Selective amplification of target polynucleotide sequences

• US 6,410,276 B1
• Filed: 04/24/1995
• Issued: 06/25/2002
• Est. Priority Date: 07/31/1987
• Status: Expired due to Term

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Boothroyd, John Charles, Pouletty, Philippe Jacques, Burg, James Lawrence
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US08/427,606
• Time in Patent Office: 2,619 Days
• Field of Search: 435/6, 435/91.2, 435/91.1, 536/24.3
• US Class Current: 435/91.2
• CPC Class Codes: C12N 15/69 Increasing the copy number of the vector
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6893 for protozoa
• CPC Class Codes: C12Q 2521/107 RNA dependent DNA polymerase,(i.e. reverse transcriptase)
• CPC Class Codes: C12Q 2521/119 RNA polymerase
• CPC Class Codes: C12Q 2525/143 incorporating a promoter sequence
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Abstract

A method is provided for multiplying the number of copies of a target polynucleotide sequence comprising a series of primer hybridization, extending, and denaturing steps to provide an intermediate double-stranded DNA molecule containing a promoter sequence (through the use of a promoter-sequence-containing primer) incorporated upstream from the target sequence. The double-stranded DNA intermediate is then used to grow multiple RNA copies of the target sequence. The resulting RNA copies can be used as target sequences to produce further copies. Multiple cycles of this sort can thereby exponentially increase the number of target sequence copies.

Claims

1. A method for increasing the number of copies of a target sequence, or the complement of said target sequence, in a polynucleotide sequence having a 3′

region and a 5′

region, and said target sequence therebetween, comprising the steps of;

(1) preparing a first double-stranded DNA comprising a first promoter sequence upstream from said target sequence by;

(a) contacting an RNA polynucleotide sequence comprising a target sequence with a first primer able to bind to a region upstream of said target sequence;

(b) extending said first primer with a DNA polymerase to form a primer extension product of said first primer having a sequence complementary to said target sequence,

(c) making said primer extension product of said first primer available for hybridization with a second primer,

(d) hybridizing said primer extension product of said first primer with a second primer able to bind to said primer extension product of said first primer at a region upstream of the sequence complementary to said target sequence, wherein one of said first and second primers comprises a 5′

promoter sequence,

(e) extending said second primer, and if necessary said primer extension product of said first primer, with a DNA polymerase to prepare said first double-stranded DNA comprising a first promoter, and

(2) transcribing multiple RNA copies from said first double-stranded DNA using a DNA-dependent RNA polymerase able to bind said promoter to thereby increase the number of copies of said target sequence, or the complement of said target sequence.

2. The method of claim 1, comprising:

(3) preparing a population of second double-stranded DNA sequences comprising a second promoter by;

(a) contacting said multiple RNA copies transcribed from said first double-stranded DNA with a third primer comprising a sequence able to bind to a region upstream of said target sequence, or the complement of said target sequence,

(b) extending said third primer with an RNA dependent DNA polymerase to form a complementary DNA sequence comprising a primer extension product of said third primer comprising said target sequence or the complement of said target sequence,

(c) making the primer extension product of said third primer available for hybridization with a fourth primer,

(d) hybridizing said primer extension product of said third primer with a fourth primer able to bind to said primer extension product of said third primer at a region upstream of said target sequence, or the complement of said target sequence, wherein at least one of said third and fourth primers comprises a 5′

promoter sequence, and wherein said third and fourth primers may be the same or different from said first and second primers,

(e) extending said fourth primer, and if necessary said primer extension product of said third primer, with a DNA polymerase to prepare said population of second double-stranded DNA comprising a second promoter, and

(4) transcribing multiple RNA copies of said second double-stranded DNA using a DNA-dependent RNA polymerase able to bind said second promoter.

3. The method of claim 1, wherein said extending comprises contacting said RNA polynucleotide sequence and said first primer with a reverse transcriptase enzyme.

4. The method of claim 1, wherein said primers comprise binding sequences of from 10 to 30 nucleotides in length.

5. The method of claim 1, wherein said primers are separated by less than 200 base pairs.

6. The method of claim 1, wherein said promoter sequence is at the 5′

terminus of a primer.

7. The method of claim 1, wherein said target single-stranded polynucleotide molecule is DNA, extending is accomplished using reverse transcriptase, and said primers are present in said intermediate no more than 150 base pairs apart.

