Global amplification using random priming by a composite primer

• US 7,402,386 B2
• Filed: 04/14/2004
• Issued: 07/22/2008
• Est. Priority Date: 04/14/2003
• Status: Active Grant

• Current Assignee: NuGEN Technologies, Inc. (Tecan Group AG)
• Original Assignee: NuGEN Technologies, Inc. (Tecan Group AG)
• Inventors: Kurn, Nurith, Wang, Shenglong
• Primary Examiner(s): Horlick; Kenneth R.
• Assistant Examiner(s): Babic; Christopher M.
• Application Number:
  US10/824,829
• Publication Number:
  US 20050019793A1
• Time in Patent Office: 1,560 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/203 incorporating a composite nucleic acid containing a polypeptide sequence other than PNA
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis

Abstract

The invention relates to the field of polynucleotide amplification. More particularly, the invention provides methods, compositions and kits for amplification of (i.e., making multiple copies of) a multiplicity of different polynucleotide template sequences using a randomly primed RNA/DNA composite primer.

Claims

1. A method for amplification of a template DNA, comprising:

(a) incubating a reaction mixture, said reaction mixture comprising;

(i) a template DNA;

(ii) a first primer, wherein the first primer is hybridizable to a multiplicity of template sites, wherein the first primer is a population of different composite primers each comprising an RNA portion and a 3′

DNA portion, wherein each composite primer comprises a 3′

random sequence, and wherein each composite primer is a tailed primer that comprises a 5′

portion that is not hybridizable to the template DNA tinder conditions in which the first primer hybridizes to the template DNA;

(iii) a DNA-dependent DNA polymerase; and

(iv) an RNA-dependent DNA polymerase;

wherein the incubation is under conditions that permit generation of a complex comprising an RNA/DNA heteroduplex, wherein said complex comprising an RNA/DNA heteroduplex is produced by hybridization of the first primer to the template DNA, primer extension to generate a first primer extension product, hybridization of a second primer to the first primer extension product, and extension of the second primer to generate a second primer extension product; and

(b) incubating a reaction mixture, said reaction mixture comprising

(i) at least a portion of the reaction products generated according to step (a);

(ii) an amplification primer, wherein said amplification primer is a composite primer comprising an RNA portion and a 3′

DNA portion, wherein the amplification primer comprises some of the sequence of the first primer, and wherein the first primer and the amplification primer are different primers;

(iii) a DNA-dependent DNA polymerase; and

(iv) an agent that cleaves RNA from an RNA/DNA heteroduplex;

wherein the incubation is under conditions that permit RNA cleavage, primer hybridization, primer extension, and displacement of the first primer extension product when its RNA is cleaved and another amplification primer binds to the second primer extension product and is extended, such that primer extension and strand displacement are repeated, whereby multiple copies of a an amplification product are generated.

2. The method of claim 1, wherein said DNA-dependent DNA polymerase and said RNA-dependent DNA polymerase of step (a) are the same enzyme.

3. The method of claim 1, wherein said DNA-dependent DNA polymerase and said RNA-dependent DNA polymerase of step (a) are different enzymes.

4. The method of claim 1, wherein said first primer and said second primer are the same primer.

5. The method of claim 1, wherein said first primer and said second primer are different primers.

6. The method of claim 1, wherein step (b) is initiated by the addition of an agent that cleaves RNA front an RNA/DNA heteroduplex to the reaction mixture of step (a).

7. The method of claim 1, wherein the agent that cleaves RNA from an RNA/DNA heteroduplex is an enzyme.

8. The method of claim 7, wherein said agent that cleaves RNA from an RNA/DNA heteroduplex is RNase H.

9. The method of claim 1, wherein the RNA portion of the first primer is 5′

with respect to the 3′

DNA portion.

10. The method of claim 9, wherein the RNA portion of the amplification primer is 5′

with respect to the 3′

DNA portion.

11. The method of claim 1, wherein the RNA portion of the amplification primer is 5′

with respect to the 3′

DNA portion.

12. The method of claim 11, wherein the 5′

RNA portion of the amplification primer is adjacent to the 3′

DNA portion.

13. The method of claim 1, wherein the RNA portion of the first primer consists of about 7 to about 50 nucleotides.

14. The method of claim 13, wherein the DNA portion of the first primer consists of about 5 to about 20 nucleotides.

15. The method of claim 1, wherein the RNA portion of the amplification primer consists of about 7 to about 50 nucleotides.

16. The method of claim 15, wherein the DNA portion of the amplification primer consists of about 5 to about 20 nucleotides.

