US4849513A
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Deoxyribonucleoside phosphoramidites in which an aliphatic amino group is attached to the sugar ring and their use for the preparation of oligonucleotides containing aliphatic amino groups
Assignee: California Institute of Technology
•
Filing: 1986-06-24
•
Granted: 1989-07-18
•
Expires: 2006-06-24
Abstract
Abstract The invention consists of compounds and methods for the synthesis of oligonucleotides which contain one or more free aliphatic amino groups attached to the sugar moieties of the nucleoside subunits. The synthetic method is versatile and general, permitting amino groups to be selectively placed at any position on oligonucleotides of any composition or length which is attainable by current DNA synthetic methods. Fluorescent dyes or other detectable moieties may be covalently attached to the amino groups to yield the corresponding modified oligonucleotide.
Inventors
- 👤 Lloyd M. Smith
- 👤 Steven Fung
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-29 22:29
CPC Classifications
C; C07; C07H; C07H21/00; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6816
Claims Analysis
Total Claims: 88
Claim 1
Independent Claim
104 words
Protected amino nucleosides having the formula: ##STR26## wherein B is selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, and inosine, R 1 , R 2 and R 5 are either H, OR, or NHR', with the proviso that one of R 1 , R 2 and R 5 is NHR', and only R 5 can be OH, wherein R is a monovalent protecting organic group containing from 1 to about 25 carbon atoms, R' is a nitrogen protecting group; R 6 is lower alkyl or heterocyclic, and R 7 is lower alkyl, cyano lower alkyl, halo lower alkyl, or nitrophenyl-lower alkyl.
Claim 2
Dependent Claim
104 words
Protected amino nucleosides having the formula: ##STR26## wherein B is selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, and inosine, R 1 , R 2 and R 5 are either H, OR, or NHR', with the proviso that one of R 1 , R 2 and R 5 is NHR', and only R 5 can be OH, wherein R is a monovalent protecting organic group containing from 1 to about 25 carbon atoms, R' is a nitrogen protecting group; R 6 is lower alkyl or heterocyclic, and R 7 is lower alkyl, cyano lower alkyl, halo lower alkyl, or nitrophenyl-lower alkyl.
Claim 3
Dependent Claim
113 words
Protected 5'-amino nucleoside phosphoramidites having the formula: ##STR27## wherein B is selected from the group consisting of thymine and uracil; X 1 is selected from trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyl-diphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y--NH--(CHR).sub.n --CO wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100; R 1 is selected from the group consisting of lower alkyl (in which case m=2) and heterocyclic (in which case m=1), and R 2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl.
Claim 4
Dependent Claim
113 words
Protected 5'-amino nucleoside phosphoramidites having the formula: ##STR27## wherein B is selected from the group consisting of thymine and uracil; X 1 is selected from trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyl-diphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y--NH--(CHR).sub.n --CO wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100; R 1 is selected from the group consisting of lower alkyl (in which case m=2) and heterocyclic (in which case m=1), and R 2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl.
Claim 5
Dependent Claim
10 words
The compounds of claim 2 wherein X 1 is trifluoroacetyl.
Claim 6
Dependent Claim
10 words
The compounds of claim 2 wherein X 1 is 9-fluorenylmethyloxycarbonyl.
Claim 7
Dependent Claim
10 words
The compounds of claim 2 wherein X 1 is p-anisyldiphenylmethyl.
Claim 8
Dependent Claim
10 words
The compounds of claim 2 wherein X 1 is triphenylmethyl.
Claim 9
Dependent Claim
10 words
The compounds of claim 2 wherein X 1 is N-tri-fluoroacetylglycol.
Claim 10
Dependent Claim
9 words
The compounds of claim 2 wherein B is thymine.
Claim 11
Dependent Claim
9 words
The compounds of claim 2 wherein B is uracil.
Claim 12
Dependent Claim
10 words
The compounds of claim 2 wherein R 2 is methyl.
Claim 13
Dependent Claim
10 words
The compounds of claim 2 wherein R 2 is beta-cyanoethyl.
Claim 14
Dependent Claim
10 words
The compounds of claim 2 wherein R 1 is methyl.
Claim 15
Dependent Claim
10 words
The compounds of claim 2 wherein R 1 is isopropyl.
Claim 16
Dependent Claim
10 words
The compounds of claim 2 wherein R 1 is morpholino.
