Highly sensitive multimeric nucleic acid probes

• US 6,077,668 A
• Filed: 08/13/1997
• Issued: 06/20/2000
• Est. Priority Date: 04/15/1993
• Status: Expired due to Term

• Current Assignee: University of Rochester
• Original Assignee: University of Rochester
• Inventors: Kool, Eric T.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): McGarry, Sean
• Application Number:
  US08/910,632
• Time in Patent Office: 1,042 Days
• Field of Search: 436/6, 436/172.3, 436/91.1, 436/91.3, 436/320.1, 536/23.1, 536/24.3, 536/24.31, 536/24.32, 536/24.33, 536/25.3, 536/25.32
• US Class Current: 435/6.16
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/1132 against retroviridae, e.g. HIV
• CPC Class Codes: C12N 2310/111 spanning the whole gene, or a large part of it
• CPC Class Codes: C12N 2310/121 Hammerhead
• CPC Class Codes: C12N 2310/122 Hairpin
• CPC Class Codes: C12N 2310/127 DNAzymes
• CPC Class Codes: C12N 2310/13 Decoys
• CPC Class Codes: C12N 2310/53 partially self-complementary or closed
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2521/307 Single strand endonuclease
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2521/337 Ribozyme
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2537/162 Helper probe

Abstract

The present invention provides detectably labeled RNA and DNA oligonucleotide multimers useful as diagnostic probes in medical, biological and chemical applications. A method for synthesizing DNA and RNA oligonucleotides, oligonucleotide multimers, and analogs, preferably those that are detectably labeled, is also provided. Oligonucleotide synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective polymerase and at least two types of nucleotide triphosphate, without the addition of auxiliary proteins, to yield an oligonucleotide multimer comprising multiple copies of a repeated oligonucleotide sequence.

Claims

1. A detectably labeled oligonucleotide multimer comprising a 5'"'"' nonrepeated region comprising a nucleotide sequence that binds a first target molecule in a sample, followed by multiple contiguous copies of a repeated oligonucleotide, wherein at least one copy of the repeated oligonucleotide comprises at least one copy of a detectable label.

2. The detectably labeled oligonucleotide multimer of claim 1 comprising multiple copies of the detectable label.

3. The detectably labeled oligonucleotide multimer of claim 1 wherein each of a multiplicity of the multiple copies of the repeated oligonucleotide comprises the detectable label.

4. The detectably labeled oligonucleotide multimer of claim 1 wherein the at least one detectable label is covalently attached to the oligonucleotide multimer.

5. The detectably labeled oligonucleotide multimer of claim 1 wherein the at least one detectable label is noncovalently attached to the oligonucleotide multimer.

6. The detectably labeled oligonucleotide multimer of claim 5 wherein the detectable label comprises a delectably labeled oligonucleotide having a nucleotide sequence complementary to at least a portion of the nucleotide sequence of the repeated oligonucleotide, wherein the detectably labeled oligonucleotide is hybridized to the oligonucleotide multimer.

7. The detectably labeled oligonucleotide multimer of claim 6 wherein the detectably labeled oligonucleotide comprises a fluorescent label, a phosphorescent label, an enzymatic label, a chemical label, or a radiolabel.

8. The detectably labeled oligonucleotide multimer of claim 7 wherein the detectably labeled oligonucleotide comprises a fluorescent label.

9. The detectably labeled oligonucleotide multimer of claim 1 comprising DNA, RNA or a derivative or analog thereof.

10. The detectably labeled oligonucleotide multimer of claim 1 wherein the 5'"'"' nonrepeated region further comprises a 5'"'"' moiety that reduces the susceptibility of the oligonucleotide multimer to enzymatic degradation.

11. The detectably labeled oligonucleotide multimer of claim 1 wherein the 5'"'"' nonrepeated region further comprises biotin.

12. The detectably labeled oligonucleotide multimer of claim 1 wherein the 5'"'"' nonrepeated region further comprises a peptide or protein.

13. The detectably labeled oligonucleotide multimer of claim 1 wherein the nucleotide sequence that binds the first target molecule comprises a RNA, DNA or a derivative or analog thereof.

14. The detectably labeled oligonucleotide multimer of claim 13 wherein the RNA, DNA or derivative or analog thereof comprises a modified backbone, a modified sugar moiety, or a modified base.

15. The detectably labeled oligonucleotide multimer of claim 13 wherein the RNA, DNA or derivative or analog thereof is selected from the group consisting of peptide nucleic acid (PNA), phosphorothioate DNA, phosphorodithioate DNA, phosphoramidate DNA, amide-linked DNA, MMI-linked DNA, 2'"'"'-O-methyl RNA, alpha-DNA, methylphosphonate DNA, 2'"'"'-O-methyl RNA, 2'"'"'-fluoro RNA, 2'"'"'-amino RNA, 2'"'"'-O-alkyl DNA, 2'"'"'-O-allyl DNA, 2'"'"'-O-alkynyl DNA, hexose DNA, pyranosyl RNA, anhydrohexitol DNA, C-5 substituted pyrimidine nucleoside, C-7 substituted 7-deazapurine nucleoside, inosine nucleoside and diaminopurine nucleoside.

