Detection of small nucleic acids

• US 7,851,150 B2
• Filed: 12/18/2003
• Issued: 12/14/2010
• Est. Priority Date: 12/18/2002
• Status: Expired due to Term

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Third Wave Technologies Incorporated (Hologic Incorporated)
• Inventors: Neri, Bruce P., Chehak, LuAnne, Olson, Sarah M., Olson-Munoz, Marilyn C., Lyamichev, Victor, Dahlberg, James E., Allawi, Hatim T.
• Primary Examiner(s): SCHULTZ, JAMES
• Application Number:
  US10/740,256
• Publication Number:
  US 20050074788A1
• Time in Patent Office: 2,553 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2525/207 siRNA, miRNA
• CPC Class Codes: C12Q 2561/109 Invader technology
• CPC Class Codes: C12Q 2565/1015 labels being on the same oligonucleotide
• CPC Class Codes: Y10T 436/145555 Hetero-N

Abstract

The present invention relates to compositions and methods for the detection and characterization of interfering RNAs such as micro RNAs (miRNAs) and small interfering RNAs (siRNAs) and other short nucleic acid molecules. More particularly, the present invention relates to methods for the detection and quantitation of interfering RNA expression. The present invention further provides for the detection of variants and types of miRNAs and siRNAs.

Claims

1. A method for analyzing microRNA, comprising:

a) contacting microRNA comprising a 3′

portion comprising a 3′

terminal end and a 5′

portion comprising a 5′

terminal end with a first hairpin probe and a second hairpin probe to form an RNA detection structure, wherein

i) said first hairpin probe comprises a 3′

region that is complementary said 3′

portion of said microRNA, and a 5′

region that is not complementary to said microRNA, wherein a first portion of said 5′

region is complementary to a second portion of said 5′

region, wherein said first portion and said second portion of said 5′

region hybridize to each other to form a first duplex when said hairpin probe is hybridized to said microRNA, and wherein said first duplex and said 3′

region of said probe are within one nucleotide of each other; and

ii) said second hairpin probe comprises a 5′

region that is complementary to said 5′

portion of said microRNA and a 3′

region that is not complementary to said microRNA, wherein a first portion of said 3′

region is complementary to a second portion of said 3′

region, wherein said first portion and said second portion of said 3′

region hybridize to each other to form a second duplex when said hairpin probe is hybridized to said microRNA, and wherein said second duplex and said 5′

region of said probe are within one nucleotide of each other;

wherein, in said RNA detection structure, said microRNA and said first and second hairpin probes form a dumbbell structure,

b) detecting formation of said RNA detection structure, wherein formation of said RNA detection structure is indicative of the presence of said microRNA.

2. The method of claim 1, wherein said detecting comprises quantitating said microRNA.

3. The method of claim 1, wherein said detecting comprises forming an invasive cleavage structure, cleaving said invasive cleavage structure, and detecting the cleavage of said invasive cleavage structure.

4. The method of claim 1, wherein said detecting comprises use of a detection assay that employs sequence analysis.

5. The method of claim 1, wherein said detecting comprises use of a detection assay that employs polymerase chain reaction.

6. The method of claim 1, wherein said detecting comprises use of a detection assay that employs microarray hybridization.

7. The method of claim 1, wherein said detecting comprises use of a detection assay that employs ligation.

8. The method of claim 1, wherein said detecting comprises use of a labeled probe.

9. The method of claim 8, wherein said labeled probe is fluorescently labeled.

10. The method of claim 8, wherein said labeled probe is configured for FRET detection.

11. The method of claim 10, wherein said labeled probe has a first conformation when not hybridized in a duplex and a second conformation when hybridized in a duplex.

12. The method of claim 10, wherein said labeled probe exhibits increased fluorescence when hybridized in a duplex.

13. The method of claim 1, wherein said detecting comprises use of a detection assay that employs polymerase chain reaction coupled with 5′

nuclease cleavage of a labeled probe.

14. The method of claim 13, wherein said labeled probe is fluorescently labeled.

15. The method of claim 13, wherein said labeled probe is configured for FRET detection upon cleavage.

16. The method of claim 1, wherein said detecting comprises exposing said RNA detection structure to a polymerase under conditions that permit primer extension.

17. The method of claim 1, wherein said detecting comprises determining the presence of said microRNA in a sample.

18. The method of claim 17, wherein said detecting comprises distinguishing said microRNA from another nucleic acid in said sample.

