Patent US6485901B1 successfully refreshed from Google Patents.
US6485901B1
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Methods, kits and compositions pertaining to linear beacons
Assignee: Applied Biosystems LLC
•
Filing: 1998-10-26
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Granted: 2002-11-26
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Expires: 2018-10-26
Abstract
Abstract This invention is directed to methods, kits and compositions pertaining to Linear Beacons. In the absence of a target sequence, Linear Beacons facilitate efficient energy transfer between the donor and acceptor moieties linked to opposite ends of the probe. Upon hybridization of the probe to a target sequence, there is a measurable change in at least one property of at least one donor or acceptor moiety of the probe which can be used to detect, identify or quantitate the target sequence in a sample.
Inventors
- 👤 Brian D. Gildea
- 👤 James M. Coull
- 👤 Jens J. Hyldig-Nielsen
- 👤 Mark J. Fiandaca
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-11-05 08:59
CPC Classifications
C; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6816; C12Q1/6818; C07; C07K; C07K14/00; C07K14/001; C07K14/003; C12Q1/6834; C12Q1/6837; Y; Y10; Y10T; Y10T436/00; Y10T436/14; Y10T436/142222; Y10T436/143333
Claims Analysis
Total Claims: 94
Claim 1
Independent Claim
148 words
A polymer comprising at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of: a) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; b) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety; c) presence or absence of magnesium in the aqueous solution; and the d) ionic strength of the aqueous solution.
Claim 2
Dependent Claim
148 words
A polymer comprising at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of: a) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; b) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety; c) presence or absence of magnesium in the aqueous solution; and the d) ionic strength of the aqueous solution.
Claim 3
Dependent Claim
12 words
The polymer of claim 1 , wherein the polymer is a PNA.
Claim 4
Independent Claim
222 words
A method for the detection, identification or quantitation of a target sequence in a sample, said method comprising: a) contacting the sample with a polymer comprising at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution is, substantially independent of at least two variables selected from the group consisting of: i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; ii) spectral overlap of the at least one linked energy donor moiety and the at least one energy acceptor moiety; iii) presence or absence of magnesium in the aqueous solution; and the iv) ionic strength of the aqueous solution; and b) detecting, identifying or quantitating the hybridization of the polymer to the target sequence, under suitable hybridization conditions, wherein the presence, absence or amount of target sequence present in the sample is correlated with a change in detectable signal associated with at least one donor or acceptor moiety of the polymer.
Claim 5
Independent Claim
222 words
A method for the detection, identification or quantitation of a target sequence in a sample, said method comprising: a) contacting the sample with a polymer comprising at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution is, substantially independent of at least two variables selected from the group consisting of: i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; ii) spectral overlap of the at least one linked energy donor moiety and the at least one energy acceptor moiety; iii) presence or absence of magnesium in the aqueous solution; and the iv) ionic strength of the aqueous solution; and b) detecting, identifying or quantitating the hybridization of the polymer to the target sequence, under suitable hybridization conditions, wherein the presence, absence or amount of target sequence present in the sample is correlated with a change in detectable signal associated with at least one donor or acceptor moiety of the polymer.
Claim 6
Dependent Claim
18 words
The method of claim 3 , wherein the nucleobase sequence of the polymer is a probing nucleobase sequence.
Claim 7
Dependent Claim
12 words
The method of claim 3 , wherein the polymer is a PNA.
Claim 8
Dependent Claim
181 words
An array comprising two or more support bound polymers wherein at least one polymer of the array comprises at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of: i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; ii) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety; iii) presence or absence of magnesium in the aqueous solution; and the iv) ionic strength of the aqueous solution; and wherein said polymer is suitable for detecting, identifying or quantitating a target sequence present in a sample.
Claim 9
Dependent Claim
181 words
An array comprising two or more support bound polymers wherein at least one polymer of the array comprises at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of: i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; ii) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety; iii) presence or absence of magnesium in the aqueous solution; and the iv) ionic strength of the aqueous solution; and wherein said polymer is suitable for detecting, identifying or quantitating a target sequence present in a sample.
Claim 10
Dependent Claim
33 words
The array of claim 6 , wherein the array is suitable for regeneration by treatment with one or more regeneration catalysts selected from the group consisting of heat, nuclease enzyme and chemical denaturant.