16. The detectably labeled oligonucleotide multimer of claim 15 wherein the substituent of the C-5 substituted pyrimidine is selected from the group consisting of fluoro, bromo, chloro, iodo, methyl, ethyl, vinyl, formyl, alkynyl, alkenyl, thiazolyl, imidazolyl and pyridyl.

17. The detectably labeled oligonucleotide multimer of claim 15 wherein the substituent of the C-7 substituted 7-deazapurine is selected from the group consisting of fluoro, bromo, chloro, iodo, methyl, ethyl, vinyl, formyl, alkynyl, alkenyl, thiazolyl, imidazolyl and pyridyl.

18. The detectably labeled oligonucleotide multimer of claim 1 wherein the first target molecule is a nucleic acid molecule, a peptide, a protein, a carbohydrate, a lipid, a hormone, a derivative thereof or an analog thereof.

19. The detectably labeled oligonucleotide multimer of claim 18 wherein the first target molecule is a nucleic acid molecule.

20. The detectably labeled oligonucleotide multimer of claim 19 wherein the nucleotide sequence that binds the first target nucleic acid molecule is complementary to at least a portion of the nucleotide sequence of the first target nucleic acid molecule.

21. The detectably labeled oligonucleotide multimer of claim 1 wherein the 5'"'"' nonrepeated region further comprises a self-complementary hairpin nucleotide sequence such that the nucleotide sequence that binds the first target molecule comprises at least a portion of the self-complementary hairpin nucleotide sequence.

22. The detectably labeled oligonucleotide multimer of claim 1 wherein the repeated oligonucleotide comprises a nucleotide sequence that binds a second target molecule.

23. The detectably labeled oligonucleotide multimer of claim 22 wherein the second target molecule is a nucleic acid molecule, and wherein the nucleotide sequence that binds the second target nucleic acid molecule is complementary to at least a portion of the nucleotide sequence of the second target nucleic acid molecule.

24. The detectably labeled oligonucleotide multimer of claim 1 wherein the nucleotide sequence of the repeated oligonucleotide has limited complexity.

25. The detectably labeled oligonucleotide multimer of claim 24 wherein the nucleotide sequence of the repeated oligonucleotide consists of less than four nucleotide types selected from the group consisting of adenine, guanine, thymidine, cytosine and uracil.

26. The detectably labeled oligonucleotide multimer of claim 24 wherein the nucleotide sequence of the repeated oligonucleotide comprises a nucleotide type that is overrepresented in the nucleotide sequence of the repeated oligonucleotide.

27. The detectably labeled oligonucleotide multimer of claim 26 wherein the overrepresented nucleotide type is present at a level of at least about 50% in the nucleotide sequence of the repeated oligonucleotide.

28. The detectably labeled oligonucleotide multimer of claim 24 wherein the nucleotide sequence of the repeated oligonucleotide is palindromic.

29. The detectably labeled oligonucleotide multimer of claim 24 wherein the nucleotide sequence of the repeated oligonucleotide is a repeating sequence.

30. The detectably labeled oligonucleotide multimer of claim 1 wherein the detectable label is a fluorescent label, a phosphorescent label, an enzymatic label, a chemical label, or a radiolabel.

31. The detectably labeled oligonucleotide multimer of claim 1 wherein the detectable label is a digoxigenin label or a biotin label.

32. The detectably labeled oligonucleotide multimer of claim 1 wherein the detectable label comprises a radiolabel selected from the group consisting of ³² p, ³³ p, ³⁵ S and ¹²⁵ I.

33. The detectably labeled oligonucleotide multimer of claim 1 wherein the detectable label is a fluorescent label.

52. A method for detecting a target molecule comprising:

(a) contacting the detectably labeled oligonucleotide multimer of claim 1 with a sample suspected of containing the target molecule to yield a detectably labeled bound multimer-target complex; and

(b) detecting the detectably labeled bound multimer-target complex.

53. The method of claim 52 wherein the 5'"'"' nonrepeated region of the detectably labeled oligonucleotide multimer further comprises biotin.

54. The method of claim 53 wherein the first target molecule comprises a nucleic acid molecule.

55. The method of claim 52 further comprising, prior to step (a), contacting the detectably labeled oligonucleotide multimer with a blocking oligonucleotide having a nucleotide sequence complementary to at least a portion of the nucleotide sequence of the repeated oligonucleotide.

56. The detectably labeled oligonucleotide multimer of claim 8 wherein each copy of the fluorescent label is separated from every other copy of the fluorescent label on the oligonucleotide multimer by a separation distance of at least about 10 nucleotides.

57. The detectably labeled oligonucleotide multimer of claim 56 wherein the separation distance is at least about 20 nucleotides.

