Late-PCR

• US 7,198,897 B2
• Filed: 12/17/2002
• Issued: 04/03/2007
• Est. Priority Date: 12/19/2001
• Status: Active Grant

• Current Assignee: Brandeis University
• Original Assignee: Brandeis University
• Inventors: Rice, John, Wangh, Lawrence J., Hartshorn, Cristina, Sanchez, J. Aquiles, Pierce, Kenneth
• Primary Examiner(s): Fredman; Jeffrey
• Assistant Examiner(s): MUMMERT, STEPHANIE KANE
• Application Number:
  US10/320,893
• Publication Number:
  US 20040053254A1
• Time in Patent Office: 1,568 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2531/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2561/113 Real time assay

Abstract

A non-symmetric polymerase chain reaction (PCR) amplification method employing a limiting primer in low concentration whose concentration-adjusted melting point at least equals, and preferably exceeds, that of the excess primer, the latter in turn not being more than 25° C. below the melting temperature of the amplicon. Assays employing such amplification and labeled hybridization probes, including assays that include a detection step following primer extension or a low-temperature probe, or both. Kits for performing such assays and primer or primer-and-probe sets for performing the foregoing amplifications and assays.

Claims

1. A non-symmetric polymerase chain reaction (PCR) amplification method comprising thermally cycling a PCR reaction mixture containing a deoxyribonucleic acid (DNA) amplification target sequence, a pair of PCR primers, dNTP'"'"'s and a thermostable polymerase repeatedly through PCR steps of strand melting, primer annealing and primer extension, wherein, at the outset of amplification (a) the reaction mixture contains up to 1,000,000 copies of the amplification target sequence, (b) the PCR primer pair comprises a limiting primer and an excess primer, the limiting primer being present at a concentration of up to 200 nM and the excess primer being present at an initial concentration at least five times higher than the limiting primer (c) an initial, concentration-adjusted melting temperature of the limiting primer that is equal to or greater than an initial, concentration-adjusted melting temperature of the excess primer when the initial, concentration-adjusted melting temperature is determined using a formula that takes into account initial primer concentration and composition, (d) if the limiting primer is not fully complementary to the target sequences the initial, concentration-adjusted melting temperature of that portion of the limiting primer which hybridizes to the target sequence is not more than 5°

C. below the initial, concentration-adjusted melting temperature of the excess primer when the initial, concentration-adjusted melting temperature is determined using a formula that takes into account initial primer concentration and composition, (e) the melting temperature of an amplicon produced by extension of the excess primer exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 18°

C., and (f) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primer following exhaustion of the limiting primer.

2. The method of claim 1, wherein the reaction mixture includes a pair of PCR primers for each of at least two amplification target sequences, and wherein the initial, concentration-adjusted melting points of the limiting primer of each primer pair is equal to or greater than the initial, concentration-adjusted melting point of the excess primer of the same primer pair.

3. The method of claim 1, further comprising reverse transcribing a ribonucleic acid (RNA) molecule to generate the DNA target sequence.

4. The method of claim 1, wherein the PCR reaction mixture contains up to 50,000 copies of the nucleic acid target.

5. The method of claim 1 wherein the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

6. The method of claim 5, wherein the excess primer is present at an initial concentration of 500–

2000 nM and at least ten times higher than the initial concentration of the limiting primer.

7. The method of claim 5 wherein the melting temperature of the amplicon is 7–

15°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

8. The method of claim 4 wherein the melting temperature of the amplicon is 7–

15°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

9. The method of claim 4 wherein the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

10. The method of claim 1 wherein the melting temperature of the amplicon is 7–

15°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

11. The method of claim 1 wherein the reaction mixture contains up to 1000 copies of the DNA target.

12. The method of claim 11 wherein the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

13. The method of claim 11 wherein the melting temperature of the amplicon is 7–

15°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

14. The method of claim 1 wherein the duration of the primer annealing step is not longer than 30 seconds.

15. The method according to claim 1, further including at least one terminal thermal cycle in which a single-stranded extension product of the excess primer is converted to a double-stranded product, wherein the PCR reaction mixture additionally includes a low-temperature primer capable of priming the extension product of the excess primer and having an initial, concentration-adjusted melting temperature at least 5°

C. below the initial, concentration-adjusted melting temperature of the excess primer, and wherein an annealing temperature is maintained above the initial, concentration-adjusted melting temperature of the low-temperature primer except for at least one terminal cycle in which the annealing temperature is lowered to hybridize the low-temperature primer.

