Pyrophosphorolysis activated polymerization (PAP): application to allele-specific amplification and nucleic acid sequence determination

• US 20020127554A1
• Filed: 02/22/2001
• Published: 09/12/2002
• Est. Priority Date: 02/23/2000
• Status: Active Grant

• Current Assignee: City of Hope
• Original Assignee: City of Hope
• Inventors: Sommer, Steve S., Liu, Qiang
• Granted Patent: US 6,534,269 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)

Abstract

A novel method of pyrophosphorolysis activated polymerization (PAP) has been developed. In PAP, pyrophosphorolysis and polymerization by DNA polymerase are coupled serially for each amplification by using an activatable oligonucleotide P* that has a non-extendable 3′-deoxynucleotide at its 3′ terminus. PAP can be applied for exponential amplification or for linear amplification. PAP can be applied to amplification of a rare allele in admixture with one or more wild type alleles by using an activatable oligonucleotide P* that is an exact match at its 3′ end for the rare allele but has a mismatch at or near its 3′ terminus for the wild type allele. PAP is inhibited by a mismatch in the 3′ specific subsequence as far as 16 nucleotides away from the 3′ terminus. PAP can greatly increase the specificity of detection of an extremely rare mutant allele in the presence of the wild type allele. Specificity results from both pyrophosphorolysis and polymerization since significant nonspecific amplification requires the combination of mismatch pyrophosphorolysis and misincorporation by the DNA polymerase, an extremely rare event. Using genetically engineered DNA polymerases greatly improves the efficiency of PAP.

Claims

1. A pyrophosphorolysis activated polymerization method of synthesizing a desired nucleic acid strand on a nucleic acid template strand which comprises serially

(a) annealing to the template strand a complementary activatable oligonucleotide P* that has a non-extendable 3′

-deoxynucleotide at its 3′

terminus and that has no nucleotides at or near its 3′

terminus that mismatch the corresponding nucleotides on the template strand, so that the terminal 3′

-deoxynucleotide is hybridized to the template strand when the oligonucleotide P* is annealed,

(b) pyrophosphorolyzing the resulting duplex with pyrophosphate and an enzyme that has phosphorolyis activity and activates the oligonucleotide P* by removal of the hybridized terminal 3′

-deoxynucleotide, and

(c) polymerizing by extending the activated oligonucleotide P* on the template strand in presence of four nucleoside triphosphates and a nucleic acid polymerase to synthesize the desired nucleic acid strand.

2. The pyrophosphorolysis activated polymerization method of claim 1 that includes amplification of the desired nucleic acid strand by

(d) separating the desired nucleic acid strand of step (c) from the template strand and

(e) repeating steps (a)-(d) until a desired level of amplification of the desired nucleic acid strand is achieved.

3. The pyrophosphorolysis activated polymerization method of claim 2 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, and step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

4. The pyrophosphorolysis activated polymerization method of claim 3 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

5. The pyrophosphorolysis activated polymerization method of claim 3 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

6. The pyrophosphorolysis activated polymerization method claim of 2 wherein steps (a) to (c) are conducted sequentially as two or more temperature stages on a thermocycler.

7. The pyrophosphorolysis activated polymerization method of claim 6 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, and step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

8. The pyrophosphorolysis activated polymerization method of claim 7 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

9. The pyrophosphorolysis activated polymerization method of claim 7 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

10. The pyrophosphorolysis activated polymerization method of claim 2 wherein steps (a) to (c) are conducted as one temperature stage on a thermocycler.

11. The pyrophosphorolysis activated polymerization method of claim 10 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, an d step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

12. The pyrophosphorolysis activated polymerization method of claim 11 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

13. The pyrophosphorolysis activated polymerization method of claim 11 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

14. The pyrophosphorolysis activated polymerization method of claim 10 wherein the DNA polymerase is also the enzyme having pyrophosphorolysis activity.

