Temperature-selectable fret cassette signaling

Abstract

To provide a multiplexed nucleic acid amplification and detection system useful for detecting the presence of multiple specific nucleic acid sequences or single nucleotide polymorphisms (i.e., "SNPs") in a temperature-dependent fashion using only a single fluorescence detection channel of a nucleic acid analyzer.SOLUTION: The technique can be carried out using standard PCR instrumentation equipped for fluorescence detection or monitoring. The disclosure relates generally to the field of biotechnology. More specifically, the disclosure relates to compositions, methods, kits, and systems for detecting and distinguishing different analyte nucleic acids using invasive cleavage reactions and a single fluorescent detection channel.SELECTED DRAWING: None

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 63 / 250,894, filed September 30, 2021. The entire disclosure of this prior application is incorporated herein by reference.

[0002] Sequence Listing The text of the computer readable sequence listing submitted herewith, entitled "DIA0105-PCT_SEQUENCE_LISTING", created on April 16, 2022, with a file size of 27,886 bytes, is incorporated herein by reference in its entirety.

[0003] Technical Field The present disclosure relates generally to the field of biotechnology. More specifically, the present disclosure relates to compositions, methods, kits, and systems for detecting and distinguishing different analyte nucleic acids using an invasive cleavage reaction and a single fluorescent detection channel. [Background technology]

[0004] background Nucleic acid quantification plays an important role in biology and medicine, for example, in cancer diagnosis and prognosis, and in the diagnosis and monitoring of infectious diseases caused by bacterial, fungal, and viral pathogens.

[0005] There is great value in detecting multiple nucleic acid analytes in a single reaction mixture. Indeed, so-called "multiplexed" detection significantly improves the value of nucleic acid assays while reducing associated reagent costs. However, different assay formats offer different levels of multiplexing capability, which means that practical tradeoffs exist. For example, next-generation sequencing technologies enable the acquisition of vast amounts of information, but the techniques are technically challenging and generally require highly specialized equipment. Another technology, called "invasive cleavage assays," allows for nucleic acid sequence detection down to the level of single-nucleotide differences ("SNPs") and is already being used in conjunction with several multiplex assay formats.

[0006] For example, Hall et al., in U.S. Patent No. 5,994,069, described two multiplexing approaches useful in connection with invasive cleavage detection methods. First, the presence of specific target sequences (or internal controls) can be designed to trigger different cascades coupled to different detectable moieties, such as different dyes in a fluorescent energy transfer format. The contribution of each specific target sequence to the final product can be tallied, allowing for quantitative detection of different nucleic acid sequences contained in a mixture of nucleic acid sequences. In a second configuration, it is desirable to determine whether any of several analytes are present in a sample, but the exact identity of each is not necessary. For example, in a blood bank, it is desirable to know whether any one of a host of infectious agents is present in a blood sample. Because blood is discarded regardless of which agents are present, different signals produced by different probes are not needed in such applications and may actually be undesirable for confidentiality reasons. Therefore, when distinguishing between analytes is unnecessary or undesirable, a single detectable label can be used.

[0007] Elsewhere, Peterson et al., in published U.S. Patent Application No. 2018 / 0163259 A1, describe the detection of different nucleic acid analytes by performing secondary invasive cleavage reactions at different temperatures and for different times, where a first secondary invasive cleavage reaction is completed by the time a second secondary invasive cleavage reaction begins. By performing the reactions at different temperatures and for different times, it is possible to distinguish between nucleic acid analytes in a single multiplex reaction.

[0008] Using a different assay format, Kozlov et al., in U.S. Patent No. 11,034,997, teach a method for performing multiplexed real-time PCR for the detection and quantification of target nucleic acids using tagged hydrolysis probes. A single probe cleavage event occurs in each cycle of the PCR reaction, as a polymerase with 5' to 3' exonuclease activity cleaves the tag portion and hydrolyzes the remaining portion of the probe. A fluorescent signal can be generated if the tag has a fluorophore separate from the quencher on the annealing portion of the probe. The fluorescent label associated with an oligonucleotide probe hybridized to a target nucleic acid can be cleaved from the target-complementary portion of the probe during one cycle of the primer extension (i.e., polymerization) reaction and subsequently decomposed. As a result, an increase in signal intensity depends on the performance of additional cycles of the PCR reaction. Similarly, Kozlov et al. teach that a "quencher molecule" (e.g., an oligo) hybridizes to the tag portion of an uncleaved hydrolysis probe at the temperature used to extend the primer in the primer extension reaction of PCR. Prior to the primer extension cycle in the PCR reaction, the fluorescence is quenched by the annealing portion of the probe and a quencher moiety linked to the quenching molecule. Despite the availability of existing nucleic acid multiplex detection platforms, there remains a need for additional approaches that can be easily adapted to automated testing platforms. More specifically, there is a need to maximize the detection capabilities of deployed testing instruments without requiring hardware modifications. [Prior art documents] [Patent documents]

[0009] [Patent Document 1] U.S. Patent No. 5,994,069 [Patent Document 2] US Patent Application Publication No. 2018 / 0163259 [Patent Document 3] U.S. Patent No. 11,034,997 Summary of the Invention [Means for solving the problem]

[0010] overview The following numbered embodiments are provided herein:

[0011] Embodiment 1 is a composition comprising a FRET cassette reporter system, the composition comprising: (i) a 5' flap FRET cassette oligonucleotide, the 5' flap portion comprising a first fluorophore moiety, a stem-loop portion comprising a first quencher moiety, and a 3' portion comprising a cleaved flap-hybridizing sequence, wherein hybridization of a cassette-specific invasive oligonucleotide complementary to the cleaved flap-hybridizing sequence of the 5' flap FRET cassette oligonucleotide forms an invasive cleavage structure cleavable by FEN-1 endonuclease at a cleavage site between the first fluorophore moiety and the first quencher moiety, and hybridization of the 5' flap FRET cassette oligonucleotide at the cleavage site forms an invasive cleavage structure cleavable by FEN-1 endonuclease. and (ii) a masking oligonucleotide comprising a second quencher moiety, wherein at least a portion of the masking oligonucleotide is capable of specifically hybridizing to the 5' flap portion of the FRET cassette oligonucleotide, and wherein hybridization of the masking oligonucleotide to the cassette cleavage flap forms a duplex having a first melting temperature exhibiting a first melting peak, and wherein fluorescent emission from the first fluorophore moiety in the duplex is quenched by the second quencher moiety.

[0012] Embodiment 2 is the composition of embodiment 1, wherein the first quencher moiety and the second quencher moiety are the same as each other.

[0013] Embodiment 3 is the composition of either embodiment 1 or embodiment 2, further comprising a FEN-1 endonuclease.

[0014] Embodiment 4 is the composition of embodiment 3, wherein the FEN-1 endonuclease is a thermostable FEN-1 endonuclease.

[0015] Embodiment 5 is the composition of embodiment 4, wherein the thermostable FEN-1 endonuclease is derived from an archaeal organism.

[0016] Embodiment 6 is the composition of any one of Embodiments 1-5, further comprising a first target-specific invasive oligonucleotide and a first target-specific primary probe oligonucleotide, each of which comprises a sequence configured to hybridize to a target nucleic acid to form an invasive cleavage structure cleavable by a FEN-1 endonuclease to produce a primary cleavage flap, wherein the primary cleavage flap is a cassette-specific invasive oligonucleotide configured to hybridize to a cleaved flap hybridizing sequence of the 5' flap FRET cassette oligonucleotide to form an invasive cleavage structure cleavable by a FEN-1 endonuclease.

[0017] Embodiment 7 is the composition of embodiment 6, further comprising a target nucleic acid.

[0018] Embodiment 8 is the composition of embodiment 7, further comprising deoxynucleoside triphosphates (dNTPs), a thermostable DNA polymerase, and a primer having a 3' end extendable by the thermostable DNA polymerase using a target nucleic acid as a template in a template-dependent nucleic acid amplification reaction.

[0019] Embodiment 9 is the composition of any one of embodiments 1-8, further comprising: (iii) a second FRET cassette oligonucleotide, the 5' portion comprising the second fluorophore moiety, a stem-loop portion comprising a third quencher moiety, and a 3' portion comprising a second cleaved flap hybridizing sequence, wherein hybridization of the second cassette-specific invasive oligonucleotide to the second cleaved flap hybridizing sequence of the second FRET cassette oligonucleotide forms an invasive cleavage structure cleavable by FEN-1 endonuclease at a cleavage site between the second fluorophore moiety and the third quencher moiety, and cleavage of the second FRET cassette oligonucleotide at the cleavage site produces a cassette cleavage product comprising the second fluorophore moiety.