19. The method of claim 18, wherein said sample comprises a cell lysate.

20. The method of claim 1, wherein said microRNA is approximately 21-22 nucleotides in length.

21. The method of claim 1, wherein a plurality of different microRNAs are detected.

22. The method of claim 21, wherein said plurality of microRNAs comprise a first microRNA and a second microRNA that is said first microRNA having a polymorphism.

23. The method of claim 1, wherein said microRNA is selected from the group consisting of Let-7, miR-1, miR-135, miR-15, miR-16, miR125b, miR-1d, and miR124a.

24. The method of claim 1, wherein at least a portion of said RNA detection structure comprises a nucleotide analog.

25. The method of claim 1, wherein at least a portion of said RNA detection structure comprises a peptide nucleic acid.

26. A method for analyzing microRNA in a sample, comprising:

a) contacting microRNA comprising a 3′

portion comprising a 3′

terminal end and a 5′

portion comprising a 5′

terminal end with a first hairpin probe and a second hairpin probe to form an RNA detection structure wherein

i) said first hairpin probe comprises a 3′

region that is complementary said 3′

portion of said microRNA, and a 5′

region that is not complementary to said microRNA, wherein a first portion of said 5′

region is complementary to a second portion of said 5′

region, wherein said first portion and said second portion of said 5′

region hybridize to each other to form a first duplex when said hairpin probe is hybridized to said microRNA, and wherein said first duplex and said 3′

region of said probe are within one nucleotide of each other; and

ii) said second hairpin probe comprises a 5′

region that is complementary to said 5′

portion of said microRNA and a 3′

region that is not complementary to said microRNA, wherein a first portion of said 3′

region is complementary to a second portion of said 3′

region, wherein said first portion and said second portion of said 3′

region hybridize to each other to form a second duplex when said hairpin probe is hybridized to said microRNA, and wherein said second duplex and said 5′

region of said probe are within one nucleotide of each other;

wherein, in said RNA detection structure, said microRNA and said first and second hairpin probes form a dumbbell structure,

b) reacting said RNA detection structure with a nucleic acid modifying enzyme to form an modified RNA detection structure;

c) detecting formation of said modified RNA detection structure, wherein formation of said modified RNA detection structure is indicative of the presence of said microRNA, and wherein said detecting formation of said modified RNA detection structure comprises use of an amplification reaction.

27. The method of claim 26, wherein said amplification reaction comprises a target amplification reaction.

28. The method of claim 27, wherein said target amplification reaction comprises a polymerase chain reaction.

29. The method of claim 26, wherein said amplification reaction comprises a signal amplification reaction.

30. The method of claim 29, wherein said signal amplification reaction comprises forming an invasive cleavage structure, cleaving said invasive cleavage structure, and detecting the cleavage of said invasive cleavage structure.

31. The method of claim 26, wherein said detecting comprises quantitating said microRNA.

32. The method of claim 26, wherein said detecting comprises use of a labeled probe.

33. The method of claim 32, wherein said labeled probe is fluorescently labeled.

34. The method of claim 33, wherein said labeled probe is configured for FRET detection.

35. The method of claim 32, wherein said labeled probe has a first conformation when not hybridized in a duplex and a second conformation when hybridized in a duplex.

36. The method of claim 32, wherein said labeled probe exhibits increased fluorescence when hybridized in a duplex.

37. The method of claim 28, wherein said polymerase chain reaction is coupled with 5′

nuclease cleavage of a labeled probe.

38. The method of claim 37, wherein said labeled probe is fluorescently labeled.

39. The method of claim 37, wherein said labeled probe is configured for FRET detection upon cleavage.

40. The method of claim 26, wherein said detecting comprises exposing said RNA detection structure to a polymerase under conditions that permit primer extension.

41. The method of claim 26, wherein said detecting comprises distinguishing said microRNA from another nucleic acid in said sample.

42. The method of claim 26, wherein said sample comprises a cell lysate.

43. The method of claim 26, wherein said microRNA is approximately 21-22 nucleotides in length.

44. The method of claim 26, wherein a plurality of different microRNAs are detected.

45. The method of claim 42, wherein said plurality of microRNAs comprise a first microRNA and a second microRNA that is said first microRNA having a polymorphism.

46. The method of claim 26, wherein said microRNA is selected from the group consisting of Let-7, miR-1, miR-135, miR-15, miR-16, miR125b, miR-1d, and miR124a.

47. The method of claim 26, wherein at least a portion of said unlabeled RNA detection structure comprises a nucleotide analog.

48. The method of claim 26, wherein at least a portion of said unlabeled RNA detection structure comprises a peptide nucleic acid.