Claim 17
Dependent Claim
14 words
The compounds of claim 2 wherein B is thymine and X 1 is trifluoroacetyl.
Claim 18
Dependent Claim
14 words
The compounds of claim 2 wherein B is thymine and X 1 is 9-fluorenylmethyloxycarbonyl.
Claim 19
Dependent Claim
14 words
The compounds of claim 2 wherein B is thymine and X 1 is p-anisyldiphenylmethyl.
Claim 20
Dependent Claim
14 words
The compounds of claim 2 wherein B is thymine and X 1 is triphenylmethyl.
Claim 21
Dependent Claim
14 words
The compounds of claim 2 wherein B is thymine and X 1 is N-trifluolroacetylglycyl.
Claim 22
Dependent Claim
14 words
The compounds of claim 2 wherein B is uracil and X 1 is trifluoroacetyl.
Claim 23
Dependent Claim
14 words
The compounds of claim 2 wherein B is uracil and X 1 is 9-fluorenylmethyloxycarbonyl.
Claim 24
Dependent Claim
14 words
The compounds of claim 2 wherein B is uracil and X 1 is p-anisyldiphenylmethyl.
Claim 25
Dependent Claim
14 words
The compounds of claim 2 wherein B is uracil and X 1 is triphenylmethyl.
Claim 26
Dependent Claim
14 words
The compounds of claim 2 wherein B is uracil and X 1 is N-trifluoroacetylglycyl.
Claim 27
Dependent Claim
6 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-methyl-N,N-diisopropylamino phosphoramidite having the formula: ##STR28##
Claim 28
Dependent Claim
6 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-methyl-N,N-diisopropylamino phosphoramidite having the formula: ##STR28##
Claim 29
Dependent Claim
6 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-dioxythymidine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite having the formula: ##STR29##
Claim 30
Dependent Claim
6 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-dioxythymidine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite having the formula: ##STR29##
Claim 31
Dependent Claim
2 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
Claim 32
Dependent Claim
2 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
Claim 33
Dependent Claim
2 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-methyl-N,N-dimethylamino phosphoramidite.
Claim 34
Dependent Claim
2 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-methyl-N,N-dimethylamino phosphoramidite.
Claim 35
Dependent Claim
2 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N-dimethylamino phosphoramidite.
Claim 36
Dependent Claim
2 words
5'-N-(9-fluorenylmethyloxycarbonyl)-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N-dimethylamino phosphoramidite.
Claim 37
Dependent Claim
2 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine-3'-O-methyl-N,N-diisopropylamino phosphoramidite.
Claim 38
Dependent Claim
2 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine-3'-O-methyl-N,N-diisopropylamino phosphoramidite.
Claim 39
Dependent Claim
2 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine-3'-O-beta-cyanoethyl-N,N-dimethylamino phosphoramidite.
Claim 40
Dependent Claim
2 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine-3'-O-beta-cyanoethyl-N,N-dimethylamino phosphoramidite.
Claim 41
Dependent Claim
2 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine-3'-O-methyl-N,N-dimethylamino phosphoramidite.
Claim 42
Dependent Claim
2 words
5'-N-p-anisyldiphenylmethyl-5'-amino-5'-deoxy-thymidine-3'-O-methyl-N,N-dimethylamino phosphoramidite.
Claim 43
Dependent Claim
2 words
5'-N-p-triphenylmethyl-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
Claim 44
Dependent Claim
2 words
5'-N-p-triphenylmethyl-5'-amino-5'-deoxythymidine-3'-O-beta-cyanoethyl-N,N-diisopropylamino phosphoramidite.
Claim 45
Dependent Claim
128 words
Protected 5'-amino nucleoside phosphoramidites having the formula: ##STR30## wherein B is selected from the group consisting of thymine and uracil; X 1 is selected from trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyl-diphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y--NH--(CHR).sub.n --CO wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100; R 1 is selected from the group consisting of lower alkyl (in which case m=2) and heterocyclic (in which case m=1), and R 2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X 2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl.
Claim 46
Dependent Claim
128 words
Protected 5'-amino nucleoside phosphoramidites having the formula: ##STR30## wherein B is selected from the group consisting of thymine and uracil; X 1 is selected from trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyl-diphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y--NH--(CHR).sub.n --CO wherein Y is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyldiphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100; R 1 is selected from the group consisting of lower alkyl (in which case m=2) and heterocyclic (in which case m=1), and R 2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, o-chlorophenyl, or p-chlorophenyl; and X 2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl.