Claim 11
Dependent Claim
186 words
A kit suitable for performing an assay which detects the presence, absence or amount of target sequence in a sample, wherein said kit comprises: a) at least one polymer having at least one linked energy donor moiety and at least one linked energy acceptor moiety, wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of: i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; ii) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety; iii) presence or absence of magnesium in the aqueous solution; and the iv) ionic strength of the aqueous solution; and b) other reagents or compositions necessary to perform the assay.
Claim 12
Dependent Claim
186 words
A kit suitable for performing an assay which detects the presence, absence or amount of target sequence in a sample, wherein said kit comprises: a) at least one polymer having at least one linked energy donor moiety and at least one linked energy acceptor moiety, wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of: i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety; ii) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety; iii) presence or absence of magnesium in the aqueous solution; and the iv) ionic strength of the aqueous solution; and b) other reagents or compositions necessary to perform the assay.
Claim 13
Dependent Claim
32 words
The kit of claim 8 , wherein one of more of the polymers of the kit have a probing nucleobase sequence that is in the range of between 11-17 subunits in length.
Claim 14
Dependent Claim
17 words
The kit of claim 8 , wherein two or more polymers are labeled with independently detectable moieties.
Claim 15
Dependent Claim
33 words
The kit of claim 10 , wherein the independently detectable moieties are used to independently detect, identify or quantitate at least two different target sequences which may be present in the same sample.
Claim 16
Dependent Claim
16 words
The kit of claim 8 , wherein the kit is used in an in-situ hybridization assay.
Claim 17
Dependent Claim
28 words
The kit of claim 8 , wherein the kit is used to detect organisms in food, beverages, water, pharmaceutical products, personal care products, dairy products or environmental samples.
Claim 18
Dependent Claim
18 words
The kit of claim 8 , wherein the kit is used to test raw materials, products or processes.
Claim 19
Dependent Claim
33 words
The kit of claim 8 , wherein the kit is used to examine clinical samples selected from the group consisting of: clinical specimens, equipment, fixtures and products used to treat humans or animals.
Claim 20
Dependent Claim
35 words
The kit of claim 8 , wherein the kit is used to detect a target sequence which is specific for a genetically based disease or is specific for a predisposition to a genetically based disease.
Claim 21
Dependent Claim
45 words
The kit of claim 16 , wherein the kit is used to detect a target sequence associated with a disease selected from the group consisting of β-Thalassemia, sickle cell anemia, Factor-V Leiden, cystic fibrosis and cancer related targets such as p53, p10, BRC-1 and BRC-2.
Claim 22
Dependent Claim
35 words
The kit of claim 8 , wherein the kit is used to detect a target sequence in a forensic technique selected from the group consisting of: prenatal screening, paternity testing, identity confirmation and crime investigation.
Claim 23
Dependent Claim
21 words
The polymer of claim 1 , wherein the probing nucleobase sequence is in the range of between 5-30 subunits in length.
Claim 24
Dependent Claim
21 words
The polymer of claim 1 , wherein the probing nucleobase sequence is in the range of between 8-18 subunits in length.
Claim 25
Dependent Claim
21 words
The polymer of claim 1 , wherein the probing nucleobase sequence is in the range of between 11-17 subunits in length.
Claim 26
Dependent Claim
216 words
The polymer of claim 1 , wherein subunits of the probing nucleobase sequence have the formula: wherein, each J is the same or different and is selected from the group consisting of: H, R 1 , OR 1 , SR 1 , NHR 1 , NR 1 2 , F, Cl, Br and I; each K is the same or different and is selected from the group consisting of: O, S, NH and NR 1 ; each R 1 is the same or different and is an alkyl group having one to five carbon atoms which may optionally contain a heteroatom or a substituted or unsubstituted aryl group; each A is selected from the group consisting of a single bond, a group of the formula; —(CJ 2 ) s — and a group of the formula; —(CJ 2 ) s C(O)— wherein, J is defined above and each s is an integer from one to five; each t is 1 or 2; each u is 1 or 2; and each L is the same or different and is independently selected from the group consisting of J, adenine, cytosine, guanine, thymine, uridine, 5-methylcytosine, 2-aminopurine, 2-amino-6-chloropurine, 2,6-diaminopurine, hypoxanthine, pseudoisocytosine, 2-thiouracil, 2-thiothymidine, other naturally occurring nucleobase analogs, other non-naturally occurring nucleobases, substituted and unsubstituted aromatic moieties, biotin and fluorescein.
Claim 27
Dependent Claim
32 words
The polymer of claim 22 , wherein each subunit consists of a naturally or a non-naturally occurring nucleobase attached to the aza nitrogen of a N-[2-(aminoethyl)]glycine backbone through a methylene carbonyl linkage.