15. The pyrophosphorolysis activated polymerization method of claim 14 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

16. The pyrophosphorolysis activated polymerization method of claim 14 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

17. The pyrophosphorolysis activated polymerization method of claim 14 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, and step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

18. The pyrophosphorolysis activated polymerization method of claim 17 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

19. The pyrophosphorolysis activated polymerization method of claim 17 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

20. The pyrophosphorolysis activated polymerization method of claim 14 wherein the DNA polymerase is thermostable Tfl, Taq, or a genetically engineered DNA polymerase.

21. The pyrophosphorolysis activated polymerization method of claim 20 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

22. The pyrophosphorolysis activated polymerization method of claim 20 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

23. The pyrophosphorolysis activated polymerization method of claim 20 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, and step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

24. The pyrophosphorolysis activated polymerization method of claim 23 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

25. The pyrophosphorolysis activated polymerization method of claim 23 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

26. The pyrophosphorolysis activated polymerization method of claim 2 applied to allele-specific amplification, wherein the nucleic acid template strand is present in admixture with a second, allelelic nucleic acid strand that differs from the template strand so that the activatable oligonucleotide P* has at least one nucleotide at or near its 3′

terminus that mismatches the corresponding nucleotide of the alleleic strand, so that in step (a) the terminal 3′

-deoxynucleotide of oligonucleotide P* is not hybridized to the allelelic strand; and

thus in step (b) the pyrophosphate and enzyme that has pyrophosphorolysis activity do not substantially remove the non-hybridized terminal 3′

-deoxynucleotide from the activatable oligonucleotide P* and in step (c) the oligonucleotide P* is not substantially extended by polymerization on the allelic strand, whereby the desired nucleic acid strand synthesized on the template strand is amplified preferentially over any nucleic acid strand synthesized on the allelelic strand.

27. The pyrophosphorolysis activated polymerization method of claim 26 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

28. The pyrophosphorolysis activated polymerization method of claim 26 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

29. The pyrophosphorolysis activated polymerization method of claim 26 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, and step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

30. The pyrophosphorolysis activated polymerization method of claim 29 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

31. The pyrophosphorolysis activated polymerization method of claim 29 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

32. The pyrophosphorolysis activated polymerization method of claim 26, wherein the desired nucleic acid strand, the template strand, and the alleleic strand are DNA strands, the activatable oligonucleotide P* is a 2′

-deoxyoligonucleotide, the terminal deoxynucleotide is a 2′

,3′

-dideoxynucleotide, the four nucleoside triphosphates are 2′

-deoxynucleoside triphosphates, and the nucleic acid polymerase is a DNA polymerase.

33. The pyrophosphorolysis activated polymerization method of claim 32 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

34. The pyrophosphorolysis activated polymerization method of claim 32 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

35. The pyrophosphorolysis activated polymerization method of claim 32 carried out in the presence of a second oligonucleotide that in step (a) anneals to the separated desired nucleic acid strand product of step (d), and wherein step (c) includes polymerizing by extending the second oligonucleotide on the desired nucleic acid strand to synthesize a copy of the nucleic acid template strand, and step (d) includes separating the synthesized nucleic acid template strand from the desired nucleic acid strand, so that amplification is exponential.

36. The pyrophosphorolysis activated polymerization method of claim 35 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide or at the first or second nucleotide from the terminal 3′

-deoxynucleotide.

37. The pyrophosphorolysis activated polymerization method of claim 35 wherein the mismatch between the activatable oligonucleotide P* and the template strand occurs at the terminal 3′

-deoxynucleotide.

38. The pyrophosphorolysis activated polymerization method of claim 26, wherein the desired nucleic acid strand, the template strand, and the alleleic strand are DNA strands, the activatable oligonucleotide P* and the second oligonucleotide are both 2′

-deoxyoligonucleotides, the terminal deoxynucleotide is a 2′

,3′

-dideoxynucleotide, the four nucleoside triphosphates are 2′

-deoxynucleoside triphosphates, and the nucleic acid polymerase is a DNA polymerase.