[0020] Embodiment 10 is the composition of embodiment 9, wherein the second FRET cassette oligonucleotide is a second 5' flap FRET cassette comprising a 5' flap portion, and the cassette cleavage product is a second cassette cleavage flap comprising a second fluorophore, and the composition further comprises: (iv) a second masking oligonucleotide comprising a fourth quencher moiety, at least a portion of the second masking oligonucleotide being specifically hybridizable to the 5' flap portion of the second FRET cassette oligonucleotide, wherein hybridization of the second masking oligonucleotide to the second cassette cleavage flap forms a second duplex having a second melting temperature higher than the first melting temperature, and wherein fluorescent emission from the second fluorophore moiety in the second duplex is quenched by the fourth quencher moiety.

[0021] Embodiment 11 is the composition of embodiment 9, wherein the second cassette cleavage product comprises no more than 5, preferably no more than 4, preferably no more than 3, preferably no more than 2 nucleotides.

[0022] Embodiment 12 is the composition of any one of embodiments 9-11, wherein the emission signals from the first fluorophore moiety and the second fluorophore moiety are detectable in the same fluorescence detection channel of a fluorescence monitoring device.

[0023] Embodiment 13 is the composition of any one of embodiments 9-12, wherein the first fluorophore moiety and the second fluorophore moiety are the same as each other.

[0024] Embodiment 14 is the composition of any one of embodiments 9-12, wherein the first fluorophore moiety and the second fluorophore moiety are not the same as one another.

[0025] Embodiment 15 is the composition of any one of embodiments 10 and 12-14, wherein the third quencher moiety and the fourth quencher moiety are the same as each other.

[0026] Embodiment 16 is a method for determining which of two different FRET cassettes in a reaction mixture has been cleaved to produce a fluorescent signal, the method comprising: (a) performing a multiple invasive cleavage reaction in the reaction mixture to cleave one or both of a first FRET cassette and a second FRET cassette to produce two different fluorescent cleavage products if cleavage occurs, wherein the first FRET cassette comprises a first 5' flap portion having a fluorophore attached thereto, the fluorophore attachment being arranged such that cleavage of the first FRET cassette by a FEN-1 endonuclease in the multiple invasive cleavage reaction produces a first cassette cleavage flap comprising the fluorophore; and wherein the reaction mixture is stably hybridized to the first cassette cleavage flap to produce a first 5' flap. wherein the first masking oligonucleotide forms a first duplex at a temperature below the Tm of the first cassette cleavage flap but not at a temperature above the first Tm, and wherein fluorescence emission from the fluorophore of the first cassette cleavage flap of the first duplex is quenched, and each of two different fluorescent cleavage products produced in the multiple invasive cleavage reaction is characterized by a different temperature-dependent fluorescence quenching profile in the reaction mixture; (b) measuring the fluorescent signals produced in the reaction mixture using a single channel of a fluorescence monitoring device under temperature conditions that differentially quench the fluorescence produced by the different fluorescent cleavage products of the multiple invasive cleavage reaction; and (c) determining which of the different FRET cassettes was cleaved in the multiple invasive cleavage reaction from the result of step (b).

[0027] Embodiment 17 is the method of embodiment 16, wherein the second FRET cassette in step (a), when cleaved, produces a fluorescent cleavage product that does not hybridize to any masking oligo in the reaction mixture, resulting in fluorescence quenching.

[0028] Embodiment 18 is the method of embodiment 17, wherein step (c) comprises comparing the fluorescence signals measured at a temperature below the first Tm and above the first Tm.

[0029] Embodiment 19 is the method of embodiment 18, wherein step (c) comprises comparing the fluorescent signals by calculating the difference between the measured fluorescent signals.

[0030] Embodiment 20 is the method of embodiment 17, wherein step (b) comprises measuring any fluorescence signal at a temperature below the first Tm, wherein fluorescence emission from the fluorophore of the first cassette cleavage flap of the first duplex is quenched, and step (c) comprises determining that the second FRET cassette has been cleaved in the reaction mixture if measurable fluorescence is detected in step (b).

[0031] Embodiment 21 is the method of embodiment 17, wherein step (b) comprises measuring any one of the fluorescent signals at a temperature below the first Tm and a temperature above the first Tm, and step (c) comprises determining that the first FRET cassette has been cleaved in the reaction mixture if the fluorescent signal measured at the temperature above the first Tm is greater than the fluorescent signal measured at the temperature below the first Tm.

[0032] Embodiment 22 is the method of any one of embodiments 16 to 21, wherein step (b) comprises measuring any of the fluorescent signals produced in the reaction mixture as a function of temperature to generate a melting / annealing curve.

[0033] Embodiment 23 is the method of embodiment 22, wherein step (c) comprises calculating a derivative of the melting / annealing curve and then determining from the calculated derivative whether the reaction mixture comprises a first duplex characterized by a first Tm as an indication that the first FRET cassette has been cleaved in the reaction mixture.

[0034] Embodiment 24 is the method of embodiment 16, wherein the second FRET cassette comprises a second 5' flap sequence having a fluorophore attached, the fluorophore attachment being arranged such that cleavage of the second FRET cassette by the FEN-1 endonuclease in a multiple invasive cleavage reaction produces a second cassette cleavage flap comprising the fluorophore, the reaction mixture comprising a second masking oligo that hybridizes to the second cassette cleavage flap to form a second duplex at a temperature below the second Tm but does not hybridize at a temperature above the second Tm, wherein fluorescence emission from the fluorophore of the second cassette cleavage flap of the second duplex is quenched, and the first Tm and the second Tm differ by at least 5°C.

[0035] Embodiment 25 is the method of embodiment 24, wherein the first Tm is greater than the second Tm, step (b) comprises measuring the fluorescent signal at either a temperature lower than the second Tm or a temperature higher than the first Tm, and step (c) comprises determining that at least one of the first FRET cassette and the second FRET cassette is cleaved in the reaction mixture if the fluorescent signal measured at the temperature higher than the first Tm is greater than the fluorescent signal measured at the temperature lower than the second Tm.

[0036] Embodiment 26 is the method of either embodiment 24 or 25, wherein step (b) comprises measuring any of the fluorescent signals produced in the reaction mixture as a function of temperature to generate a melting / annealing curve.

[0037] Embodiment 27 is the method of embodiment 26, wherein step (c) comprises calculating a derivative of the melting / annealing curve and then determining from the calculated derivative whether the reaction mixture comprises a first duplex characterized by a first Tm as an indication that the first FRET cassette has been cleaved in the reaction mixture.

[0038] Embodiment 28 is the method of embodiment 26, wherein step (c) comprises calculating a derivative of the melting / annealing curve and then determining from the calculated derivative whether the reaction mixture contains a second duplex characterized by a second Tm as an indication that the second FRET cassette has been cleaved in the reaction mixture.

[0039] Embodiment 29 is the method of any one of embodiments 16 to 28, wherein the first and second FRET cassettes are labeled with the same fluorophore.

[0040] Embodiment 30 is the method of any one of embodiments 16 to 28, wherein the first and second FRET cassettes are not labeled with the same fluorophore.

[0041] Embodiment 31 is the method of any one of embodiments 16 to 30, wherein the FEN-1 endonuclease of the multiply invasive cleavage reaction in step (a) comprises a thermostable FEN-1 endonuclease.

[0042] Embodiment 32 is the method of any one of embodiments 16-31, wherein step (c) comprises determining using a computer programmed with software.

[0043] Embodiment 33 is a method of analyzing a sample containing a target nucleic acid, comprising: (a) contacting in a reaction mixture any first target nucleic acid of the sample with a first primary probe oligonucleotide comprising a sequence complementary thereto and a FEN-1 endonuclease under conditions such that, when the first primary probe oligonucleotide hybridizes to the first target nucleic acid, the first primary probe is cleaved by the FEN-1 endonuclease to generate a first primary cleavage flap, wherein the first primary cleavage flap hybridizes to a cleaved flap hybridizing sequence of a first FRET cassette oligonucleotide contained in the reaction mixture and is cleaved by the FEN-1 endonuclease at a cleavage site between a first fluorophore moiety and a first quencher moiety of the first FRET cassette oligonucleotide to form an invasive cleavage structure that releases a first cassette cleavage flap comprising the first fluorophore moiety. (b) hybridizing a first masking oligonucleotide comprising a second quencher moiety to a first cassette cleavage flap to form a duplex at a temperature below a first Tm of the first masking oligonucleotide and the first cassette cleavage flap, wherein fluorescent emission from the first fluorophore moiety of the duplex is quenched by the second quencher moiety, and wherein at a second temperature higher than the first Tm, the first masking oligonucleotide and the first cassette cleavage flap do not form a stable duplex; and (c) determining whether the sample contains the first target nucleic acid if fluorescence emitted from the first fluorophore moiety is detected in step (b), or whether the sample does not contain the first target nucleic acid if fluorescence emitted from the first fluorophore moiety is not detected in step (b).

