US5585481A
Expired / Lapsed
US
⏱️ 0.0 years remaining
Linking reagents for nucleotide probes
Assignee: Gen Probe Inc
•
Filing: 1994-01-14
•
Granted: 1996-12-17
•
Expires: 2014-01-14
Abstract
Abstract A versatile reagent with a non-nucleotide monomeric unit having a ligand, and first and second coupling groups which are linked to the non-nucleotide monomeric unit. The ligand can be either a chemical moiety, such as a label or intercalator, or a linking arm which can be linked to such a moiety. Such reagent permits preparation of versatile nucleotide/non-nucleotide polymers, having any desired sequence of nucleotide and non-nucleotide monomeric units, each of the latter of which bear a desired ligand. These polymers can for example, be used as probes which can exhibit enhanced sensitivity and/or which are capable of detecting a genus of nucleotides each species of which has a common target nucleotide sequence of interest bridged by different sequences not of interest.
Inventors
- 👤 Lyle J. Arnold, Jr.
- 👤 Mark A. Reynolds
- 👤 Ram S. Bhatt
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-28 23:43
CPC Classifications
C; C07; C07H; C07H21/00; C07F; C07F9/00; C07F9/02; C07F9/06; C07F9/22; C07F9/24; C07F9/2404; C07F9/2408
Claims Analysis
Total Claims: 53
Claim 1
Independent Claim
185 words
A linking reagent having the formula: D--X.sup.1 --R.sup.2 (X.sup.3 --M).sub.n --Z wherein: Z is a reactive phosphorus-containing group attached to the end of R 2 , wherein said reactive phosphorus-containing group is able to couple to, or is activatable for coupling to, an OH group of a first nucleotide; R 2 comprises a chain of atoms which is 2-20 atoms in length joined to X 1 and Z, wherein R 2 is stable to DNA synthesis and deprotection conditions; X l is either O, S, NH or NNH; D is a protecting group which may be removed to permit X 1 to be coupled to the phosphorus group of a second nucleotide; each X 3 is independently a linker-arm joined at a first end to R 2 and joined at a second end to M, wherein each X 3 is stable to DNA synthesis and deprotection conditions; each M is independently either a label stable to DNA synthesis and deprotection conditions or a protecting group which can be removed to permit X 3 to be coupled to a label; and n is a positive integer.
Claim 2
Dependent Claim
185 words
A linking reagent having the formula: D--X.sup.1 --R.sup.2 (X.sup.3 --M).sub.n --Z wherein: Z is a reactive phosphorus-containing group attached to the end of R 2 , wherein said reactive phosphorus-containing group is able to couple to, or is activatable for coupling to, an OH group of a first nucleotide; R 2 comprises a chain of atoms which is 2-20 atoms in length joined to X 1 and Z, wherein R 2 is stable to DNA synthesis and deprotection conditions; X l is either O, S, NH or NNH; D is a protecting group which may be removed to permit X 1 to be coupled to the phosphorus group of a second nucleotide; each X 3 is independently a linker-arm joined at a first end to R 2 and joined at a second end to M, wherein each X 3 is stable to DNA synthesis and deprotection conditions; each M is independently either a label stable to DNA synthesis and deprotection conditions or a protecting group which can be removed to permit X 3 to be coupled to a label; and n is a positive integer.
Claim 3
Dependent Claim
81 words
The linking reagent of claim 1, wherein Z has the formula: ##STR3## wherein, X 2 is either a halogen or a substituted amino; R 3 is selected from the group consisting of alkyl, alkoxy and phenoxy; X 4 is selected from the group consisting of halogen, amino and O - ; and R 5 is selected from the group consisting of alkyl, alkoxy, aryloxy and H, provided that R 5 may be H only if X 4 is O - .
Claim 4
Dependent Claim
12 words
The linking reagent of claim 2, wherein Z has the formula: ##STR4##
Claim 5
Dependent Claim
31 words
The linking reagent of claim 3, wherein X 2 is either Cl or a secondary amino; and R 3 is selected from the group consisting of chlorophenoxy, methoxy, ethoxy and beta-cyanoethoxy.