16. The method according to claim 15 wherein the initial, concentration-adjusted melting temperature of the low-temperature primer is at least 10°

C. below the initial, concentration-adjusted melting point of the excess primer.

17. The method of claim 1, wherein the PCR reaction mixture additionally contains a complementary oligonucleotide that hybridizes to a 3′

end of the excess primer and has an initial, concentration-adjusted melting temperature at least 3°

C. lower than the initial, concentration-adjusted melting temperature of the excess primer.

18. The method of claim 17 wherein the complementary oligonucleotide is present at the outset in a concentration greater than the concentration of the excess primer.

70. The method of claim 1, wherein the formula is:

T_m=Δ

H/(Δ

S+R ln(C/2))−

273.15+12 log [M], wherein

Δ

H is enthalpy,

Δ

S is entropy,

C is concentration of the primer,

R is universal gas constant, and

[M] is molar concentration of monovalent cations.

75. The method of claim 1, wherein the thermostable polymerase is Taq polymerase.

19. A non-symmetric polymerase chain reaction (PCR) method comprising thermally cycling a PCR reaction mixture containing a deoxyribonucleic acid (DNA) amplification target sequence, a pair of matched limiting PCR primers, an excess primer, dNTP'"'"'s and a thermostable polymerase repeatedly through PCR steps of strand melting, primer annealing and primer extension, wherein the matched limiting PCR primers are present in approximately equimolar initial concentration of up to 200 nM, the excess primer is present at an initial concentration at least five times higher than the limiting primers, an initial, concentration-adjusted melting temperatures of the excess primer is at least 5°

C. below an initial, concentration-adjusted melting temperature of the limiting primers when the initial, concentration-adjusted melting temperature is determined using a formula that takes into account initial primer concentration and composition, and wherein the method comprises a first phase wherein an annealing temperature is higher than the initial, concentration-adjusted melting temperature of the excess primer and the matched limiting primers generate a first amplicon, and a second phase wherein the annealing temperature is lowered and the excess primer generates a second amplicon, shorter than the first amplicon, utilizing the first amplicon as a template strand, and wherein the melting temperature of the second amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 25°

C.

20. The method according to claim 19, wherein the initial, concentration-adjusted melting temperature of the excess primer is at least 10°

C. below the initial, concentration-adjusted melting temperatures of the limiting primers.

21. The method according to claim 20 wherein the melting temperature of the second amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 18°

C.

71. The method of claim 19, wherein the formula is:

T_m=Δ

H/(Δ

S+R ln(C/2))−

273.15+12 log [M], wherein

Δ

H is enthalpy,

Δ

S is entropy,

C is concentration of the primer,

R is universal gas constant, and

[M] is molar concentration of monovalent cations.

76. The method of claim 19, wherein the thermostable polymerase is Taq polymerase.

22. A non-symmetric polymerase chain reaction (PCR) method with removal of single-stranded amplicon comprising a) thermally cycling a PCR reaction mixture containing a DNA amplification target sequence, a pair of PCR primers for the amplification target sequence, dNTP'"'"'s and a thermostable DNA polymerase through repeated cycles of strand melting, primer annealing and primer extension, wherein (i) the PCR primer pair comprises a limiting primer and an excess primer, (ii) the limiting primer is present at an initial concentration of up to 200 nM, and the excess primer is present at an initial concentration at least five times higher than the limiting primer, (iii) an initial, concentration-adjusted melting temperature of the limiting primer is at least equal to an initial, concentration-adjusted melting temperature of the excess primer when in initial, concentration-adjusted melting temperature is determined using a formula that takes into account initial primer concentration and composition, and (iv) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primer following exhaustion of the limiting primer;

and b) during at least some cycles of linear amplification, following the step of primer extension, removing a single-stranded extension product of the excess primer from the reaction mixture by hybridizing the single-stranded extension product to capture probes.

23. The method of claim 22, wherein the capture probes are in a thermally isolated product removal zone and the step of removing comprises passing the reaction mixture through the zone.

