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METHOD FOR DETECTING TARGET NUCLEIC ACID SEQUENCES

20220017949 · 2022-01-20

    Inventors

    Cpc classification

    International classification

    Abstract

    The present application relates to multiplex detection of nucleic acid molecules. In particular, the present application provides a method for detecting target nucleic acid sequences, said method can simultaneously detect the presence of multiple target nucleic acid sequences in a sample. In addition, the present application further provides a probe set, and a kit comprising one or more said probe sets, said probe set and said kit can be used to carry out the method of the invention.

    Claims

    1-40. (canceled)

    41. A probe set, comprising a detection probe, and at least two mediator probes, wherein, said mediator probe each independently comprises in 5′ to 3′ direction, a mediator sequence and a target specific sequence, said target specific sequence comprises a sequence complementary to a target nucleic acid sequence, said mediator sequence comprises a sequence not complementary to said target nucleic acid sequence, and, the mediator sequences comprised in at least two mediator probes are different from each other; and said detection probe comprises in 3′ to 5′ direction, at least two capture sequences which are complementary to the mediator sequences or parts thereof of the at least two mediator probes, and are able to hybridize with and capture the mediator sequences of the at least two mediator probes, and a templating sequence; and, said detection probe is labeled with a reporter group and a quencher group, wherein, said reporter group can generate a signal, and, said quencher group can absorb or quench the signal generated by said reporter group; and, the signal, as generated by said detection probe when hybridizing with its complementary sequence, is different from the signal, as generated when not hybridizing with its complementary sequence.

    42. The probe set according to claim 41, wherein said probe set has one or more of the following features: (i) said probe set comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 15, or at least 20 mediator probes; (ii) the mediator sequences comprised in at least two or all the mediator probes are different from each other; (iii) the target specific sequences comprised in at least two or all the mediator probes are different from each other; (iv) at least two or all the mediator probes target to different target nucleic acid sequences, respectively; and (v) said probe set comprises one or more detection probes; and the one or more detection probes are independently labeled with identical or different reporter groups.

    43. The probe set according to claim 41, wherein, said mediator probe has one or more of the following features: (a) said mediator probes each independently comprise or consist of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; (b) the mediator sequence of at least one mediator probe comprises a modified nucleotide, an unnatural nucleotide, or any combination thereof; (c) said mediator probes each independently have a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-200 nt, 200-300 nt, 300-400 nt, 400-500 nt, 500-600 nt, 600-700 nt, 700-800 nt, 800-900 nt, or 900-1000 nt; (d) the target specific sequences in said mediator probes each independently have a length of 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-150 nt, 150-200 nt, 200-250 nt, 250-300 nt, 300-350 nt, 350-400 nt, 400-450 nt, or 450-500 nt; (e) the mediator sequences in said mediator probes each independently have a length of 5-10 nt, 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-110 nt, 110-120 nt, 120-130 nt, or 130-140 nt; and (f) at least one mediator probe has a 3′-OH end, or the 3′-end thereof is blocked.

    44. The probe set according to claim 41, wherein said detection probe has one or more of the following features: (a) said detection probe each independently comprises or consists of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; (b) said detection probe each independently has a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-200 nt, 200-300 nt, 300-400 nt, 400-500 nt, 500-600 nt, 600-700 nt, 700-800 nt, 800-900 nt, or 900-1000 nt; (c) each capture sequence in said detection probe independently has a length of 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-150 nt, 150-200 nt, 200-250 nt, 250-300 nt, 300-350 nt, 350-400 nt, 400-450 nt, or 450-500 nt; (d) the templating sequence in said detection probe each independently has a length of 1-5 nt, 5-10 nt, 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-200 nt, 200-300 nt, 300-400 nt, 400-500 nt, 500-600 nt, 600-700 nt, 700-800 nt, or 800-900 nt; (e) at least one detection probe has 3′-OH end, or its 3′-end is blocked; (f) at least one detection probe is a self-quenching probe; (g) in said detection probe, the reporter group is independently a fluorescent group; and, the quencher group is a molecule or a group capable of absorbing or quenching fluorescence; (h) at least one detection probe is resistant to nuclease activity; (i) said detection probe each independently is linear or has a hairpin structure; and (j) at least one detection probe comprises multiple capture sequences; and, said multiple capture sequences are arranged in a contiguous manner, arranged in such a manner that they are spaced by a linking sequence, or arranged in an overlapping manner.

    45. The probe set according to claim 41, wherein said detection probe has one or more of the following features: (a) said detection probe is labeled with a reporter group at its 5′ end or upstream and is labeled with a quencher group at its 3′ end or downstream, or is labeled with a reporter group at its 3′ end or downstream and is labeled with a quencher group at its 5′ end or upstream; (b) the distance between said reporter group and said quencher group is 10-80 nt or longer; (c) the reporter group is selected from the group consisting of ALEX-350, FAM, VIC, TET, CAL Fluor® Gold 540, JOE, HEX, CAL Fluor Orange 560, TAMRA, CAL Fluor Red 590, ROX, CAL Fluor Red 610, TEXAS RED, CAL Fluor Red 635, Quasar 670, CY3, CYS, CY5.5, and Quasar 705; (d) the quencher group is selected from the group consisting of DABCYL, BHQ, ECLIPSE, and TAMRA; (e) at least one detection probe is resistant to 5′ nuclease activity; (f) at least one detection probe has a main chain comprising a modification resistant to nuclease activity; and (g) at least one detection probe has a main chain comprising phosphorothioate bond, alkyl phosphate triester bond, aryl phosphate triester bond, alkyl phosphonate bond, aryl phosphonate bond, hydrogenated phosphate bond, alkyl phosphoramidate bond, aryl phosphoramidate bond, 2′-O-aminopropyl modification, 2′-O-alkyl modification, 2′-O-allyl modification, 2′-O-butyl modification, and/or 1-(4′-thio-PD-ribofuranosyl) modification.

    46. A kit comprising one or more probe sets as defined in claim 41.

    47. The kit according to claim 46, wherein said kit has one or more of the following features: (i) said kit comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 probe sets; (ii) at least two or all the mediator probes in the kit target to different target nucleic acid sequences, respectively; (iii) the mediator sequences comprised in at least two or all the mediator probes in the kit are different from each other; (iv) the target specific sequences comprised in at least two or all the mediator probes in the kit are different from each other; and (v) the detection probes in the kit are independently labeled with identical or different reporter groups.

    48. The kit according to claim 46, wherein the kit further comprises: an upstream oligonucleotide sequence, a downstream oligonucleotide sequence, a common primer, an enzyme having 5′ nuclease activity, a nucleic acid polymerase, an agent for nucleic acid hybridization, an agent for cleavage of a mediator probe, an agent for nucleic acid extension, an agent for nucleic acid amplification, an agent for reverse transcription, or any combination thereof.

    49. The kit according to claim 48, wherein said upstream oligonucleotide sequence has one or more of the following features: (1) said upstream oligonucleotide sequence comprises a sequence complementary to a target nucleic acid sequence; and, when hybridizing with the target nucleic acid sequence, said upstream oligonucleotide sequence is located upstream to the target specific sequence of a mediator probe; (2) said upstream oligonucleotide sequences each independently comprise or consist of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; (3) said upstream oligonucleotide sequences each independently have a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-110 nt, 110-120 nt, 120-130 nt, 130-140 nt, or 140-150 nt; (4) said upstream oligonucleotide sequence, upon hybridization with a target nucleic acid sequence, is each independently located far from the upstream of the mediator probe, or located near the upstream of the mediator probe, or has a partially overlapping sequence with the target specific sequence of the mediator probe; and (5) said upstream oligonucleotide sequence is each independently a primer specific for a target nucleic acid sequence or a probe specific for a target nucleic acid sequence.

    50. The kit according to claim 48, wherein said downstream oligonucleotide sequence has one or more of the following features: (1) said downstream oligonucleotide sequence comprises a sequence complementary to a target nucleic acid sequence; and, when hybridizing with said target nucleic acid sequence, said downstream oligonucleotide sequence is located downstream to the target specific sequence of a mediator probe; (2) said downstream oligonucleotide sequences each independently comprise or consist of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; and (3) said downstream oligonucleotide sequences each independently have a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-110 nt, 110-120 nt, 120-130 nt, 130-140 nt, or 140-150 nt.

    51. The kit according to claim 48, wherein the upstream oligonucleotide sequence and the downstream oligonucleotide sequence have an identical oligonucleotide sequence at 5′ end; and, the common primer has a sequence complementary to the identical oligonucleotide sequence; optionally, said common primer has one or more of the following features: (a) said common primer comprises or consists of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; and (b) said common primer has a length of 8-15 nt, 15-20 nt, 20-30 nt, 30-40 nt, or 40-50 nt.

    52. The kit according to claim 48, wherein said enzyme having 5′ nuclease activity or said nucleic acid polymerase has one or more of the following features: (1) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is a nucleic acid polymerase having 5′ nuclease activity; (2) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is a DNA polymerase having 5′ nuclease activity; (3) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is a DNA polymerase originated from a bacterium selected from: Thermus aquaticus (Taq), Thermus thermophiles (Tth), Thermus filiformis, Therrnis flavus, Thermococcus literalis, Thermus antranildanii, Thermus caldophllus, Thermus chliarophilus, Thermus flavus, Thermus igniterrae, Thermus lacteus, Thermus oshimai, Thermus ruber, Thermus rubens, Thermus scotoductus, Thermus silvanus, Thermus thermophllus, Thermotoga maritima, Thermotoga neapolitana, Thermosipho africanus, Thermococcus litoralis, Thermococcus barossi, Thermococcus gorgonarius, Thermotoga maritima, Thermotoga neapolitana, Thermosiphoafricanus, Pyrococcus woesei, Pyrococcus horikoshii, Pyrococcus abyssi, Pyrodictium occultum, Aquifexpyrophilus and Aquifex aeolieus; and (4) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is Taq polymerase.