Claim 6
Dependent Claim
20 words
The linking reagent of claim 4, wherein X 2 is selected from the group consisting of diisopropylamino, dimethyl and morpholino.
Claim 7
Dependent Claim
12 words
The linking reagent of claim 2, wherein Z has the formula: ##STR5##
Claim 8
Dependent Claim
52 words
The linking reagent of claim 6, wherein X 4 is selected from the group consisting of Cl, secondary amino and O - ; and R 5 is selected from the group methoxy, ethoxy, monochlorophenoxy, beta-cyanoethoxy and H, provided that R 5 may be H only if X 4 is O - .
Claim 9
Dependent Claim
11 words
The linking reagent of claim 2, wherein X 1 is O.
Claim 10
Dependent Claim
96 words
The linking reagent of any one of claims 1-8, wherein R 2 consists essentially of a hydrocarbon chain optionally substituted by one or more heteroatoms, each independently selected from the group consisting of oxygen, nitrogen and sulfur; and each X 3 is independently either NH, O, S, NNH, or a chain 1-25 atoms in length ending in either NH, O, S or NNH, wherein each of said X 3 chain of atoms consists essentially of a hydrocarbon chain optionally substituted by one or more heteroatoms independently selected from the group consisting of oxygen, nitrogen and sulfur.
Claim 11
Dependent Claim
10 words
The linking reagent claim 9, wherein R 2 is acyclic.
Claim 12
Dependent Claim
14 words
The linking reagent of claim 10, wherein R 2 in an acyclic hydrocarbon chain.
Claim 13
Dependent Claim
19 words
The linking reagent of claim 11, wherein said hydrocarbon chain has a length of 2 to 10 carbon atoms.
Claim 14
Dependent Claim
19 words
The linking reagent of claim 12, wherein said hydrocarbon chain has a length of 2 to 3 carbon atoms.
Claim 15
Dependent Claim
10 words
The linking reagent of claim 13, wherein n is 1.
Claim 16
Dependent Claim
17 words
The linking reagent of any one of claims 1-8, wherein R 2 is an acyclic hydrocarbon chain.
Claim 17
Dependent Claim
19 words
The linking reagent of claim 15, wherein said hydrocarbon chain has a length of 2 to 10 carbon atoms.
Claim 18
Dependent Claim
19 words
The linking reagent of claim 16, wherein said hydrocarbon chain has a length of 2 to 3 carbon atoms.
Claim 19
Dependent Claim
10 words
The linking reagent of claim 17, wherein n is 1.
Claim 20
Dependent Claim
32 words
The linking reagent of claim 2, wherein each X 3 is linked to R 2 by a carbon and to M by a nitrogen and each M is independently trifluoroacetyl or 9-trifluorenylmethoxycarbonyl.
Claim 21
Dependent Claim
14 words
The linking reagent of claim 2, or 8, wherein D is triphenylmethyl or dimethoxytriphenylmethyl.
Claim 22
Dependent Claim
18 words
The linking reagent of claim 2, wherein M is said label stable to DNA synthesis and deprotection conditions.
Claim 23
Dependent Claim
26 words
The linking reagent of claim 2, wherein M is said protecting group which may be removed to permit X 3 to be coupled to said label.
Claim 24
Dependent Claim
168 words
A linking reagent composition having the formula: Q--X.sup.1 --R.sup.2 (X.sup.3 --M).sub.n --T wherein: T is a DNA synthesis support attached to the end of R 2 through a cleavable ester linkage, R 2 comprises a chain of atoms which is 2-20 atoms in length joining X 1 to T, wherein each R 2 is stable to DNA synthesis and deprotection conditions, X 1 is O, S, NH or NNH, Q is a nucleotide or a protecting group which may be removed to permit X 1 to be coupled to the phosphorus group of a nucleotide, each X 3 is independently a linker-arm joined at a first end to R 2 and joined at a second end to M, wherein each X 3 is stable to DNA synthesis and deprotection conditions, each M is independently a label stable to DNA synthesis and deprotection conditions or a protecting group which can be removed to permit X 3 to be coupled to a label, and each n is a positive integer.