[0044] Embodiment 34 further comprises contacting any of the second target nucleic acids of the sample in a reaction mixture with a second primary probe oligonucleotide comprising a sequence complementary thereto and a FEN-1 endonuclease under conditions such that, when the second primary probe oligonucleotide hybridizes to the second target nucleic acid, the second primary probe is cleaved by the FEN-1 endonuclease to generate a second primary cleavage flap different from the first primary cleavage flap, wherein the second primary cleavage flap hybridizes to a cleaved flap hybridizing sequence of a second FRET cassette oligonucleotide contained in the reaction mixture and is cleaved by the FEN-1 endonuclease at a cleavage site between the second fluorophore moiety and a third quencher moiety of the second FRET cassette oligonucleotide to form an invasive cleavage structure that releases a second cassette cleavage flap comprising a second fluorophore moiety; and at a third temperature lower than the second Tm, a second masking oligonucleotide comprising a fourth quencher moiety. 34. The method of embodiment 33, wherein the second masking oligonucleotide hybridizes to the second cassette cleavage flap to form a duplex, and fluorescent emission from the second fluorophore moiety of the duplex is quenched by the fourth quencher moiety, and at a fourth temperature higher than the second Tm, the second masking oligonucleotide and the second cassette cleavage flap do not form a stable duplex, and the first Tm and the second Tm differ from each other by at least 5°C, step (b) further comprises detecting any fluorescence emitted from the second fluorophore moiety at the fourth temperature, and step (c) further comprises determining whether the sample contains the second target nucleic acid if fluorescence emitted from the second fluorophore moiety of the 5' flap cleavage product of the second FRET cassette oligonucleotide is detected in step (b), or whether the sample does not contain the first target nucleic acid if fluorescence emitted from the second fluorophore moiety of the 5' flap cleavage product of the second FRET cassette oligonucleotide is not detected in step (b).

[0045] Embodiment 35 is a preferred embodiment of the present invention, wherein step (a) further comprises contacting any of the second target nucleic acids of the sample with a second primary probe oligonucleotide comprising a sequence complementary thereto and a FEN-1 endonuclease in a reaction mixture under conditions such that, when the second primary probe oligonucleotide hybridizes to the second target nucleic acid, the second primary probe is cleaved by the FEN-1 endonuclease to generate a second primary cleavage flap, wherein the second primary cleavage flap hybridizes to a cleaved flap hybridizing sequence of a second FRET cassette oligonucleotide contained in the reaction mixture, thereby forming a cleavage flap between the second fluorophore moiety and the third quencher moiety of the second FRET cassette oligonucleotide. 34. The method of embodiment 33, wherein the FEN-1 endonuclease cleaved the first target nucleic acid at the site to form an invasive cleavage structure that releases a cleavage product comprising a second fluorophore moiety, and the cleavage product does not hybridize to any masking oligonucleotide in the reaction mixture, resulting in fluorescence quenching; step (b) further comprises detecting any fluorescence emitted from the second fluorophore moiety of the cleavage product; and step (c) further comprises determining whether the sample contains the second target nucleic acid if fluorescence emitted from the second fluorophore moiety is detected in step (b), or whether the sample does not contain the first target nucleic acid if fluorescence emitted from the second fluorophore moiety is not detected in step (b).

[0046] Embodiment 36 is the method of either embodiment 34 or embodiment 35, wherein step (b) comprises detecting any fluorescence emitted from the first and second fluorophore moieties using a single channel of a fluorescence monitoring device.

[0047] Embodiment 37 is the method of embodiment 36, wherein step (b) is performed while a nucleic acid amplification reaction is occurring in the reaction mixture, and the products of the nucleic acid amplification reaction comprise the first target nucleic acid and the second target nucleic acid.

[0048] Embodiment 38 is the method of embodiment 37, wherein the nucleic acid amplification reaction includes a step for thermal cycling and the reaction mixture further comprises a thermostable DNA polymerase.

[0049] Embodiment 39 is the method of any one of embodiments 33 to 36, wherein step (b) is performed when the temperature of the reaction mixture is reduced to allow annealing of the masking oligonucleotide and the complementary cassette cleavage flap.

[0050] Embodiment 40 is the method of 36, wherein the first and second fluorophore moieties are the same as each other.

[0051] Embodiment 41 is the method of embodiment 36, wherein the step (b) of detecting any fluorescence comprises measuring any fluorescence.

[0052] Embodiment 42 is the method of embodiment 41, further comprising any step of detecting or measuring fluorescence at the first temperature.

[0053] Embodiment 43 is the method of any one of embodiments 34 or 35, wherein both the first fluorophore moiety and the second fluorophore moiety are detectable in the same fluorescence detection channel of the energy sensor device.

[0054] Embodiment 44 is the method of embodiment 43, wherein the second fluorophore moiety is the same as the first fluorophore moiety.

[0055] Embodiment 45 is the method of embodiment 43, wherein the second fluorophore moiety is not the same as the first fluorophore moiety.

[0056] Embodiment 46 is the method of any one of embodiments 33 to 43, wherein fluorescence from the second fluorophore is detected and / or measured at the first temperature.

[0057] Embodiment 47 is the method of any one of embodiments 33-44, wherein the third quencher moiety is the same as the first quencher moiety and / or the second quencher moiety.

[0058] Embodiment 48 is the method of any one of embodiments 33 to 47, wherein the reaction mixture comprises primer oligonucleotides that amplify a target nucleic acid, and at least one primer oligonucleotide acts as an invasive oligonucleotide in the presence of the primary probe oligonucleotide and the target nucleic acid and / or target amplicon to form an invasive cleavage structure that is cleaved by the thermostable FEN-1 endonuclease.

[0059] Embodiment 49 is the method of any one of embodiments 33 to 48, wherein step (c) comprises determining using a computer programmed with software.

[0060] Embodiment 50 is a system for determining which of a plurality of target nucleic acid analytes are present in a reaction mixture, wherein each target nucleic acid analyte of the plurality of target nucleic acid analytes is detectable by a fluorescent signal, the system comprising: a thermocycler; a fluorometer in optical communication with the thermocycler, the fluorometer measuring, in a single optical channel, a fluorescent signal indicative of production of nucleic acid amplification products by the thermocycler; and a computer in communication with the fluorometer, the system causing the computer to (a) obtain a melting / annealing curve dataset generated from measurements made by the fluorometer; and (b) measure, in the melting / annealing curve dataset, a fluorescent signal indicative of production of nucleic acid amplification products by the reaction mixture. (c) determining the presence of a first target nucleic acid in the reaction mixture by detecting a fluorescent signal from a first fluorescent cleavage product at a temperature at which fluorescence in the mixture is maximally quenched; (c) generating a derivative plot from the melting / annealing curve dataset; and (d) determining the presence of a second target nucleic acid in the reaction mixture if the derivative plot contains features characteristic of the first duplex, wherein the first duplex comprises a first masking oligonucleotide and a second fluorescent cleavage product that is produced in the reaction mixture when the second target nucleic acid is present.

[0061] Embodiment 51 is the system of embodiment 50, wherein the computer is programmed with software instructions that cause the computer to determine that a third target nucleic acid is present in the reaction mixture if (e) the derivative plot contains a feature characteristic of a second duplex, the second duplex containing a second masking oligonucleotide and a third fluorescent cleavage product that is produced in the reaction mixture when the third target nucleic acid is present.

[0062] Embodiment 52 is the system of embodiment 50 or embodiment 51, wherein the characteristic feature of the first duplex comprises a maximum, minimum, or zero crossing point of the calculated derivative.

[0063] Embodiment 53 is the system of embodiment 52, wherein the calculated derivative comprises a calculated first derivative, the feature characteristic of the first duplex comprises a first maximum of the calculated first derivative of the melt / annealing curve dataset as a first melt peak, and the feature characteristic of the second duplex comprises a second maximum of the calculated first derivative of the melt / annealing curve dataset as a second melt peak.

[0064] Embodiment 54 is the system of any one of embodiments 50 to 53, wherein the thermocycler, the fluorometer, and the computer are all components of a real-time PCR instrument.

[0065] Embodiment 55 is the system of embodiment 50, wherein the computer-generated melting / annealing curve data set comprises data points showing fluorescence as a function of temperature. [Brief explanation of the drawings]

[0066] [Figure 1]Figure 1 provides a schematic diagram of an assay using two invasive cleavage reactions performed sequentially in the same reaction mixture. In the primary reaction, an "invasive oligonucleotide" (SEQ ID NO: 1) and a "primary probe oligo" (SEQ ID NO: 2) (i.e., a 5' flap oligonucleotide) hybridize to a "target strand" nucleic acid (SEQ ID NO: 3) to form an invasive cleavage structure cleavable by FEN-1 endonuclease, releasing a cleaved 5' flap ("primary cleavage flap") (SEQ ID NO: 4). In the secondary reaction, the primary cleavage flap from the primary reaction hybridizes to a FRET cassette ("FRET cassette 1") (SEQ ID NO: 5), a hairpin oligonucleotide labeled with a fluorescent dye and a quencher molecule, to form a second invasive cleavage structure cleavable by FEN-1 endonuclease at a site between the fluorophore (denoted as "HEX") and the quencher ("Q"). Cleavage of "FRET cassette 1" (SEQ ID NO: 5) produces "cleaved FRET cassette 1" (SEQ ID NO: 6), separating the quencher from the fluorophore so that fluorescent signal from the fluorophore can be detected. Each primary cleavage flap can hybridize to a series of new uncleaved FRET cassettes to form further fluorescent cleavage products.

