Producing, cataloging and classifying sequence tags
First Claim
1. A method of forming a population of nucleic acid sequence tags, comprising:
- covalently coupling a first target nucleic acid to a first end of a first nucleic acid bridge and a second target nucleic acid to a second end of the first nucleic acid bridge to form a linear chimeric nucleic acid intermediate, wherein the first nucleic acid bridge is disposed between the first target nucleic acid and the second target nucleic acid; and
producing from the linear chimeric nucleic acid intermediate a first sequence tag and a second sequence tag, wherein the first sequence tag comprises at least a portion of the first target nucleic acid and at least a portion of the first nucleic acid bridge, and wherein the second sequence tag comprises at least a portion of the second target nucleic acid and at least a portion of the first nucleic acid bridge, wherein the at least a first portion of the first target nucleic acid comprises a first addressable portion and wherein the at least a first portion of the second target nucleic acid comprises a second addressable portion.
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Abstract
The described method provides, methods, and kits to produce, identify, catalog and classify a comprehensive collection of nucleic acid targets produced from a nucleic acid sample. The method, referred to as Cataloging and Classification of Sequence Tags, involves generating a set of target nucleic acid fragments; coupling the target nucleic acid fragments to a nucleic acid bridge comprising, for example, two or more primer binding sites and two recognition sites for cleavage at a site offset from the recognition site to the fragment'"'"'s end; and cleaving the fragments to generate chimeric nucleic acids of known length. The nucleic acid bridge is thus disposed between the two nucleic acid fragments in the chimeric nucleic acid. The resulting duplex nucleic acids comprise a set of sequence tags (i.e., by amplification using universal primers), comprising an addressable portion, a target nucleic portion and a portion of the nucleic acid bridge. Single-stranded or partial duplex sequence tags may be captured by coupling to a complementary capture probe. Capture probe-sequence tag hybrids, may be detected employing a labeled detector probe. The method allows a complex sample of nucleic acids to be cataloged in a reproducible and sequence-specific manner. The method further provides methods for analysis of the above sample to classify the sequence tags; determine the presence and relative amounts of sequences of interest; derive expressed genes signatures and differential gene expression signatures; and identify putative expressed sequence tags (EST).
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Citations
89 Claims
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1. A method of forming a population of nucleic acid sequence tags, comprising:
- covalently coupling a first target nucleic acid to a first end of a first nucleic acid bridge and a second target nucleic acid to a second end of the first nucleic acid bridge to form a linear chimeric nucleic acid intermediate, wherein the first nucleic acid bridge is disposed between the first target nucleic acid and the second target nucleic acid; and
producing from the linear chimeric nucleic acid intermediate a first sequence tag and a second sequence tag, wherein the first sequence tag comprises at least a portion of the first target nucleic acid and at least a portion of the first nucleic acid bridge, and wherein the second sequence tag comprises at least a portion of the second target nucleic acid and at least a portion of the first nucleic acid bridge, wherein the at least a first portion of the first target nucleic acid comprises a first addressable portion and wherein the at least a first portion of the second target nucleic acid comprises a second addressable portion. - View Dependent Claims (2, 4, 5, 6, 7, 10, 12, 20, 24, 25, 26, 29, 34, 60, 62, 86, 87, 89)
- covalently coupling a first target nucleic acid to a first end of a first nucleic acid bridge and a second target nucleic acid to a second end of the first nucleic acid bridge to form a linear chimeric nucleic acid intermediate, wherein the first nucleic acid bridge is disposed between the first target nucleic acid and the second target nucleic acid; and
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3. (canceled)
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8-9. -9. (canceled)
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11. (canceled)
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13-19. -19. (canceled)
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21-23. -23. (canceled)
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27-28. -28. (canceled)
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30-33. -33. (canceled)
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35-59. -59. (canceled)
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61. (canceled)
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63-73. -73. (canceled)
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74. A kit for use in a sequence tag detection assay, comprising:
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a cleaving agent;
a nucleic acid bridge;
a detector probe;
a detector array; and
a means for detecting a presence, an amount, or an absence of binding of the detector probe to the detector array.
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75-85. -85. (canceled)
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88. A method of forming a population of nucleic acid sequence tags, comprising:
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a) obtaining a first target nucleic acid and a second target nucleic acid by cleaving a nucleic acid sample with a first cleaving agent;
b) covalently coupling the first target nucleic acid to a first end of a first nucleic acid bridge and the second target nucleic acid to a second end of the first nucleic acid bridge to form a linear chimeric nucleic acid intermediate, wherein the first nucleic acid bridge is disposed between the first target nucleic acid and the second target nucleic acid; and
wherein the first nucleic acid bridge comprises a first restriction enzyme recognition site and a second restriction enzyme recognition site, andc) amplifying the linear chimeric nucleic acid intermediate in the presence of a first primer and a second primer to form a first sequence tag and a second sequence tag, wherein the first sequence tag comprises at least a portion of the first target nucleic acid and at least a portion of the first nucleic acid bridge, and wherein the second sequence tag comprises at least a portion of the second target nucleic acid and at least a portion of the first nucleic acid bridge, wherein the at least a first portion of the first target nucleic acid comprises a first addressable portion and wherein the at least a first portion of the second target nucleic acid comprises a second addressable portion.
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Specification