    53. A kit comprising m detection probes and n mediator probes, wherein, n is an integer of ≥2, m is an integer less than n and greater than 0, and, each mediator probe independently comprises in 5′ to 3′ direction, a mediator sequence and a target specific sequence, said target specific sequence comprises a sequence complementary to a target nucleic acid sequence, said mediator sequence comprises a sequence not complementary to said target nucleic acid sequence, and, the mediator sequences comprised in at least two mediator probes are different from each other; and each detection probe independently comprises in 3′ to 5′ direction, one or more capture sequences complementary to one or more mediator sequences or parts thereof, and a templating sequence; and, said m detection probes comprise a plurality of capture sequences, which are complementary to the mediator sequences or parts thereof of the mediator probes, respectively; and, wherein at least one of the detection probes comprises at least two capture sequences, which are complementary to the mediator sequences or parts thereof of at least two mediator probes, and are able to hybridize with and capture the mediator sequences of the at least two mediator probes; and each detection probe is independently labeled with a reporter group and a quencher group, wherein, said reporter group can generate a signal, and, said quencher group can absorb or quench the signal generated by said reporter group; and, the signal, as generated by each detection probe when hybridizing with its complementary sequence, is different from the signal, as generated when not hybridizing with its complementary sequence.

    54. The kit according to claim 53, wherein the kit has one or more of the following features: (a) n is an integer of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40 or greater; (b) m is an integer of 1, 2, 3, 4, 5, 6, 8, 10 or greater; (c) when m≥2, said m detection probes are independently labeled with identical or different reporter groups; (d) said target nucleic acid sequence is DNA or RNA; (e) said target nucleic acid sequence is single-stranded or double-stranded; (f) said target nucleic acid sequence is obtained from prokaryotes, eukaryotes, viruses or viroids; (g) the kit comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 8, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, or at least 45 mediator probes; and (h) the kit comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 8, or at least 10 detection probes.

    55. The kit according to claim 53, wherein said mediator probe has one or more of the following features: (a) said mediator probes each independently comprise or consist of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; (b) the mediator sequence of at least one mediator probe comprises a modified nucleotide, an unnatural nucleotide, or any combination thereof; (c) said mediator probes each independently have a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-200 nt, 200-300 nt, 300-400 nt, 400-500 nt, 500-600 nt, 600-700 nt, 700-800 nt, 800-900 nt, or 900-1000 nt; (d) the target specific sequences in said mediator probes each independently have a length of 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-150 nt, 150-200 nt, 200-250 nt, 250-300 nt, 300-350 nt, 350-400 nt, 400-450 nt, or 450-500 nt; (e) the mediator sequences in said mediator probes each independently have a length of 5-10 nt, 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-110 nt, 110-120 nt, 120-130 nt, or 130-140 nt; and (f) at least one mediator probe has a 3′-OH end, or the 3′-end thereof is blocked; (g) the mediator sequences comprised in at least two or all the mediator probes are different from each other; (h) the target specific sequences comprised in at least two or all the mediator probes are different from each other; and (i) at least two or all the mediator probes target to different target nucleic acid sequences, respectively.

    56. The kit according to claim 53, wherein said detection probe has one or more of the following features: (a) said detection probe each independently comprises or consists of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; (b) said detection probe each independently has a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-200 nt, 200-300 nt, 300-400 nt, 400-500 nt, 500-600 nt, 600-700 nt, 700-800 nt, 800-900 nt, or 900-1000 nt; (c) each capture sequence in said detection probe independently has a length of 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-150 nt, 150-200 nt, 200-250 nt, 250-300 nt, 300-350 nt, 350-400 nt, 400-450 nt, or 450-500 nt; (d) the templating sequence in said detection probe each independently has a length of 1-5 nt, 5-10 nt, 10-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-200 nt, 200-300 nt, 300-400 nt, 400-500 nt, 500-600 nt, 600-700 nt, 700-800 nt, or 800-900 nt; (e) at least one detection probe has 3′-OH end, or its 3′-end is blocked; (f) at least one detection probe is a self-quenching probe; (g) in said detection probe, the reporter group is independently a fluorescent group; and, the quencher group is a molecule or a group capable of absorbing or quenching fluorescence; (h) at least one detection probe is resistant to nuclease activity; (i) said detection probe each independently is linear or has a hairpin structure; (j) at least one detection probe comprises multiple capture sequences; and, said multiple capture sequences are arranged in a contiguous manner, arranged in such a manner that they are spaced by a linking sequence, or arranged in an overlapping manner; (k) said detection probe is labeled with a reporter group at its 5′ end or upstream and is labeled with a quencher group at its 3′ end or downstream, or is labeled with a reporter group at its 3′ end or downstream and is labeled with a quencher group at its 5′ end or upstream; (l) the distance between said reporter group and said quencher group is 10-80 nt or longer; (m) the reporter group is selected from the group consisting of ALEX-350, FAM, VIC, TET, CAL Fluor® Gold 540, JOE, HEX, CAL Fluor Orange 560, TAMRA, CAL Fluor Red 590, ROX, CAL Fluor Red 610, TEXAS RED, CAL Fluor Red 635, Quasar 670, CY3, CYS, CY5.5, and Quasar 705; (n) the quencher group is selected from the group consisting of DABCYL, BHQ, ECLIPSE, and TAMRA; (o) at least one detection probe is resistant to 5′ nuclease activity; (p) at least one detection probe has a main chain comprising a modification resistant to nuclease activity; and (q) at least one detection probe has a main chain comprising phosphorothioate bond, alkyl phosphate triester bond, aryl phosphate triester bond, alkyl phosphonate bond, aryl phosphonate bond, hydrogenated phosphate bond, alkyl phosphoramidate bond, aryl phosphoramidate bond, 2′-O-aminopropyl modification, 2′-O-alkyl modification, 2′-O-allyl modification, 2′-O-butyl modification, and/or 1-(4′-thio-PD-ribofuranosyl) modification.

    57. The kit according to claim 53, wherein the kit further comprises: an upstream oligonucleotide sequence, a downstream oligonucleotide sequence, a common primer, an enzyme having 5′ nuclease activity, a nucleic acid polymerase, an agent for nucleic acid hybridization, an agent for cleavage of a mediator probe, an agent for nucleic acid extension, an agent for nucleic acid amplification, an agent for reverse transcription, or any combination thereof.

    58. The kit according to claim 57, wherein said kit has one or more of the following features: (1) said upstream oligonucleotide sequence comprises a sequence complementary to a target nucleic acid sequence; and, when hybridizing with the target nucleic acid sequence, said upstream oligonucleotide sequence is located upstream to the target specific sequence of a mediator probe; (2) said upstream oligonucleotide sequences each independently comprise or consist of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; (3) said upstream oligonucleotide sequences each independently have a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-110 nt, 110-120 nt, 120-130 nt, 130-140 nt, or 140-150 nt; (4) said upstream oligonucleotide sequence, upon hybridization with a target nucleic acid sequence, is each independently located far from the upstream of the mediator probe, or located near the upstream of the mediator probe, or has a partially overlapping sequence with the target specific sequence of the mediator probe; (5) said upstream oligonucleotide sequence is each independently a primer specific for a target nucleic acid sequence or a probe specific for a target nucleic acid sequence; (6) said downstream oligonucleotide sequence comprises a sequence complementary to a target nucleic acid sequence; and, when hybridizing with said target nucleic acid sequence, said downstream oligonucleotide sequence is located downstream to the target specific sequence of a mediator probe; (7) said downstream oligonucleotide sequences each independently comprise or consist of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; and (8) said downstream oligonucleotide sequences each independently have a length of 15-20 nt, 20-30 nt, 30-40 nt, 40-50 nt, 50-60 nt, 60-70 nt, 70-80 nt, 80-90 nt, 90-100 nt, 100-110 nt, 110-120 nt, 120-130 nt, 130-140 nt, or 140-150 nt.

    59. The kit according to claim 57, wherein the upstream oligonucleotide sequence and the downstream oligonucleotide sequence have an identical oligonucleotide sequence at 5′ end; and the common primer has a sequence complementary to the identical oligonucleotide sequence; optionally, said common primer has one or more of the following features: (a) said common primer comprises or consists of naturally occurring nucleotides, modified nucleotides, unnatural nucleotides, or any combination thereof; and (b) said common primer has a length of 8-15 nt, 15-20 nt, 20-30 nt, 30-40 nt, or 40-50 nt.

    60. The kit according to claim 57, wherein said enzyme having 5′ nuclease activity or said nucleic acid polymerase has one or more of the following features: (1) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is a nucleic acid polymerase having 5′ nuclease activity; (2) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is a DNA polymerase having 5′ nuclease activity; (3) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is a DNA polymerase originated from a bacterium selected from: Thermus aquaticus (Taq), Thermus thermophiles (Tth), Thermus filiformis, Thermis flavus, Thermococcus literalis, Thermus antranildanii, Thermus caldophllus, Thermus chliarophilus, Thermus flavus, Thermus igniterrae, Thermus lacteus, Thermus oshimai, Thermus ruber, Thermus rubens, Thermus scotoductus, Thermus silvanus, Thermus thermophllus, Thermotoga maritima, Thermotoga neapolitana, Thermosipho africanus, Thermococcus litoralis, Thermococcus barossi, Thermococcus gorgonarius, Thermotoga maritima, Thermotoga neapolitana, Thermosiphoafricanus, Pyrococcus woesei, Pyrococcus horikoshii, Pyrococcus abyssi, Pyrodictium occultum, Aquifexpyrophilus and Aquifex aeolieus; and (4) said enzyme having 5′ nuclease activity or said nucleic acid polymerase is Taq polymerase.