17. The method of claim 1, wherein the reaction mixture of step (b) further comprises a non-canonical nucleotide.

18. The method of claim 17, wherein the non-canonical nucleotide is dUTP.

19. The method of claim 1, wherein the reaction mixture of step (b) further comprises a labeled nucleotide.

73. The method of any of claims 1, 20, 34, or 48, wherein said template DNA is genomic DNA.

74. The method of claim 73, wherein said genomic DNA comprises a multiplicity of genomic DNA templates.

20. A method for amplification of a template DNA, comprising:

incubating a reaction mixture, said reaction mixture comprising;

(a) a complex comprising a RNA/DNA partial heteroduplex, wherein the complex is generated by incubating a first reaction mixture, said first reaction mixture comprising;

(i) a template DNA;

(ii) a first primer;

wherein the first primer is hybridizable to a multiplicity of template sites, wherein the first primer is a population of different composite primers each comprising an RNA portion and a 3′

DNA portion, wherein the composite primer comprises a 3′

random sequence, and wherein the composite primer is a tailed primer that comprises a 5′

portion that is not hybridizable to the template DNA under conditions in which the first primer hybridizes to the template DNA;

(iii) a DNA-dependent DNA polymerase; and

(iv) an RNA-dependent DNA polymerase;

wherein the incubation is under conditions that permit hybridization of the first primer to the template DNA, primer extension to generate a first primer extension product, hybridization of a second primer to the first primer extension product, and extension of the second primer to generate a second primer extension product, whereby a complex comprising an RNA/DNA partial heteroduplex is generated;

(b) an amplification primer, wherein the amplification primer is a composite primer comprising an RNA portion and a 3′

DNA portion, wherein the amplification primer comprises some of the sequence of the first primer, and wherein the first primer and the amplification primer are different primers;

(c) a DNA-dependent DNA polymerase; and

(d) an agent that cleaves RNA from an RNA/DNA heteroduplex;

wherein the incubation is under conditions that permit RNA cleavage, primer hybridization, primer extension, and displacement of the first primer extension product when its RNA is cleaved and another amplification primer binds to the second primer extension product and is extended, such that primer extension and strand displacement are repeated, whereby multiple copies of an amplification product are generated.

21. The method of claim 20, wherein the agent that cleaves RNA from an RNA/DNA heteroduplex is an enzyme.

22. The method of claim 21, wherein the enzyme that cleaves RNA from an RNA/DNA heteroduplex is RNase H.

23. The method of claim 21, wherein said DNA-dependent DNA polymerase and said enzyme that cleaves RNA from an RNA/DNA heteroduplex are the same enzyme.

24. The method of claim 23, wherein said DNA-dependent DNA polymerase and said enzyme that cleaves RNA from an RNA/DNA heteroduplex are different enzymes.

25. The method of claim 20, wherein the RNA portion of the amplification primer is 5′

with respect to the 3′

-DNA portion.

26. The method of claim 25, wherein the 5′

RNA portion of the amplification primer is adjacent to the 3′

DNA portion.

27. The method of claim 20, wherein the RNA portion of the amplification primer consists of about 7 to about 50 nucleotides.

28. The method of claim 27, wherein the DNA portion of the amplification primer consists of about 5 to about 20 nucleotides.

29. The method of claim 20, wherein the RNA portion of the amplification primer consists of about 10 to about 50 nucleotides.

30. The method of claim 29, wherein the DNA portion of the amplification primer consists of about 7 to about 20 nucleotides.

31. The method of claim 20, wherein the reaction mixture further comprises a non-canonical nucleotide.

32. The method of claim 31, wherein the non-canonical nucleotide is dUTP.

33. The method of claim 20, wherein the reaction mixture further comprises a labeled nucleotide.

65. The method of claim 20, wherein the RNA portion of the first primer is 5′

with respect to the 3′

-DNA portion.

66. The method of claim 65, wherein the 5′

RNA portion of the first primer is adjacent to the 3′

DNA portion.

67. The method of claim 20, wherein said first primer and said second primer are the same primer.

68. The method of claim 67, wherein said first primer and said second primer are different primers.

34. A method for amplification of a template DNA, comprising:

incubating a reaction mixture, said reaction mixture comprising;

(a) a complex of a first primer extension product and a second primer extension product, wherein the first primer extension product is generated by extension of a first primer hybridized to the template DNA with a DNA polymerase, wherein the first primer is a hybridizable to a multiplicity of template polynucleotide sites, wherein the first primer is a population of different composite primers each comprising an RNA portion and a 3′

DNA portion, wherein each composite primer comprises a 3′

random sequence, and wherein each composite primer is a tailed primer that comprises a 5′

portion that is not hybridizable to the template DNA under conditions in which the first primer hybridizes to the template DNA, and wherein the second primer extension product is generated by extension of a second primer hybridized to the first primer extension product;

(b) an amplification primer, wherein the amplification is a composite primer comprising an RNA portion and a 3′

DNA portion, wherein the amplification primer comprises some of the sequence of the first primer, wherein the first primer and the amplification primer are different primers, and wherein the amplification primer is hybridizable to the second primer extension product;

(c) a DNA-dependent DNA polymerase; and

(d) an agent that cleaves RNA from an RNA/DNA heteroduplex;

wherein the incubation is under conditions that permit RNA cleavage, primer hybridization, primer extension, and displacement of the first primer extension product from the second primer extension product when its RNA is cleaved and another amplification primer binds and is extended, such that primer extension and strand displacement are repeated, whereby multiple copies of an amplification product are generated.