Claim 28
Dependent Claim
40 words
The polymer of claim 1 , wherein the efficiency of transfer of energy between the at least one linked donor moiety and the at least one linked acceptor moiety is substantially independent of at least three of the selected variables.
Claim 29
Dependent Claim
37 words
The polymer of claim 1 , wherein the efficiency of transfer of energy between the at least one linked donor moiety and the at lease one linked acceptor moiety is substantially independent of all four selected variables.
Claim 30
Dependent Claim
48 words
The polymer of claim 1 , wherein the polymer is a PNA and the at least one energy acceptor moiety is linked to the C-terminus of the probing nucleobase sequence and the at least one energy donor moiety is linked to the N-terminus of the probing nucleobase sequence.
Claim 31
Dependent Claim
37 words
The polymer of claim 1 , wherein the at least one energy donor moiety is a fluorophore selected from the group consisting of 5(6)-carboxyfluorescein, 5-(2′-aminoethyl)-aminonaphthalene-1-sulfonic acid (EDANS), bodipy, rhodamine, Cy2, Cy3, Cy3.5, Cy5, Cy5.5 and texas red.
Claim 32
Dependent Claim
18 words
The polymer of claim 1 , wherein the at least one energy acceptor moiety is 4-((-4-(dimethylamino)phenyl)azo)benzoic acid (dabcyl).
Claim 33
Dependent Claim
14 words
The polymer of claim 1 , wherein the polymer is immobilized to a support.
Claim 34
Dependent Claim
16 words
The polymer of claim 1 , wherein the polymer is one component polymer of an array.
Claim 35
Dependent Claim
81 words
A polymer comprising; a) a probing nucleobase sequence for probing a target sequence to which the probing nucleobase sequence is complementary or substantially complementary; b) at least one energy donor moiety that is linked to the probing nucleobase sequence; and c) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence.
Claim 36
Dependent Claim
81 words
A polymer comprising; a) a probing nucleobase sequence for probing a target sequence to which the probing nucleobase sequence is complementary or substantially complementary; b) at least one energy donor moiety that is linked to the probing nucleobase sequence; and c) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence.
Claim 37
Dependent Claim
55 words
The polymer of claim 31 , wherein the at least one energy donor moiety is linked to one of a first or second end of the probing nucleobase sequence and the at least one energy acceptor moiety is linked to the other one of the first or the second end of the probing nucleobase sequence.
Claim 38
Dependent Claim
48 words
The polymer of claim 32 , wherein the polymer is a PNA and the at least one energy acceptor moiety is linked to the C-terminus of the probing nucleobase sequence and the at least one energy donor moiety is linked to the N-terminus of the probing nucleobase sequence.
Claim 39
Dependent Claim
216 words
The polymer of claim 31 , wherein subunits of the probing nucleobase sequence have the formula: wherein, each J is the same or different and is selected from the group consisting of: H, R 1 , OR 1 , SR 1 , NHR 1 , NR 1 2 , F, Cl, Br and I; each K is the same or different and is selected from the group consisting of: O, S, NH and NR 1 ; each R 1 is the same or different and is an alkyl group having one to five carbon atoms which may optionally contain a heteroatom or a substituted or unsubstituted aryl group; each A is selected from the group consisting of a single bond, a group of the formula; —(CJ 2 ) s — and a group of the formula; —(CJ 2 ) s C(O)— wherein, J is defined above and each s is an integer from one to five; each t is 1 or 2; each u is 1 or 2; and each L is the same or different and is independently selected from the group consisting of J, adenine, cytosine, guanine, thymine, uridine, 5-methylcytosine, 2-aminopurine, 2-amino-6-chloropurine, 2,6-diaminopurine, hypoxanthine, pseudoisocytosine, 2-thiouracil, 2-thiothymidine, other naturally occurring nucleobase analogs, other non-naturally occurring nucleobases, substituted and unsubstituted aromatic moieties, biotin and fluorescein.
Claim 40
Dependent Claim
32 words
The polymer of claim 34 , wherein the subunit consists of a naturally or a non-naturally occurring nucleobase attached to the aza nitrogen of a N-[2-(aminoethyl)]glycine backbone through a methylene carbonyl linkage.
Claim 41
Dependent Claim
21 words
The polymer of claim 31 , wherein the probing nucleobase sequence is in the range of between 5-30 subunits in length.
Claim 42
Dependent Claim
20 words
The polymer of claim 31 , wherein the probing nucleobase sequence is the range of between 8-18 subunits in length.