    Description

    DESCRIPTION OF THE DRAWINGS

    [0246] FIGS. 1A-1B illustrate exemplary embodiments for the method of the invention, to describe the basic principle of the method of the invention.

    [0247] FIG. 1A illustrates exemplary embodiments in which 1 detection probe and 5 mediator probes are used to detect 5 target nucleic acid molecules. In the embodiments, a self-quenched detection probe (which carries a fluorescent group and quencher group) is provided, and an upstream primer (Upstream primers 1-5), a downstream primer (Downstream primers 1-5), and a mediator probe (Mediator probes 1-5) are designed and provided for each of the target nucleic acid molecules (T1-T5); wherein, the mediator probe each comprises a unique mediator sequence (Mediator sequences 1-5), which can hybridize with said detection probe. The hybridization position for each mediator sequence on a detection probe is unique, but there may be an overlapping region between them. For example, as shown in FIG. 1A, the hybridization position for Mediator sequence 1 on the detection probe partially overlaps with that for Mediator sequence 2, and the hybridization position for Mediator sequence 4 on the detection probe partially overlaps with that for Mediator sequence 5, while the hybridization position for Mediator sequence 3 on the detection probe does not overlap with those for other mediator sequences. During detection, 5 upstream primers, 5 downstream primers, and 5 mediator probes hybridized (annealed) with their corresponding target nucleic acid molecules, respectively; later, in the presence of a nucleic acid polymerase, all the upstream primer and downstream primers were extended, respectively, and due to the extension of each of the upstream primers (Upstream primer 1-5), the corresponding mediator probe (Mediator probes 1-5) was cleaved by an enzyme having 5′ nuclease activity, so as to release a mediator fragment (Mediator fragments 1-5); later, Mediator fragments 1-5 hybridized to the detection probe at different positions, respectively, and were extended by a nucleic acid polymerase, so as to produce five extension products; the five extension products had different lengths, and together with the detection probe, formed five duplexes having different T.sub.m values. Therefore, by melting curve analysis, the presence of a duplex having a specific Tm value can be determined, and the presence of the target nucleic acid molecules corresponding to the duplex can be further determined. Therefore, in the method of the invention, the detection of 5 target nucleic acid molecules can be achieved by using 1 detection probe and 5 mediator probes.

    [0248] FIG. 1B illustrates exemplary embodiments in which 2 detection probes and 10 mediator probes were used to detect 10 target nucleic acid molecules (T1-T10). In the embodiments, two self-quenching detection probes (a first and second detection probe) are provided, each of which carries a different fluorescent group (fluorescent groups 1-2) and a different quencher group (Quencher groups 1-2); and, an upstream primer (Upstream primers 1-10), a downstream primer (Downstream primers 1-10), and a mediator probe (Mediator probe 1-10) are designed and provided for each target nucleic acid molecule (T1-T10); wherein, each mediator probe comprises a unique mediator sequence (Mediator sequences 1-10), and Mediator sequences 1-5 can hybridize with the first detection probe, and Mediator sequences 6-10 can hybridize with the second detection probe. The hybridization position for each mediator sequence on a detection probe is unique, but there may be an overlapping region between them. For example, as shown in FIG. 1B, the hybridization position for Mediator sequence 1 on the first detection probe partially overlaps with that for Mediator sequence 2, the hybridization position for Mediator sequence 4 on the first detection probe partially overlaps with that for Mediator sequence 5, the hybridization position for Mediator sequence 3 on the first detection probe does not hybridize with those for other mediator sequences; the hybridization position for Mediator sequence 6 on the second detection probe partially overlaps with that for Mediator sequence 7, the hybridization position for Mediator sequence 9 on the second detection probe partially overlaps with that for Mediator sequence 10, the hybridization position for Mediator sequence 8 on the second detection probe does not overlap with those for other mediator sequences. During the detection, 10 upstream primers, 10 downstream primers, 10 mediator probes hybridized (annealed) with their corresponding target nucleic acid molecules, respectively; later, in the presence of a nucleic acid polymerase, all the upstream primers and downstream primers were extended, respectively; and due to the extension of each upstream primer (Upstream primers 1-10), the corresponding mediator probe (Mediator probe 1-10) was cleaved by an enzyme having 5′ nuclease activity, so as to release a mediator fragment (Mediator fragment 1-10); later, Mediator fragments 1-5 hybridized to the first detection probe at different positions, and were extended by a nucleic acid polymerase, so as to produce 5 extension products; the 5 extension products had different lengths, and together with the first detection probe, formed 5 duplexes having different Tm values. Similarly, Mediator fragments 6-10 hybridized to the second detection probe at different positions, and were extended by a nucleic acid polymerase, so as to produce another 5 extension products; the 5 extension products had different lengths, and together with the second detection probe, formed another 5 duplexes having different T.sub.m values. Later, fluorescent groups (fluorescent group 1-2) on the first and second detection probe were used to carry out melting curve analysis, respectively, and the presence of a duplex having a specific T.sub.m value could be determined, and the presence of the target nucleic acid molecule corresponding to the duplex could be determined. Therefore, in the method of the invention, 2 detection probes and 10 mediator probes can be used to achieve the detection of 10 target nucleic acid molecules.

    [0249] FIGS. 2A-2D show the amplification curves of 4 real-time PCRs using the mediator probe BRAF-MP1 and the liner fluorescent probe UP-L2, wherein, Reaction A uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 2A); Reaction B uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 2B); Reaction C uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 2C); Reaction D uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 2D); and, in FIGS. 2A-2D, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0250] FIGS. 3A-3D show the amplification curves of 4 real-time PCRs using the mediator probe BRAF-MP1 and the fluorescent probe UP-MB having a hairpin structure, wherein, Reaction A uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 3A); Reaction B uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 3B); Reaction C uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 3C); Reaction D uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 3D); and, in FIG. 3A-3D, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0251] FIGS. 4A-4B show the amplification curves and melting curves of 4 real-time PCRs using the mediator probe BRAF-MP1 and the fluorescent probe UP-L2 (FIG. 4A) or UP-MB (FIG. 4B), wherein, in the assay of FIG. 4A, the mediator probe BRAF-MP1, the fluorescent probe UP-L2 and polymerase Taq are used; in the assay of FIG. 4B, the mediator probe BRAF-MP1, the fluorescent probe UP-MB and polymerase Taq are used; and, in the assays of FIGS. 4A-4B, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0252] FIGS. 5A-5C show the amplification curves and melting curves of 3 real-time PCRs using the mediator probe (BRAF-MP1, BRAF-MP2, or BRAF-MP3) and the linear fluorescent probe UP-L2; wherein, in the assay of FIG. 5A, the mediator probe BRAF-MP1, the fluorescent probe UP-L2 and polymerase Taq are used; in the assay of FIG. 5B, the mediator probe BRAF-MP2, the fluorescent probe UP-L2 and polymerase Taq are used; in the assay of FIG. 5C, the mediator probe BRAF-MP3, the fluorescent probe UP-L2 and polymerase Taq are used; and, in the assays of FIGS. 5A-5C, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0253] FIGS. 6A-6C show the amplification curves and melting curves of 3 real-time PCRs using the mediator probe (BRAF-MP1, BRAF-MP2, or BRAF-MP3) and the hairpin fluorescent probe UP-MB; wherein, in the assay of FIG. 6A, the mediator probe BRAF-MP1, the fluorescent probe UP-MB and polymerase Taq; in the assay FIG. 6B, the mediator probe BRAF-MP2, the fluorescent probe UP-MB and polymerase Taq are used; in the assay of FIG. 6C, the mediator probe BRAF-MP3, the fluorescent probe UP-MB and polymerase Taq are used; and, in the assays of FIGS. 6A-6C, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0254] FIG. 7 shows the amplification curves and melting curves of 5 real-time PCRs using a specific amount (100 ng, 10 ng, 1 ng, 100 pg or 10 pg) of 293T cell genomic DNA as a template; wherein, in said real-time PCR, the mediator probe BRAF-MP2, the hairpin fluorescent probe UP-MB and polymerase Taq are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0255] FIGS. 8A-8B show the amplification curves and melting curves of real-time PCRs in which the amplification is carried out in a symmetric manner (FIG. 8A) or in an asymmetric manner (FIG. 8B); wherein, in said real-time PCR, the mediator probe BRAF-MP2, the hairpin fluorescent probe UP-MB, polymerase Taq and a specified amount (100 ng, 10 ng, 1 ng or 100 pg) of 293T cell genomic DNA are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0256] FIGS. 9A-9B show the amplification curves and melting curves of real-time PCRs in which the amplification is carried out by a two-step method (FIG. 9A) or a three-step method (FIG. 9B); wherein, in said real-time PCR, the mediator probe BRAF-MP2, the hairpin fluorescent probe UP-MB, polymerase Taq and a specified amount (100 ng, 10 ng, 1 ng, 100 pg or 10pg) of 293T cell genomic DNA are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0257] FIG. 10 shows the amplification curves and melting curves of 3 real-time PCRs using a plasmid carrying wild-type KRAS gene or mutant KRAS gene or water as a template; wherein, in said real-time PCR, the mediator probe KRAS-MP2, the hairpin fluorescent probe UP-MB and polymerase Taq are used; and, and the black solid line represents the experimental result using a plasmid carrying wild-type KRAS gene as a template; the grey solid line represents the experimental result using a plasmid carrying mutant KRAS gene as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0258] FIG. 11 shows the amplification curves and melting curves of real-time PCRs using 2 mediator probes and 1 fluorescent probe; wherein, in said real-time PCR, 4 primers (BRAF-F, BRAF-R, KRAS-F and KRAS-R), 2 mediator probes (BRAF-MP2 and KRAS-MP3), the hairpin fluorescent probe UP-MB, polymerase Taq and a specified amount (100 ng, 10 ng, 1 ng, 100 pg or 10 pg) of 293T cell genomic DNA are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0259] FIG. 12 shows the melting curves of real-time PCRs using 4 mediator probes and 1 fluorescent probe; wherein, in said real-time PCR, 9 primers, 4 mediator probes, and 1 fluorescent probe as described in Table 4, polymerase TaqHS and a specified amount (100 ng, 10 ng, 1 ng, or 100 pg) of cellular genomic DNA obtained from a normal male are used; and, the solid line in the figure shows the experimental result using the genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0260] FIGS. 13A-13C show the melting curves of 83 real-time PCRs using 20 mediator probes and 6 fluorescent probes; wherein, in said real-time PCR, 41 primers, 20 mediator probes, and 6 fluorescent probes as described in Table 5, polymerase TaqHS and cellular genomic DNA obtained from normal males (83 samples in total) are used; FIG. 13A shows the melting curve obtained from ROX detection channel; FIG. 13B shows the melting curve obtained from FAM detection channel; FIG. 13C shows the melting curve obtained from Cy5 detection channel; and, the solid line in the figure shows the experimental result using the cellular genomic DNA (83 samples) as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0261] FIG. 14 shows the representative experimental result obtained by detecting 92 samples by using 20-plex PCR MCA; wherein, the black solid line shows the experimental result using cellular genomic DNA from males having microdeletions on Y chromosome, as a template; the grey solid line shows the experimental result using normal male cellular genomic DNA as a template; the dashed black line represents the experimental result using normal female cellular genomic DNA as a template; the dashed grey line represents the experimental result using water as a template.