Claim 25
Dependent Claim
168 words
A linking reagent composition having the formula: Q--X.sup.1 --R.sup.2 (X.sup.3 --M).sub.n --T wherein: T is a DNA synthesis support attached to the end of R 2 through a cleavable ester linkage, R 2 comprises a chain of atoms which is 2-20 atoms in length joining X 1 to T, wherein each R 2 is stable to DNA synthesis and deprotection conditions, X 1 is O, S, NH or NNH, Q is a nucleotide or a protecting group which may be removed to permit X 1 to be coupled to the phosphorus group of a nucleotide, each X 3 is independently a linker-arm joined at a first end to R 2 and joined at a second end to M, wherein each X 3 is stable to DNA synthesis and deprotection conditions, each M is independently a label stable to DNA synthesis and deprotection conditions or a protecting group which can be removed to permit X 3 to be coupled to a label, and each n is a positive integer.
Claim 26
Dependent Claim
29 words
The composition of claim 23, wherein Q is said protecting group which may be removed to permit X 1 to be coupled to the phosphorus group of said nucleotide.
Claim 27
Dependent Claim
10 words
The composition of claim 24, wherein X 1 is 0.
Claim 28
Dependent Claim
92 words
The composition of claim 23, wherein R 2 consists essentially of a hydrocarbon chain optionally substituted by one or more heteroatoms each independently selected from the group consisting of oxygen, nitrogen and sulfur; and each X 3 is independently either NH, O, S, NNH, or a chain of 1-25 atoms in length ending in NH, O, S or NNH, wherein each of said X 3 chain of atoms consists essentially of a hydrocarbon chain optionally substituted by one or more heteroatoms independently selected from the group consisting of oxygen, nitrogen and sulfur.
Claim 29
Dependent Claim
10 words
The composition of claim 26, wherein X 1 is 0.
Claim 30
Dependent Claim
13 words
The composition of any one of claims 23-27, wherein R 2 is acyclic.
Claim 31
Dependent Claim
14 words
The linking reagent of claim 28, wherein R 2 in an acyclic hydrocarbon chain.
Claim 32
Dependent Claim
18 words
The composition of claim 29, wherein said hydrocarbon chain has a length of 2 to 10 carbon atoms.
Claim 33
Dependent Claim
18 words
The composition of claim 30, wherein said hydrocarbon chain has a length of 2 to 3 carbon atoms.
Claim 34
Dependent Claim
10 words
The composition of claim 31, wherein each n is 1.
Claim 35
Dependent Claim
197 words
A linking reagent having the formula: ##STR6## wherein: Z is a reactive phosphorus-containing group, OH or a cleavable ester attached to a DNA synthesis support, wherein said reactive phosphorus-containing group is able to couple, to or is activatable for coupling to, an OH group of a first nucleotide; D is a protecting group which may be removed to permit said non-nucleotide linking reagent to be coupled to a second nucleotide; i is either 0, 1, 2 or 3, and j is either 0, 1, 2 or 3, provided that i+j is at least 1; L 1 is a first linker-arm; L 2 is either H or a second linker-arm; wherein said first linker-arm, and said second linker-arm each independently have the formula: (CH.sub.2).sub.k --NH--(CO--(CH.sub.2).sub.q NH).sub.r --M wherein each M is independently H, fluorenylmethoxycarbonyl, trifluoroacetyl or a label stable to DNA synthesis and deprotection conditions, each k is independently an integer between 0 and 4, inclusive, each q is independently an integer between 1 and 11, inclusive, each r is independently either 0, 1, or 2, provided that each k+1+(2+q)r in said first linker-arm, and in said second linker-arm are independently an integer between 1 and 25, inclusive.