[0067] [Figure 2] Figure 2 is a series of schematic diagrams illustrating the structure and use of 5' flap FRET cassettes. Figure 2A shows the structure of an example "5' flap FRET cassette" (SEQ ID NO: 7). Figure 2B shows an example "5' flap FRET cassette 1" (SEQ ID NO: 7) hybridized to a "flap cleaved from primary probe" (SEQ ID NO: 8) (i.e., the primary cleavage flap functions as the invasive oligonucleotide). Figure 2C shows the temperature-dependent interaction between a "cassette cleavage flap" (SEQ ID NO: 9) (i.e., the 5' flap cleaved from the 5' flap FRET cassette) and a complementary "masking oligo" (SEQ ID NO: 10).

[0068] [Figure 3]Figure 3 shows a schematic diagram of how the fluorescent signals produced by the cleavage of three different FRET cassettes ("Flapless FRET Cassette" (SEQ ID NO: 11), "5' Flap FRET Cassette 1" (SEQ ID NO: 7), and "5' Flap FRET Cassette 2" (SEQ ID NO: 13)) can be distinguished by temperature-dependent quenching. The "Flap Cleaved from Target 2 Primary Probe" (SEQ ID NO: 8) hybridizes to "5' Flap FRET Cassette 1" (SEQ ID NO: 7) to promote the enzyme-dependent cleavage reaction. The "Cassette Cleaved Flap 1" (SEQ ID NO: 9), or the 5' flap cleaved from "5' Flap FRET Cassette 1" (SEQ ID NO: 7), can hybridize to "Masking Oligo 1" (SEQ ID NO: 10) to form a first hybrid duplex that exhibits quenched fluorescence. The "Flap Cleaved from Target 3 Primary Probe" (SEQ ID NO: 14) hybridizes to "5' Flap FRET Cassette 2" (SEQ ID NO: 13) to promote the enzyme-dependent cleavage reaction. "Cassette Cleavage Flap 2" (SEQ ID NO: 15), or the 5' flap cleaved from "5' Flap FRET Cassette 2" (SEQ ID NO: 13), can hybridize to "Masking Oligo 2" (SEQ ID NO: 16) to form a second duplex that exhibits quenched fluorescence. The two hybrid duplexes are designed to have unique melting / annealing properties, which allow one to be distinguished from the other. The signal produced by cleavage of the "Flapless FRET Cassette" (SEQ ID NO: 11) remains detectable under all temperature conditions.

[0069] [Figure 4]Figure 4 is a schematic diagram of cleavage products prepared using a flapless FRET cassette and two different 5' flap FRET cassettes, in which all three FRET cassettes are labeled with the same reporter dye (HEX). The different FRET cassettes allow for the detection of different nucleic acid target sequences using only a single fluorescence detection channel of a nucleic acid analyzer. In the illustrated embodiment, temperature 1 is lower than temperature 2 (e.g., temperature 1 can be 40°C and temperature 2 can be 50°C). Target 1 is detected using a flapless FRET cassette (e.g., SEQ ID NO: 11 in Figure 3) that does not have a corresponding masking oligonucleotide, so that the signal from target 1 is detectable at all temperatures. Target 2 is detected using a 5' flap FRET cassette (e.g., SEQ ID NO: 7 in Figure 3) that produces "cassette cleavage flap 1" (SEQ ID NO: 9), which is masked by hybridization with "masking oligo 1" (SEQ ID NO: 10) when the reaction mixture is below temperature 1. Above temperature 1 but below temperature 2, signals reflecting the detection of both target 1 and target 2 are detectable. Detection of target 3 is performed using a 5' flap FRET cassette (e.g., SEQ ID NO: 13 in Figure 3) that produces "Cassette Cleavage Flap 2" (SEQ ID NO: 15), which is masked by hybridization with "Masking Oligo 2" (SEQ ID NO: 16) when the reaction mixture is below temperature 2. Above temperature 2, signals from all three targets 1, 2, and 3 are detectable. In the illustrated embodiment, the temperatures selected for detection of cleavage of the different FRET cassettes are independent of the sequences of the three different target nucleic acids.

[0070] [Figure 5] 5 provides a set of graphs showing fluorescence measured in the HEX channel as a function of cycle number. Reactions contain target analyte A (FIG. 5A), target analyte B (FIG. 5B), or target analytes A and B together (FIG. 5C), as described in Example 1.

[0071] [Figure 6]FIG. 6 is a graph showing melting curve analysis using fluorescence detected in the HEX channel for reactions containing target analyte A, target analyte B, and target analytes A and B together, as described in Example 2.

[0072] [Figure 7] Figures 7A-7D provide a set of graphs showing fluorescence measured in the HEX channel as a function of cycle number and temperature at which fluorescence measurements were made. Figures 7A and 7B show results obtained for reactions containing only target analyte B (using a 5' flap FRET cassette and a masking oligonucleotide that quenches at low temperature) when fluorescence was measured at 63°C and 39°C, respectively. Figures 7C and 7D show results obtained for reactions containing target analytes A and B together, where analyte A was detected using a flapless FRET cassette (without a 5' flap), producing a product that fluoresced at both temperatures, and fluorescence was measured at 63°C and 39°C, respectively. The procedure is described in Example 3.

[0073] [Figure 8] FIG. 8 is a graph showing melting curve analysis detected in the HEX channel for reactions containing target analyte A, target analyte B, target analyte C, and a combination of all three target analytes, as described in Example 4.

[0074] [Figure 9] Figure 9 provides a graph showing the unique melting / annealing curve profiles observed for additional analyte combinations, as described in Example 4. The left panel of the figure shows the melting / annealing curve results for reactions that amplified either analyte B or analyte C. The right panel of the figure shows the melting / annealing curve analysis results for reactions that amplified analyte B alone, analyte C alone, or a combination of analytes B and C.

[0075] [Figure 10] FIG. 10 provides first derivative plots of the measured fluorescence data shown in two panels of FIG. DETAILED DESCRIPTION OF THE INVENTION

[0076] definition To facilitate the understanding of this disclosure, several terms and phrases are defined below. Further definitions are set forth throughout the detailed description. Throughout the specification and claims, the following terms shall take the meanings explicitly associated therewith, unless the context clearly dictates otherwise.

[0077] As used herein, the phrase "in one embodiment" may, but does not necessarily, refer to the same embodiment. Further, as used herein, the phrase "in another embodiment" does not necessarily, but may, refer to different embodiments. Thus, as described below, various embodiments of the present technology can be readily combined without departing from the scope or spirit of the technology.

[0078] The term "based on" is not exclusive and allows for the basis of additional factors not listed, unless the context clearly dictates otherwise. Additionally, throughout this specification, the meanings of "a," "an," and "the" include plural references. The meaning of "in" includes "in" and "on."

[0079] As used in the claims of this application, the transitional phrase "consisting essentially of" extends the claim to As discussed in Herz, 537 F.2d 549,551-52,190 USPQ 461,463 (CCPA 1976), limitations are placed on the specific materials or steps of the claimed invention "as well as those which do not substantially affect the basic and novel characteristic(s)." For example, a composition "consisting essentially of" recited elements may contain unrecited contaminants, although present, at levels such that the contaminants do not alter the function of the recited composition compared to the pure composition (i.e., a composition "consisting of" the recited components). As used herein, the term "sample" refers to a specimen that may contain an analyte of interest (e.g., nucleic acid, such as a microorganism, virus, gene, or a component thereof, including a nucleic acid sequence in or derived from the specimen). A sample may be from any source, such as a biological specimen or an environmental source. A biological specimen includes any tissue or material from a living or dead organism that may contain analyte or nucleic acid in or derived from the specimen. Examples of biological samples include nasal swab samples, vaginal swab samples, respiratory tissue, exudates (e.g., bronchoalveolar lavage), biopsies, sputum, peripheral blood, plasma, serum, lymph nodes, gastrointestinal tissue, feces, urine, or other fluids, tissues, or materials. Examples of environmental samples include water, ice, soil, slurries, debris, biofilms, suspended particles, and aerosols. A sample may be a processed specimen or material, such as that obtained from processing a sample by using filtration, centrifugation, sedimentation, or adhesion to a medium such as a matrix or support. Other sample processing may include physically or mechanically disrupting tissues, cell aggregates, or cells to release intracellular components, including nucleic acids, into a solution that may contain other components, such as enzymes, buffers, salts, detergents, etc. A sample being tested for the presence of an analyte may be referred to as a "test sample."