    Specific Modes for Carrying Out the Invention

    [0262] The invention is illustrated by reference to the following examples which are used only for the purpose of illustration (not intended to limit the protection scope of the invention). It should be understood that the examples are only used to illustrate the principle and technical effects of the invention, rather than showing all the possibility of the invention. The invention is not limited to the materials, reaction conditions or parameters mentioned in these examples. A person skilled in the art, based on the principle of the invention, can use other similar materials or reaction conditions to carry out other technical solutions. Such technical solutions do not depart from the basic principle and concept of the invention, and fall into the scope of the invention.

    Example 1

    Real-Time PCR Assay Using Mediator Probes and Fluorescent Probes

    [0263] In the example, BRAF gene was used as an exemplary target sequence to be detected, to establish a real-time PCR assay using a mediator probe and a fluorescent probe, and to evaluate the effect of using a linear fluorescent probe and a hairpin fluorescent probe (i.e. a fluorescent probe having a hairpin structure) in said real-time PCR assay. The fluorescent probes (linear or hairpin) used were self-quenching fluorescent probes, one end of which was labeled with a fluorescent group (e.g. ROX), the other end of which was labeled with a quencher group (e.g. BHQ2).

    [0264] In brief, a 25-μL PCR reaction system was used to carry out real-time PCR, said PCR reaction system comprised 1× buffer A (67 mM Tris-HCl, 16.6 mM (NH.sub.4).sub.2SO.sub.4, 6.7 μM EDTA and 0.085 mg/mL BSA), 3.0 mM MgCl.sub.2, 0.2 mM dNTPs, 2.0 U polymerase Taq (Linglan Biotechnology Co., Ltd., Shanghai) or KlenTaq 1 (AB Bioscience, UK), 400 nM Upstream primer and 400 nM Downstream primer, 0 or 200 nM mediator probe, 200 nM fluorescent probe (linear or hairpin), 0.1 μL Single Strand DNA-Binding Protein (SSB), and 5 μL 293T cell genomic DNA. The reaction conditions of real-time PCR were: 95° C., 5 min; and then 50 cycles of (95° C., 20 s and 61° C., 1 min); and, collecting fluorescence at 61° C. The experimental apparatus used was Bio-Rad CFX96 real-time PCR instrument (Bio-Rad, USA). The primers and probes used were synthesized by Shanghai Sangon Co., Ltd. The sequences of primers and probes used were shown in Table 1.

    TABLE-US-00001 TABLE 1 Sequences of primers and probes used SEQ ID Sequence (5′ .fwdarw. 3′) NO Upstream primer TGTTTTCCTTTACTTA 1 BRAF-F CTACACCTCAG Downstream primer TCAGTGGAAAAATAGC 2 BRAF-R CTCAATTC mediator probe AAATCGTTCTGGGCTC 3 BRAF-MP1 TACGCTACAGTGAAAT CTCGATGGAGTGGGTC C-C.sub.7NH.sub.2 Fluorescent probe UP-L2 (linear) ROX-5′-TTGTCACCT 4 GTCCTAGAGAGCGTAG AGCCCAGAACGATTT- BHQ2 UP-MB (hairpin) ROX-5′-CCCGGCTTG 5 TCACCTGTCCTAGAGA GCGTAGAGCCCAGAAC GATTTGCCGGG-BHQ2 Note: -C.sub.7NH.sub.2 was used to block 3′-OH of a mediator probe (the same below).

    [0265] The experimental results were shown in FIGS. 2A-3D. FIGS. 2A-2D show the amplification curves of 4 real-time PCRs using the mediator probe BRAF-MP1 and the liner fluorescent probe UP-L2, wherein, Reaction A uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 2A); Reaction B uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 2B); Reaction C uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 2C); Reaction D uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 2D); and, in FIGS. 2A-2D, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0266] The result of FIGS. 2A-2D show that real-time PCR fluorescent signal was generated only in Reaction A, and no fluorescent signal was generated in Reaction B, C or D. These results show that when a polymerase having 5′.fwdarw.3′ exonuclease activity (e.g. Taq polymerase) was used, mediator probes and linear fluorescent probes could be used in real-time PCR.

    [0267] FIGS. 3A-3D show the amplification curves of 4 real-time PCRs using the mediator probe BRAF-MP1 and the fluorescent probe UP-MB having a hairpin structure, wherein, Reaction A uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 3A); Reaction B uses Taq DNA polymerase having 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 3B); Reaction C uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 200 nM mediator probe (FIG. 3C); Reaction D uses KlenTaq 1 DNA polymerase having no 5′.fwdarw.3′ exonuclease activity and 0 nM mediator probe (FIG. 3D); and, in FIGS. 3A-3D, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0268] The result of FIGS. 3A-3D show that real-time PCR fluorescent signal was generated only in Reaction A, and no fluorescent signal was generated in Reaction B, C or D. These results show that when a polymerase having 5′.fwdarw.3′ exonuclease activity (e.g. Taq polymerase) was used, mediator probes and fluorescent probes having a hairpin structure could be used in real-time PCR.

    EXAMPLE 2

    Post-PCR MCA Assay Using Mediator Probes and Fluorescent Probes

    [0269] In the example, BRAF gene was used as an exemplary target sequence to be detected, to evaluate the effect of using a linear fluorescent probe and a hairpin fluorescent probe in post-PCR MCA method.

    [0270] As described in Example 1, a 25-μL PCR reaction system was used to carry out real-time PCR. The PCR reaction system used was the same as the one used in Example 1. The PCR reaction conditions used were: 95° C., 5 min; 50 cycles (95° C., 20 s and 61° C., 1 min); and 35° C., 10 min; and, collecting fluorescence at 61° C. After PCR was finished, melting curve analysis was carried out according to the following procedures: 95° C., 2 min; 45° C., 2 min; and then increasing the temperature of the reaction system from 45° C. to 95° C. at a heating rate of 0.5° C./step (the duration for each step was 5 s), during which fluorescent signal was collected. The experimental results were shown in FIGS. 4A-4B.

    [0271] FIGS. 4A-4B show the amplification curves and melting curves of 4 real-time PCRs using the mediator probe BRAF-MP1 and the fluorescent probe UP-L2 (FIG. 4A) or UP-MB (FIG. 4B), wherein, in the assay of FIG. 4A, the mediator probe BRAF-MP1, the fluorescent probe UP-L2 and polymerase Taq are used; in the assay of FIG. 4B, the mediator probe BRAF-MP1, the fluorescent probe UP-MB and polymerase Taq are used; and, in the assays of FIGS. 4A-4B, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0272] The result of FIGS. 4A-4B show that when a reaction system comprising a mediator probe and a fluorescent probe (linear or hairpin) was used to carry out real-time PCR and the subsequent MCA, the target peaks could be detected at about 78° C. in the experimental groups. These results show that a mediator probe and a fluorescent probe (linear or hairpin) could be used to carry out post-PCR MCA assay. In addition, the result of FIGS. 4A-4B also show that when a linear fluorescent probe was used to carry out MCA assay, a non-specific peak could be detected at about 60° C. (which represents the duplex formed by the mediator probe and the linear fluorescent probe). By contrast, when a hairpin fluorescent probe was used to carry out MCA assay, the non-specific peak was significantly weakened. These results show that a hairpin fluorescent probe had better specificity than a linear fluorescent probe. Therefore, under some situations, a hairpin fluorescent probe may be preferred.

    Example 3

    Selection of the Length of Mediator Sequences

    [0273] In the example, multiple mediator probes having mediator sequences of different lengths were designed and synthesized, and the method described in Example 2 was used to evaluate the effect of the length of a mediator sequence on post-PCR MCA assay.

    [0274] In brief, 3 mediator probes were designed and synthesized, and the lengths of the mediator sequences comprised therein were 19, 15 and 13 bases, respectively. The particular sequences of the 3 mediator probes were shown in Table 2.

    TABLE-US-00002 TABLE 2 Sequences of mediator probes SEQ mediator ID probe Sequence (5′ .fwdarw. 3′) NO: BRAF-MP1 AAATCGTTCTGGGCTCTACGC 3 TACAGTGAAATCTCGATGGAG TGGGTCC-C.sub.7NH.sub.2 BRAF-MP2 AAATCGTTCTGGGCTCTACAG 6 TGAAATCTCGATGGAGTGGGT CC-C.sub.7NH.sub.2 BRAF-MP3 AAATCGTTCTGGGCAGTGAAA 7 TCTCGATGGAGTGGGTCC- C.sub.7NH.sub.2

    [0275] As described in Example 2, a 25-μL PCR reaction system was used to carry out real-time PCR and the subsequent MCA assay. Except for the mediator probes used, the PCR reaction system, the PCR reaction conditions and the MCA assay conditions as used were the same as those used in Example 2. The experimental results were shown in FIGS. 5-6.

