Assays and kits incorporating nucleic acid probes containing improved molecular switch
First Claim
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1. A method for the detection of at least one predetermined nucleic acid target sequence in a sample containing nucleic acid and comprising the steps of:
- a) adding to the sample hybridization probes comprising a molecular switch consisting essentially of three oligonucleotide sequences;
i) a probe sequence of from about 20 to about 60 nucleotides, having a 5'"'"' side and a 3'"'"' side, which probe sequence is complementary to said target sequence,ii) a 5'"'"' sequence of from about 10 to about 40 nucleotides, including a first switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 5'"'"' side of the probe sequence, andiii) a 3'"'"' sequence of from about 10 to about 40 nucleotides, including a second switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 3'"'"' side of the probe sequence, said second switch sequence being hybridized with said first switch sequence only when said probe sequence is not hybridized to said target sequence, wherein said molecular switch includes a preselected nucleic acid sequence for selectively generating a detectable signal when the probe sequence is hybridized with said target sequence,b) specifically hybridizing probes with said target sequence,c) destroying the ability of probes which did not hybridize specifically with said target sequence in step b to generate a signal,d) generating a signal from probes which did hybridize specifically with said target sequence in step b, ande) detecting the signal in order to detect the predetermined nucleic acid target sequence.
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Abstract
A probe for the detection of a nucleic acid target sequence containing a molecular switch comprising three essential elements: a probe sequence of 20-60 nucleotides surrounded by switch sequences of 10-40 nucleotides which are complementary to each other, wherein the state of the switch is useful for selectively generating a detectable signal if the probe is hybridized to a target; also, assays and kits utilizing such probes.
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23 Claims
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1. A method for the detection of at least one predetermined nucleic acid target sequence in a sample containing nucleic acid and comprising the steps of:
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a) adding to the sample hybridization probes comprising a molecular switch consisting essentially of three oligonucleotide sequences; i) a probe sequence of from about 20 to about 60 nucleotides, having a 5'"'"' side and a 3'"'"' side, which probe sequence is complementary to said target sequence, ii) a 5'"'"' sequence of from about 10 to about 40 nucleotides, including a first switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 5'"'"' side of the probe sequence, and iii) a 3'"'"' sequence of from about 10 to about 40 nucleotides, including a second switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 3'"'"' side of the probe sequence, said second switch sequence being hybridized with said first switch sequence only when said probe sequence is not hybridized to said target sequence, wherein said molecular switch includes a preselected nucleic acid sequence for selectively generating a detectable signal when the probe sequence is hybridized with said target sequence, b) specifically hybridizing probes with said target sequence, c) destroying the ability of probes which did not hybridize specifically with said target sequence in step b to generate a signal, d) generating a signal from probes which did hybridize specifically with said target sequence in step b, and e) detecting the signal in order to detect the predetermined nucleic acid target sequence. - View Dependent Claims (2, 3, 4, 5, 6, 17)
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7. A method for the detection of at least one predetermined nucleic acid target sequence in a sample containing nucleic acid comprising the steps of
a) adding to the sample hybridization probes comprising a molecular switch consisting essentially of three oligonucleotide sequence: -
i) a probe sequence of from about 20 to about 60 nucleotides, having a 5'"'"' side and a 3'"'"' side, which probe sequence is complementary to said target sequence, ii) a 5'"'"' sequence of from about 10 to about 40 nucleotides, including a first switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 5'"'"' side of the probe sequence, and iii) a 3'"'"' sequence of from about 10 to about 40 nucleotides, including a second switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 3'"'"' side of the probe sequence, said second switch sequence being hybridized with said first switch sequence only when said probe sequence is not hybridized to said target sequence, wherein said molecular switch includes a preselected nucleic acid sequence for selectively generating a detectable signal when the probe sequence is hybridized with said target sequence, said detectable signal resulting from exponential replication of replicable RNA, b) specifically hybridizing probes with said target sequence, c) exponentially replicating the replicatable RNA, and d) detecting the replication products in order to detect the predetermined nucleic acid target sequence. - View Dependent Claims (8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23)
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15. A method for the detection of at least one predetermined nucleic acid target sequence in a sample containing nucleic acid comprising the steps of
a) adding to the sample hybridization probes comprising a molecular switch consisting essentially of three oligonucleotides sequences: -
i) a probe sequence of from about 20 to about 60 nucleotides, having a 5'"'"' side and a 3'"'"' side, which probe sequence is complementary to said target sequence, ii) a 5'"'"' sequence of from about 10 to about 40 nucleotides, including a first switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 5'"'"' side of the probe sequence, and iii) a 3'"'"' sequence of from about 10 to about 40 nucleotides, including a second switch sequence of at least about 10 nucleotides, immediately adjacent to and linked to the 3'"'"' side of the probe sequence, said second switch sequence being hybridized with said first switch sequence being when said probe sequence is not hybridized to said target sequence, wherein said molecular switch includes a preselected nucleic acid sequence for selectively generating a detectable signal from an RNA signal generator sequence of said hybridization probe when the probe sequence is hybridized with said target sequence, b) specifically hybridizing probes with said target sequence, c) cleaving said RNA-signal generator sequence from probes which hybridized with target sequences in step b, d) generating an amplified signal using said RNA-signal generator, and e) detecting said amplified signal in order to detect the predetermined nucleic acid target sequence. - View Dependent Claims (16)
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Specification