Claim 47
Dependent Claim
10 words
The compounds of claim 34 wherein X 1 is trifluoroacetyl.
Claim 48
Dependent Claim
10 words
The compounds of claim 34 wherein X 1 is 9-fluorenylmethyloxycarbonyl.
Claim 49
Dependent Claim
10 words
The compounds of claim 34 wherein X 1 is N-trifluoroacetylglycol.
Claim 50
Dependent Claim
9 words
The compounds of claim 34 wherein B is uracil.
Claim 51
Dependent Claim
10 words
The compounds of claim 34 wherein R 1 is methyl.
Claim 52
Dependent Claim
10 words
The compounds of claim 34 wherein R 1 is isopropyl.
Claim 53
Dependent Claim
10 words
The compounds of claim 34 wherein R 1 is morpholino.
Claim 54
Dependent Claim
10 words
The compounds of claim 34 wherein R 2 is methyl.
Claim 55
Dependent Claim
10 words
The compounds of claim 34 wherein R 2 is beta-cynaoethyl.
Claim 56
Dependent Claim
14 words
The compounds of claim 34 wherein B is uracil and X 1 is trifluoroacetyl.
Claim 57
Dependent Claim
14 words
The compounds of claim 34 wherein B is uracil and X 1 is fluorenylmethyloxycarbonyl.
Claim 58
Dependent Claim
14 words
The compounds of claim 34 wherein B is uracil and X 1 is N-trifluoroacetylglycyl.
Claim 59
Dependent Claim
9 words
5'-O-di-p-anisylphenylmethyl-2'-N -trifluoacetyl-2 -amino-2'-deoxyuridine-3'-O-methyl-N, N-diisopropylamino phosphoramidite having the formula: ##STR31##
Claim 60
Dependent Claim
9 words
5'-O-di-p-anisylphenylmethyl-2'-N -trifluoacetyl-2 -amino-2'-deoxyuridine-3'-O-methyl-N, N-diisopropylamino phosphoramidite having the formula: ##STR31##
Claim 61
Dependent Claim
7 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoacetylglycol) -2'-amino-2'-deoxyuridine-3'-O-methyl-N,N-diisopropylamino phosphoramidite having the formula: ##STR32##
Claim 62
Dependent Claim
7 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoacetylglycol) -2'-amino-2'-deoxyuridine-3'-O-methyl-N,N-diisopropylamino phosphoramidite having the formula: ##STR32##
Claim 63
Dependent Claim
5 words
5'-O-di-p-anisylphenylmethyl-2'-N-trifluoacetyl -2'-amino-2'-deoxyuridine-3 -O-beta-cyanoethyl-N, N-diisopropylamino phosphoramidite.
Claim 64
Dependent Claim
5 words
5'-O-di-p-anisylphenylmethyl-2'-N-trifluoacetyl -2'-amino-2'-deoxyuridine-3 -O-beta-cyanoethyl-N, N-diisopropylamino phosphoramidite.
Claim 65
Dependent Claim
4 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoacetylglycol) -2'-amino-2'-deoxyuridine-3'-O-beta-cyanoethyl-N, N-diisopropylamino phosphoramidite.
Claim 66
Dependent Claim
4 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoacetylglycol) -2'-amino-2'-deoxyuridine-3'-O-beta-cyanoethyl-N, N-diisopropylamino phosphoramidite.
Claim 67
Dependent Claim
129 words
Protected 2'-amino-nucleoside phosphoramidites having the formula: ##STR33## wherein B is selected from the the group consisting of thymine and uracil; X 1 is selected from trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyl-diphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y--NH--(CHR).sub.n --CO wherein Y is selected from the group consisting of trofluoroacetyl, 9- fluorenylmethoxycarbonyl, p-anisylphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100; R 1 is selected from the group consisting of lower alkyl (in which case m=2) and heterocyclic (in which case m=1), and R 2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, O-chlorophenyl, or p-chlorophenyl; and X 2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl.