[0080] The terms "target nucleic acid" and "target sequence" refer to the nucleic acid to be detected or analyzed. Therefore, a "target" nucleic acid must be distinguished from other nucleic acids or nucleic acid sequences. For example, when used in reference to an amplification reaction, these terms can refer to the nucleic acid or portion of a nucleic acid amplified by the reaction, and when used in reference to a polymorphism, they can refer to the locus in the nucleic acid of a suspected polymorphism. When used in reference to an invasive cleavage reaction, these terms typically refer to a nucleic acid molecule containing a sequence that selectively hybridizes to a first nucleic acid molecule (e.g., a probe oligonucleotide) and a second nucleic acid molecule (an invasive oligonucleotide) to form an overlapping invasive cleavage structure. Generally, a target nucleic acid (e.g., present in a sample, isolated from a sample, enriched from a sample, or amplified from or within a sample) is located within a target region and can be identified by the successful formation of an invasive cleavage structure in combination with the first and second nucleic acid molecules (e.g., a probe oligonucleotide and an invasive oligonucleotide) that are cleavable by a cleavage agent. Target nucleic acids derived from organisms are not limited to genomic DNA and RNA. Target nucleic acids from organisms can include any nucleic acid species, including, but not limited to, genomic DNA and RNA, messenger RNA, structural RNA, ribosomal and tRNA, and small RNA such as snRNA, siRNA, and microRNA (miRNA). See, for example, U.S. Patent No. 7,851,150, the entire contents of which are incorporated herein by reference. A "segment" is defined as a region of nucleic acid within a target sequence.

[0081] Mononucleotides react to form oligonucleotides by unidirectionally attaching the 5' phosphate attached to one mononucleotide pentose ring to the 3' oxygen of the next mononucleotide via a phosphodiester bond. Therefore, when the 5' phosphate of an oligonucleotide is not linked to the 3' oxygen of the mononucleotide pentose ring, the end of the oligonucleotide is referred to as the "5' end." When the 3' oxygen is not linked to the 5' phosphate of the next mononucleotide pentose ring, the end of the oligonucleotide is referred to as the "3' end." As used herein, a nucleic acid sequence may also be referred to as having a 5' end and a 3' end, even if it is within a larger oligonucleotide. A first region along a nucleic acid chain is said to be upstream of another region if, moving in the 5' to 3' direction along the nucleic acid chain, the 3' end of the first region precedes the 5' end of the second region.

[0082] As used herein, the term "5' end" refers to a portion of a nucleic acid having a 5' end (i.e., a 5' end where the 5' phosphate is not linked to the 3' oxygen of a mononucleotide pentose ring). The term "3' end" refers to a portion of a nucleic acid having a 3' end (i.e., a 3' end where the 3' oxygen is not linked to the 5' phosphate of a subsequent mononucleotide pentose ring).

[0083] As used herein, the terms "hybridization" or "hybridize" (and grammatical equivalents) are used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acid strands involved in a duplex) depend on the degree of complementarity between the nucleic acids, the stringency of the conditions involved, the T of the hybrid formed, and the degree of complementarity between the nucleic acids. m and the G:C ratio within the nucleic acid.

[0084] When two different non-overlapping oligonucleotides anneal to different regions of the same linear complementary nucleic acid, and the 3' end of one oligonucleotide is adjacent to the 5' end of the other, the former can be called the "upstream" oligonucleotide, and the latter can be called the "downstream" oligonucleotide.Similarly, when two overlapping oligonucleotides hybridize to the same linear complementary nucleic acid, and the first oligonucleotide is positioned so that its 5' end is upstream of the 5' end of the second oligonucleotide, and the 3' end of the first oligonucleotide is upstream of the 3' end of the second oligonucleotide, the first oligonucleotide can be called the "upstream" oligonucleotide, and the second oligonucleotide can be called the "downstream" oligonucleotide.

[0085] As used herein, the term "Tm" refers to the "melting temperature" of a nucleic acid strand relative to a complementary nucleic acid strand. The melting temperature of a nucleic acid duplex is the temperature at which a population of double-stranded nucleic acid molecules becomes half-dissociated into single strands. Measuring the melting temperature of a labeled nucleic acid duplex typically involves plotting fluorescence as a function of temperature to generate a melting curve characteristic of duplex dissociation. Graphing the negative first derivative of the melting curve as a function of temperature yields the T m are identifiable as peaks. See, e.g., KM Ririe et al., Analytical Biochemistry 245:154-160 (1997).

[0086] "Calculated T m " refers to the melting temperature calculated from the physical sequence of complementary nucleic acids, along with factors of the reaction conditions (e.g., salt concentration, concentration of complementary strands in the mixture). m Several formulas for calculating T are well known in the art. As indicated by standard references, mA simple estimate of the value is that when a nucleic acid is in an aqueous solution of 1 M NaCl (see, e.g., Young and Anderson, (1985) in Nucleic Acid Hybridisation: A Practical Approach (Hames & Higgins, Eds.) pp 47-71, IRL Press, Oxford), the formula: T m T = 81.5 + 0.41 (% G + C) m Other calculations for calculating σ are known in the art and take into account structural and environmental as well as sequence characteristics (see, e.g., Allawi, HT and SantaLucia, J., Jr. Biochemistry 36, 10581-94 (1997)); and SantaLucia, Proc Natl Acad Sci U S A., 95(4):1460 (1998)).

[0087] As used herein, the term "cycling hybridization" refers to the process of cycling the T of a hybridized nucleic acid strand such that an oligonucleotide is continually annealed to and dissociated from a target strand without temperature cycling (i.e., the probe-target nucleic acid duplex is alternately melted and annealed without shifting the temperature of the reaction mixture). m It refers to incubation of a reaction mixture containing nucleic acids (e.g., probe oligonucleotides and their complementary target nucleic acids) at or near (e.g., within 4°C, more preferably within 3°C, even more preferably within 2°C, and even more preferably within 1°C) the temperature.

[0088] As used herein, an "invasive cleavage assay" is a procedure for detecting or quantifying a target nucleic acid by enzymatic cleavage of one or more different invasive cleavage structures, at least one of which contains a FRET cassette. In a preferred embodiment, the invasive cleavage assay combines two invasive signal amplification reactions (e.g., a "primary reaction" and a "secondary reaction") in series in a single reaction mixture. Reagents for the invasive cleavage assay may include a structure-specific 5' nuclease (e.g., FEN-1 endonuclease), an "invasive oligonucleotide," a "primary probe," and a "FRET cassette."

[0089] As used herein, the term "INVADER assay" refers to a structure-specific flap endonuclease cleavage assay (Hologic, Inc.), such as those described in, e.g., U.S. Patent Nos. 5,846,717; 5,985,557; 5,994,069; 6,001,567; 6,090,543; 6,872,816; 7,935,800; 9,133, 503; 9,096,893; Lyamichev et al., Nat. Biotech., 17:292 (1999); Hall et al., Proc. Natl. Acad. Sci. USA, 97:8272 (2000); Allawi et al., RNA (2004), 10:1153-1161 (2004), each of which is incorporated herein by reference in its entirety for all purposes.

[0090] As used herein, the term "invasive cleavage structure" (sometimes simply "cleavage structure") refers to an overlapping nucleic acid duplex structure that is a substrate for cleavage by a flap endonuclease (e.g., FEN-1 endonuclease). The enzyme-catalyzed cleavage reaction does not require any nucleic acid strand extension. In some embodiments, the invasive cleavage structure includes: (i) a continuous nucleic acid strand (e.g., a target DNA or target RNA); (ii) an upstream nucleic acid that hybridizes to a first portion of the target strand to form an upstream duplex (e.g., an invasive oligonucleotide, sometimes referred to as an INVADER oligonucleotide); and (iii) a downstream nucleic acid that hybridizes to form a downstream duplex (e.g., a 5' flap probe, or a primary probe oligonucleotide with a 5' flap that is not complementary to the target strand). The upstream and downstream nucleic acids anneal to adjacent regions of the target nucleic acid, forming an overlap between the 3' portion of the upstream nucleic acid and the duplex formed between the downstream nucleic acid and the target nucleic acid. When one or more bases from the upstream and downstream nucleic acids occupy the same position relative to the target nucleic acid base, overlapping occurs, regardless of whether the overlapping base(s) of the upstream nucleic acid are complementary to the target nucleic acid and whether the bases are natural or unnatural bases. In some embodiments, the 3' portion of the upstream nucleic acid that overlaps with the downstream duplex is a non-basic chemical moiety such as an aromatic ring structure (e.g., as disclosed in U.S. Pat. No. 6,090,543, the entire contents of which are incorporated herein by reference). In some embodiments, one or more of the nucleic acids can be attached to each other by a covalent linkage, such as a nucleic acid stem-loop, or by a non-nucleic acid chemical linkage (e.g., a multi-carbon chain). When the cleaved 5' flap hybridizes to the FRET cassette, an invasive cleavage structure is also created (e.g., the "target nucleic acid" and the "downstream nucleic acid" are covalently linked in a stem-loop configuration). The "target nucleic acid" sequence of the FRET cassette that hybridizes to the cleaved 5' flap can be referred to as the "cleaved flap hybridizing sequence."