8. A method of detecting a target polynucleotide sequence in a sample, which comprises:

multiplying the number of copies of said target sequence according to claim 1; and

detecting the presence of said multiplied copies.

9. The method of claim 2 wherein said steps (3) and (4) are repeated a plurality of times.

10. The method of claim 9 wherein a labeled ribonucleoside triphosphate is provided as a substrate for one enzyme in said method.

11. The method of claim 10 wherein said labeled ribonucleoside triphosphate is labeled with a radioactive label.

12. The method of claim 11 wherein said labeled ribonucleoside triphosphate is labeled with biotin.

13. The method of claim 12 wherein said labeled ribonucleoside triphosphate is labeled with avidin.

14. The method of claim 1 wherein labeled mononucleotide triphosphates are provided in at least one of said extending steps.

15. The method of claim 1 wherein said target sequence includes a sequence recognized by a restriction endonuclease.

16. The method of claim 2 wherein said multiple RNA copies or said second double-stranded DNA sequence are detected by use of a probe labeled with an antibody or ligand.

17. The method of claim 2 wherein one said primer is located adjacent a specific restriction endonuclease site so that said second double-stranded DNA sequences can be cleaved with said restriction endonuclease to produce a fragment that will not hybridize to said primers.

18. The method of claim 1 wherein one said primer contains additional nucleotides at one end which do not adversely affect said method.

19. The method of claim 2 wherein said first and second primers differ from said third and fourth primers, respectively.

20. The method of claim 2 wherein said first and second primers are the same as said third and fourth primers, respectively.

21. A method for increasing the number of copies of a target polynucleotide sequence or the complement of said target polynucleotide sequence which comprises:

(1) sequentially hybridizing a target single-stranded polynucleotide molecule with primer sequences followed by extending said primers and denaturing, wherein at least one of said primers contains a promoter sequence, to produce a double-stranded DNA intermediate having a promoter sequence upstream from a target sequence;

(2) growing multiple RNA copies of said target sequence from said intermediate using an RNA polymerase capable of binding said promoter;

(3) preparing a second collection of double-stranded DNA intermediates having a promoter sequence upstream from said target sequence from said RNA copies by hybridizing said RNA copies with primer sequences, extending, and denaturing; and

(4) transcribing multiple RNA copies from said second collection of double-stranded DNA intermediates.

22. The method of claim 21, wherein said primers comprise binding sequences of from 10 to 30 nucleotides in length.

23. The method of claim 21, wherein said primers are separated by less than 200 base pairs.

24. The method of claim 21, wherein said promoter sequence is at the 5′

terminus of a primer.

25. The method of claim 21, wherein said target single-stranded polynucleotide molecule is DNA, extending is accomplished using reverse transcriptase, and said primers are present in said intermediate no more than 150 base pairs apart.

26. A method of detecting a target polynucleotide sequence in a sample, which comprises:

multiplying the number of copies of said target sequence according to claim 21; and

detecting the presence of said multiplied copies.

27. The method of claim 21 wherein said steps (3) and (4) are repeated a plurality of times.

28. The method of claim 34 wherein a labeled ribonucleoside triphosphate is provided as a substrate for one enzyme in said method.

29. The method of claim 28 wherein said labeled ribonucleoside triphosphate is labeled with a radioactive label.

30. The method of claim 29 wherein said labeled ribonucleoside triphosphate is labeled with biotin.

31. The method of claim 30 wherein said labeled ribonucleoside triphosphate is labeled with avidin.

32. The method of claim 21 wherein labeled mononucleotide triphosphates are provided in at least one of said extending steps.

33. The method of claim 21 wherein said target sequence includes a sequence recognized by a restriction endonuclease.

34. The method of claim 21 wherein said multiple RNA copies of said second double-stranded DNA sequence are detected by use of a probe labeled with an antibody or ligand.

35. The method of claim 21 wherein one of said primers is located adjacent to a specific restriction endonuclease site so that said second double-stranded DNA sequence s can be cleaved with said restriction endonuclease to produce a fragment that will not hybridize to said primers.

36. The method of claim 21 wherein one of said primers contains additional nucleotides at one end which do not adversely affect said method.

37. The method of claim 21 wherein said first and second primers differ from said third and fourth primers, respectively.

38. The method of claim 21 wherein said first and second primers are the same as said third and fourth primers, respectively.