24. The method according to claim 23, wherein the product removal zone is physically isolatable from the at least one reaction zone, further including periodically isolating the product removal zone and harvesting product hybridized to the capture probes while the reaction mixture is in the at least one reaction zone.

25. The method of claim 22 wherein the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

26. The method of claim 22, wherein the melting temperature of the amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 18°

C.

27. The method of claim 22, wherein the excess primer is present at an initial concentration of 500–

2000 nM and at least ten times higher than the initial concentration of the limiting primer.

72. The method of claim 22, wherein the formula is:

T_m=Δ

H/(Δ

S+R ln(C/2))−

273.15+12 log [M], wherein

Δ

H is enthalpy,

Δ

S is entropy,

C is concentration of the primer,

R is universal gas constant, and

[M] is molar concentration of monovalent cations.

77. The method of claim 22, wherein the thermostable polymerase is Taq polymerase.

28. A homogeneous detection assay for at least one DNA amplification target sequence employing non-symmetric polymerase chain reaction (PCR) amplification, comprising (a) thermally cycling through multiple cycles of PCR steps of strand melting, primer annealing and primer extension a PCR reaction mixture containing the at least one DNA amplification target sequence, a thermostable DNA polymerase, dNTP'"'"'s, and for each amplification target sequence a pair of PCR primers for amplifying the amplification target sequence and at least one labeled hybridization probe that hybridizes to an amplicon produced by the primers and (b) detecting signal produced by the at least one probe as an indication of the presence of the at least one amplification target sequence, wherein (i) each PCR primer pair comprises a limiting primer and an excess primer, (ii) the limiting primer is present at an initial concentration of up to 200 nM, and for each primer pair the excess primer is present at an initial concentration of at least five times higher than the limiting primer concentration, (iii) an initial, concentration-adjusted melting temperature of the limiting primer of each primer pair is at least equal to an initial, concentration-adjusted melting temperature the excess primer of the same pair when the initial, concentration-adjusted melting temperature is determined using a formula that takes into account initial primer concentration and composition, (iv) for each primer pair the melting temperature of the amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 25°

C., (v) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primers following exhaustion of the limiting primers, and (vi) the probes is selected from the group consisting of probes that hybridize to an extension product of the limiting primer, and probes that hybridize to an extension product of the excess primer and signal upon hybridization, and (viii) the probes hybridize to the amplicons during the PCR step of primer annealing.

29. The assay according to claim 28, wherein the step of detecting is an end-point detection.

30. The assay according to claim 28, wherein the step of detection is real-time detection performed during the annealing step of at least some cycles of linear amplification.

31. The assay according to claim 28, wherein the step of detection is real-time detection performed following the extension step of at least some cycles of linear amplification and prior to strand melting of the following cycles.

32. The assay according to claim 31 wherein the duration of the primer annealing step is not longer than 30 seconds.

33. The assay according to claim 32 wherein, for each primer pair, the melting temperature of the amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 18°

C.

34. The assay according to claim 32 wherein, for each primer pair, the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusting melting temperature of the excess primer.

35. The assay according to claim 32, wherein the at least on hybridization probe hybridizes to the extension products of the excess primer and signals upon hybridization.

36. The assay according to claim 28 wherein, the at least one hybridization probe is a dual-labeled fluorescent probe that hybridizes to the extension product of the limiting primer and that is hydrolyzed by the polymerase during extension of the excess primer, thereby generating a detectable signal, and wherein the signal is detected in real time during at least some cycles of the linear amplification.

37. The assay according to claim 36, wherein the reaction mixture contains up to 50,000 copies of the at least one amplification target sequence.

38. The assay according to claim 37 wherein, for each primer pair, the melting temperature of the amplicon is not more than 18°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

39. The assay according to claim 37 wherein, for each primer pair, the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

40. The assay according to claim 39 wherein the duration of the primer annealing step is not longer than 30 seconds.

41. The assay according to claim 37, wherein the signal from the at least one hybridization probe is detected between the PCR steps of primer extension and strand melting.

42. The assay according to claim 28, wherein the at least one hybridization probe is a dual-labeled fluorescent probe that hybridizes to the extension product of the limiting primer and that is hydrolyzed by the polymerase during extension of the excess primer, thereby generating a detectable signal.