Claim 43
Dependent Claim
20 words
The polymer of claim 31 , wherein the probing nucleobase sequence is the range of between 11-17 subunits in length.
Claim 44
Dependent Claim
41 words
The method of claim 3 , wherein the efficiency of transfer of energy between the at least one donor moiety and the at least one acceptor moiety of the polymer is substantially independent of at least three of the selected variables.
Claim 45
Dependent Claim
38 words
The method of claim 3 , wherein the efficiency of transfer of energy between the at least one donor moiety and the at least one acceptor moiety of the polymer is substantially independent of all four selected variables.
Claim 46
Dependent Claim
21 words
The method of claim 3 , wherein the target sequence is detected, identified or quantitated in a closed tube (homogeneous) assay.
Claim 47
Dependent Claim
30 words
The method of claim 41 , wherein the target sequence that is detected, identified or quantitated is synthesized or amplified in a reaction occurring in the closed tube (homogeneous) assay.
Claim 48
Dependent Claim
45 words
The method of claim 42 , wherein the target sequence is synthesized or amplified using a process selected from the group consisting of: Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), Transcription-Mediated Amplification (TMA), Rolling Circle Amplification (RCA) and Q-beta replicase.
Claim 49
Dependent Claim
17 words
The method of claim 43 , wherein the synthesized or amplified target sequence is measured in real-time.
Claim 50
Dependent Claim
15 words
The method of claim 43 , wherein the PCR reaction is an asymmetric PCR reaction.
Claim 51
Independent Claim
156 words
A method for the detection, identification or quantitation of a target sequence in a sample, said method comprising: a) contacting the sample with a polymer comprising: i) a probing nucleobase sequence for probing the target sequence to which the probing nucleobase sequence is complementary or substantially complementary; ii) at least one energy donor moiety that is linked to the probing nucleobase sequence; and iii) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence; and b) detecting, identifying or quantitating the hybridization of the polymer to the target sequence, under suitable hybridization conditions, wherein the presence, absence or amount of target sequence present in the sample is correlated with a change in detectable signal associated with at least one donor or acceptor moiety of the polymer.
Claim 52
Independent Claim
156 words
A method for the detection, identification or quantitation of a target sequence in a sample, said method comprising: a) contacting the sample with a polymer comprising: i) a probing nucleobase sequence for probing the target sequence to which the probing nucleobase sequence is complementary or substantially complementary; ii) at least one energy donor moiety that is linked to the probing nucleobase sequence; and iii) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence; and b) detecting, identifying or quantitating the hybridization of the polymer to the target sequence, under suitable hybridization conditions, wherein the presence, absence or amount of target sequence present in the sample is correlated with a change in detectable signal associated with at least one donor or acceptor moiety of the polymer.
Claim 53
Dependent Claim
62 words
The method of claim 46 , wherein the at least one energy donor moiety is linked to one of a first or a second end of the probing nucleobase sequence of the polymer and the at least one energy acceptor moiety is linked to the other one of the first or the second end of the probing nucleobase sequence of the polymer.
Claim 54
Dependent Claim
48 words
The method of claim 47 , wherein the polymer is a PNA and the at least one energy acceptor moiety is linked to the C-terminus of the probing nucleobase sequence and the at least one energy donor moiety is linked to the N-terminus of the probing nucleobase sequence.
Claim 55
Dependent Claim
24 words
The method of claim 46 , wherein the probing nucleobase sequence of the polymer is in the range of between 5-30 subunits in length.
Claim 56
Dependent Claim
24 words
The method of claim 46 , wherein the probing nucleobase sequence of the polymer is in the range of between 8-18 subunits in length.
Claim 57
Dependent Claim
24 words
The method of claim 46 , wherein the probing nucleobase sequence of the polymer is in the range of between 11-17 subunits in length.
Claim 58
Dependent Claim
219 words
The method of claim 46 , wherein subunits of the probing nucleobase sequence of the polymer have the formula: wherein, each J is the same or different and is selected from the group consisting of: H, R 1 , OR 1 , SR 1 , NHR 1 , NR 1 2 , F, Cl, Br and I; each K is the same or different and is selected from the group consisting of: O, S, NH and NR 1 ; each R 1 is the same or different and is an alkyl group having one to five carbon atoms which may optionally contain a heteroatom or a substituted or unsubstituted aryl group; each A is selected from the group consisting of a single bond, a group of the formula; —(CJ 2 ) s — and a group of the formula; —(CJ 2 ) s C(O)— wherein, J is defined above and each s is an integer from one to five; each t is 1 or 2; each u is 1 or 2; and each L is the same or different and is independently selected from the group consisting of J, adenine, cytosine, guanine, thymine, uridine, 5-methylcytosine, 2-aminoptirine, 2-amino-6-chloropurine, 2,6-diaminopurine, hypoxanthine, pseudoisocytosine, 2-thiouracil, 2-thiothymidine, other naturally occurring nucleobase analogs, other non-naturally occurring nucleobases, substituted and unsubstituted aromatic moieties, biotin and fluorescein.
