MicroRNA and Messenger RNA Detection On Arrays
First Claim
1. A method of detecting a plurality of short target nucleic acids, and a plurality of messenger RNAs on a same solid support, wherein each short target nucleic acid is 18-25 nucleotides in length, said method comprising;
- contacting the plurality of different short target nucleic acids with a plurality of target-specific stem-loop reverse transcription primers, wherein each of the plurality of stem-loop reverse transcription primers comprises a 3′
target-specific portion, a zip-code stem, and a promoter;
contacting, in the same reaction mixture as the short target nucleic acids, a plurality of messenger RNAs with an oligo-dT-promoter-containing reverse transcription primer;
extending the plurality of reverse transcription primers and the oligo-dT-promoter-containing reverse transcription primer in a reverse transcription reaction to form a collection of reverse transcription products;
amplifying the reverse transcription products in an in vitro transcription reaction comprising an enzyme corresponding to the promoter, to form a plurality of in vitro transcription products; and
,detecting the plurality of in vitro transcription products on the same solid support.
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Abstract
The present teachings provide methods for reverse transcribing, and detecting, a plurality of small nucleic acids such as micro RNAs, from the same reaction mixture as a plurality of messenger RNAs. High levels of multiplexing are provided by the use of a plurality of zip-coded stem-loop reverse transcription primers, along with an oligo-dT-promoter-containing reverse transcription primer, in the same reverse transcription reaction mixture. The resulting products can be amplified in an in vitro transcription reaction, and detected on a solid support such as an array. The present teachings also provide compositions, kits, and devices for performing and detecting the reverse transcription reactions described herein.
24 Citations
20 Claims
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1. A method of detecting a plurality of short target nucleic acids, and a plurality of messenger RNAs on a same solid support, wherein each short target nucleic acid is 18-25 nucleotides in length, said method comprising;
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contacting the plurality of different short target nucleic acids with a plurality of target-specific stem-loop reverse transcription primers, wherein each of the plurality of stem-loop reverse transcription primers comprises a 3′
target-specific portion, a zip-code stem, and a promoter;contacting, in the same reaction mixture as the short target nucleic acids, a plurality of messenger RNAs with an oligo-dT-promoter-containing reverse transcription primer; extending the plurality of reverse transcription primers and the oligo-dT-promoter-containing reverse transcription primer in a reverse transcription reaction to form a collection of reverse transcription products; amplifying the reverse transcription products in an in vitro transcription reaction comprising an enzyme corresponding to the promoter, to form a plurality of in vitro transcription products; and
,detecting the plurality of in vitro transcription products on the same solid support. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A reaction composition comprising;
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(A) a plurality of target-specific stem-loop reverse transcription primers, wherein each of the plurality of target-specific stem-loop reverse transcription primers comprises a 3′
target-specific portion, a zip-code stem, a promoter; and
,(B) an oligo-dT-promoter-containing reverse transcription primer. - View Dependent Claims (8)
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9. A kit for quantitating a plurality of short target nucleic acids, and a plurality of messenger RNAs on a single solid support, wherein each short target nucleic acid is 18-25 nucleotides in length, said method comprising;
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A) a plurality of target-specific stem-loop reverse transcription primers, wherein each of the plurality of target-specific stem-loop reverse transcription primers comprises a 3′
target-specific portion, a zip-code stem, and a promoter; and
,B) an oligo-dT-promoter-containing reverse transcription primer. - View Dependent Claims (10, 11, 12, 13, 14, 15)
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16. A device comprising a solid support comprising a plurality of immobilized probes, wherein the plurality of immobilized probes comprises;
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A) a plurality of probes complementary to, or complementary to the complement of, a plurality of messenger RNAs; and
,B) a plurality of probes complementary to, or complementary to the complement of, a plurality of short target nucleic acids and a corresponding zip-code introduced in a reverse transcription reaction. - View Dependent Claims (17, 18, 19, 20)
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Specification