39. The pyrophosphorolysis activated polymerization method of claim 38 wherein the mismatch between the activatable 2′

-deoxyoligonucleotide P* and the template strand occurs at the terminal 2′

,3′

-deoxynucleotide or at the first or second 2′

-deoxynucleotide from the terminal 2′

,3′

-deoxynucleotide.

40. The pyrophosphorolysis activated polymerization method of claim 38 wherein the mismatch between the activatable 2′

-deoxyoligonucleotide P* and the template strand occurs at the terminal 2′

,3′

-deoxynucleotide.

41. The method of claim 1 wherein the nucleic acid polymerase used in step (c) is a genetically modified DNA polymerase.

42. The method of claim 41 wherein PAP efficiency is enhanced or PAP efficiency is less discriminated against any kind of dideoxynucleotide, such as ddAMP, ddTMP, ddGMP, ddCMP, at the 3′

terminus of P*.

43. The method of claim 42 wherein PAP efficiency is enhanced or PAP efficiency is less discriminated against any kind of dideoxynucleotide, such as ddAMP, ddTMP, ddGMP, ddCMP, at the 3′

terminus of P* by using genetically modified DNA polymerase.

44. The method of claim 41 wherein the genetically modified DNA polymerase contains a mutation F667Y in the active site, such as AmplTaqFS and ThermoSequenase DNA polymerases.

45. The method of claim 41 wherein the dideoxynucleotide at the 3′

terminus of P*, such as ddAMP, ddTMP, ddGMP, and ddCMP, may be labeled by dyes, such as fluorescence dyes.

46. The method of claim 41 wherein the nucleotide triphosphate may be dideoxynucleotide triphosphates as substrates of DNA polymerase, such as ddATP, ddTTP, ddGTP and ddCTP, and the dideoxynucleotide triphosphates may be labeled by dyes, such as fluorescence dyes.

47. The method of claim 1 wherein P* has a 3′

specific subsequence with length n>

3 nucleotides, and P* is not substantially amplified when one or more mismatches to its template strand is located within the 3′

specific subsequence, while P* is substantially amplified with its perfectly matched template strand within the 3′

specific subsequence.

48. The method of claim 47 wherein the mismatch in the 3′

specific subsequence is within 16 nucleotides of the 3′

terminus of P*.

49. The method of claim 47 wherein each PAP may be applied with one P* or two oligonucleotides.

50. The method of claim 1 to compare two DNA sequences or to monitor gene expression profiling, wherein a set of P*s with different 3′

specific subsequences are applied for PAP.

51. The method of claim 50 wherein each P* has a 3′

specific subsequence.

52. The method of claim 50 wherein the set of P* is incomplete with different 3′

specific subsequences.

53. The method of claim 50 wherein the list of the specific PAP amplifications with the pre-known P*s are scored and then the unknown complementary sequence is determined by ordering the 3′

specific subsequences.

54. The method of claim 53 wherein each PAP may be applied with one P* or two oligonucleotides.

55. The pyrophosphorolysis activated polymerization method for exponential amplification of a mutant allele that is present in admixture with a wild-type allele, which comprises separating the strands of the alleles to provide single-stranded DNA and then serially

(a) annealing to the sense or antisense strands of each allele a complementary activatable 2′

-deoxyoligonucleotide P* that has a non-extendable 2′

,3′

-deoxynucleotide at its 3′

terminus and that has no 2′

-deoxynucleotides at or near its 3′

terminus that mismatch the corresponding 2′

-deoxynucleotides on the mutant strand but that has at least one 2′

-deoxynucleotide at or near its 3′

terminus that mismatches the corresponding 2′

-deoxynucleotide on the wild type stand, so that the terminal 2′

,3′

-deoxynucleotide is hybridized to the mutant strand but not to the wild-type strand when the oligonucleotide P* is annealed, and simultaneously annealing to the anti-parallel strands of each allele a second, complementary 2′

