled Oligonucleotides
[0083] Oligonucleotides to be cleaved and deprotected by the novel
reagents and methods of the invention may be conjugated, "labelled"
with label reagents. Such conjugates may find utility as DNA
sequencing primers, PCR primers, oligonucleotide hybridization
probes, oligonucleotide ligation probes, double-labelled
5'-exonuclease (TaqMan.TM.) probes, size standards for
electrophoresis, i.e. "lane standards" or "lane markers", and the
like (U.S. Pat. No. 4,757,141; Andrus, "Chemical methods for 5'
non-isotopic labelling of PCR probes and primers" (1995) in PCR 2:
A Practical Approach, Oxford University Press, Oxford, pp. 39-54;
Hermanson, Bioconjugate Techniques, (1996) Academic Press, San
Diego, Calif. pp. 40-55, 643-71; Mullah (1998) Nucl. Acids Res.
26:1026-1031).
[0084] Certain labels provide a signal for detection of the
labelled oligonucleotide by fluorescence, chemiluminescence, or
electrochemical luminescence (Kricka, L. in Nonisotopic DNA Probe
Techniques (1992), Academic Press, San Diego, pp. 3-28).
Fluorescent dyes useful for labelling oligonucleotides include
fluoresceins, rhodamines (U.S. Pat. Nos. 5,366,860; 5,847,162;
5,936,087; 6,008,379; 6,191,278), energy-transfer dyes (U.S. Pat.
Nos. 5,863,727; 5,800,996; 5,945,526), and cyanines (Kubista, WO
97/45539). Examples of fluorescein dyes include
6-carboxyfluorescein; 2',4',1,4,-tetrachlorofluorescein; and
2',4',5',7',1,4-hexachlorofluorescein (Menchen, U.S. Pat. No.
5,118,934). Fluorescence has largely supplanted radioactivity as
the preferred detection method for many ligation experiments and
applications, such as the oligonucleotide ligation assay and other
in vitro DNA probe-based diagnostic tests.
[0085] Another class of labels includes fluorescence quenchers. The
emission spectra of a quencher overlaps with a proximal
intramolecular or intermolecular fluorescent dye such that the
fluorescence of the fluorescent dye is substantially diminished, or
quenched, by the phenomenon of fluorescence resonance energy
transfer "FRET" (Clegg (1992) "Fluorescence resonance energy
transfer and nucleic acids", Meth. Enzymol. 211:353-388). An
example of FRET in the present invention is where the
oligonucleotide is labelled with a fluorescent dye and a
fluorescence quencher. Particular quenchers include but are not
limited to (i) rhodamine dyes selected from the group consisting of
tetramethyl-6-carboxyrhodamine (TAMRA),
tetrapropano-6-carboxyrhodamine (ROX); (ii) diazo compounds, e.g.
DABSYL, DABCYL (Matayoshi (1990) Science 247:954-58; Tyagi, WO
95/13399), Fast Black, (Nardone, U.S. Pat. No. 6,117,986); (iii)
cyanine dyes (Lee, U.S. Pat. No. 6,080,868) and, (iv) other
chromophores e.g. anthraquinone, malachite green, nitrothiazole,and
nitroimidazole compounds and the like.
[0086] Energy-transfer dyes are another type of oligonucleotide
label. An energy-transfer dye label includes a donor dye linked to
an acceptor dye (U.S. Pat. No. 5,800,996). Light, e.g. from a
laser, at a first wavelength is absorbed by a donor dye, e.g. FAM.
The donor dye emits excitation energy absorbed by the acceptor dye.
The acceptor dye fluoresces at a second, longer wavelength. The
donor dye and acceptor dye moieties of an energy-transfer label may
be attached by a linkage linking the 4' or 5' positions of the
donor dye, e.g. FAM, and a 5- or 6-carboxyl group of the acceptor
dye. Other rigid and non-rigid linkages may be useful.