43. The assay according to claim 28, wherein the at least one hybridization probe emits a detectable signal upon hybridization to the extension product of the excess primer.

44. The assay according to claim 43, wherein, for at least one PCR primer pair, the reaction mixture additionally contains a complementary oligonucleotide that hybridizes to a 3′

end of the excess primer and has an initial, concentration-adjusted melting temperature at least 3°

C. lower than the initial, concentration-adjusted melting temperature of the excess primer.

45. The assay according to claim 44 wherein the complementary oligonucleotide is present at the outset in a concentration greater than the concentration of the excess primer.

46. The assay according to claim 28, wherein the at least one hybridization probe comprises a first probe for one allelic variant and a second probe for another allelic variant.

47. The assay according to claim 28, further comprising reverse transcribing of ribonucleic acid (RNA) molecule to generate a DNA target sequence.

48. The assay according to claim 28, wherein the reaction mixture contains up to 50,000 copies of the amplification target sequence.

49. The assay according to claim 28, wherein the initial, concentration-adjusted melting temperature of the limiting primer is at least 3°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

50. The assay according to claim 28 wherein the melting temperature of the amplicon is not more than 18°

C. higher than the initial, concentration-adjusted melting temperature of the excess primer.

51. The assay according to claim 28, wherein the at least one amplification target sequence comprises at least two amplification target sequences.

73. The assay of claim 28, wherein the formula is:

T_m=Δ

H/(Δ

S+R ln(C/2))−

273.15+12 log [M], wherein

Δ

H is enthalpy,

Δ

S is entropy,

C is concentration of the primer,

R is universal gas constant, and

[M] is molar concentration of monovalent cations.

78. The method of claim 28, wherein the thermostable polymerase is Taq polymerase.

52. A homogeneous detection assay for at least one DNA amplification target sequence employing non-symmetric polymerase chain reaction (PCR) amplification, comprising (a) thermally cycling through multiple cycles of PCR steps of strand melting, primer annealing and primer extension a PCR reaction mixture containing the at least one amplification target sequence, a thermostable DNA polymerase, dNTP'"'"'s, and for each amplification target sequence a pair of PCR primers for amplifying the amplification target sequence and at least one labeled low-temperature hybridization probe that hybridizes to an amplicon produced by the primers and (b) detecting signal produced by the at least one probe as an indication of the presence of the at least one amplification target sequence, wherein (i) each PCR primer pair comprises a limiting primer and an excess primer, (ii) each limiting primer is present at an initial concentration of up to 200 nM, and for each primer pair the excess primer is present at an initial concentration at least five times higher than the limiting primer concentration, (iii) for each amplification target sequence, the low-temperature hybridization probe binds to the extension product of the excess primer and emits a detectable signal upon hybridization, (iv) for each amplification target sequence an initial, concentration-adjusted melting temperature of the low-temperature hybridization probe is at least 5°

C. below an initial, concentration-adjusted melting temperature of the limiting primer when the initial, concentration-adjusted melting temperature is determined using a formula that takes into account initial primer concentration and composition, (v) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primers following exhaustion of the limiting primers, and (vi) detection is performed at a temperature sufficiently low for the low-temperature probes to hybridize and signal.

53. The assay according to claim 52, wherein the initial, concentration-adjusted melting temperature of the low-temperature hybridization probe is at least 10°

C. below the initial, concentration-adjusted melting temperature of the limiting primer.

54. The assay according to claim 52, wherein each probe is present in the reaction mixture at a concentration of at least 1 uM.

55. The assay according to claim 52 wherein the PCR step of primer annealing during at least some cycles of linear amplification is of sufficiently low temperature and of sufficient duration that the low-temperature probe hybridizes during primer annealing, and detection is performed during that step.

56. The assay according to claim 52, wherein the initial, concentration-adjusted melting temperature of limiting primer of each primer pair is equal to or greater than the initial, concentration-adjusted melting temperature of the excess primer of the same primer pair.

57. The assay according to claim 52, wherein the PCR amplification includes an added detection step following primer extension during at least some cycles of linear amplification, the detection step being of sufficiently low temperature and sufficient duration for the low-temperature hybridization probes to hybridize and signal, and wherein the PCR step of primer annealing is not of sufficiently low temperature and sufficient duration for said probes to hybridize and signal.