-deoxyoligonucleotide, where the activatable 2′

-deoxyoligonucleotide P* and the second 2′

-deoxyoligonucleotide flank the region of the gene to be amplified;

(b) pyrophosphorolyzing the activatable 2′

-deoxyoligonucleotide P* that is annealed to a mutant strand with pyrophosphate and an enzyme that has phosphorolyis activity to activate the 2′

-deoxyoligonucleotide P* by removal of the hybridized terminal 2′

,3′

-deoxynucleotide, and

(c) polymerizing by extending the activated oligonucleotide P* on the mutant strand in presence of four nucleoside triphosphates and a DNA polymerase and simultaneously extending the second 2′

-deoxyoligonucleotide on both mutant and wild-type anti-parallel strands,

(d) separating the extension products of step (c); and

(e) repeating steps (a)-(d) until the desired level of exponential amplification of the mutant allele has been achieved.

56. The pyrophosphorolysis activated polymerization method of claim 55 wherein the mismatch between the activatable 2′

-deoxyoligonucleotide P* and the wild-type strand occurs at the terminal 2′

,3′

-deoxynucleotide or at the first or second 2′

-deoxynucleotide from the terminal 2′

,3′

-deoxynucleotide.

57. The pyrophosphorolysis activated polymerization method of claim 56 wherein the mismatch between the activatable 2′

-deoxyoligonucleotide P* and the wild-type strand occurs at the terminal 2′

,3′

-deoxynucleotide.

58. The pyrophosphorolysis activated polymerization method of claim 55 wherein the activatable 2′

-deoxyoligonucleotide P* is annealed to the antisense strands of the alleles and the second 2′

-deoxyoligonucleotide is annealed to the sense strands.

59. The pyrophosphorolysis activated polymerization method of claim 58 wherein the mismatch between the activatable 2′

-deoxyoligonucleotide P* and the wild-type strand occurs at the terminal 2′

,3′

-deoxynucleotide or at the first or second 2′

-deoxynucleotide from the terminal 2′

,3′

-deoxynucleotide.

60. The pyrophosphorolysis activated polymerization method of claim 58 wherein the mismatch between the activatable 2′

-deoxyoligonucleotide P* and the wild-type strand occurs at the terminal 2′

,3′

-deoxynucleotide.

61. The pyrophosphorolysis activated polymerization method claim of 55 wherein steps (a) to (c) are conducted sequentially as two or more temperature stages on a thermocycler.

62. The pyrophosphorolysis activated polymerization method of claim 55 wherein steps (a) to (c) are conducted as one temperature stage on a thermocycler.

63. The pyrophosphorolysis activated polymerization method of claim 55 wherein the DNA polymerase is thermostable Tfl, Taq, or a genetically engineered DNA polymerase.

64. A pyrophosphorolysis activated polymerization method which comprises serially

(a) annealing to a template nucleic acid strand a complementary activatable oligonucleotide P* that has a non-extendable 3′

-deoxynucleotide at its 3′

terminus and that has no nucleotides at or near its 3′

terminus that mismatch the corresponding nucleotides on the template strand, so that the terminal 3′

-deoxynucleotide is hybridized to the template strand when the oligonucleotide P* is annealed,

(b) pyrophosphorolyzing the resulting duplex with pyrophosphate and an enzyme that has phosphorolyis activity and activates the oligonucleotide P* by removal of the hybridized terminal 3′

-deoxynucleotide, and

(c) extending the activated oligonucleotide P* on the template strand in presence of a non-extendable 3′

-deoxynucleoside triphosphate and a nucleic acid polymerase.

65. The pyrophosphorolysis activated polymerization method of claim 64 wherein the non-extendable 3′

-deoxynucloside triphosphate is labeled with a radioactive or fluorescent label.