[0087] Metal porphyrin complexes, e.g. aluminum phthalocyanine
tetrasulfonate (Stanton, WO 88/04777) and chemiluminescent
compounds. e.g 1,2-dioxetane chemiluminescent moieties (Bronstein,
U.S. Pat. No. 4,931,223) are other examples of useful
oligonucleotide labels.
[0088] Another class of labels, referred to herein as
hybridization-stabilizing moieties, include but are not limited to
minor groove binders (Blackburn, M. and Gait, M. Nucleic Acids in
Chemistry and Biology (1996) Oxford University Press, p.337-46),
intercalators, polycations, such as poly-lysine and spermine, and
cross-linking functional groups. Hybridization-stabilizing moieties
may increase the stability of base-pairing, i.e. affinity, or the
rate of hybridization, exemplified by high thermal melting
temperatures, Tm, of the duplex. Hybridization-stabilizing moieties
may also increase the specificity of base-pairing, exemplified by
large differences in Tm between perfectly complementary
oligonucleotide and target sequences and where the resulting duplex
contains one or more mismatches of Watson/Crick base-pairing
(Blackburn, M. and Gait, M. Nucleic Acids in Chemistry and Biology
(1996) Oxford University Press, pp. 15-81). Labels which enhance
hybridization specificity and affinity are desirable, e.g.
minor-groove binders and affinity ligand labels. Biotin and
digoxigenin are useful affinity ligand labels for the capture and
isolation of oligonucleotides. Minor groove binders include Hoechst
33258, CDPI.sub.1-3 (U.S. Pat. No. 6,084,102; WO 96/32496; Kutyavin
(2000) Nucleic Acids Res. 28:655-61), netropsin, and distamycin.
Other useful labels include electrophoretic mobility modifiers,
amino acids, peptides, and enzymes.
[0089] A labelled oligonucleotide may have formula IV: 7
[0090] where the oligonucleotide comprises 2 to 1000 nucleotides.
LABEL is a protected or unprotected form of a fluorescent dye, an
exemplary class of labels, which includes an energy-transfer dye. B
is any nucleobase, e.g. uracil, thymine, cytosine, adenine,
7-deazaadenine, guanine, and 8-deazaguanosine. L is a linkage, such
as a propargyl amine (U.S. Pat. Nos. 5,047,519; 5,770,716;
5,821,356; 5,948,648). R.sup.6 is H, OH, halide, azide, amine,
C.sub.1-C.sub.6 aminoalkyl, C.sub.1-C.sub.6 alkyl, allyl, protected
hydroxyl, trialkylsilyloxy, tert-butyldimethylsilyloxy,
C.sub.1-C.sub.6alkoxy, OCH.sub.3, or OCH.sub.2CH.dbd.CH.sub.2.
R.sup.7 is H, phosphate, internucleotide phosphodiester, or
internucleotide analog. R.sup.8 is H, phosphate, internucleotide
phosphodiester, or internucleotide analog. In this embodiment, the
nucleobase-labelled oligonucleotide IV may bear multiple labels
attached through the nucleobases. Nucleobase-labelled
oligonucleotide IV may be formed by: (i) coupling of a nucleoside
phosphoramidite reagent by automated synthesis or (ii)
post-synthesis coupling with a label reagent. Oligonucleotides
labelled at the 5' terminus have structure V: 8
[0091] where X is O, NH, or S; R.sup.6 is H, OH, halide, azide,
amine, C.sub.1-C.sub.6 aminoalkyl, C.sub.1-C.sub.6 alkyl, allyl,
C.sub.1-C.sub.6 alkoxy, --OCH.sub.3, or --OCH.sub.2CH.dbd.CH.sub.2;
R.sup.7 is H, phosphate, internucleotide phosphodiester, or
internucleotide analog; and L is C.sub.1-C.sub.12 alkyldiyl,
C.sub.6-C.sub.20 aryldiyl, or polyethyleneoxy of up to 100
ethyleneoxy units.
