Coupled amplification and ligation method
First Claim
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1. A method for detecting a target polynucleotide in a sample comprising:
- amplifying the target polynucleotide by primer extension to form an amplification product that is complementary to the target polynucleotide, the amplification being performed (a) in the presence of at least one pair of oligonucleotide probes capable of hybridizing to contiguous sequences of the amplification product; and
(b) at a higher temperature than a melting point temperature of the oligonucleotide probes;
ligating those oligonucleotide probes which hybridize to contiguous sequences of the amplification product to form a ligation product; and
detecting the ligation product.
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Abstract
A method based on polymerase chain reaction (PCR) amplification and oligonucleotide ligase assay (OLA) reaction is provided for analyzing complex genetic systems in a single reaction vessel. The method involves simultaneously incubating a sample containing one or more target polynucleotides with PCR primers and OLA probes in a single reaction mixture. The presence of variant polynucleotide sequences in the sample is determined by detecting and identifying the products of the OLA reaction.
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Citations
34 Claims
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1. A method for detecting a target polynucleotide in a sample comprising:
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amplifying the target polynucleotide by primer extension to form an amplification product that is complementary to the target polynucleotide, the amplification being performed (a) in the presence of at least one pair of oligonucleotide probes capable of hybridizing to contiguous sequences of the amplification product; and
(b) at a higher temperature than a melting point temperature of the oligonucleotide probes;ligating those oligonucleotide probes which hybridize to contiguous sequences of the amplification product to form a ligation product; and detecting the ligation product. - View Dependent Claims (2, 3, 4, 5, 6, 7)
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8. A method for detecting a plurality of target polynucleotides in a sample comprising:
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amplifying the plurality of target polynucleotides by primer extension to form a plurality of amplification products that are complementary to the plurality of target polynucleotides, the amplification being performed (a) in the presence of a plurality of pairs of oligonucleotide probes capable of hybridizing to contiguous sequences of the amplification products, and (b) at a higher temperature than a melting point temperature of the oligonucleotide probes; ligating those oligonucleotide probes which hybridize to contiguous sequences of the plurality of amplification products to form a plurality of ligation products; and detecting the plurality of ligation products. - View Dependent Claims (9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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20. A kit for detecting a target polynucleotide of known sequence in a sample comprising:
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a sufficient quantity of amplification primers to perform an amplification reaction on the target polynucleotide to form an amplification product; and a sufficient quantity of two isolated oligonucleotide probes capable of hybridizing to contiguous sequences of the amplification product to perform a ligation reaction on the oligonucleotide probes, the amplification primers having a melting point temperature sufficiently high to enable performance of the amplification reaction at a temperature above the melting point temperature of the oligonucleotide probes. - View Dependent Claims (21, 22, 23, 24, 25, 26)
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27. A kit for detecting a plurality of target polynucleotides of known sequence in a sample comprising:
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sufficient quantities of amplification primers to perform amplification reactions on the plurality of target polynucleotides to form a plurality of amplification products; and sufficient quantities of a plurality of pairs of isolated oligonucleotide probes capable of hybridizing to contiguous sequences of the plurality of amplification products to perform ligation reactions on the pairs of oligonucleotide probes, each amplification primer having a melting point temperature sufficiently high to enable performance of the amplification reactions at a temperature above a melting point temperature of the oligonucleotide probes. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34)
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Specification