    [0276] FIGS. 5A-5C show the amplification curves and melting curves of 3 real-time PCRs using the mediator probe (BRAF-MP1, BRAF-MP2, or BRAF-MP3) and the linear fluorescent probe UP-L2; wherein, in the assay of FIG. 5A, the mediator probe BRAF-MP1, the fluorescent probe UP-L2 and polymerase Taq are used; in the assay of FIG. 5B, the mediator probe BRAF-MP2, the fluorescent probe UP-L2 and polymerase Taq are used; in the assay of FIG. 5C, the mediator probe BRAF-MP3, the fluorescent probe UP-L2 and polymerase Taq are used; and, in the assays of FIGS. 5A-5C, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0277] FIGS. 6A-6C show the amplification curves and melting curves of 3 real-time PCRs using the mediator probe (BRAF-MP1, BRAF-MP2, or BRAF-MP3) and the hairpin fluorescent probe UP-MB; wherein, in the assay of FIG. 6A, the mediator probe BRAF-MP1, the fluorescent probe UP-MB and polymerase Taq; in the assay FIG. 6B, the mediator probe BRAF-MP2, the fluorescent probe UP-MB and polymerase Taq are used; in the assay of FIG. 6C, the mediator probe BRAF-MP3, the fluorescent probe UP-MB and polymerase Taq are used; and, in the assays of FIGS. 6A-6C, the solid line represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0278] The results in FIGS. 5A-6C show that three mediator probes having mediator sequences of different lengths together with fluorescent probes (linear or hairpin), could be used to carry out post-PCR MCA assay. Therefore, these results show that according to practical need, a mediator probe of a suitable length could be selected to carry out post-PCR MCA assay. In addition, the results of FIGS. 5-6 also show that with the decrease in the mediator length of mediator probes, the T. value of the nonspecific peak decreased gradually, and the signal intensity reduced continuously. Therefore, according to practical need, the mediator length of a mediator probe can be properly optimized, so as to reduce the interference of nonspecific peaks.

    [0279] In addition, the results of FIGS. 5A-6C also show that when a linear fluorescent probe was used to carry out MCA assay, a nonspecific peak (which represented a duplex formed by the mediator probe and the linear fluorescent probe) could be detected. By contrast, when a hairpin fluorescent probe was used to carry out MCA assay, the signal of the non-specific peak was significantly decreased or even undetected. These results show that a hairpin fluorescent probe had better specificity than a linear fluorescent probe, could better overcome the interference of a nonspecific peak resulted from hybridization between a mediator probe and a fluorescent probe. Therefore, under some situations, a hairpin fluorescent probe may be preferred.

    Example 4

    Sensitivity of Mediator Probe and Hairpin Fluorescent Probe-Based Post-PCR MCA Assay

    [0280] In the example, sensitivity of mediator probe and hairpin fluorescent probe-based post-PCR MCA assay was studied. In brief, as described in Example 2, a 25-μL PCR reaction system was used to carry out real-time PCR and the subsequent MCA assay, wherein, the mediator probe used was BRAF-MP2, the fluorescent probe used was UP-MB, the polymerase used was Taq, and the template used was 293T cell genomic DNA (the amount of which was 100 ng, 10 ng, 1 ng, 100 pg or 10 pg; the assay was repeated for three times for each amount). Except for the amount of genomic DNA, the PCR reaction system, the PCR reaction conditions and the MCA assay conditions used were the same as those used in Example 2. The result was shown in FIG. 7.

    [0281] FIG. 7 shows the amplification curves and melting curves of 5 real-time PCRs using a specific amount (100 ng, 10 ng, 1 ng, 100 pg or 10 pg) of 293T cell genomic DNA as a template; wherein, in said real-time PCR, the mediator probe BRAF-MP2, the hairpin fluorescent probe UP-MB and polymerase Taq are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0282] The result of FIG. 7 shows that when genomic DNA at an amount as low as 10 pg was used as a template, a specific target peak could still be detected by the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay. This shows that said post-PCR MCA assay had a very high sensitivity and could even be used to detect a single human genome.

    Example 5

    Selection of PCR Amplification Conditions

    [0283] In the example, PCR amplification conditions were evaluated for their effect on mediator probe and hairpin fluorescent probe-based post-PCR MCA assay.

    [0284] (1) Symmetric amplification and asymmetric amplification

    [0285] In brief, as described in Example 4, a 25-μL PCR reaction system was used to carry out real-time PCR and the subsequent MCA assay, wherein, the mediator probe used was BRAF-MP2, the fluorescent probe used was UP-MB, the polymerase used was Taq, and the template used was a specified amount (100 ng, 10 ng, 1 ng or 100 pg) of 293T cell genomic DNA. Except for the concentrations of primers, the PCR reaction system, the PCR reaction conditions and the MCA assay conditions used were the same as those used in Example 4. In symmetric PCR, the primers used were 400 nM upstream primer and 400 nM downstream primer. In asymmetric PCR, the primers used were 800 nM upstream primer (the primer and a probe were in reverse directions, i.e. an extension product thereof bound to the probe) and 80 nM downstream primer. The experimental results were shown in FIGS. 8.

    [0286] FIGS. 8A-8B show the amplification curves and melting curves of real-time PCRs in which the amplification is carried out in a symmetric manner (FIG. 8A) or in an asymmetric manner (FIG. 8B); wherein, in said real-time PCR, the mediator probe BRAF-MP2, the hairpin fluorescent probe UP-MB, polymerase Taq and a specified amount (100 ng, 10 ng, 1 ng or 100 pg) of 293T cell genomic DNA are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0287] The result of FIGS. 8A-8B show that under conditions of symmetric amplification or asymmetric amplification, the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay could detect the specific target peak; and under the two conditions, there were no significant difference in Cq value of PCR and specific peaks generated in MCA assay. Therefore, in said post-PCR MCA assay, PCR amplification could be carried out in a symmetric or an asymmetric manner.

    [0288] (2) Two-Step PCR and Three-Step PCR

    [0289] In brief, as described in Example 4, a 25-μL PCR reaction system was used to carry out real-time PCR and the subsequent MCA assay, wherein, the mediator probe used was BRAF-MP2, the fluorescent probe used was UP-MB, the polymerase used was Taq, and the template used was a specified amount (100 ng, 10 ng, 1 ng, 100 pg or 10 pg) of 293T cell genomic DNA. Except for PCR reaction conditions, the PCR reaction system and the MCA assay conditions used were the same as those used in Example 4. The amplification conditions used in two-step PCR were: 95° C., 5 min; and then 50 cycles of (95° C., 20 s and 61° C., 1 min). The amplification conditions used in three-step PCR were: 95° C., 5 min; and then 50 cycles of (95° C., 20 s; 61° C., 40 s; and 72° C., 20 s). The experimental results were shown in FIG. 9.

    [0290] FIGS. 9A-9B show the amplification curves and melting curves of real-time PCRs in which the amplification is carried out by a two-step method (FIG. 9A) or a three-step method (FIG. 9B); wherein, in said real-time PCR, the mediator probe BRAF-MP2, the hairpin fluorescent probe UP-MB, polymerase Taq and a specified amount (100 ng, 10 ng, 1 ng, 100 pg or 10pg) of 293T cell genomic DNA are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0291] The result of FIGS. 9A-9B show that under the conditions of two-step PCR or three-step PCR, the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay could detect the specific target peak. In addition, the result of FIGS. 9A-9B also show that under the conditions of two-step PCR, said post-PCR MCA assay could be used to detect genomic DNA at a concentration as low as 10 pg; under the conditions of three-step PCR, said post-PCR MCA assay could be used to detect genomic DNA at a concentration as low as 100 pg. These results show that in said post-PCR MCA assay, PCR amplification could be carried out in a two-step manner or a three-step manner; and, when a two-step method was used to carry out PCR amplification, said post-PCR MCA assay have a higher sensitivity.

    Example 6

    Effect of Target Sequence Variation on the Mediator Probe and Hairpin Fluorescent Probe-Based Post-PCR MCA Assay

    [0292] One characteristic of the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay, is that the detected melting point depends on the mediator sequence and fluorescent probe, and is not associated with the target sequence. Therefore, even if there was variation in the target sequence to be detected (as a result, the target sequence did not completely match with the target specific sequence in the mediator probe (e.g. there was one or more mismatched bases)), said post-PCR MCA assay could detect the specific peak, and the melting point of the specific peak retained unchanged, as long as the mediator probe could bind to the target sequence during real-time PCR annealing/extension. In order to verify this characteristic, in the example, target sequence variation/mutation was evaluated for its effect on the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay.

    [0293] In brief, a 25-μL PCR reaction system was used to carry out real-time PCR, said PCR reaction system comprised 1× buffer A (67 mM Tris-HCl, 16.6 mM (NH.sub.4).sub.2SO.sub.4, 6.7 μM EDTA and 0.085 mg/mL BSA), 3.0 mM MgC1.sub.2, 0.2 mM dNTPs, 2.0 U polymerase Taq, 400 nM Upstream primer and 400 nM Downstream primer, 200 nM Mediator probe KRAS-MP2, 200 nM fluorescent probe UP-MB, 0.1 μL single strand DNA-binding protein (SSB), and 5 pL plasmid carrying wild-type KRAS gene or mutant KRAS gene (as a template). Sequences of the primers and probes used were shown in Table 3.