[0092] A variety of labels may be covalently attached at the 3'
terminus of oligonucleotides. A solid support bearing a label, or
bearing functionality which can be labelled by a post-synthesis
reaction, can be utilized as a solid support for oligonucleotide
synthesis (U.S. Pat. Nos. 5,141,813; 5,231,191, 5,401,837;
5,736,626). By this approach, the label or the functionality is
present during synthesis of the oligonucleotide. During cleavage
and deprotection, the label or the functionality remains covalently
attached to the oligonucleotide. Oligonucleotides labelled at the
3' terminus may have structure VI: 9
[0093] The linkage L in formulas IV, V, VI may be attached at any
site on the label, LABEL.
[0094] Labelling can be accomplished using any one of a large
number of known techniques employing known labels, linkages,
linking groups, standard reagents and reaction conditions, and
analysis and purification methods. Generally, the linkage linking
the label and the oligonucleotide should not (i) interfere with
hybridization, (ii) inhibit enzymatic activity, or (iii) adversely
affect the properties of the label, e.g. quenching or bleaching
fluorescence of a dye. Oligonucleotides can be labelled at sites
including a nucleobase, a sugar, an internucleotide linkage, and
the 5' and 3' terminii. Oligonucleotides can be functionalized to
bear reactive amino, thiol, sulfide, disulfide, hydroxyl, and
carboxyl groups at any of these sites. Nucleobase label sites
generally include the 7-deaza or C-8 positions of the purine or
deazapurine, and the C-5 position of the pyrimidine. The linkage
between the label and the nucleobase may be acetylenic-amido or
alkenic-amido linkages. Typically, a carboxyl group on the label is
activated by forming an active ester, e.g. N-hydroxysuccinimide
(NHS) ester and reacted with an amino group on the alkynylamino- or
alkenylamino-derivatized nucleobase. Labels are most conveniently
and efficiently introduced at the 5' terminus (Andrus, A. "Chemical
methods for 5' non-isotopic labelling of PCR probes and primers"
(1995) in PCR 2: A Practical Approach, Oxford University Press,
Oxford, pp. 39-54) with fluorescent dyes and other labels which
have been functionalized as phosphoramidite reagents, as part of
the automated protocol.
[0095] Oligonucleotides may be labelled at both the 5' and 3'
terminii. Each terminii may bear one or more labels. For example,
Examples 1-4 include oligonucleotides with a 5' fluorescent dye and
two labels, a quencher Q and a minor groove binder CDPI.sub.3, at
the 3' terminus.
[0096] In a first method for labelling synthetic oligonucleotides,
a nucleophilic functionality, e.g. a primary aliphatic amine, is
introduced at a labelling attachment site on an oligonucleotide,
e.g. a 5' terminus. After automated, solid-support synthesis is
complete, the oligonucleotide is cleaved from the support and all
protecting groups are removed. The nucleophile-oligonucleotide is
reacted with an excess of a label reagent containing an
electrophilic moiety, e.g. isothiocyanate or activated ester, e.g.
N-hydroxysuccinimide (NHS), under homogeneous solution conditions
(Hermanson, Bioconjugate Techniques, (1996) Academic Press, San
Diego, Calif. pp. 40-55, 643-71; Andrus, A. "Chemical methods for
5' non-isotopic labelling of PCR probes and primers" (1995) in PCR
2: A Practical Approach, Oxford University Press, Oxford, pp.
39-54). Labelled oligonucleotides IV, V, or VI may be formed by
reacting a reactive linking group form, e.g. NHS, of a dye, with an
oligonucleotide functionalized with an amino, thiol, or other
nucleophile (U.S. Pat. No. 4,757,141).
[0097] In a second method, a label is directly incorporated into
the oligonucleotide during or prior to automated synthesis, for
example as a support reagent (U.S. Pat. Nos. 5,736,626 and
5,141,813) or as a non-nucleoside phosphoramidite reagent. Certain
fluorescent dyes and other labels have been functionalized as
phosphoramidite reagents for 5' labelling (Theisen (1992) Nucleic
Acid Symposium SeriesNo. 27, Oxford University Press, Oxford, pp.
99-100).