58. The detectably labeled oligonucleotide multimer of claim 33 wherein each copy of the fluorescent label is separated from every other copy of the fluorescent label on the oligonucleotide multimer by a separation distance of at least about 10 nucleotides.

59. The detectably labeled oligonucleotide multimer of claim 58 wherein the separation distance is at least about 20 nucleotides.

34. A method for synthesizing a detectable labeled oligonucleotide multimer comprising:

(a) providing a single-stranded circular template comprising at least one copy of a nucleotide sequence complementary to the nucleotide sequence of a selected oligonucleotide;

(b) annealing an effective amount of an oligonucleotide primer to the single-stranded circular template to yield a primed single-stranded circular template; and

(c) combining the primed single-stranded circular template with an effective amount of at least two types of nucleotide triphosphate, at least one of the at least two types of nucleotide triphosphate comprising a detectable label and an effective amount of a polymerase enzyme, without the addition of auxiliary proteins, to yield a detectably labeled oligonucleotide multimer comprising a 5'"'"' nonrepeated region comprising a nucleotide sequence that binds a first target molecule followed by multiple contiguous copies of the selected oligonucleotide, wherein at least one copy of the selected oligonucleotide comprises at least one copy of a detectable label.

35. The method of claim 34 wherein the size of the single-stranded circular template is about 15-1500 nucleotides.

36. The method of claim 34 wherein the nucleotide triphosphate comprising the detectable label is a ribonucleotide triphosphate.

37. The method of claim 34 wherein the nucleotide triphosphate comprising the detectable label is selected from the group consisting of rATP, rTTP, rUTP, rGTP, rCTP, r(isoG)TP and r(isoC)TP.

38. The method of claim 37 wherein the nucleotide triphosphate comprising the detectable label is rUTP.

39. The method of claim 34 wherein the nucleotide triphosphate comprising the detectable label is a deoxyribonucleotide triphosphate.

40. The method of claim 34 wherein the nucleotide triphosphate comprising the detectable label is selected from the group consisting of dATP, dTTP, dUTP, dGTP, dCTP, d(isoG)TP and d(isoC)TP.

41. The method of claim 40 wherein the nucleotide triphosphate comprising the detectable label is dUTP.

42. The method of claim 34 wherein the detectable label is a fluorescent label, a phosphorescent label, an enzymatic label, a chemical label, or a radiolabel.

43. The method of claim 34 wherein the single-stranded circular template comprises only one nucleotide complementary to the nucleotide triphosphate comprising the detectable label.

44. The method of claim 34 wherein the single-stranded circular template comprises a plurality of nucleotides complementary to the nucleotide triphosphate comprising the detectable label, and wherein each of said complementary nucleotides is separated from every other said complementary nucleotide on the circular template by a separation distance of at least about 10 nucleotides.

45. The method of claim 44 wherein the separation distance is at least about 20 nucleotides.

46. The method of claim 34 further comprising (c) separating the oligonucleotide multimers from other components of the reaction mixture.

47. The method of claim 46 wherein step (c) further comprises separating oligonucleotide multimers of at least about 1000 nucleotides in length from other components of the reaction mixture.

48. The method of claim 34 wherein the oligonucleotide multimer comprises RNA.

49. The method of claim 34 wherein the oligonucleotide primer is at least 6 nucleotides in length.

50. The method of claim 34 wherein the oligonucleotide primer comprises the nucleotide sequence that binds the first target molecule.

51. The method of claim 34 wherein the oligonucleotide multimer comprises DNA.

60. A detectably labeled oligonucleotide multimer comprising multiple copies of a fluorescent label, the oligonucleotide multimer further comprising a 5'"'"' nonrepeated region comprising a nucleotide sequence that binds a target molecule in a sample, followed by multiple contiguous copies of a repeated oligonucleotide wherein at least one copy of the repeated oligonucleotide comprises at least one copy of a fluorescent label and wherein the multiple copies of the fluorescent label are positioned within the oligonucleotide multimer such that each copy of the fluorescent label is separated from every other copy of the fluorescent label on the oligonucleotide multimer by a separation distance of at least about 10 nucleotides.

61. The detectably labeled oligonucleotide multimer of claim 60 wherein the separation distance is at least about 20 nucleotides.

62. The detectably labeled oligonucleotide multimer of claim 60 comprising DNA, RNA or a derivative or analog thereof.

63. The detectably labeled oligonucleotide multimer of claim 60 wherein the target molecule is a nucleic acid molecule, a peptide, a protein, a carbohydrate, a lipid, a hormone, a derivative thereof or an analog thereof.

64. The detectably labeled oligonucleotide multimer of claim 63 wherein the target molecule is a nucleic acid molecule.

65. The detectably labeled oligonucleotide multimer of claim 64 wherein the binding region comprises a nucleotide sequence complementary to at least a portion of the nucleotide sequence of the target nucleic acid molecule.

66. The detectably labeled oligonucleotide multimer of claim 60 wherein the nucleotide sequence of the repeated oligonucleotide has limited complexity.