[0091] In some embodiments, the target nucleic acid is amplified (e.g., by PCR), and the amplification product is detected using an invasive cleavage assay while the amplification reaction is occurring. Assays configured to perform a detection assay (e.g., an invasive cleavage assay) in combination with an amplification assay are described in U.S. Patent No. 9,096,893, which is incorporated herein by reference in its entirety for all purposes. In further embodiments, an RNA target nucleic acid can be reverse transcribed, amplified, and detected in a single reaction using an invasive cleavage assay, as described in International Publication No. WO 2006 / 050499, which is incorporated herein by reference in its entirety for all purposes.

[0092] As used herein, the term "probe oligonucleotide" refers to an oligonucleotide that interacts with a target nucleic acid to form a detectable complex. In some embodiments, the complex between the probe and the target is detected while it exists. In other embodiments, the formation of the complex can be detected when it no longer exists (e.g., by detecting an event, such as a cleavage event, that occurs as a result of the formation of the probe / target complex).

[0093] As used herein, the term "flap probe" refers to a probe oligonucleotide that includes a target-specific portion that specifically hybridizes to a target nucleic acid and a 5' flap portion that does not hybridize to the target nucleic acid. Typically, the 5' flap portion is not complementary to a region of the target nucleic acid adjacent to the duplex formed between the target nucleic acid and the target-specific portion of the flap probe.

[0094] As used herein with respect to a sequential invasive cleavage assay, a "primary probe" is a flap probe that includes a 3' sequence or portion complementary to a target nucleic acid to be detected and a 5' flap portion that is not complementary to the target nucleic acid (i.e., the non-complementary 5' flap portion does not hybridize to the target nucleic acid). The 5' flap portion is configured such that upon cleavage of the primary probe involved in the invasive cleavage structure in the "primary" reaction of the sequential invasive cleavage assay, the cleaved 5' flap released from the primary probe can hybridize to a FRET cassette to promote the secondary reaction of the sequential invasive cleavage assay.

[0095] As used herein, the term "primary reaction" generally refers to flap endonuclease cleavage of a primary probe, thereby generating a cleaved 5' flap. When a primary probe is cleaved with FEN-1 endonuclease, the sequence of the 5' flap cleaved from the primary probe typically comprises the 5' flap portion of the primary probe plus the first (5'-most) nucleotide of the target-specific portion of the primary probe.

[0096] As used herein, the term "secondary reaction" generally refers to hybridization of the cleaved 5' flap from the primary reaction to a FRET cassette to form a secondary invasive cleavage structure, and cleavage of the secondary invasive cleavage structure by a flap endonuclease to produce a detectable signal.

[0097] As used herein, a reaction is "active" if a reaction product is produced. For example, a secondary reaction is active when a reaction mixture containing the necessary components (e.g., a FRET cassette, a cleaved 5' flap specific to the FRET cassette, and a FEN enzyme) is incubated at a temperature that allows cycling hybridization of the cleaved 5' flap to the FRET cassette in the reaction mixture, resulting in cleavage of the FRET cassette and separation of the donor (e.g., fluorophore) and acceptor (e.g., quencher) moieties.

[0098] The term "invasive oligonucleotide" (sometimes "INVADER oligonucleotide") refers to an oligonucleotide that hybridizes to a target nucleic acid at a position near the hybridization region between the probe and target nucleic acid, and the invasive oligonucleotide includes a portion (e.g., a chemical moiety or nucleotide, whether or not complementary to the target) that overlaps the hybridization region between the probe and target. In some embodiments, the invasive oligonucleotide contains a sequence at its 3' end that is substantially the same as a sequence located at the 5' end of the probe oligonucleotide.

[0099] As used herein, the term "FRET" refers to fluorescence resonance energy transfer, a process in which chemical moieties (e.g., fluorophores) transfer energy between themselves or from a fluorophore to a non-fluorophore (e.g., a quencher molecule). In some situations, FRET involves an excited donor fluorophore transferring energy to a low-energy acceptor fluorophore via a short-range (e.g., about 10 nm or less) dipole-dipole interaction. In other situations, FRET involves a loss of fluorescence energy from the donor and an increase in fluorescence in the acceptor fluorophore. In yet other forms of FRET, energy can be exchanged from an excited donor fluorophore to a non-fluorescent molecule (e.g., a quencher molecule). FRET is known to those of skill in the art and has been described (see Stryer et al., 1978, Ann. Rev. Biochem., 47:819; Selvin, 1995, Methods Enzymol., 246:300; Orpana, 2004 Biomol Eng 21, 45-50; Olivier, 2005 Mutant Res 573, 103-110, each of which is incorporated herein by reference in its entirety).

[0100] As used herein, the term "FRET cassette" refers to an oligonucleotide containing a stem-loop or hairpin structure (i.e., a region of nucleic acid that intramolecularly base-pairs to form a double-helical stem, with a loop of nucleotides connecting the base-paired strands at one end of the stem) that includes a donor moiety (e.g., a "fluorophore") and a nearby acceptor moiety (e.g., a "quencher"), where attachment of the donor moiety and the acceptor moiety to the same FRET cassette substantially suppresses (e.g., quenches) detectable energy emission from the donor moiety (e.g., fluorescence emission). The FEN-1 enzyme catalyzes hydrolytic cleavage of the phosphodiester bond 3' adjacent to the junction of single- and double-stranded DNA, generally one nucleotide, toward the 5' end of the stem-loop portion of the oligonucleotide, releasing a 5' nucleotide or 5' flap from the stem-loop portion of the FRET cassette. The fluorophore moiety is typically attached to the 5' end or 5' flap of the FRET cassette oligonucleotide, and the quencher moiety is typically attached to the stem-loop portion of the oligonucleotide.

[0101] The "cleaved flap hybridizing sequence" of a FRET cassette refers to a nucleotide base sequence in the 3' portion of the FRET cassette that specifically hybridizes to the 3' end of a complementary nucleic acid or oligonucleotide, e.g., a 5' flap cleaved from a primary probe (the "primary cleavage flap"), such that when the flap cleavage product hybridizes to the FRET cassette, the 3' end of the complementary oligonucleotide is positioned to form an invasive cleavage structure (i.e., a substrate for a FEN enzyme) such that the cleavage site on the FRET cassette is located between the fluorophore moiety and the quencher moiety.

[0102] As used herein, the term "5' flap FRET cassette" refers to a FRET cassette oligonucleotide having a single-stranded 5' flap portion, a stem-loop portion, and a single-stranded 3' portion comprising a cleaved flap-hybridizing sequence, wherein the 5' flap portion and the cleaved flap-hybridizing sequence are not complementary to each other.

[0103] As used herein, the term "flapless FRET cassette" refers to a FRET cassette that does not have a single-stranded 5' portion, e.g., one or more non-complementary 5' nucleotides, and in which the 5' terminal nucleotide of the oligonucleotide is capable of base pairing as the last base pair on the non-loop end of the stem-loop portion of the FRET cassette.

[0104] Because amplification of the fluorescent signal from cleavage of the FRET cassette results from repeated or cycling hybridization of a complementary oligonucleotide (e.g., the 5' flap cleaved from the primary probe) to the cleaved flap-hybridizing sequence in the population of FRET cassettes, the primary probe is typically designed so that the cleaved 5' flap is not extendable by a polymerase using the FRET cassette as a template. For example, the primary probe is typically designed so that, when hybridized to a FRET cassette, it produces a 5' cleaved flap product having a 3' end that is not complementary to the cleaved flap-hybridizing sequence in the FRET cassette.

[0105] In some embodiments, a mixture of FRET cassettes having two or more different cleaved flap hybridizing sequences can be used (e.g., in a multiplex invasive cleavage reaction). Two cleaved flap hybridizing sequences are said to be "different" from one another if the cleaved flap product (e.g., under invasive cleavage assay conditions) is hybridizable to one cleaved flap hybridizing sequence but not measurably hybridizable to the other cleaved flap hybridizing sequence, or vice versa. Cleavage of the FRET cassette by a FEN enzyme (e.g., FEN-1 endonuclease) in a secondary reaction separates the donor and acceptor moieties, thereby relieving inhibition and allowing signal generation. In some embodiments, the donor and acceptor moieties interact via fluorescence resonance energy transfer (e.g., "FRET"). In other embodiments, the donor and acceptor of a FRET cassette interact via a non-FRET mechanism.

[0106] As used herein, an "interactive" label pair refers to a donor moiety and an acceptor moiety that are attached to the same FRET cassette and are in an energy transfer relationship with each other (i.e., via a FRET mechanism or a non-FRET mechanism). A signal (e.g., a fluorescent signal) can be generated when the donor moiety and the acceptor moiety are separated, for example, by cleavage of the FRET cassette in a secondary reaction. Different FRET cassettes that specifically hybridize to different cleaved 5' flaps can each contain the same interactive label pair.

[0107] As used herein, the term "unlabeled" when used with respect to a probe oligonucleotide refers to a probe oligonucleotide that does not contain a chromophore or fluorophore to facilitate detection. Unlabeled probes may contain modifications, such as a 3' blocking group, to prevent extension by a polymerase.

