US5770716A
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Substituted propargylethoxyamido nucleosides, oligonucleotides and methods for using same
Assignee: Applied Biosystems LLC
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Filing: 1997-04-10
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Granted: 1998-06-23
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Expires: 2017-04-10
Abstract
Abstract Substituted propargylethoxyamido nucleosides are disclosed having the structure <IMAGE> wherein X is selected from the group consisting of amino alkanoic acid, alkylamino benzoic acid, alpha -amino acid, and 4-amino-2-butynoic acid. R1 and R2 taken separately are selected from the group consisting of -H, lower alkyl, protecting group, and label; R3 is selected from the group consisting of -H and lower alkyl. B is a 7-deazapurine, purine, or pyrimidine nucleoside base. When B is purine or 7-deazapurine, the sugar moiety is attached at the N9-position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N1-position of the pyrimidine. When B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine. W1 is selected from the group consisting of -H and -OH. W2 is -OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position. W3 is selected from the group consisting of -PO4, -P2O7, -P3O10, phosphate analog, and -OH. Additionaly, a primer extension method is provided employing the above X-substituted propargylethoxyamido nucleosides, and polynucleotides including the above X-substituted propargylethoxyamido nucleosides is provided.
Inventors
- 👤 Shaheer H. Khan
- 👤 Steven M. Menchen
- 👤 Barnett B. Rosenblum
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-30 04:22
CPC Classifications
C; C07; C07H; C07H21/00; C07H19/00; C07H19/02; C07H19/04; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6869; Y; Y02; Y02P; Y02P20/00; Y02P20/50; Y02P20/55
Claims Analysis
Total Claims: 15
Claim 1
Independent Claim
220 words
A polynucleotide comprising a nucleotide compound having the structure: ##STR20## wherein: X is selected from the group consisting of ##STR21## where n ranges from 1 to 5, ##STR22## where n ranges from 1 to 5, ##STR23## R 1 and R 2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R 3 is selected from the group consisting of --H and lower alkyl; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; wherein when B is purine or 7-deazapurine, the sugar moiety is attached at the N 9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N 1 -position of the pyrimidine; and wherein when B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine; W 1 is selected from the group consisting of --H and --OH; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is selected from the group consisting of --PO 4 , phosphate analog, and --OH.
Claim 2
Dependent Claim
220 words
A polynucleotide comprising a nucleotide compound having the structure: ##STR20## wherein: X is selected from the group consisting of ##STR21## where n ranges from 1 to 5, ##STR22## where n ranges from 1 to 5, ##STR23## R 1 and R 2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R 3 is selected from the group consisting of --H and lower alkyl; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; wherein when B is purine or 7-deazapurine, the sugar moiety is attached at the N 9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N 1 -position of the pyrimidine; and wherein when B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine; W 1 is selected from the group consisting of --H and --OH; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is selected from the group consisting of --PO 4 , phosphate analog, and --OH.
Claim 3
Dependent Claim
227 words
A nucleoside compound having the structure: ##STR24## wherein: X is selected from the group consisting of ##STR25## where n ranges from 1 to 5, ##STR26## where n ranges from 1 to 5, ##STR27## R 1 and R 2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R 3 is selected from the group consisting of --H and lower alkyl; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; wherein when B is purine or 7-deazapurine, the sugar moiety is attached at the N 9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N 1 -position of the pyrimidine; and wherein when B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine; W 1 is selected from the group consisting of --H and --OH; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is selected from the group consisting of --PO 4 , --P 2 O 7 , --P 3 O 10 , phosphate analog, and --OH.
Claim 4
Dependent Claim
227 words
A nucleoside compound having the structure: ##STR24## wherein: X is selected from the group consisting of ##STR25## where n ranges from 1 to 5, ##STR26## where n ranges from 1 to 5, ##STR27## R 1 and R 2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R 3 is selected from the group consisting of --H and lower alkyl; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; wherein when B is purine or 7-deazapurine, the sugar moiety is attached at the N 9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N 1 -position of the pyrimidine; and wherein when B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine; W 1 is selected from the group consisting of --H and --OH; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is selected from the group consisting of --PO 4 , --P 2 O 7 , --P 3 O 10 , phosphate analog, and --OH.
Claim 5
Dependent Claim
16 words
The nucleoside compound of claim 2 wherein one of R 1 and R 2 is label.
Claim 6
Dependent Claim
13 words
The nucleoside compound of claim 3 wherein the label is a fluorescein-type dye.
Claim 7
Dependent Claim
23 words
The nucleoside compound of claim 3 wherein the label is selected from a group consisting of a rhodamine-type dye and a FLAN-type dye.
Claim 8
Dependent Claim
40 words
The nucleoside compound of claim 2 wherein: W 1 is --H; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is --P 3 P 10 .
Claim 9
Dependent Claim
22 words
The nucleoside compound of claim 2 wherein W 2 selected from the group consisting of --OH, --H, azido, amino, halo, and methoxy.
Claim 10
Dependent Claim
18 words
The nucleoside compound of claim 2 wherein W 2 selected from the group consisting of --H and fluoro.
Claim 11
Dependent Claim
19 words
The nucleoside of claim 2 wherein B is selected from the group consisting of uracil, cytosine, 7-deazaadenine, and 7-deazaguanosine.
Claim 12
Dependent Claim
18 words
The nucleoside compound of claim 2 wherein X is alkylamino benzoic acid having a para configuration and n=1.
Claim 13
Independent Claim
272 words
A method for performing a primer extension reaction comprising the steps of: providing a template nucleic acid; annealing an oligonucleotide primer to a portion of the template nucleic acid; and adding primer-extension reagents to the primer-template hybrid for extending the primer, the primer extension reagents including a nucleoside compound having the structure: ##STR28## wherein X is selected from the group consisting of ##STR29## where n ranges from 1 to 5, ##STR30## where n ranges from 1 to 5, ##STR31## R 1 and R 2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R 3 is selected from the group consisting of --H and lower alkyl; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; wherein when B is purine or 7-deazapurine, the sugar moiety is attached at the N 9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N 1 -position of the pyrimidine; and wherein when B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine; W 1 is selected from the group consisting of --H and --OH; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is selected from the group consisting of --PO 4 , --P 2 O 7 , --P 3O 10 , phosphate analog, and --OH.
Claim 14
Independent Claim
272 words
A method for performing a primer extension reaction comprising the steps of: providing a template nucleic acid; annealing an oligonucleotide primer to a portion of the template nucleic acid; and adding primer-extension reagents to the primer-template hybrid for extending the primer, the primer extension reagents including a nucleoside compound having the structure: ##STR28## wherein X is selected from the group consisting of ##STR29## where n ranges from 1 to 5, ##STR30## where n ranges from 1 to 5, ##STR31## R 1 and R 2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R 3 is selected from the group consisting of --H and lower alkyl; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; wherein when B is purine or 7-deazapurine, the sugar moiety is attached at the N 9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N 1 -position of the pyrimidine; and wherein when B is a purine, the adjacent triple-bonded carbon is attached to the 8-position of the purine, when B is 7-deazapurine, the adjacent triple-bonded carbon is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, the adjacent triple-bonded carbon is attached to the 5-position of the pyrimidine; W 1 is selected from the group consisting of --H and --OH; W 2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W 3 is selected from the group consisting of --PO 4 , --P 2 O 7 , --P 3O 10 , phosphate analog, and --OH.
Claim 15
Dependent Claim
20 words
The method of claim 11 wherein one of R 1 and R 2 is label and the other is --H.
References Cited (Backward Citations)
US5047518A
Cited
US5151507A
Cited
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