58. The assay according to claim 57, wherein the initial, concentration-adjusted melting temperature of the low-temperature hybridization probe is at least 10°

C. below the initial, concentration-adjusted melting temperature of the limiting primer.

59. The assay according to claim 57, wherein the initial, concentration-adjusted melting temperature of the low-temperature hybridization probe is at least 5°

C. below a mean temperature of the annealing step of the exponential phase of the amplification reaction.

60. The assay according to claim 59, wherein the initial, concentration-adjusted melting temperature of the low-temperature hybridization probe is at least 10°

C. below the mean temperature of the annealing step of the exponential phase of the amplification reaction.

61. The assay according to claim 57, wherein the detection step is performed only beginning a few cycles prior to the threshold cycle of the reaction.

62. The assay according to claim 57, wherein the low-temperature detection step is not more than 30 seconds duration.

63. The assay according to claim 57, wherein detection is end-point detection performed following completion of the amplification reaction.

64. The assay according to claim 52, wherein for each primer pair the melting temperature of the amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 25°

C.

74. The assay of claim 52, wherein the formula is:

T_m=Δ

H/(Δ

S+R ln(C/2))−

273.15+12 log [M], wherein

Δ

H is enthalpy,

Δ

S is entropy,

C is concentration of the primer,

R is universal gas constant, and

[M] is molar concentration of monovalent cations.

79. The method of claim 52, wherein the thermostable polymerase is Taq polymerase.

65. A non-symmetric polymerase chain reaction (PCR) amplification method comprising thermally cycling a PCR reaction mixture containing a deoxyribonucleic acid (DNA) amplification target sequence, a pair of PCR primers, dNTP'"'"'s and a thermostable polymerase repeatedly through PCR steps of strand melting, primer annealing and primer extension, wherein, at the outset of amplification (a) the reaction mixture contains up to 1,000,000 copies of the amplification target sequence, (b) the PCR primer pair comprises a limiting primer and an excess primer, the limiting primer being present at an initial concentration of up to 200 nM and the excess primer being present at an initial concentration at least five times higher than the limiting primer (c) an initial, concentration-adjusted melting temperature of the limiting primer that is equal to or greater than an initial, concentration-adjusted melting temperature of the excess primer when the initial, concentration-adjusted melting temperature is determined using a Nearest Neighbor formula, (d) if the limiting primer is not fully complementary to the target sequences the initial, concentration-adjusted melting temperature of that portion of the limiting primer which hybridizes to the target sequence is not more than 5°

C. below the initial, concentration-adjusted melting temperature of the excess primer when the initial, concentration-adjusted melting temperature is determined using a Nearest Neighbor formula, (e) the melting temperature of the amplicon produced by extension of the excess primer exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 18°

C., and (f) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primer following exhaustion of the limiting primer.

80. The method of claim 65, wherein the thermostable polymerase is Taq polymerase.

66. A non-symmetric polymerase chain reaction (PCR) method comprising thermally cycling a PCR reaction mixture containing a deoxyribonucleic acid (DNA) amplification target sequence, a pair of matched limiting PCR primers, an excess primer, dNTP'"'"'s and a thermostable polymerase repeatedly through PCR steps of strand melting, primer annealing and primer extension, wherein the matched limiting PCR primers are present in approximately equimolar initial concentrations of up to 200 nM, the excess primer is present at an initial concentration at least five times higher than the limiting primers, an initial, concentration-adjusted melting temperatures of the excess primer is at least 5°

C. below an initial, concentration-adjusted melting temperature of the limiting primers when the initial, concentration-adjusted melting temperature is determined using a Nearest Neighbor formula, and wherein the reaction comprises a first phase wherein the annealing temperature is higher than the initial, concentration-adjusted melting temperature of the excess primer and the matched limiting primers generate a first amplicon, and a second phase wherein the annealing temperature is lowered and the excess primer generates a second amplicon, shorter than the first amplicon, utilizing the first amplicon as a template strand, and wherein the melting temperature of the second amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 25°

C.