[0108] As used herein, the term "donor" refers to a moiety (e.g., a fluorophore) that absorbs at a first wavelength and emits at a second, longer wavelength. The term "acceptor" refers to a moiety, such as a fluorophore, chromophore, or quencher, that can absorb some or most of the energy emitted by the donor when the donor is in close proximity (typically 1-100 nm) to the donor group. The acceptor may have an absorption spectrum that overlaps with the emission spectrum of the donor. Generally, if the acceptor is a fluorophore, it re-emits at a third, longer wavelength. If the acceptor is a chromophore or quencher, it emits the energy absorbed from the donor without emitting a photon. In some preferred embodiments, changes in the energy levels of the donor and / or acceptor moieties are detected (e.g., by measuring energy transfer between or from the donor and / or acceptor moieties). This can include detecting emission. In some preferred embodiments, the emission spectrum of the acceptor moiety is different from the emission spectrum of the donor moiety such that emissions (eg, of light and / or energy) from the moieties can be distinguished (eg, spectrally resolved) from one another.

[0109] In some embodiments, a donor moiety is used in combination with multiple acceptor moieties. In preferred embodiments, a donor moiety is used in combination with a non-fluorescent quencher moiety and an acceptor moiety, such that when the donor moiety is close to the quencher (e.g., between 1 and 100 nm, or more preferably between 1 and 25 nm, or even more preferably about 10 nm or less), its excitation is transferred to the quencher moiety rather than the acceptor moiety, and when the quencher moiety is removed (e.g., by cleavage of the probe), excitation of the donor moiety is transferred to the acceptor moiety. In some preferred embodiments, emission from the acceptor moiety is detected (e.g., using wavelength-shifting molecular beacons) (see Tyagi et al., Nature Biotechnology 18:1191 (2000); Mhlanga and Malmberg, 2001 Methods 25, 463-471; Olivier, 2005 Mutant Res 573, 103-110, and U.S. Patent Application No. 20030228703, each of which is incorporated herein by reference in its entirety).

[0110] As used herein, the term "distinct" with respect to signals (e.g., one or more labels) refers to signals that can be distinguished from one another by spectral properties, such as, for example, fluorescence emission wavelength, color, absorbance, mass, size, fluorescence polarization characteristics, charge, etc., or by their ability to interact with another moiety, such as with a chemical reagent, enzyme, antibody, etc.

[0111] As used herein, the term "synthetic" when used with respect to a polynucleotide or oligonucleotide (e.g., a probe) refers to a nucleic acid produced in a cell-free in vitro reaction (e.g., an enzymatic or chemical synthesis reaction). Examples of enzymatic formation of synthetic nucleic acids include formation by restriction enzyme digestion, polymerization (templated or non-templated), ligation, etc. Examples of chemical synthesis of nucleic acids include, but are not limited to, phosphodiester and phosphotriester chemistry, phosphoramidite and H-phosphonate chemistry, etc. See, for example, Methods in Molecular Biology, Vol. 20: Protocols for Oligonucleotides and Analogs, pp. 165-189 (S. Agrawal, Ed., Humana Press, 1993); Oligonucleotides and Analogues: A Practical Approach, pp. 87-108 (F. Eckstein, Ed., 1991); and Uhlmann and Peyman, supra. See Agrawal and Iyer, Curr. Op. in Biotech. 6:12 (1995); and Anti-sense Research and Applications (Crooke and Lebleu; Eds., CRC Press, Boca Raton, 1993), Beaucage and Caruthers, Tetrahedron Lett. 22:1859-1862 (1981), and Agrawal and Zamecnik, U.S. Patent No. 5,149,798 (1992). In some embodiments, preformed synthetic oligonucleotides are introduced into the reaction, while in other embodiments, synthetic oligonucleotides are formed or modified in situ (e.g., by the action of a polymerase, ligase, cleavage enzyme, etc.).

[0112] As used herein, the term "flap endonuclease" or "FEN" (e.g., "FEN enzyme") refers to a class of nucleolytic enzymes that act as structure-specific endonucleases on DNA structures with a duplex containing a single-stranded 5' overhang or 5' flap on one strand that is displaced by the other strand of the nucleic acid such that there are overlapping nucleotides at the junction between the single-stranded and double-stranded DNA. FEN enzymes catalyze the hydrolytic cleavage of the phosphodiester bond adjacent to the 3' side of the junction between the single-stranded and double-stranded DNA, releasing the overhang or "flap" (see Trends Biochem. Sci. 23:331-336 (1998) and Annu. Rev. Biochem. 73:589-615 (2004)). FEN enzymes can be individual enzymes or multi-subunit enzymes. In certain embodiments, FEN enzyme activity can exist as the activity of another enzyme or protein complex, such as a DNA polymerase. In some preferred embodiments, the FEN enzyme does not have DNA polymerization activity (e.g., does not polymerize DNA even in the presence of a template, primer, and dNTPs). In other preferred embodiments, the FEN enzyme has DNA polymerization activity, but does not demonstrate this activity by extending an oligo (e.g., a 5' flap cleaved from a primary probe or derived from another source) in a manner that substantially precludes cycling hybridization to the FRET cassette. For example, a FEN enzyme involved in a secondary invasive cleavage reaction to cleave a fluorophore or fluorescent 5' flap from a FRET cassette does not extend the cleaved 5' flap from the primary probe (i.e., the invasive probe that reversibly hybridizes to the FRET cassette and catalyzes the cleavage reaction). The flap endonuclease may be thermostable. Examples of FEN enzymes useful in the methods disclosed herein are described in U.S. Pat. Nos. 5,614,402; 5,795,763; 6,090,606, and the published PCT applications identified in WO 98 / 23774; WO 02 / 070755; WO 01 / 90337; and WO 03 / 073067, each of which is incorporated by reference in its entirety.Specific examples of commercially available FEN enzymes include Cleavase® enzymes (Hologic, Inc.).

[0113] As used herein, "FEN-1" refers to the non-polymerase flap endonuclease from eukaryotic or archaeal organisms, which is encoded by the FEN-1 (flap structure-specific endonuclease 1) gene.See, for example, U.S. Patent No. 6,562,611 to Kaiser et al., and Kaiser MW et al. (1999) J.Biol.Chem., 274:21387; International Publication No. WO 02 / 070755 and U.S. Patent No. 7,122,364 (which are incorporated herein by reference in their entirety for all purposes).The term "FEN-1 activity" refers to any enzymatic activity of the FEN-1 enzyme. FEN-1 endonucleases also include modified FEN-1 proteins (e.g., chimeric proteins containing portions of FEN-1 enzymes from different organisms) and enzymes containing one or more mutations (e.g., substitutions, deletions, insertions, etc.), as described in WO 02 / 070755 and U.S. Patent No. 7,122,364. Archaeal organisms are any generally unicellular organisms of the biological kingdom Archaea.

[0114] References to "first," "second," "third," etc. (e.g., target nucleic acid, FRET cassette, invasive cleavage assay, etc.) do not necessarily indicate that one precedes the other, but merely provide identifiers to distinguish one from the other.

[0115] A "reaction mixture" is a combination of reagents (e.g., oligonucleotides, target nucleic acids, enzymes, etc.) in a single reaction vessel.

[0116] As used herein, a "multiplex" assay is a type of assay that detects or measures multiple analytes (two or more) in a single assay run. This is distinct from procedures that measure one analyte per reaction mixture. A multiplex invasive cleavage assay is performed by combining reagents for detecting or measuring two or more different analytes using independent invasive cleavage assays in a single reaction vessel. In some embodiments, the same species of fluorescent reporter is detected in each of the multiplex assays. In other embodiments, different species of fluorescent reporters are used, but the different reporters are detectable in the same channel of an instrument that detects a range of fluorescent wavelengths.

[0117] As used herein, the term "complementary" refers to a nucleic acid base sequence that can form a double-stranded hydrogen-bonding region. The nucleic acid base sequence can be "fully complementary" (i.e., each nucleic acid base in one sequence can pair with a corresponding nucleic acid base in a second sequence) or "partially complementary" (i.e., at least one nucleic acid base in one sequence cannot hydrogen bond with a corresponding nucleic acid base in a second sequence). The nucleic acid base sequences can be in the same or different polynucleotides.

[0118] As used herein, the terms "duplex" and "hybrid duplex" refer to a nucleic acid structure comprising a double-stranded hydrogen-bonded region. Such structures can be fully or partially double-stranded and include RNA:RNA, RNA:DNA, and DNA:DNA molecules and their analogs. By way of example, a "duplex" comprises a cleaved 5' flap sequence (e.g., a primary cleavage flap) hybridized to a complementary cleaved flap hybridizing sequence of a FRET cassette, and a cassette cleavage flap hybridized to a complementary masking oligonucleotide.