[0098] Polynucleotides may be labelled with moieties that affect
the rate of electrophoretic migration, i.e. mobility-modifying
labels. Mobility-modifying labels include polyethyleneoxy units,
--(CH.sub.2CH.sub.2O).sub.n-- where n may be 1 to 100 (U.S. Pat.
No. 5,624,800). The polyethyleneoxy units may be interspersed with
phosphate groups. Specifically labelling polynucleotides with
labels of polyethyleneoxy of discrete and known size allows for
separation by electrophoresis, substantially independent of the
number of nucleotides in the polynucleotide. That is,
polynucleotides of the same length may be discriminated upon by the
presence of spectrally resolvable dye labels and mobility-modifying
labels. Polynucleotides bearing both dye labels and
mobility-modifying labels may be formed enzymatically by ligation
or polymerase extension of the single-labelled polynucleotide or
nucleotide constituents.
[0099] The present invention is particularly well suited for
cleaving and deprotecting polynucleotides with multiple and
different labels.
VI.6 EXAMPLES
[0100] The invention will be further clarified by a consideration
of the following examples, which are intended to be purely
exemplary of the invention and not to in any way limit its
scope.
Example 1
[0101]
1 An oligonucleotide T.sub.8-Q-CDPI.sub.3: 5' TTT TTT
TT-Q-CDPI.sub.3 3' (SEQ ID. NO. 1)
[0102] was synthesized on the Model 3948 DNA Synthesizer (Applied
Biosystems, Foster City, Calif.). Eight cycles of phosphoramidite
chemistry was conducted with thymidine 3' phosphoramidite in a
column containing 16 mg (200 nmoles) highly cross-linked
polystyrene bead support loaded with 12 .mu.mole/gm of a linkage
including quencher label Q and minor groove binder label
CDPI.sub.3. The quencher label, Q, has the structure: 10
[0103] where X is the attachment site to a linkage. The
minor-groove-binder label, CDPI.sub.3, has the following structure:
11
[0104] where X is the attachment site to a linkage.
[0105] The support was divided into two portions. The first portion
was treated with 15% ethanolic ammonia (15:85 v/v EtOH:conc.
NH.sub.4OH) for 2 hours at 55.degree. C. to effect cleavage and
deprotection. The second portion was treated with 3%
diethylmalonate (DEM) dissolved in 15% ethanolic ammonia (3:15:82
v/v/v DEM:EtOH:conc. NH4OH), for 2 hours at 55.degree. C.
[0106] After cooling, an aliquot from each portion was analyzed by
reverse phase HPLC. The adsorbent was 2-5 .mu.m particles of C-18
polystyrene/divinylbenzene. The mobile phases were a gradient of
acetonitrile in TEAA (triethylammonium acetate) at about pH 7.
(Transgenomic WAVE, Transgenomic, Inc., San Jose, Calif.). Other
mobile phases, conditions, and HPLC equipment are also useful for
analyzing the oligonucleotides which are cleaved and deprotected by
the methods and reagents of the invention. The major, product peak
and the major (first) late-eluting contaminant were separated and
isolated from each aliquot. The late-eluting contaminant(s) from
the first portion, cleaved and deprotected without DEM, were
analyzed by MALDI-TOF mass spectrometry (PerSeptive Biosystems
Voyager-DE, Framingham, Mass.) and found to have a mass of 3485.5
[M+26] mass units. This mass is consistent with an additional vinyl
group modification (--CH.sub.2.dbd.CH.sub.2). The major peak in the
HPLC from each portion was assigned to T.sub.8-Q-CDPI.sub.3 from
the strong molecular ion peak at 3459.41 mass units (positive
mode), as expected.