    TABLE-US-00003 TABLE 3 Sequences of the primers and probes used SEQ ID Sequence (5′ .fwdarw. 3′) NO: Upstream primer ATTATAAGGCCTGCTGAAAATGAC  8 KRAS-F Downstream primer GCACCAGTAATATGCATATTAAAAC  9 KRAS-R Mediator probe AAATCGTTCTGGGCTCTACGTGGTA 10 KRAS-MP2 GTTGGAGCTGGTGGCGT-C.sub.7NH.sub.2 Fluorescent ROX-5′-CCCGGCTTGTCACCTGTC  5 probe UP-MB CTAGAGAGCGTAGAGCCCAGAACGA TTTGCCGGG-BHQ2

    [0294] As compared with wild-type KRAS gene, mutant KRAS gene had a G.fwdarw.A base mutation in Exon 2, and was used to simulate target sequence variation. The target specific sequence in the mediator probe used completely matched with the sequence of the wild-type KRAS gene, but had one mismatch with the mutant KRAS gene.

    [0295] The reaction conditions of real-time PCR were: 95° C., 5 min; 50 cycles of (95° C., 20 s and 61° C., 1 min); and 35° C., 10 min; and, collecting fluorescence at 61° C. After PCR was finished, melting curve analysis was carried out according to the following procedures: 95° C., 2 min; 45° C., 2 min; and then increasing the temperature of the reaction system from 45° C. to 95° C. at a heating rate of 0.5° C/step (the duration was 5 s for each step), during which ROX fluorescent signal was collected. The experimental apparatus used was Bio-Rad CFX96 real-time PCR instrument (Bio-Rad, USA). The experimental results were shown in FIGS. 10.

    [0296] FIG. 10 shows the amplification curves and melting curves of 3 real-time PCRs using a plasmid carrying wild-type KRAS gene or mutant KRAS gene or water as a template; wherein, in said real-time PCR, the mediator probe KRAS-MP2, the hairpin fluorescent probe UP-MB and polymerase Taq are used; and, and the black solid line represents the experimental result using a plasmid carrying the wild-type KRAS gene as a template; the grey solid line represents the experimental result using a plasmid carrying the mutant KRAS gene as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0297] The result of FIG. 10 shows that when the plasmid carrying the wild-type or mutant KRAS gene was used as a template, the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay could detect a specific target peak, and under said two conditions, the detected specific target peaks had the same melting point. These experimental results show that the mediator probe and hairpin fluorescent probe-based post-PCR MCA assay could tolerate certain target sequence variation/mutation; and, as long as the target sequence variation or mutation did not affect the binding of the mediator probe to the varied or mutated target sequence during real-time PCR annealing/extension, said post-PCR MCA assay could still be used to detect the varied/mutated target sequence, and the melting point of the detected specific peak retained unchanged.

    [0298] Example 7. Duplex detection In the example, two mediator probes and one fluorescent probe were used in a single post-PCR MCA assay to achieve simultaneous detection and discrimination (i.e. duplex detection) of 2 target sequences. In the experiment, BRAF gene and KRAS gene were used as exemplary target sequences to be detected, and a specified amount of 293T cell genomic DNA was used as a sample to be detected.

    [0299] In brief, a 25-μL PCR reaction system was used to carry out real-time PCR, said PCR reaction system comprised 1× buffer A (67 mM Tris-HCl, 16.6 mM (NH.sub.4).sub.2SO.sub.4, 6.7 μM EDTA and 0.085 mg/mL BSA), 3.0 mM MgCl.sub.2, 0.2 mM dNTPs, 2.0 U polymerase Taq, 400 nM primers BRAF-F (SEQ ID NO: 1), BRAF-R (SEQ ID NO: 2), KRAS-F (SEQ ID NO: 8) and KRAS-R (SEQ ID NO: 9), 100 nM mediator probe BRAF-MP2 (SEQ ID NO: 6, comprising a target specific sequence specific for BRAF gene), 200 nM mediator probe KRAS-MP3 (5′-CTC TCT AGG ACA GGT GGT GGC GTA GGC AAG AGT GC-C7NH.sub.2-3′ (SEQ ID NO: 11); comprising a target specific sequence specific for KRAS gene), 200 nM fluorescent probe UP-MB (SEQ ID NO: 5), 0.1 μL single strand DNA-binding protein (SSB), and a specified amount of 293T cell genomic DNA (100 ng, 10 ng, 1 ng, 100 pg or 10pg; the assay was repeated for three times for each amount). The PCR reaction conditions and MCA assay conditions used were the same as those used in Example 6. The result was shown in FIG. 11.

    [0300] FIG. 11 shows the amplification curves and melting curves of real-time PCRs using 2 mediator probes and 1 fluorescent probe; wherein, in said real-time PCR, 4 primers (BRAF-F, BRAF-R, KRAS-F and KRAS-R), 2 mediator probes (BRAF-MP2 and KRAS-MP3), the hairpin fluorescent probe UP-MB, polymerase Taq and a specified amount (100 ng, 10 ng, 1 ng, 100 pg or 10 pg) of 293T cell genomic DNA are used; and, the solid line in the figure represents the experimental result using 293T cell genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0301] The result of FIG. 11 shows that in the melting curve, two distinguishable specific peaks (marked as peak of BRAF and marked as peak of KRAS) appeared, the melting points of which corresponded to the duplexes formed by the fluorescent probe UP-MB and the extension products of the mediator sequences in the mediator probes BRAF-MP2 and KRAS-MP3, respectively. This result shows that by using two mediator probes and a fluorescent probe, simultaneous detection and discrimination (i.e. duplex detection) of two target sequences can be achieved in a single post-PCR MCA assay. In addition, the result of FIG. 11 also shows that the sensitivity of said duplex PCR MCA assay was very high (the detection limit could be as low as 10 pg genomic DNA), and could even be used in detection of a single human genome.

    Example 8

    Quadruplex Detection

    [0302] In the example, by using four mediator probes and a fluorescent probe, simultaneous detection and discrimination (i.e. quadruplex detection) of 4 target sequences was achieved in a single post-PCR MCA assay. In this experiment, three detection sites (sY82, sY86 and sY242) on Y chromosome and an internal reference gene (ZFX/Y gene) were used as exemplary target sequences to be detected, and a specified amount of cellular genomic DNA obtained from a normal male was used as a sample to be detected.

    [0303] In brief, a 25-μL PCR reaction system was used to carry out real-time PCR, said PCR reaction system comprised 1× buffer A (67 mM Tris-HCl, 16.6 mM (NH.sub.4).sub.2SO.sub.4, 6.7 μM EDTA and 0.085 mg/mL BSA), 11.0 mM MgCl.sub.2, 0.7 mM dNTPs, 5.0 U polymerase TaqHS (TaKaRa, Dalian), the primers (8 primers and 1 common amplification primer) and the probes (4 mediator probes and 1 fluorescent probe) as shown in Table 4, and a specified amount of cellular genomic DNA obtained from a normal male (100 ng, 10 ng, 1 ng, or 100 pg; the assay was repeated for three times for each amount).

    [0304] The PCR reaction conditions used were as followed: 95° C., 5 min; 4 cycles of (95° C., 20 s and 61° C., 1 min); 46 cycles of (95° C., 20 s and 62° C., 1 min); and 35° C., 30 min. After PCR was finished, melting curve analysis was carried out according to the following procedures: 95° C., 2 min; 40° C., 2 min; and then increasing the temperature of the reaction system from 40° C. to 95° C. at a heating rate of 0.4° C./step (the duration was 5 s for each step), during which ROX fluorescent signal was collected. The experimental apparatus used was Bio-Rad CFX96 real-time PCR instrument (Bio-Rad, USA). The result was shown in FIG. 12.

    [0305] FIG. 12 shows the melting curves of real-time PCRs using 4 mediator probes and 1 fluorescent probe; wherein, in said real-time PCR, 9 primers, 4 mediator probes and 1 fluorescent probe as described in Table 4, polymerase TaqHS and a specified amount (100 ng, 10 ng, 1 ng, or 100 pg) of cellular genomic DNA obtained from a normal male were used; and, the solid line in the figure shows the experimental result using genomic DNA as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0306] The result of FIG. 12 shows that in the melting curve, four distinguishable specific peaks (marked as 4 peaks, i.e. 242, ZF, 82 and 86, respectively) appeared, the melting points of which corresponded to the duplexes formed by said fluorescent probes and the extension products of the mediator sequences in the mediator probes 242-MP, ZF-MP, 82-MP and 86-MP. This result shows that by using four mediator probes and a fluorescent probe, simultaneous detection and discrimination (i.e. quadruplex detection) of 4 target sequences could be achieved in a single post-PCR MCA assay. In addition, the result of FIG. 12 also shows that the sensitivity of said quadruplex PCR MCA assay was high (the detection limit could be as low as 100 pg genomic DNA).

    Example 9

    20-plex Detection

    [0307] In the example, by using 20 mediator probes and 6 fluorescent probes, simultaneous detection and discrimination (i.e. 20-plex detection) of 20 target sequences was achieved in a single post-PCR MCA assay. In this experiment, 18 detection sites (sY242, sY82, sY86, sY152, sY145, sY84, sY124, sY127, sY128, sY133, sY143, sY134, sY155, sY154, sY157, sY254, sY239 and sY255) on Y chromosome and two internal reference genes (SRY gene and ZFX/Y gene) were used as exemplary target sequences to be detected, and cellular genomic DNA obtained from 83 normal males were used as samples to be detected.

    [0308] In brief, a 25-μL PCR reaction system was used to carry out real-time PCR, said PCR reaction system comprised lxbuffer A (67 mM Tris-HCl, 16.6 mM (NH.sub.4).sub.2SO.sub.4, 6.7 μM EDTA and 0.085 mg/mL BSA), 11.0 mM MgCl.sub.2, 0.7 mM dNTPs, 5.0 U polymerase TaqHS (TaKaRa, Dalian), the primers (40 primers and 1 common amplification primer) and probes (20 mediator probes and 6 fluorescent probes) as shown in Table 5, and 5 μL cell genomic DNA.