Claim 36
Dependent Claim
197 words
A linking reagent having the formula: ##STR6## wherein: Z is a reactive phosphorus-containing group, OH or a cleavable ester attached to a DNA synthesis support, wherein said reactive phosphorus-containing group is able to couple, to or is activatable for coupling to, an OH group of a first nucleotide; D is a protecting group which may be removed to permit said non-nucleotide linking reagent to be coupled to a second nucleotide; i is either 0, 1, 2 or 3, and j is either 0, 1, 2 or 3, provided that i+j is at least 1; L 1 is a first linker-arm; L 2 is either H or a second linker-arm; wherein said first linker-arm, and said second linker-arm each independently have the formula: (CH.sub.2).sub.k --NH--(CO--(CH.sub.2).sub.q NH).sub.r --M wherein each M is independently H, fluorenylmethoxycarbonyl, trifluoroacetyl or a label stable to DNA synthesis and deprotection conditions, each k is independently an integer between 0 and 4, inclusive, each q is independently an integer between 1 and 11, inclusive, each r is independently either 0, 1, or 2, provided that each k+1+(2+q)r in said first linker-arm, and in said second linker-arm are independently an integer between 1 and 25, inclusive.
Claim 37
Dependent Claim
80 words
The linking reagent of claim 33, wherein Z has the formula: ##STR7## wherein X 2 is a halogen or a substituted amino; R 3 is selected from the group consisting of alkyl, alkoxy and phenoxy; X 4 is selected from the group consisting of halogen, amino and O - ; and R 5 is selected from the group consisting of alkyl, alkoxy, aryloxy and H, provided that R 5 may be H only if X 4 is O - .
Claim 38
Dependent Claim
12 words
The linking reagent of claim 34, wherein Z has the formula: ##STR8##
Claim 39
Dependent Claim
30 words
The linking reagent of claim 35, wherein X 2 is Cl or a secondary amino; and R 3 is selected from the group consisting of chlorophenoxy, methoxy, ethoxy and beta-cyanoethoxy.
Claim 40
Dependent Claim
20 words
The linking reagent of claim 36, wherein X 2 is selected from the group consisting of diisopropylamino, dimethylamino and morpholino.
Claim 41
Dependent Claim
12 words
The linking reagent of claim 34, wherein Z has the formula: ##STR9##
Claim 42
Dependent Claim
52 words
The linking reagent of claim 38, wherein X 4 is selected from the group consisting of Cl, secondary amino and O - ; and R 5 is selected from the group methoxy, ethoxy, monochlorophenoxy, beta-cyanoethoxy and H, provided that R 5 may be H only if X 4 is O - .
Claim 43
Dependent Claim
12 words
The linking reagent of claim 33 or 34, wherein j is 0.
Claim 44
Dependent Claim
13 words
The linking reagent of claim 33 or 34, wherein L 2 is H.
Claim 45
Dependent Claim
17 words
The linking reagent of claim 33 or 34, wherein L 2 is H and j is 0.
Claim 46
Dependent Claim
12 words
The linking reagent of claim 33 or 34, wherein i is 1.
Claim 47
Dependent Claim
16 words
The linking reagent of claim 33 or 34, wherein i is 1 and j is 1.
Claim 48
Dependent Claim
13 words
The linking reagent of claim 33 or 34, wherein each r is 0.
Claim 49
Dependent Claim
18 words
The linking reagent of claim 33 or 34, wherein each r is 0 and X 5 is H.
Claim 50
Dependent Claim
19 words
The linking reagent of claim 33 or 34, wherein each q is an integer between 1 and 6, inclusively.
Claim 51
Dependent Claim
17 words
The linking reagent of claim 42, wherein each q is an integer between 1 and 6, inclusively.
Claim 52
Dependent Claim
20 words
The linking reagent of claim 33 or 34, wherein each k is independently an integer between 1 and 3, inclusively.
Claim 53
Dependent Claim
17 words
The linking reagent of claim 44, wherein each q is an integer between 1 and 6, inclusively.
References Cited (Backward Citations)
US4500707A
Cited
US4415732A
Cited
US4835263A
Cited
US4725677A
Cited
US4599303A
Cited
US5039796A
Cited
US4757141A
Cited
US5071974A
Cited
US4968742A
Cited
US5324831A
Cited
USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 1999-12-17 | 2000-06-17 | 2000-12-17 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2003-12-17 | 2004-06-17 | 2004-12-17 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2007-12-17 | 2008-06-17 | 2008-12-17 | $7700.00 | Window Closed / Lapsed |