Example 2
[0107]
2 An oligonucleotide T.sub.15-Q-CDPI.sub.3: 5' TTT TTT TTT TTT
TTT-Q-CDPI.sub.3 3' (SEQ ID. NO. 2)
[0108] was synthesized on the Model 3948 DNA Synthesizer (Applied
Biosystems, Foster City, Calif.). Fifteen cycles of phosphoramidite
chemistry was conducted with thymidine 3' phosphoramidite in a
column containing 16 mg (200 nmoles) highly cross-linked
polystyrene bead support loaded with 12 .mu.mole/gm of a linkage
including quencher label Q and minor groove binder label
CDPI.sub.3. The support was divided into two portions. The first
portion was treated with 15% ethanolic ammonia (15:85 v/v
EtOH:conc. NH4OH) for 2 hours at 55.degree. C. to effect cleavage
and deprotection. The second portion was treated with 3%
diethylmalonate (DEM) dissolved in 15% ethanolic ammonia (3:15:82
v/v/v DEM:EtOH:conc. NH.sub.4OH), for 2 hours at 55.degree. C.
After cooling, an aliquot from each portion was analyzed by reverse
phase HPLC. The portion cleaved and deprotected without DEM shows a
complex-product mixture containing only 26.5% of the desired
product eluting at 6.1 minutes (FIG. 1a). The product mixture is
contaminated with significant (50%) later eluting impurities. The
portion cleaved and deprotected with 3% DEM shows improved purity,
76.8% of the desired product eluting at 6.1 minutes and a
diminished level of later eluting impurities (FIG. 1b).
EXAMPLE 3
[0109] Oligonucleotides labelled with a fluorescent dye
(F=6-carboxyfluorescein) at the 5' terminus, and a quencher moiety
(Q) and minor groove binder (CDPI.sub.3) at the 3' terminus:
3 5' F-CAG TCG CCC TGC C-Q-CDPI.sub.3 3' (SEQ ID. NO. 3) 5' F-CTT
CTT GCT AAT TCC-Q- (SEQ ID. NO. 4) CDPI.sub.3 3'
[0110] were synthesized on a Model 3900 DNA Synthesizer (Applied
Biosystems, Foster City, Calif.). Phosphoramidite chemistry was
conducted with nucleoside 3' phosphoramidites, including A.sup.bz,
G.sup.dmf, C.sup.bz and T, in a column containing 16 mg (200
nmoles) highly cross-linked polystyrene bead support loaded with 12
.mu.mole/gm of a linkage including quencher label Q and minor
groove binder label CDPI.sub.3.
[0111] After each synthesis, the support was divided into four
portions. Each portion was treated with a reagent containing 0%,
0.1%, 1% or 3% diethylmalonate (DEM) in 15% ethanolic ammonia
(15:85 v/v EtOH:conc. NH.sub.4OH) for 2 hours at 65.degree. C. to
effect cleavage and deprotection.
[0112] After cooling, an aliquot from each portion was analyzed by
reverse phase HPLC. The portions cleaved and deprotected without
DEM shows a complex product mixture containing only 21.8% of the
desired product eluting at 6.5 minutes (FIG. 2a) and 32.7% of the
desired product eluting at 6.4 minutes (FIG. 3a) for SEQ ID. NO 3
and SEQ ID. NO 4 respectively. The product mixtures are
contaminated with significant (50%) later eluting impurities. The
portions cleaved and deprotected with 0.1% DEM show improved
purities; 65.8% (FIG. 2b) and 64.4% (FIG. 3b) and diminished levels
of later eluting impurities for SEQ ID. NO 3 and SEQ ID. NO 4
respectively. The portions cleaved and deprotected with 1% DEM show
again improved purities; 76.7% (FIG. 2c) and 76.7% (FIG. 3c) for
SEQ ID. NO 3 and SEQ ID. NO 4 respectively. The portions cleaved
and deprotected with 3% DEM show again improved purities, 79.5%
(FIG. 2d) and 77.5% (FIG. 3d) for SEQ ID. NO 3 and SEQ ID. NO 4
respectively.
[0113] The fluorescent dye, 6-carboxyfluorescein, (F) has the
following structure: 12
[0114] where X is the attachment site to a linkage.