Claim 59
Dependent Claim
32 words
The method of claim 52 , wherein each subunit consists of a naturally or a non-naturally occurring nucleobase attached to the aza nitrogen of a N-[2-(aminoethyl)]glycine backbone through a methylene carbonyl linkage.
Claim 60
Dependent Claim
48 words
The method of claim 46 , wherein the polymer is a polyamide and the at least one energy acceptor moiety is linked to the C-terminus of the probing nucleobase sequence and the at least one energy donor moiety is linked to the N-terminus of the probing nucleobase sequence.
Claim 61
Dependent Claim
40 words
The method of claim 46 , wherein the at least one energy donor moiety of the polymer is a fluorophore selected from the group consisting of 5(6)-carboxyfluorescein, 5-(2′-aminoethyl)-aminonaphthalene-1-sulfonic acid (EDANS), bodipy, rhodamine, Cy2, Cy3, Cy3.5, Cy5, Cy5.5 and texas red.
Claim 62
Dependent Claim
21 words
The method of claim 46 , wherein the at least one energy acceptor moiety of the polymer is 4-((-4-(dimethylamino)phenyl)azo)benzoic acid (dabcyl).
Claim 63
Dependent Claim
21 words
The method of claim 46 , wherein the target sequence is detected, identified or quantitated in a closed tube (homogeneous) assay.
Claim 64
Dependent Claim
30 words
The method of claim 57 , wherein the target sequence that is detected, identified or quantitated is synthesized or amplified in a reaction occurring in the closed tube (homogeneous) assay.
Claim 65
Dependent Claim
45 words
The method of claim 58 , wherein the target sequence is synthesized or amplified using a process selected from the group consisting of: Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), Transcription-Mediated Amplification (TMA), Rolling Circle Amplification (RCA) and Q-beta replicase.
Claim 66
Dependent Claim
17 words
The method of claim 58 , wherein the synthesized or amplified target sequence is measured in real-time.
Claim 67
Dependent Claim
15 words
The method of claim 59 , wherein the PCR reaction is an asymmetric PCR reaction.
Claim 68
Dependent Claim
24 words
The method of claim 46 , wherein the target sequence is detected, identified or quantitated in a cell or tissue, whether living or not.
Claim 69
Dependent Claim
25 words
The method of claim 62 , wherein the target sequence in the cell or tissue is detected, identified or quantitated or using in situ hybridization.
Claim 70
Dependent Claim
20 words
The method of claim 46 , wherein the sample is contacted with said polymer and one or more blocking probes.
Claim 71
Dependent Claim
28 words
The method of claim 46 , wherein detection, identification or quantitation of the target sequence determines the presence or amount of an organism or virus in the sample.
Claim 72
Dependent Claim
31 words
The method of claim 46 , wherein detection, identification or quantitation of the target sequence determines the presence or amount of one or more species of an organism in the sample.
Claim 73
Dependent Claim
32 words
The method of claim 46 , wherein detection, identification or quantitation of the target sequence determines the effect of antimicrobial agents on the growth of one or more microorganisms in the sample.
Claim 74
Dependent Claim
29 words
The method of claim 46 , wherein detection, identification or quantitation of the target sequence determines the presence or amount of a taxonomic group of organisms in the sample.
Claim 75
Dependent Claim
24 words
The method of claim 46 , wherein detection, identification or quantitation of the target sequence facilitates a diagnosis of a condition of medical interest.
Claim 76
Dependent Claim
15 words
The method of claim 46 , wherein the target sequence is immobilized to a surface.
Claim 77
Dependent Claim
14 words
The method of claim 46 , wherein the polymer is immobilized to a surface.
Claim 78
Dependent Claim
16 words
The method of claim 46 , wherein the polymer is one component polymer of an array.