35. The method of claim 34, wherein said agent that cleaves RNA from a RNA/DNA heteroduplex is an enzyme.

36. The method of claim 35, wherein the enzyme that cleaves RNA from a RNA/DNA heteroduplex is RNase H.

37. The method of claim 35, wherein said DNA-dependent DNA polymerase and the enzyme that cleaves RNA from an RNA/DNA heteroduplex are the same enzyme.

38. The method of claim 35, wherein said DNA-dependent DNA polymerase and the enzyme that cleaves RNA from an RNA/DNA heteroduplex are different enzymes.

39. The method of claim 34, wherein the RNA portion of the amplification primer is 5′

with respect to the 3′

DNA portion.

40. The method of claim 39, wherein the 5′

RNA portion of the amplification primer is adjacent to the 3′

DNA portion.

41. The method of claim 34, wherein the RNA portion of the amplification primer consists of about 7 to about 50 nucleotides.

42. The method of claim 41, wherein the DNA portion of the amplification primer consists of about 5 to about 20 nucleotides.

43. The method of claim 34, wherein the RNA portion of the amplification primer consists of about 10 to about 50 nucleotides.

44. The method of claim 43, wherein the DNA portion of the amplification primer consists of about 7 to about 20 nucleotides.

45. The method of claim 34, wherein the reaction mixture further comprises a non-canonical nucleotide.

46. The method of claim 45, wherein the non-canonical nucleotide is dUTP.

47. The method of claim 34, wherein the reaction mixture further comprises a labeled nucleotide.

69. The method of claim 34, wherein the RNA portion of the first primer is 5′

with respect to the 3′

-DNA portion.

70. The method of claim 69, wherein the 5′

RNA portion of the first primer is adjacent to the 3′

DNA portion.

71. The method of claim 34, wherein said first primer and said second primer are the same primer.

72. The method of claim 71, wherein said first primer and said second primer are different primers.

48. A method for amplification of a template DNA, comprising:

(a) randomly priming a template DNA with a first primer, wherein said first primer is hybridizable to a multiplicity of template polynucleotide sites, wherein the first primer is a population of different composite primers each comprising an RNA portion and a 3′

DNA portion, and wherein each composite primer is a tailed primer that comprises a 5′

portion that is not hybridizable to the template DNA under conditions in which the first primer hybridizes to the template DNA;

(b) extending said first primer with a DNA polymerase to generate a first primer extension product;

(c) hybridizing a second primer to the first primer extension product;

(d) extending said second primer with a DNA-dependent DNA polymerase and an RNA-dependent polymerase to generate a second primer extension product, whereby a complex comprising an RNA/DNA heteroduplex is generated;

(e) cleaving RNA from the first primer with an agent that cleaves RNA from a RNA/DNA heteroduplex;

(f) hybridizing an amplification primer to the second primer extension product, wherein said amplification primer is a composite primer comprising a RNA portion and a 3′

DNA portion, wherein the amplification primer comprises some of the sequence of the first primer, and wherein the first primer and the amplification primer are different primers;

(g) extending the hybridized amplification primer by strand displacement DNA synthesis;

(h) cleaving RNA from the amplification primer with an agent that cleaves RNA from a RNA/DNA heteroduplex, such that another amplification primer hybridizes and is extended, whereby multiple copies of an amplification product are generated.

49. The method of claim 48, wherein the agent that cleaves RNA from an RNA/DNA heteroduplex is an enzyme.

50. The method of claim 49, wherein the enzyme that cleaves RNA from an RNA/DNA heteroduplex is RNase H.

51. The method of claim 48, wherein the DNA polymerase of step (b) is a DNA-dependent DNA polymerase.

52. The method of claim 48, wherein the DNA-dependent DNA polymerase and the RNA-dependent DNA polymerase are the same enzyme.

53. The method of claim 48, wherein the DNA-dependent DNA polymerase and the RNA-dependent DNA polymerase are different enzymes.

54. The method of claim 48, wherein the RNA portion of the first primer is 5′

with respect to the 3′

DNA portion.

55. The method of claim 48, wherein the RNA portion of the amplification primer is 5′

with respect to the 3′

DNA portion.

56. The method of claim 55, wherein the 5′

RNA portion of the amplification primer is adjacent to the 3′

DNA portion.

57. The method of claim 54, wherein the 5′

RNA portion of the first primer is adjacent to the 3′

DNA portion.

58. The method of claim 48, wherein the RNA portion of the first primer consists of about 7 to about 50 nucleotides.

59. The method of claim 58, wherein the DNA portion of the first primer consists of about 5 to about 20 nucleotides.

60. The method of claim 48, wherein the RNA portion of the amplification primer consists of about 7 to about 50 nucleotides.

61. The method of claim 60, wherein the DNA portion of the amplification primer consists of about 5 to about 20 nucleotides.

62. The method of claim 48, wherein step (g) is carried out in the presence of a non-canonical nucleotide.

63. The method of claim 62, wherein the non-canonical nucleotide is dUTP.

64. The method of claim 48, wherein step (g) is carried out in the presence of a labeled nucleotide.