Microarray analysis of RNA
First Claim
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1. A method of analyzing RNAs comprising:
- a) contacting a sample comprising RNAs and interfering sequences that are complementary to said RNAs with an analogous DNA set to provide a DNA/RNA duplex comprising an analogous DNA of said set and a complementary interfering sequence, wherein the analogous DNA set comprises at least one sequence comprising the same sequence of bases as an RNA of said sample, except that uracils in the sequence of said RNA are substituted with thymines, and wherein said sample is isolated from a biological source;
b) contacting the DNA/RNA duplex with an enzyme having a DNA;
RNA nuclease activity to provide a digested RNA sample;
c) contacting the digested RNA sample with an array of probes that are complementary to the analogous DNAs of said analogous DNA set under conditions sufficient to provide for specific binding of said RNA to a probe of said array; and
d) interrogating the array.
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Abstract
In certain embodiments, the invention provides a method of performing an array analysis, the method including contacting a sample of RNA with an analogous DNA set to provide a DNA/RNA duplex, contacting the DNA/RNA duplex with an enzyme having a DNA:RNA nuclease activity to provide a digested RNA sample, and contacting the digested RNA sample with an array under conditions sufficient to provide for specific binding to the array. The array typically is then interrogated. Kits in accordance with the invention are also described which include an analogous DNA set and an array.
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Citations
24 Claims
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1. A method of analyzing RNAs comprising:
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a) contacting a sample comprising RNAs and interfering sequences that are complementary to said RNAs with an analogous DNA set to provide a DNA/RNA duplex comprising an analogous DNA of said set and a complementary interfering sequence, wherein the analogous DNA set comprises at least one sequence comprising the same sequence of bases as an RNA of said sample, except that uracils in the sequence of said RNA are substituted with thymines, and wherein said sample is isolated from a biological source; b) contacting the DNA/RNA duplex with an enzyme having a DNA;
RNA nuclease activity to provide a digested RNA sample;c) contacting the digested RNA sample with an array of probes that are complementary to the analogous DNAs of said analogous DNA set under conditions sufficient to provide for specific binding of said RNA to a probe of said array; and d) interrogating the array. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22)
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19. A method for analyzing a RNA comprising:
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contacting a sample of RNA comprising an interfering sequence complementary to said RNA with an oligodeoxynucleotide to provide a DNA/RNA duplex, wherein the oligodeoxynucleotide is complementary to the interfering sequence and analogous to the RNA, and wherein said oligodeoxynucleotide has the same sequence of bases as said RNA, except that uracils in the sequence of said small RNA are substituted with thymines, and wherein said sample is isolated from a biological source; contacting the DNA/RNA duplex with an enzyme having a DNA;
RNA nuclease activity to provide a digested RNA sample;contacting the digested RNA sample with a capture agent under conditions sufficient to provide for specific binding to the capture agent to result in the RNA bound to the capture agent; and detecting the RNA bound to the capture agent. - View Dependent Claims (23, 24)
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Specification