    [0309] In said 6 fluorescent probes, fluorescent probes UP1 and UP2 were labeled with ROX and BHQ2, and their fluorescent signal was detected by ROX channel; fluorescent probes UP3 and UP4 were labeled with FAM and BHQ1, and their fluorescent signal was detected by FAM channel; fluorescent probes UP5 and UP6 were labeled with Cy5 and BHQ2, and their fluorescent signal was detected by Cy5 channel. The mediator sequences in Mediator probes 82-MP, 86-MP, 242-MP, ZF-MP could bind to fluorescent probe UP1, and were used to detect the target sequences sY82, sY86, sY242, and ZFX/Y, respectively. The mediator sequences in Mediator probes 152-MP, 145-MP, 84-MP, and SRY-MP could bind to fluorescent probe UP2, and were used to detect the target sequences sY152, sY145, sY84, SRY, respectively. The mediator sequences in mediator probes 124-MP, 127-MP, 128-MP could bind to fluorescent probe UP3, and were used to detect the target sequences sY124, sY127, and sY128, respectively. The mediator sequences in Mediator probes 133-MP, 143-MP, and 134-MP could bind to fluorescent probe UP4, and were used to detect the target sequences sY133, sY143 and sY134. The mediator sequences in Mediator probes 155-MP, 154-MP, and 157-MP could bind to fluorescent probe UP5, and were used to detect the target sequences sY155, sY154, and sY157. The mediator sequences in Mediator probes 254-MP, 239-MP, and 255-MP could bind to fluorescent probe UP6, and were used to detect the target sequences sY254, sY239 and sY255.

    [0310] In this experiment, cellular genomic DNA from 83 normal males were used as samples to be tested (83 samples in total), and 83 real-time PCRs were carried out. The PCR reaction conditions used were as followed: 95° C., 5 min; 4 cycles of (95° C., 20 s and 61° C., 1 min); 46 cycles of (95° C., 20 s and 62° C., 1 min); and 35° C., 30 min. After PCR was finished, melting curve analysis was carried out according to the following procedures: increasing the temperature of the reaction system from 45° C. to 98° C. at a heating rate of 0.1° C./step (the duration was 5 s for each step); and then keeping it at 45° C. for 2 min; later, increasing the temperature of the reaction system from 45° C. to 98° C. at a heating rate of 0.04° C./step (the duration was 5 s for each step). During the whole process of MCA assay, the fluorescent signal from 3 detection channels (ROX, FAM and Cy5) was collected. The experimental apparatus used was Bio-Rad CFX96 real-time PCR instrument (Bio-Rad, USA). The result was shown in FIGS. 13A-13C.

    [0311] FIGS. 13A-13C show the melting curves of 83 real-time PCRs using 20 mediator probes and 6 fluorescent probes; wherein, in said real-time PCR, 41 primers, 20 mediator probes and 6 fluorescent probe as described in Table 5, polymerase TaqHS and cellular genomic DNA obtained from normal males (83 samples in total) are used; FIG. 13A shows the melting curve obtained from ROX detection channel; FIG. 13B shows the melting curve obtained from FAM detection channel; FIG. 13C shows the melting curve obtained from Cy5 detection channel; and, the solid line in the figure shows the experimental result using cellular genomic DNA (83 samples) as a template; the dashed line represents the experimental result using water as a template (negative control).

    [0312] The result of FIGS. 13A-13C show that in the melting curve obtained from ROX detection channel, 8 specific distinguishable peaks (marked as 8 peaks, i.e. 242, ZF, 82, 86, 152, 145, SRY, and 84, respectively) appeared, the melting points of which corresponded to the duplexes formed by fluorescent probe UP1 or UP2 and the extension products of the mediator sequences in Mediator probes 242-MP, ZF-MP, 82-MP, 86-MP, 152-MP, 145-MP, SRY-MP, and 84-MP; in the melting curve obtained from FAM detection channel, 6 distinguishable specific peaks (marked as 6 peaks, i.e. 124, 127, 128, 133, 143, and 134, respectively), the melting points of which corresponded to the duplexes formed by fluorescent probe UP3 or UP4 and the extension products of the mediator sequences in Mediator probes 124-MP, 127-MP, 128-MP, 133-MP, 143-MP, and 134-MP, respectively; in the melting curve obtained from Cy5 detection channel, 6 specific distinguishable peaks (marked as 6 peaks, i.e. 155, 154, 157, 254, 239, and 255, respectively) appeared, the melting points of which corresponded to the duplexes formed by fluorescent probe UP5 or UP6 and the extension products of the mediator sequences in Mediator probes 155-MP, 154-MP, 157-MP, 254-MP, 239-MP, and 255-MP, respectively. These experimental results show that by using 20 mediator probes and 6 fluorescent probes, simultaneous detection and discrimination (i.e. 20-plex detection) of 20 target sequences could be achieved in a single post-PCR MCA assay.

    [0313] In addition, the result of FIGS. 13A-13C also show that for the detected 83 samples, the shapes of the 83 melting curves obtained were substantively the same, and in these melting curves, the T.sub.m values of 20 specific peaks were substantively the same (CV<0.5%). This shows that said 20-plex PCR MCA assay had very excellent repeatability and reliability.

    [0314] In order to further confirm the reliability of said methods above, another 92 samples were subjected to blind test by using said methods. Among said 92 samples, 33 samples were cellular genomic DNA obtained from different normal males; 58 samples were cellular genomic DNA obtained from different males having microdeletions on Y chromosome; 1 sample was cellular genomic DNA obtained from a normal female. The 92 samples were detected by using said 20-plex PCR MCA assay.

    [0315] Later, traditional PCR-agarose gel electrophoresis was also used to detect the 92 samples. The result shows that the detection result of 20-plex PCR MCA assay was completely concordant with the detection result of PCR-agarose gel electrophoresis. This also shows that the 20-plex PCR MCA assay of the invention had very excellent reliability. Some typical detection results of said 20-plex PCR MCA assay were shown in FIG. 14.

    [0316] FIG. 14 shows the representative experimental result obtained by detecting 92 samples by using 20-plex PCR MCA assay; wherein, the black solid line shows the experimental result using cellular genomic DNA from males having microdeletions on Y chromosome, as a template; the grey solid line shows the experimental result using cellular genomic DNA from normal males as a template; the dashed black line represents the experimental result using cellular genomic DNA from a normal female as a template; the dashed grey line represents the experimental result using water as a template. These experimental results show again that by using 20 mediator probes and 6 fluorescent probes, it can achieve the simultaneous detection and discrimination (i.e. 20-plex detection) of 20 target sequences in a single post-PCR MCA assay.

    [0317] Although the specific embodiments of the invention have been described in detail, those skilled in the art would understand that, based on all the disclosed teachings, various modifications and changes can be made to details, and such modifications and changes are within the scope of the invention. The scope of the invention is given by the appended claims and any equivalents thereof.

    TABLE-US-00004 TABLE 4 Sequences and amounts of the primers and probes used in Example 8 Target Conc. SEQ gene Primer and probe (μM) Sequence (5′ .fwdarw. 3′) ID NO Common amplification 0.8 GCAAGCCCTCACGTAGCGAA 12 primer Fluorescent probe UP1  0.0375 ROX-CGAGCAAAAAGAAGTGTGAGAGGTGTGATGAGCTCG-BHQ2 13 sY82 Upstream primer H-82-F 0.006 GCAAGCCCTCACGTAGCGAAATCCTGCCCTTCTGAATCTC 14 Downstream primer H-82-R 0.006 GCAAGCCCTCACGTAGCGAACTGATGGATGATGGGATGTTTG 15 Mediator probe 82-MP 0.006 CACCTCTCACATGTATTTAGCAGCAACATGGCTAGAACTGGAGG-C.sub.7NH.sub.2 16 sY86 Upstream primer H-86-F 0.006 GCAAGCCCTCACGTAGCGAAGCCCCTTAAACAACAACCT 17 Downstream primer H-86-R 0.006 GCAAGCCCTCACGTAGCGAAACAGGGAGAAGACAGCATCT 18 Mediator probe 86-MP 0.006 TCATCACACCTCTGAGATCAAGCTATGGCCAGGGCTGG-C.sub.7NH.sub.2 19 sY242 Upstream primer H-242-F 0.015 GCAAGCCCTCACGTAGCGAAGCAATGGAGTAGCCAGACA 20 Downstream primer H-242-R 0.015 GCAAGCCCTCACGTAGCGAATCTGCCACTAAACTGTAAGCTC 21 Mediator probe242-MP 0.02 CGCACTTCTTTTGATGGGGGGCAAGGCTGACAGC-C.sub.7NH.sub.2 22 ZFX/Y Upstream primer H-ZF-F 0.01 GCAAGCCCTCACGTAGCGAAGAAATACCGCTGTACTGACTG 23 Downstream primer H-ZF-R 0.01 GCAAGCCCTCACGTAGCGAAGGAAAGTTCTTGCTGTGGAC 24 Mediator probe ZF-MP 0.01 TCTCACACTTCTTCACAGAATTTACACTTGTGCATTTTGTTGGCTCC-C.sub.7NH.sub.2 25

