Reverse transcription on microarrays
First Claim
1. A method for detecting a target RNA in a sample, the method comprising, (a) providing an array comprising a DNA primer comprising a sequence complementary to the target RNA;
- (b) contacting the primer with an RNA sample under conditions that promote specific hybridization between the primer and the target RNA;
(c) incubating the primer-RNA heteroduplex with a reverse transcriptase enzyme, under conditions that allow reverse transcription of the RNA into cDNA such that a detectable label is incorporated into the cDNA; and
(d) detecting the detectable label incorporated into the nascent cDNA strand synthesized by the reverse transcriptase, wherein the presence of the label in the cDNA is indicative of the presence of the target RNA in the sample.
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Abstract
The present invention provides novel methods for detection of gene. A method for detecting RNA molecules of interest in which oligonucleotide primers uniquely complementary to specific RNA molecules are used as primers for reverse transcribing target RNAs with reverse transcriptase, or any enzyme that possesses reverse transcription activity, is provided. The invention eliminates the need for labeling or converting the target RNA by incorporating detectable labels in the elongation product of reverse transcription of the probe-bound target RNA in the sample.
143 Citations
54 Claims
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1. A method for detecting a target RNA in a sample, the method comprising,
(a) providing an array comprising a DNA primer comprising a sequence complementary to the target RNA; -
(b) contacting the primer with an RNA sample under conditions that promote specific hybridization between the primer and the target RNA;
(c) incubating the primer-RNA heteroduplex with a reverse transcriptase enzyme, under conditions that allow reverse transcription of the RNA into cDNA such that a detectable label is incorporated into the cDNA; and
(d) detecting the detectable label incorporated into the nascent cDNA strand synthesized by the reverse transcriptase, wherein the presence of the label in the cDNA is indicative of the presence of the target RNA in the sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 42)
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27. A method for detecting a target RNA in a sample, the method comprising,
(a) providing a microarray comprising at least one DNA primer comprising a sequence complementary to a sequence of the target RNA; -
(b) contacting the microarray with an RNA sample under conditions that allow specific hybridization between the primer and the target RNA;
(c) incubating the primer-RNA heteroduplex with a reverse transcriptase enzyme, under conditions that allow reverse transcription of the RNA into cDNA; and
(d) detecting the cDNA-RNA heteroduplex synthesized by the reverse transcriptase enzyme, wherein presence of the cDNA-RNA heteroduplex is indicative of the presence of the target RNA in the sample, wherein the detection is not mediated by an antibody against a DNA-RNA hybrid. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46)
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47. A method for detecting a target RNA in a sample, the method comprising,
(a) providing an array comprising a DNA primer comprising a sequence complementary to the target RNA; -
(b) contacting the primer with an RNA sample under conditions that promote specific hybridization between the primer and the target RNA;
(c) incubating the primer-RNA heteroduplex with a thermostable reverse transcriptase enzyme, under conditions that allow reverse transcription of the RNA into cDNA such that a detectable label is incorporated into the cDNA;
(d) performing at least two cycles of hybridization and reverse transcription, under conditions comprising a temperature higher than a melting temperature of the RNA;
cDNA duplex; and
(e) detecting the detectable label incorporated into the nascent cDNA strand synthesized by the reverse transcriptase, wherein the presence of the label in the cDNA is indicative of the presence of the target RNA in the sample. - View Dependent Claims (48, 49, 50)
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51. A kit for identifying sequence variations in a target polynucleotide as compared to a reference sequence, comprising:
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a) an array of at least two oligonucleotide primers immobilized on a solid phase support, wherein each oligonucleotide primer is selected to comprise a sequence complementary to a target RNA, and occupies an identifiable and discrete area of the array;
b) reagents suitable for a reverse transcription reaction on the array; and
c) detection means for detecting a nascent cDNA strand on the array. - View Dependent Claims (52, 53, 54)
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Specification