81. The method of claim 66, wherein the thermostable polymerase is Taq polymerase.

67. A non-symmetric polymerase chain reaction (PCR) method with removal of single-stranded amplicon comprising a) thermally cycling a PCR reaction mixture containing a DNA amplification target sequence, a pair of PCR primers for the amplification target sequence, dNTP'"'"'s and a thermostable DNA polymerase through repeated cycles of strand melting, primer annealing and primer extension, wherein (i) the PCR primer pair comprises a limiting primer and an excess primer, (ii) the limiting primer is present at an initial concentration of up to 200 nM, and the excess primer is present at an initial concentration at least five times higher than the limiting primer, (iii) an initial, concentration-adjusted melting temperature of the limiting primer is at least equal to an initial, concentration-adjusted melting temperature of the excess primer when the initial, concentration-adjusted melting temperature is determined using a Nearest Neighbor formula, and (iv) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primer following exhaustion of the limiting primer;

and b) during at least some cycles of linear amplification, following the step of primer extension, removing single-stranded extension product of the excess primer from the reaction mixture by hybridizing the product to capture probes.

82. The method of claim 67, wherein the thermostable polymerase is Taq polymerase.

68. A homogeneous detection assay for at least one DNA amplification target sequence employing non-symmetric polymerase chain reaction (PCR) amplification, comprising (a) thermally cycling through multiple cycles of PCR steps of strand melting, primer annealing and primer extension a PCR reaction mixture containing the at least one amplification target sequence, a thermostable DNA polymerase, dNTP'"'"'s, and for each amplification target sequence a pair of PCR primers for amplifying the amplification target sequence and at least one labeled hybridization probe that hybridizes to the amplicon produced by the primers and (b) detecting signal produced by the at least one probe as an indication of the presence of the at least one amplification target sequence, wherein (i) each PCR primer pair comprises a limiting primer and an excess primer, (ii) the limiting primer is present at an initial concentration of up to 200 nM, and for each primer pair the excess primer is present at an initial concentration of at least five times higher than the limiting primer concentration, (iii) an initial, concentration-adjusted melting temperature of the limiting primer of each primer pair is equal to or greater than the initial, concentration-adjusted melting temperature of the excess primer of the same primer pair when the initial, concentration-adjusted melting temperature is determined using a Nearest Neighbor formula, (iv) for each primer pair the melting temperature of the amplicon exceeds the initial, concentration-adjusted melting temperature of the excess primer by not more than 25°

C., (v) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primers following exhaustion of the limiting primers, and (vi) the probes are selected from the group consisting of probes that hybridize to the extension product of the limiting primer, and probes that hybridize to the extension product of the excess primer and signal upon hybridization, and (viii) the probes hybridize to the amplicons during the PCR step of primer annealing.

83. The method of claim 68, wherein the thermostable polymerase is Taq polymerase.

69. A homogeneous detection assay for at least one DNA amplification target sequence employing non-symmetric polymerase chain reaction (PCR) amplification, comprising (a) thermally cycling through multiple cycles of PCR steps of strand melting, primer annealing and primer extension a PCR reaction mixture containing the at least one amplification target sequence, a thermostable DNA polymerase, dNTP'"'"'s, and for each amplification target sequence a pair of PCR primers for amplifying the amplification target sequence and at least one labeled low-temperature hybridization probe that hybridizes to the amplicon produced by the primers and (b) detecting signal produced by the at least one probe as an indication of the presence of the at least one amplification target sequence, wherein (i) each PCR primer pair comprises a limiting primer and an excess primer, (ii) each limiting primer is present at an initial concentration of up to 200 nM, and for each primer pair the excess primer is present at an initial concentration at least five times higher than the limiting primer concentration, (iii) for each amplification target sequence, the low-temperature hybridization probe binds to the extension product of the excess primer and emits a detectable signal upon hybridization, (iv) for each amplification target sequence an initial, concentration-adjusted melting temperature of the low-temperature hybridization probe is at least 5°

C. below an initial, concentration-adjusted melting temperature of the limiting primer when the initial, concentration-adjusted melting temperature is determined using a Nearest Neighbor formula, (v) thermal cycling is repeated a number of times sufficient to include multiple cycles of linear amplification using the excess primers following exhaustion of the limiting primers, and (vi) detection is performed at a temperature sufficiently low for the low-temperature probes to hybridize and signal.

84. The method of claim 69, wherein the thermostable polymerase is Taq polymerase.