39. A method for increasing the number of copies of a target sequence, or the complement of said target sequence, in a polynucleotide sequence having a 3′

region and a 5′

region, and said target sequence therebetween, comprising the steps of;

(1) preparing a first double-stranded DNA comprising a first promoter sequence upstream from said target sequence by;

(a) contacting a single stranded DNA polynucleotide sequence comprising a target sequence with a first primer able to bind to a region upstream of said target sequence,

(b) extending said first primer with a DNA polymerase to form a primer extension product of said first primer having a sequence complementary to said target sequence,

(c) making said primer extension product of said first primer available for hybridization with a second primer,

(d) hybridizing said primer extension product of said first primer with a second primer able to bind to said primer extension product of said first primer at a region upstream of the sequence complementary to said target sequence, wherein one of said first and second primers comprises a 5′

promoter sequence,

(e) extending said second primer, and if necessary said primer extension product of said first primer, with a DNA polymerase to prepare said first double-stranded DNA comprising a first promoter,

(2) transcribing multiple RNA copies from said first double-stranded DNA using a DNA-dependent RNA polymerase able to bind said promoter to thereby increase the number of copies of said target sequence, or the complement of said target sequence.

(3) preparing a population of second double-stranded DNA sequences comprising a second promoter by;

(a) contacting said multiple RNA copies transcribed from said first double-stranded DNA with a third primer comprising a sequence able to bind to a region upstream of said target sequence, or the complement of said target sequence,

(b) extending said third primer with an RNA dependent DNA polymerase to form a complementary DNA sequence comprising a primer extension product of said third primer comprising said target sequence or the complement of said target sequence,

(c) making the primer extension product of said third primer available for hybridization with a fourth primer,

(d) hybridizing said primer extension product of said third primer with a fourth primer able to bind to said primer extension product of said third primer at a region upstream of said target sequence, or the complement of said target sequence, wherein at least one of said third and fourth primers comprises a 5′

promoter sequence, and wherein said third and fourth primers may be the same or different from said first and second primers,

(e) extending said fourth primer, and if necessary said primer extension product of said third primer, with a DNA polymerase to prepare said population of second double-stranded DNA comprising a second promoter, and

(4) transcribing multiple RNA copies of said second double-stranded DNA using a DNA-dependent RNA polymerase able to bind said second promoter.

40. The method of claim 39, wherein said primers comprise binding sequences of from 10 to 30 nucleotides in length.

41. The method of claim 39, wherein said primers are separated by less than 200 base pairs.

42. The method of claim 39, wherein said promoter sequence is at the 5′

terminus of a primer.

43. The method of claim 39, wherein said target single-stranded polynucleotide molecule is DNA, extending is accomplished using reverse transcriptase, and said primers are present in said intermediate no more than 150 base pairs apart.

44. A method of detecting a target polynucleotide sequence in a sample, which comprises:

multiplying the number of copies of said target sequence according to claim 46; and

detecting the presence of said multiplied copies.

45. The method of claim 39 wherein said steps (3) and (4) are repeated a plurality of times.

46. The method of claim 45, wherein a labeled ribonucleoside triphosphate is provided as a substrate for one enzyme in said method.

47. The method of claim 46 wherein said labeled ribonucleoside triphosphate is labeled with a radioactive label.

48. The method of claim 47 wherein said labeled ribonucleoside triphosphate is labeled with biotin.

49. The method of claim 48 wherein said labeled ribonucleoside triphosphate is labeled with avidin.

50. The method of claim 39 wherein labeled mononucleotide triphosphates are provided in at least one of said extending steps.

51. The method of claim 39 wherein said target sequence includes a sequence recognized by a restriction endonuclease.

52. The method of claim 40 wherein said multiple RNA copies or said second double-stranded DNA sequence are detected by use of a probe labeled with an antibody or ligand.

53. The method of claim 40 wherein one said primer is located adjacent a specific restriction endonuclease site so that said second double-stranded DNA sequences can be cleaved with said restriction endonuclease to produce a fragment that will not hybridize to said primers.

54. The method of claim 39 wherein one said primer contains additional nucleotides at one end which do not adversely affect said method.

55. The method of claim 39 wherein said first and second primers differ from said third and fourth primers, respectively.

56. The method of claim 39 wherein said first and second primers are the same as said third and fourth primers, respectively.