    TABLE-US-00005 TABLE 5 Sequences and amounts of the primers and probes used in Example 9 Target Conc. SEQ gene Primers and probes (nM) Sequence (5′ .fwdarw. 3′) ID NO Common amplification 3200 GCAAGCCCTCACGTAGCGAA 12 primers Fluorescent probe UP1 60 ROX-CGAGCAAAAAGAAGTGTGAGAGGTGTGATGAGCTCG-BHQ2 13 sY82 Upstream primer H-82-F 7.5 GCAAGCCCTCACGTAGCGAAATCCTGCCCTTCTGAATCTC 14 Downstream primer H-82-R 7.5 GCAAGCCCTCACGTAGCGAACTGATGGATGATGGGATGTTTG 15 Mediator probe 82-MP 6.0 CACCTCTCACATGTATTTAGCAGCAACATGGCTAGAACTGGAGG-C.sub.7NH.sub.2 16 sY86 Upstream primer H-86-F 7.5 GCAAGCCCTCACGTAGCGAAGCCCCTTAAACAACAACCT 17 Downstream primer H-86-R 7.5 GCAAGCCCTCACGTAGCGAAACAGGGAGAAGACAGCATCT 18 Mediator probe 86-MP 6.0 TCATCACACCTCTGAGATCAAGCTATGGCCAGGGCTGG-C.sub.7NH.sub.2 19 sY242 Upstream primer H-242-F 27.5 GCAAGCCCTCACGTAGCGAAGCAATGGAGTAGCCAGACA 20 Downstream primer H-242-R 27.5 GCAAGCCCTCACGTAGCGAATCTGCCACTAAACTGTAAGCTC 21 Mediator probe 242-MP 200.0 CGCACTTCTTTTGATGGGGGGCAAGGCTGACAGC-C.sub.7NH.sub.2 22 ZFX/Y Upstream primer H-ZF-F 7.5 GCAAGCCCTCACGTAGCGAAGAAATACCGCTGTACTGACTG 23 Downstream primer H-ZF-R 7.5 GCAAGCCCTCACGTAGCGAAGGAAAGTTCTTGCTGTGGAC 24 Mediator probe ZF-MP 8.0 TCTCACACTTCTTCACAGAATTTACACTTGTGCATTTTGTTGGCTCC-C.sub.7NH.sub.2 25 Fluorescent probe UP2 50 ROX-CGGCGGAGTGGGCACGGAGAGCGCTGGACAGTGT + G + GA + C + 26 CCACGTCTCGCAGCAGGCCGCCG-BHQ2 sY152 Upstream primer H-152-F 7.5 GCAAGCCCTCACGTAGCGAAGCGCTCTAAGAATTGGGTAAAG 27 Downstream primer H-152-R 7.5 GCAAGCCCTCACGTAGCGAAACAGGAGGGTACTTAGCAG 28 Mediator probe 152-MP 60 AGCGCTCTCCGTCTGCCATGTTTCAGCTCTTTGACAGCA-C.sub.7-NH.sub.2 29 sY145 Upstream primer H-145-F 7.5 GCAAGCCCTCACGTAGCGAACTTCCTACATTTGTCTTCATAACTTC 30 Downstream primer H-145-R 7.5 GCAAGCCCTCACGTAGCGAAAGAGTGTGATTTCTCATATTTGGTC 31 Mediator probe 145-MP 200 ACACTGTCCAGCGACTTTTGGCTGGGCTGACTACCAGT-C.sub.7-NH.sub.2 32 SRY Upstream primer H-SRY-F 7.5 GCAAGCCCTCACGTAGCGAACCAGTGGAAAATGCTTACTGA 33 Downstream primer H-SRY-R 7.5 GCAAGCCCTCACGTAGCGAAATCTGCGGGAAGCAAACTG 34 Mediator probe SRY-MP 200 GTCCACACTGTATCGACCTCGTCGGAAGGCGAAGATG-C.sub.7-NH.sub.2 35 sY84 Upstream primer H-84-F 30 GCAAGCCCTCACGTAGCGAACCTATTTGTTTTAAGGTGCCATTC 36 Downstream primer H-84-R 30 GCAAGCCCTCACGTAGCGAAAGCTTGCATTAGGCAGACAC 37 Mediator probe 84-MP 200 CCTGCTGCGAGAGCAAATTCCCTTAATCTGCACGAAACATGGG-C.sub.7-NH.sub.2 38 Fluorescent probe UP3 40 FAM-AAGCCCAAAAAAGAGAACAGTATCAGTCACACGGGGCTT-BHQ1 39 sY124 Upstream primer H-124-F 30 GCAAGCCCTCACGTAGCGAATGCCACAGTAAAATGAAGCATC 40 Downstream primer H-124-R 30 GCAAGCCCTCACGTAGCGAATGTTTTCTTCCAGGGCAATG 41 Mediator probe 124-MP 200 TTCTCTTTTTTGGGTCTAGAAGTGCCAtTCGGAAACCA-C.sub.7-NH.sub.2 42 sY127 Upstream primer H-127-F 22.5 GCAAGCCCTCACGTAGCGAAGAATATAGCCCAAAACTAATCAGCA 43 Downstream primer H-127-R 22.5 GCAAGCCCTCACGTAGCGAAAACATCTGGCTCACCCATATAAG 44 Mediator probe 127-MP 200 ATACTGTTCTCTAGCACCCACTGGAATCTACCAAAGCCCA-C.sub.7-NH.sub.2 45 sY128 Upstream primer H-128-F 7.5 GCAAGCCCTCACGTAGCGAAAGTGAACAGGATTGGCAAAGA 46 Downstream primer H-128-R 7.5 GCAAGCCCTCACGTAGCGAAGCAAAACTTTCAACTTCCAAATTCA 47 Mediator probe 128-MP 200 GTGACTGATACCATGAGTGGACATAAGCAAAGCACTTTGGATCA-C.sub.7-NH.sub.2 48 Fluorescent probe UP4 75 FAM-GCGCGCCAGCGGACGAGGCTGTGCACCGGTCGGAGGTGGGGGCGCGC- 49 BHQ1 sY133 Upstream primer H-133-F 7.5 GCAAGCCCTCACGTAGCGAATTCACCAGGACAGAGCCA 50 Downstream primer H-133-R 7.5 GCAAGCCCTCACGTAGCGAATGGCAATGTTTTCTCCCTTCA 51 Mediator probe 133-MP 200 CACAGCCTCGTCCCATCATGAACTCACACATGCACACACATCC-C.sub.7-NH.sub.2 52 sY143 Upstream primer H-143-F 15 GCAAGCCCTCACGTAGCGAAGCAGGATGAGAAGCAGGTAG 53 Downstream primer H-143-R 15 GCAAGCCCTCACGTAGCGAACCTGACATCTAAATAATCTGTGGTG 54 Mediator probe 143-MP 200 GACCGGTGCACCAATGAAAGAACCCCTCCACAATGAAAAGCCT-C.sub.7-NH.sub.2 55 sY134 Upstream primer H-134-F 7.5 GCAAGCCCTCACGTAGCGAAATTCTACTTGAAGCGTTCTGTGA 56 Downstream primer H-134-R 7.5 GCAAGCCCTCACGTAGCGAACAACCACTGCCAAAACTTTCA 57 Mediator probe 134-MP 100 CCCACCTCCGACCACCCAAGACAAAACACCTACTTTCCACT-C.sub.7-NH.sub.2 58 Fluorescent probe UP5 60 Cy5-GCTGCAAAAAACTCAACGATGTGGAAGTCAGCAGC-BHQ2 59 sY155 Upstream primer H-155-F 15 GCAAGCCCTCACGTAGCGAAAGCTCAGAGAAACTTACAACACT 60 Downstream primer H-155-R 15 GCAAGCCCTCACGTAGCGAATGCATTTGAATGTGTAGTGGAGA 61 Mediator probe 155-MP 200 GCTGAGTTTTTTGGGTGGTACAGAGATATTTATGACGGATCCCAACA-C.sub.7-NH.sub.2 62 sY154 Upstream primer H-154-F 15 GCAAGCCCTCACGTAGCGAATTTGCACCAGGATTAAGTGAAGA 63 Downstream primer H-154-R 15 GCAAGCCCTCACGTAGCGAAGTCAGATGTAAGATTGATGCCA 64 Mediator probe 154-MP 200 ATCGTTGAGTTGGTTCCTCCAGAGCCAGGATGTAACC-C.sub.7NH.sub.2 65 sY157 Upstream primer H-157-F 7.5 GCAAGCCCTCACGTAGCGAAGCAAAACATTGGGAATATCTTGGA 66 Downstream primer H-157-R 7.5 GCAAGCCCTCACGTAGCGAATACAGGTTATCCACATTTCTTATCT 67 Mediator probe 157-MP 40 TTCCACATCGTCGTTGTAATAGCAGAAGGTAGGAGATCACTAAAGTGGC- 68 C.sub.7-NH.sub.2 Fluorescent probe UP6 60 Cy5-CCGGCGGGGAGGGACCGTCGTGGCAGGAGGAGCAGCTCACCAGGCCGCC 69 GG-BHQ2 sY254 Upstream primer H-254-F 7.5 GCAAGCCCTCACGTAGCGAATTTTGTACTTCCTGGAGGTTTAG 70 Downstream primer H-254-R 7.5 GCAAGCCCTCACGTAGCGAACCAATCTCAGTTTCATCCATCT 71 Mediator probe254-MP 200 CCACGACGGTCTGGTCATTCGGGGATAAATGGGGGAGAAATTTCCA-C.sub.7-NH.sub.2 72 sY239 Upstream primer H-239-F 7.5 GCAAGCCCTCACGTAGCGAAGTGTGTTTGTTTTTGTTTTTGTGAC 73 Downstream primer H-239-R 7.5 GCAAGCCCTCACGTAGCGAACAGGAAATCTTTCTAAGTGGACA 74 Mediator probe 239-MP 200 CTCCTGCCACGAGGAGCCATGTGCAGAAAAATTCACTGATGC-C.sub.7-NH.sub.2 75 sY255 Upstream primer H-255-F 7.5 GCAAGCCCTCACGTAGCGAATTACAGGATTCGGCGTGA 76