Example 4
[0115] Following the procedures of Example 3, the 13 nt
oligonucleotide:
5' F-CCA TGC GTT AGC C -Q-CDPI.sub.3 3 (SEQ ID. NO. 5)
[0116] was synthesized and the support was divided into two
portions. One portion was cleaved and deprotected with 15%
ethanol:NH.sub.4OH only and with 3% DEM in 15% ethanol:NH.sub.4OH.
An aliquot from each portion was analyzed by reverse phase HPLC.
The portion cleaved and deprotected without DEM shows a complex
product mixture containing only 26% of the desired product eluting
at 6.1 minutes (FIG. 4a). The product mixture is contaminated with
significant later eluting impurities. The portion cleaved and
deprotected with 3% DEM shows improved purity, 67% of the desired
product eluting at 6.1 minutes and a diminished level of later
eluting impurities (FIG. 4b).
Example 5
[0117] Liquid Phase Cleavage/deprotection:
[0118] A set of up to 48 oligonucleotides are synthesized on the
Model 3948 DNA Synthesizer (Applied Biosystems, Foster City,
Calif.). Each oligonucleotide is synthesized at 50-100 nmolar scale
on about 20 mg of 3' nucleoside, high-crosslink polystyrene in a
OneStep.TM. synthesis/purification column (Applied Biosystems,
Foster City, Calif.; Andrus, U.S. Pat. Nos. 5,935,527 and
6,175,006; Baier (1996) BioTechniques 20:298-303). Oligonucleotides
may be 15-50 nt, or longer. Oligonucleotides may be unlabelled or
labelled with labels such as fluorescent dyes or
hybridization-stabilizing moieties. Synthesis is conducted with the
FastPhoramidite.TM. set of 3' phosphoramidite nucleosides
(A.sup.bz, G.sup.dmf, C.sup.bz, T) dissolved in acetonitrile and
coupled to the 5' terminus of the growing oligonucleotide with
tetrazole, or a tetrazole analog, e.g. 5-ethylthiotetrazole, as a
proton-source activator. Synthesis may be programmed to either
remove the 5' DMT group from the 5' terminus of the oligonucleotide
by acidic detritylation, or leave it intact by omitting the final
detritylation step. When a set of three oligonucleotides finishes
the synthesis stage under the synthesis fluid delivery head, the
set of three columns rotates under the cleavage/deprotection
delivery head. The deprotection reagent of the invention may be
delivered to the columns, e.g. 0.5 to 1.5 ml of a mixture of
concentrated ammonium hydroxide and an active methylene compound.
The active methylene compound may be 1 to 10% by volume of the
reagent. The deprotection reagent may further contain 1 to 30% of
an alcohol solvent, by volume. The deprotection reagent is allowed
to stand in, or circulate through, the column at ambient or higher
temperature for several minutes to an hour. The oligonucleotide is
thereby cleaved from the solid support and can be delivered to
enclosed tubing which is heated at about 65.degree. C. for about
1-2 hours to complete deprotection, i.e. removal of nucleobase and
internucleotide protecting groups.
[0119] When the 5' DMT group has been left intact, the solution
containing the deprotected oligonucleotide may be purified by
trityl-selective hydrophobic interaction by absorption onto the
polystyrene in the OneStep column in which it was synthesized.
Following absorption (loading), the column is treated with reagents
to effect washing away of impurities, detritylation of the
oligonucleotide, and elution of the deprotected, purified, and
detritylated oligonucleotide.
