Detection of Nucleic Acids
First Claim
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1. A method of genotyping a single nucleotide polymorphism (SNP), which comprises:
- providing a sample comprising or suspected of comprising a target nucleic acid comprising at least one SNP;
incubating at least two label extender probes each comprising a different L-1 sequence, at least two capture extender probes each comprising a different C-1 sequence, and a label probe system with the sample comprising or suspected of comprising the target nucleic acid comprising the at least one SNP, wherein at least one L-1 sequence is perfectly complementary to the at least one allele of a SNP;
adding one or more subsets of particles comprising covalently bound thereto at least two capture probes, under conditions in which the particles bind to the capture extender probes, wherein the capture probes are covalently bound to the particles, wherein one or more particles within a subset of particles is distinguishable from one or more particles in any other subset of particles;
detecting whether the particles have bound thereto the label probe system, thereby genotyping the at least one allele of the SNP.
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Abstract
Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Compositions, kits, and systems related to the methods are also described.
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Citations
36 Claims
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1. A method of genotyping a single nucleotide polymorphism (SNP), which comprises:
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providing a sample comprising or suspected of comprising a target nucleic acid comprising at least one SNP; incubating at least two label extender probes each comprising a different L-1 sequence, at least two capture extender probes each comprising a different C-1 sequence, and a label probe system with the sample comprising or suspected of comprising the target nucleic acid comprising the at least one SNP, wherein at least one L-1 sequence is perfectly complementary to the at least one allele of a SNP; adding one or more subsets of particles comprising covalently bound thereto at least two capture probes, under conditions in which the particles bind to the capture extender probes, wherein the capture probes are covalently bound to the particles, wherein one or more particles within a subset of particles is distinguishable from one or more particles in any other subset of particles; detecting whether the particles have bound thereto the label probe system, thereby genotyping the at least one allele of the SNP. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A method of genotyping a single nucleotide polymorphism (SNP), which comprises:
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providing a sample comprising or suspected of comprising a target nucleic acid comprising at least one SNP; incubating at least two label extender probes each comprising a different L-1 sequence, and a label probe system with the sample comprising or suspected of comprising the target nucleic acid comprising the at least one SNP, wherein at least one L-1 sequence is perfectly complementary to the at least one SNP allele; detecting whether the label probe system is associated with the sample. - View Dependent Claims (14, 15, 16, 17, 18, 19)
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20. A method of detecting a microRNA or siRNA, which comprises:
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providing a sample comprising or suspected of comprising a microRNA or siRNA; incubating at least two label extender probes each comprising a different L-1 sequence, and a label probe system with the sample comprising or suspected of comprising the microRNA or siRNA, wherein at least one L-1 sequence is complementary to at least part of the microRNA or siRNA sequence; detecting whether the label probe system is associated with the sample. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28)
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29. A method of detecting a translocation event or fusion event, which comprises:
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providing a sample comprising or suspected of comprising a translocation event or fusion event at a translocation site; incubating at least two label extender probes each comprising a different L-1 sequence, and a label probe system with the sample comprising or suspected of comprising the translocation event or fusion event, wherein at least one L-1 sequence is perfectly complementary to a translocation sequence, wherein the translocation sequence is centered at the translocation site; detecting whether the label probe system is associated with the sample. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36)
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Specification