66. The pyrophosphorolysis activated polymerization method of claim 64 wherein the non-extendable 3′

-deoxynucleoside triphosphate is a non-extendable 2′

,3′

-didedoxynucleoside triphosphate.

67. The pyrophosphorolysis activated polymerization method of claim 66 wherein, in step (c), the activated oligonucleotide P* is extended in presence of a mixture of a non-extendable 2′

,3′

-dideoxynucleoside triphosphate and four 2′

-deoxy- nucleoside triphosphates.

68. The pyrophosphorolysis activated polymerization method of claim 66 wherein the non-extendable 3′

-deoxynucleoside triphosphate is labeled with a radioactive or fluorescent label.

69. The pyrophosphorolysis activated polymerization method of claim 67 wherein the non-extendable 3′

-deoxynucleoside triphosphate is labeled with a radioactive or fluorescent label.

70. The pyrophosphorolysis activated polymerization method of claim 64 wherein, in step (c), the activated oligonucleotide P* is extended in presence of a mixture of a non-extendable 3′

-deoxynucleoside triphosphate and four nucleoside triphosphates.

71. The pyrophosphorolysis activated polymerization method of claim 70 wherein the non-extendable 3′

-deoxynucleoside triphosphate is labeled with a radioactive or fluorescent label.

72. A process which comprises serial coupling of two reactions, the second reaction being amplification of a nucleic acid by extension of an oligonucleotide on a nucleic acid template in the presence of four nucleoside triphosphates and a nucleic acid polymerase, the first reaction being activation of the oligonucleotide by removal of a 3′

end block which, if not removed, would prevent the oligonucleotide from being extended on the template.

73. Process of claim 72 where the oligonucleotide is at least partially hybridized to the template before and during the first reaction.

74. Process of claim 73 where the 3′

end block on the oligonucleotide is a 3′

chemical cap or 3′

mismatch of the template.

75. Process of claim 74 where the 3′

block is removed by 3′

base repair, dephosphorylation or restriction endonuclease cleavage.

76. Process of claim 75 where the oligonucleotide contains a methylated endonuclease recognition sequence and is annealed to the target with the unmethylated restriction endonuclease sequence, and the oligonucleotide is activated by restriction endonuclease cleavage of the methylated site.

77. Process of claim 76 where the methylated endonuclease recognition sequence is G^mATC

78. Process of claim 77 where the restriction endonuclease is DpnI.

80. The method of claim 79 wherein the nucleotide triphosphate may be didexonucleotide triphosphates as substrates of DNA polymerase for single nucleotide extensions, such as, ddATP, ddTTP, ddGTP and ddCTP.

81. The method of claim 80 wherein the dideoxynucleotide triphosphates may be labeled by dyes, such as fluorescence dyes, and the PAP signal is represented by the intensity increase of each dye.

82. The method of claim 79 wherein there is one P* corresponding to a nucleotide position of downstream or upstream which 3′

terminal nucleotide corresponds to the reference sequence or one of the three possible single base substitutions.

83. The method of claim 79 wherein there are four P*s corresponding to a nucleotide position of downstream or upstream strand which have identical sequence except that at the 3′

terminus, either ddAMP, ddTMP, ddGMP or ddCMP corresponds to the reference sequence and the three possible single base substitutions.

84. The method of claim 83 wherein the four P*s are immobilized on a single spot.

85. The method of claim 83 wherein each two successive P*s are stacked arranged with the stacked region≦

the 3′

specific subsequence to reduce the number of P*s, which can provide information regarding mutation position.

86. The method of claim 83 wherein the list of the specific PAP amplifications with the pre-known P* are scored and then the DNA complementary sequence is reconstructed by using the Watson-Crick pairing rules.