Example 6
[0120] Gas Phase Cleavage/deprotection:
[0121] A set of 48 oligonucleotides were synthesized in a single
pre-programmed run on the Model 3900 DNA Synthesizer (Applied
Biosystems, Foster City, Calif.). Each oligonucleotide was
synthesized at a 200 nmolar scale on about 10 mg of polystyrene
support in a column with inlet and outlet openings. The
oligonucleotides ranged in size from 15 to 30 nt in length. After
synthesis of the 48 oligonucleotides was complete, 200 .mu.l of a
1% DEM in acetonitrile solution was delivered to each column. Argon
gas was flushed through the openings for about 30 seconds to expel
most of the solution. The columns were then transferred to a
holder, e.g. 96 well microtiter format. The holder was placed in a
sealable stainless steel, pressure vessel with an internal volume
of approximately one gallon. Up to four such holders could be
placed in the vessel for parallel cleavage and deprotection
operations. The holders were placed on a mesh screen affixed
approximately 1 inch from the bottom of the vessel. Approximately
450 ml of chilled, concentrated ammonium hydroxide solution was
added to the bottom floor of the vessel, or into a shallow pan that
sits on the bottom floor of the vessel, below the mesh screen. The
columns or holders were not in direct contact with the ammonium
hydroxide solution. The vessel was sealed and heated to 65.degree.
C. for about 2 hours. The pressure generated inside during the
heating period was about 45 psi. The vessel was cooled, vented, and
opened.
[0122] The holders containing the columns were removed from the
vessel and placed in a device whereby a vacuum can be applied to
draw liquids and air through the inlet opening of the columns. To
each column, 250 .mu.l of water was delivered and pulled through to
waste. The cleaved and deprotected oligonucleotides were eluted by
delivering 250 .mu.l of 20% (50% for labelled oligonucleotides)
acetonitrile in water to each column and collecting the eluant in a
vessel mounted below the outlet opening of the column.
Alternatively, the liquid reagents, i.e. water wash or eluant
solution, can be drawn through the column by centrifugation where
the holder is rotated in a centrifuge. The eluted oligonucleotides
can be dried under vacuum and resuspended in an aqueous medium,
further diluted, or used directly by aliquot in experiments.
Example 7
[0123] Following the procedures of Example 3, the 25 nt
oligonucleotide:
5' H.sub.2N--(PEO).sub.2-- AAA ATC AAG AAC TAC AAG ACC GCC C3' (SEQ
ID. NO. 6)
[0124] was synthesized on C polystyrene support. After the final A
phosphoramidite was coupled, two PEO (pentaethyleneoxy;
--(CH.sub.2CH.sub.2O).sub.5--) linkers were coupled as PEO
phosphoramidite, followed by Aminolink TFA (Applied Biosystems,
Foster City, Calif.) phosphoramidite to give the 5' amino with 2
PEO linkages (Vinayak, WO 00/50432; Andrus, WO 98/39353). The
support was divided into two portions. One portion was cleaved and
deprotected with NH.sub.4OH only. The other portion was cleaved an
deprotected with 1% DEM in 15% ethanol:NH.sub.4OH. An aliquot from
each portion was analyzed by reverse phase HPLC. The portion
cleaved and deprotected with NH4OH only shows a complex product
mixture containing only 25.8% of the desired product eluting at 6.5
minutes (FIG. 5a). The product mixture is contaminated with
significant later eluting impurities. The portion cleaved and
deprotected with 1% DEM shows improved purity, 48.9% of the desired
product eluting at 6.5 minutes and diminished levels of earlier and
later eluting impurities (FIG. 5b).
[0125] All publications, patents, and patent applications referred
to herein are hereby incorporated by reference, and to the same
extent as if each individual publication, patent or patent
application was specifically and individually indicated to be
incorporated by reference.
[0126] Although only a few embodiments have been described in
detail above, those having ordinary skill in the chemical arts will
clearly understand that many modifications are possible in these
embodiments without departing from the teachings thereof. All such
modifications are intended to be encompassed within the scope of
the following claims.
Sequence CWU 1
1
6 1 8 DNA Unknown Synthetic DNA 1 tttttttt 8 2 15 DNA Unknown
Synthetic DNA 2 tttttttttt ttttt 15 3 13 DNA Unknown Synthetic DNA
3 cagtcgccct gcc 13 4 15 DNA Unknown Synthetic DNA 4 cttcttgcta
attcc 15 5 13 DNA Unknown Synthetic DNA 5 ccatgcgtta gcc 13 6 25
DNA Unknown Synthetic DNA 6 aaaatcaaga actacaagac cgccc 25
* * * * *