Claim 68
Dependent Claim
129 words
Protected 2'-amino-nucleoside phosphoramidites having the formula: ##STR33## wherein B is selected from the the group consisting of thymine and uracil; X 1 is selected from trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, p-anisyl-diphenylmethyl, triphenylmethyl, and protected amino acyl having the formula: Y--NH--(CHR).sub.n --CO wherein Y is selected from the group consisting of trofluoroacetyl, 9- fluorenylmethoxycarbonyl, p-anisylphenylmethyl, and triphenylmethyl; R is an amino acid side chain or hydrogen when n=1; and R is hydrogen when n is an integer from 2 to 100; R 1 is selected from the group consisting of lower alkyl (in which case m=2) and heterocyclic (in which case m=1), and R 2 is selected from the group consisting of methyl, beta-cyanoethyl, p-nitrophenethyl, O-chlorophenyl, or p-chlorophenyl; and X 2 is a hydroxyl protecting group selected from triphenylmethyl, p-anisyl-diphenylmethyl, di-p-anisylphenylmethyl, and 9-phenylxanthenyl.
Claim 69
Dependent Claim
10 words
The compounds of claim 51 wherein X 1 is trifluoroacetyl.
Claim 70
Dependent Claim
10 words
The compounds of claim 51 wherein X 1 is 9-fluorenylmethyloxycarbonyl.
Claim 71
Dependent Claim
10 words
The compounds of claim 51 wherein X 1 is N-trifluoroacetylglycyl.
Claim 72
Dependent Claim
9 words
The compounds of claim 51 wherein B is uracil.
Claim 73
Dependent Claim
10 words
The compounds of claim 51 wherein R 1 is methyl.
Claim 74
Dependent Claim
10 words
The compounds of claim 49 wherein R 1 is isopropyl.
Claim 75
Dependent Claim
10 words
The compounds of claim 49 wherein R 1 is morpholino.
Claim 76
Dependent Claim
10 words
The compounds of claim 49 wherein R 2 is methyl.
Claim 77
Dependent Claim
10 words
The compounds of claim 49 wherein R 2 is beta-cyanoethyl.
Claim 78
Dependent Claim
14 words
The compounds of claim 49 wherein B is uracil and X 1 is trifluoroacetyl.
Claim 79
Dependent Claim
14 words
The compounds of claim 49 wherein B is uracil and X 1 is fluorenylmethyloxycarbonyl.
Claim 80
Dependent Claim
14 words
The compounds of claim 49 wherein B is uracil and X 1 is N-trifluoroacetylglycyl.
Claim 81
Dependent Claim
4 words
5'-O-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl -2'-amino-2'-deoxy-ara-uridine-3'-O-methyl-N, N-diisopropylamino phosphoramidite.
Claim 82
Dependent Claim
4 words
5'-O-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl -2'-amino-2'-deoxy-ara-uridine-3'-O-methyl-N, N-diisopropylamino phosphoramidite.
Claim 83
Dependent Claim
2 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycol)-2'-amino-2'-deoxy-ara-uridine-3'-O-methyl-N,N-diiso-propylamino phosphoramidite.
Claim 84
Dependent Claim
2 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycol)-2'-amino-2'-deoxy-ara-uridine-3'-O-methyl-N,N-diiso-propylamino phosphoramidite.
Claim 85
Dependent Claim
2 words
5'-O-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxy-ara-uridine-3'-O-beta-cyanoethyl-N,N-diiso-propylamino phosphoramidite.
Claim 86
Dependent Claim
2 words
5'-O-di-p-anisylphenylmethyl-2'-N-trifluoroacetyl-2'-amino-2'-deoxy-ara-uridine-3'-O-beta-cyanoethyl-N,N-diiso-propylamino phosphoramidite.
Claim 87
Dependent Claim
3 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycol)-2'-amino-2'-deoxy-ara-uridine-3'-O-beta cyanoethyl-N,N-diisopropylamino phosphoramidite.
Claim 88
Dependent Claim
3 words
5'-O-di-p-anisylphenylmethyl-2'-N-(N-trifluoroacetylglycol)-2'-amino-2'-deoxy-ara-uridine-3'-O-beta cyanoethyl-N,N-diisopropylamino phosphoramidite.
References Cited (Backward Citations)
USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 1992-07-17 | 1993-01-16 | 1993-07-18 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 1996-07-17 | 1997-01-16 | 1997-07-18 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2000-07-17 | 2001-01-16 | 2001-07-18 | $7700.00 | Window Closed / Lapsed |