87. The method of claim 83 wherein each PAP may be applied with one P* or two oligonucleotides.

79. A method of scanning for unknown sequence variants in a nucleic acid sequence or re-sequencing of a predetermined sequence in a nucleic acid by pyrophosphorolysis activated polymerization which comprises

(a) mixing under hybridization conditions a template strand of the nucleic acid with multiple sets of four activatable oligonucleotides P* which are sufficiently complementary to the template strand to hybridize therewith and which, within each set differ, from each other in having a different 3′

-terminal non-extendable nucleotide, so that the 3′

terminal non-extendable nucleotide is hybridized to the template strand if the template strand is complementary to the 3′

terminal non-extendable nucleotide, the number of sets corresponding to the number of nucleotides in the sequence;

(b) treating the resulting duplexes with pyrophosphate and an enzyme that has phosphorolyis activity to activate by pyrophosphorolysis only those oligonucleotides P* which have a 3′

terminal non-extendable nucleotide that is hybridized to the template strand,

(c) polymerizing by extending the activated oligonucleotides P* on the template strand in presence of four nucleoside triphosphates and a nucleic acid polymerase,

(d) separating the nucleic acid strands synthesized in step (c) from the template strand,

(e) repeating steps (a)-(d) until a desired level of amplification is achieved, and

(f) arranging the nucleic acid sequence in order by analyzing overlaps of oligonuclotides P* that produced amplifications.

88. A method of determining de novo the sequence of a nucleic acid by pyrophosphorolysis activated polymerization which comprises

(a) mixing under hybridization conditions a template strand of the nucleic acid with multiple activatable oligonucleotides P*, all having the same number n of nucleotides and constituting collectively all possible sequences having n nucleotides, and all having a non-extendable nucleotide at the 3′

terminus, whereby any oligonucleotides P* that are sufficiently complementary will hybridize to the template strand, and the 3′

terminal non-extendable nucleotide will hybridize to the template strand only if the template strand is complementary at the position corresponding to the 3′

terminus;

(b) treating the resulting duplexes with pyrophosphate and an enzyme that has phosphorolyis activity to activate only those hybridized oligonucleotides P* which have a 3′

terminal non-extendable nucleotide that is hybridized to the template strand, by pyrophosphorolysis of those hybridized 3′

terminal non-extendable nucleotides;

(c) polymerizing by extending the activated oligonucleotides P* on the template strand in presence of four nucleoside triphosphates and a nucleic acid polymerase,

(d) separating the nucleic acid strands synthesized in step (c) from the template strand,

(e) repeating steps (a)-(d) until a desired level of amplification has been achieved, and

(f) determining the sequence of oligonucleotides P* that produced amplifications, then arranging the nucleic acid sequence in order by analyzing overlaps of these oligonucleotides.

89. The method of claim 88 wherein the nucleotide triphosphate may be didexonucleotide triphosphates as substrates of DNA polymerase for single nucleotide extensions, such as, ddATP, ddTTP, ddGTP and ddCTP.

90. The method of claim 89 wherein the dideoxynucleotide triphosphates may be labeled by dyes, such as fluorescence dyes, and the PAP signal is represented by the intensity increase of each dye.

91. The method of claim 88 wherein the dideoxynucleotide at the 3′

terminus of P*, such as ddAMP, ddTMP, ddGMP, and ddCMP, may be labeled by dyes, such as fluorescence dyes, and the PAP signal is represented by the intensity decrease of each dye.

92. The method of claim 88 wherein a set of P*s with different 3′

specific subsequences are applied for PAP.

93. The method of claim 92 wherein each P* has a 3′

specific subsequence.

94. The method of claim 92 wherein the set of P*s is a complete set of different 3′

specific subsequences or an incomplete set of different 3′

specific subsequences.

95. The method of claim 92 wherein the list of the specific PAP amplifications with the pre-known P*s are scored and then the unknown DNA complementary sequence is reconstructed by ordering the 3′

specific subsequences by using the Watson-Crick pairing rules.

96. The method of claim 92 wherein each PAP may be applied with one or two P* or two oligonucleotides.