Claim 79
Dependent Claim
114 words
An array comprising two or more support bound polymers wherein at least one polymer of the array comprises: a) a probing nucleobase sequence for probing a target sequence to which the probing nucleobase sequence is complementary or substantially complementary; b) at least one energy donor moiety that is linked to the probing nucleobase sequence; and c) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence; and wherein said polymer is suitable for detecting, identifying or quantitating a target sequence present in a sample.
Claim 80
Dependent Claim
114 words
An array comprising two or more support bound polymers wherein at least one polymer of the array comprises: a) a probing nucleobase sequence for probing a target sequence to which the probing nucleobase sequence is complementary or substantially complementary; b) at least one energy donor moiety that is linked to the probing nucleobase sequence; and c) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence; and wherein said polymer is suitable for detecting, identifying or quantitating a target sequence present in a sample.
Claim 81
Dependent Claim
67 words
The array of claim 73 , wherein the at least one energy donor moiety of the at least one polymer is linked to one of a first or a second end of the probing nucleobase sequence and the at least one energy acceptor moiety of the at least one polymer is linked to the other one of the first or second end of the probing nucleobase sequence.
Claim 82
Dependent Claim
33 words
The array of claim 73 , wherein the array is suitable for regeneration by treatment with one or more regeneration catalysts selected from the group consisting of heat, nuclease enzyme and chemical denaturant.
Claim 83
Dependent Claim
119 words
A kit suitable for performing an assay which detects the presence, absence or amount of target sequence in a sample, wherein said kit comprises: a) at least one polymer having: i) a probing nucleobase sequence for probing a target sequence to which the probing nucleobase sequence is complementary or substantially complementary; ii) at least one energy donor moiety that is linked to the probing nucleobase sequence; and iii) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence; and b) other reagents or compositions necessary to perform the assay.
Claim 84
Dependent Claim
119 words
A kit suitable for performing an assay which detects the presence, absence or amount of target sequence in a sample, wherein said kit comprises: a) at least one polymer having: i) a probing nucleobase sequence for probing a target sequence to which the probing nucleobase sequence is complementary or substantially complementary; ii) at least one energy donor moiety that is linked to the probing nucleobase sequence; and iii) at least one energy acceptor moiety that is linked to the probing nucleobase sequence wherein the at least one donor moiety is separated from the at least one acceptor moiety by at least a portion of the probing nucleobase sequence; and b) other reagents or compositions necessary to perform the assay.
Claim 85
Dependent Claim
67 words
The kit of claim 76 , wherein the at least one energy donor moiety of the at least one polymer is linked to one of a first or a second end of the probing nucleobase sequence and the at least one energy acceptor moiety of the at least one polymer is linked to the other one of the first or second end of the probing nucleobase sequence.
Claim 86
Dependent Claim
27 words
The kit of claim 76 , wherein one of more of the polymers of the kit have a probing nucleobase sequence that is 11-17 subunits in length.
Claim 87
Dependent Claim
20 words
The kit of claim 76 , wherein two or more polymers of the kit are labeled with independently detectable moieties.
Claim 88
Dependent Claim
33 words
The kit of claim 79 , wherein the independently detectable moieties are used to independently detect, identify or quantitate at least two different target sequences which may be present in the same sample.
Claim 89
Dependent Claim
37 words
The polymer of claim 31 , wherein the at least one energy donor moiety is a fluorophore selected from the group consisting of 5(6)-carboxyfluorescein, 5-(2′-aminoethyl)-aminonaphthalene-1-sulfonic acid (EDANS), bodipy, rhodamine, Cy2, Cy3, Cy3.5, Cy5, Cy5.5, and texas red.
Claim 90
Dependent Claim
18 words
The polymer of claim 31 , wherein the at least one energy acceptor moiety is 4-((-4-(dimethylamino)phenyl)azo)benzoic acid (dabcyl).
Claim 91
Dependent Claim
32 words
The polymer of claim 31 , wherein at least one spacer moiety separates one or both of the donor and acceptor moieties from the probing nucleobase sequence to which it is linked.
Claim 92
Dependent Claim
18 words
The polymer of claim 31 , wherein the probing nucleobase sequence is perfectly complementary to the target sequence.
Claim 93
Dependent Claim
14 words
The polymer of claim 31 , wherein the polymer is immobilized to a support.
Claim 94
Dependent Claim
16 words
The polymer of claim 31 , wherein the polymer is one component polymer of an array.
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USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 2005-11-25 | 2006-05-27 | 2006-11-26 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2009-11-25 | 2010-05-27 | 2010-11-26 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2013-11-25 | 2014-05-27 | 2014-11-26 | $7700.00 | Window Closed / Lapsed |