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US5484908A
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Oligonucleotides containing 5-propynyl pyrimidines
Assignee: Ionis Pharmaceuticals Inc
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Filing: 1991-11-26
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Granted: 1996-01-16
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Expires: 2011-11-26
Abstract
Abstract Oligonucleotides with enhanced hybridization binding possessing 5-propynyluracil and/or 5-propynylcytosine in place of uracil and cytosine, respectively. These oligonucleotides are useful in traditional hybridization assays for detection of a specific DNA sequence.
Inventors
- 👤 Brian Froehler
- 👤 Robert J. Jones
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-29 06:46
CPC Classifications
C; C07; C07H; C07H19/00; C07H19/02; C07H19/04; C07H19/06; C07H19/10; C07H19/16; C07H19/20; C07H21/00; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6839
Claims Analysis
Total Claims: 21
Claim 1
Independent Claim
109 words
A nucleoside analog having the general structural formula: ##STR14## wherein in each of formula 4 and formula 5 one R 1 is a protecting group and the other is an activated group for oligonucleotide synthesis or is a solid support; R 2 is selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl, o-pyridinyl, m-pyridinyl and p-pyridinyl; and R 3 is selected from the group consisting of H, OH, F, OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 .
Claim 2
Dependent Claim
109 words
A nucleoside analog having the general structural formula: ##STR14## wherein in each of formula 4 and formula 5 one R 1 is a protecting group and the other is an activated group for oligonucleotide synthesis or is a solid support; R 2 is selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl, o-pyridinyl, m-pyridinyl and p-pyridinyl; and R 3 is selected from the group consisting of H, OH, F, OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 .
Claim 3
Dependent Claim
16 words
The nucleoside analog of claim 1, wherein the protecting group is DMT (dimethoxytrityl) or MMT (monomethoxytrityl).
Claim 4
Dependent Claim
13 words
The nucleoside analog of claim 1 wherein R 3 is H or OH.
Claim 5
Dependent Claim
11 words
The nucleoside analog of claim 1 wherein R 2 is propynyl.
Claim 6
Dependent Claim
13 words
The nucleoside analog of claim 1 wherein the nucleoside is an α anomer.
Claim 7
Dependent Claim
58 words
An o-xyloso nucleoside dimer having the general structural formula: ##STR15## wherein each R 1 is H or a blocking group; and each B is independently a purine or pyrimidine base, provided that at least one B is ##STR16## wherein R 2 is selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl, o-pyridinyl, m-pyridinyl and p-pyridinyl.
Claim 8
Dependent Claim
58 words
An o-xyloso nucleoside dimer having the general structural formula: ##STR15## wherein each R 1 is H or a blocking group; and each B is independently a purine or pyrimidine base, provided that at least one B is ##STR16## wherein R 2 is selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl, o-pyridinyl, m-pyridinyl and p-pyridinyl.
Claim 9
Dependent Claim
11 words
The nucleoside dimer of claim 6 wherein R 2 is propynyl.
Claim 10
Dependent Claim
29 words
The nucleoside dimer of claim 7 wherein the blocking group is selected from the group consisting of PO 3 -2 , DMT MMT H-phosphonate, methyl phosphonate, methylphosphoramidite, or β-cyanoethylphosphoramidite.
Claim 11
Dependent Claim
129 words
A nucleoside analog dimer having the general structural formula 8: ##STR17## wherein X is selected from the group consisting of O and S; B is independently a purine or pyrimidine base, provided that at least one B is ##STR18## wherein each R 1 is independently selected from the group consisting of H and a blocking group; each R 2 is independently selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl o-pyridinyl, m-pryridinyl and p-pyridinyl; and each R 3 is independently selected from the group consisting of H, OH, F, OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , or SC 3 H 5 .
Claim 12
Dependent Claim
129 words
A nucleoside analog dimer having the general structural formula 8: ##STR17## wherein X is selected from the group consisting of O and S; B is independently a purine or pyrimidine base, provided that at least one B is ##STR18## wherein each R 1 is independently selected from the group consisting of H and a blocking group; each R 2 is independently selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl o-pyridinyl, m-pryridinyl and p-pyridinyl; and each R 3 is independently selected from the group consisting of H, OH, F, OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , or SC 3 H 5 .
Claim 13
Dependent Claim
20 words
The dimer of claim 9 wherein R 1 is H, PO 3 -2 , DMT, MMT, H-phosphonate, methylphosphoramidite or β-cyanoethylphosphoramidite.
Claim 14
Dependent Claim
15 words
The dimer of claim 9 wherein at least one B is 5-propynyluracil, 3-methyl-1-butynyluracil or 5-propynylcytosine.
Claim 15
Dependent Claim
24 words
The dimer of claim 9 wherein at least one R 2 is propynyl, R 3 is OC 3 H 5 and X is S.
Claim 16
Dependent Claim
17 words
The nucleoside analog of claim 1 wherein the activated group is H-phosphonate, methyl phosphonate, methylphosphoramidite or β-cyanoethylphosphoramidite.
Claim 17
Dependent Claim
41 words
The nucleoside analog of claim 1 wherein R 1 at the 5' position is DMT (dimethoxytrityl) or MMT (monomethoxytrityl); R 1 at the 3' position is H-phosphonate, β-cyanoethylphosphoramidite or methylphosphoramidite; R 2 is propynyl or 3-methyl-1-butynyl; and R 3 is H.
Claim 18
Dependent Claim
32 words
The dimer of claim 6 wherein one of R 1 is a protecting group and the other of R 1 is an activated group for oligonucleotide synthesis or is a solid support.
Claim 19
Dependent Claim
16 words
The dimer of claim 15 wherein the activated group is H-phosphonate, methyl phosphonate, methylphosphoramidite or β-cyanoethylphosphoramidite.
Claim 20
Dependent Claim
32 words
The dimer of claim 9 wherein one of R 1 is a protecting group and the other of R 1 is an activated group for oligonucleotide synthesis or is a solid support.
Claim 21
Dependent Claim
16 words
The dimer of claim 17 wherein the activated group is H-phosphonate, methyl phosphonate, methylphosphoramidite or β-cyanoethylphosphoramidite.
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) | 1999-01-15 | 1999-07-17 | 2000-01-16 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2003-01-15 | 2003-07-17 | 2004-01-16 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2007-01-15 | 2007-07-17 | 2008-01-16 | $7700.00 | Window Closed / Lapsed |