[0119] As used herein, the term "cleaved form" refers to a portion of a polynucleotide that has been cleaved from the remainder of the polynucleotide by the action of one or more nucleases. By way of example, a 5' flap sequence is "cleaved form" when the primary probe has been cleaved by an endonuclease (e.g., a FEN enzyme), thereby separating the 5' flap portion from the target-hybridizing portion of the flap probe.

[0120] As used herein with respect to a polynucleotide (e.g., an oligonucleotide, a target nucleic acid, etc.), the term "single-stranded state" refers to a region of the polynucleotide that is available for base pairing. In the case of a single-stranded polynucleotide having a self-complementary region, the term "single-stranded state" refers to the region of the self-complementary polynucleotide that is available for base pairing. For example, a cassette cleavage flap is in a single-stranded state before hybridizing to a masking oligonucleotide or after melting to separate the cassette cleavage flap from the masking oligonucleotide.

[0121] As used herein, the "temperature conditions" used to carry out a reaction refer to the temperature or temperature range that allows the reaction to occur. Different temperature profiles for different reactions mean that the temperature conditions that allow one reaction to occur may not allow a different reaction to occur. This term also applies to the temperature profile that allows the hybridization of a masking oligo to a complementary oligo sequence that contains a fluorophore moiety.

[0122] As used herein, "optimal" (and grammatical variations thereof) reaction conditions refer to the most favorable reaction conditions for promoting or allowing a reaction to occur. For example, the optimal temperature for carrying out a secondary reaction would be the temperature at which the FRET cassette is most efficiently cleaved in the reaction mixture (e.g., corresponding to a peak on a plot of the fluorescent signal as a function of reaction temperature). Similarly, an optimal temperature range is the range of most favorable temperature conditions for promoting or allowing a reaction to occur. In certain exemplary embodiments, a preferred optimal temperature range may include the optimal temperature plus or minus 5°C, more preferably plus or minus 4°C, more preferably plus or minus 3°C, even more preferably plus or minus 2°C, and even more preferably plus or minus 1°C.

[0123] As used herein, "attached" (e.g., two things are "attached") means chemically linked together. For example, a fluorophore moiety is "attached" to a FRET cassette if it is chemically bound to the structure of the FRET cassette.

[0124] As used herein, "equivalent" (e.g., in the context of "equivalent donor-acceptor pairs" or "equivalent donors" or "equivalent fluorophore" moieties) means that the excitation and emission spectra of the detectable chemical species are sufficiently similar or overlapping in wavelength range to permit detection of the fluorescent emission wavelengths within the same channel of an instrument used to monitor the signal.

[0125] As used herein, the term "spectral overlap" refers to two or more optical spectra that have at least one common wavelength.

[0126] As used herein, the emission from a donor moiety (e.g., a fluorophore) is "quenched" when an acceptor moiety (e.g., a quencher) is close enough to suppress or prevent the detectable emission of photons from the donor.For example, when both the donor moiety and the acceptor moiety are attached to the same FRET cassette, the emission from the donor moiety is quenched.Similarly, the emission from the donor or fluorophore moiety attached to the 5' flap cleaved from the FRET cassette can be quenched when the cleaved 5' flap (cassette cleavage flap) is hybridized to a complementary oligo containing a quencher moiety.

[0127] As used herein, "specific" means relating to only one (or only the specifically designated group), such as having a specific effect on or affecting only one (or only the specifically designated group) in a specific way. For example, a cleavage 5' flap specific to a FRET cassette (e.g., a primary cleavage flap) can hybridize to that FRET cassette, form an invasive cleavage structure, and promote the cleavage reaction, but cannot hybridize to a different FRET cassette (e.g., a FRET cassette with a different cleaved flap hybridization sequence) and promote the cleavage reaction. Similarly, a fluorescent 5' flap cleaved from a FRET cassette (a cassette cleavage flap) can hybridize to a masking oligonucleotide specific to that cassette cleavage flap if the sequences of the two oligonucleotides are complementary to each other.

[0128] As used herein, the term "specifically hybridize" means that under given hybridization conditions, a probe or primer detectably hybridizes substantially only to a target sequence in a sample containing the target sequence (i.e., there is little or no detectable hybridization to non-target sequences). Similarly, a cleaved 5' flap that is "specific" for a FRET cassette specifically hybridizes to that FRET cassette to form an invasive cleavage structure and can promote the cleavage reaction, but does not hybridize to a different FRET cassette in a manner that forms an invasive cleavage structure.

[0129] The term "thermostable," when used with respect to an enzyme, such as a FEN enzyme, indicates that the enzyme is functional or active (i.e., capable of performing catalysis) at elevated temperatures (e.g., about 55°C or higher). In some embodiments, the enzyme is functional or active at temperatures as high as 65°C or higher (e.g., 75°C, 85°C, or even 95°C).

[0130] As used herein, the term "amplified" refers to an increase in the abundance of a molecule, moiety, or effect. A target nucleic acid can be amplified by in vitro replication, such as by PCR.

[0131] As used herein, the term "amplification method" in reference to nucleic acid amplification refers to a process that specifically amplifies the abundance of a nucleic acid of interest. Some amplification methods (e.g., polymerase chain reaction or PCR) involve repeated cycles of heat denaturation, oligonucleotide primer annealing to a template molecule, and nucleic acid polymerase extension of the annealed primer. The conditions and time required for each of these steps are well known in the art. Some amplification methods are performed at a single temperature and are considered "isothermal." The accumulation of amplification product can be exponential or linear. Some amplification methods (e.g., "target amplification" methods) amplify the abundance of a target sequence by copying the target sequence multiple times (e.g., PCR, NASBA, TMA, strand displacement amplification, ligase chain reaction, LAMP, ICAN, RPA, SPA, HAD, etc.), while some amplification methods amplify the abundance of a nucleic acid species that may or may not contain a target sequence, but whose amplification indicates the presence of a specific target sequence in the reaction. Some signal amplification methods can increase the abundance of a nucleic acid species by converting the starting nucleic acid, for example, by cleaving it to form a cleavage product, or by extending it, for example, by polymerization or ligation. Target amplification methods can be applied to the signal molecule (e.g., PCR can be used to produce more copies of the product of a ligation, cleavage, or non-target copying reaction), or vice versa.

[0132] As used herein, the terms "polymerase chain reaction" and "PCR" refer to an enzymatic reaction in which a segment of DNA is replicated in vitro from a target nucleic acid. The reaction generally involves extending a primer on each strand of the target nucleic acid with a template-dependent DNA polymerase to produce a complementary copy of a portion of that strand. The chain reaction involves repeated cycles of denaturing the DNA strands, for example, by heating, followed by cooling to allow primer annealing and extension, resulting in the exponential accumulation of copies of the region of the target nucleic acid adjacent to and including the primer binding site. When an RNA target nucleic acid is amplified by PCR, it is generally converted into a DNA copy strand by an enzyme capable of reverse transcription. Exemplary enzymes include MMLV reverse transcriptase, AMV reverse transcriptase, and others familiar to those skilled in the art.

[0133] As used herein, the term "oligonucleotide" (e.g., deoxyribonucleotide or ribonucleotide) is defined as a molecule containing two or more nucleotides, preferably at least five nucleotides, more preferably at least about 10-15 nucleotides, and more preferably at least about 15-30 nucleotides or longer. Oligonucleotides are typically less than 200 residues in length (e.g., between 15 and 100 nucleotides), although as used herein, the term is intended to encompass longer polynucleotide chains as well. The exact size depends on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. Oligonucleotides are often referred to by their length. For example, a 24-nucleotide oligonucleotide is referred to as a "24mer." Oligonucleotides can form secondary and tertiary structures by self-hybridization or by hybridizing to other polynucleotides. Such structures can include, but are not limited to, duplexes, hairpins, cruciforms, bends, and triplexes. Oligonucleotides can be generated in any manner, including chemical synthesis, DNA replication, reverse transcription, PCR, or a combination thereof. In some embodiments, the oligonucleotide that forms the invasive cleavage structure is generated in a reaction (e.g., by extension of a primer in an enzymatic extension reaction). As used herein, the terms "oligonucleotide" and "polynucleotide" can be used interchangeably and can include non-naturally occurring monomers or portions thereof. More specifically, oligonucleotides can include linear or cyclic oligomers of natural and / or modified monomers or linkages, including, for example, deoxyribonucleosides, ribonucleosides, their substituted and alpha-anomeric forms, peptide nucleic acids (PNAs), locked nucleic acids (LNAs), 2'-O-methyl modifications, phosphorothioates, methylphosphonates, spacers, etc.

[0134] As used herein, a "signal" is a detectable quantity or impulse of energy, such as electromagnetic energy (e.g., light). The emission of light from an appropriately stimulated fluorophore is an example of a fluorescent signal. In some embodiments, a "signal" refers to the aggregate energy detected in a single channel of a detection instrument (e.g., a fluorometer).

[0135] As used herein, "background" signal refers to the signal (e.g., fluorescent signal) generated under the condition that target nucleic acid-specific reaction does not occur.For example, the signal generated in the secondary reaction that contains FRET cassette and FEN enzyme but does not contain cassette-specific invasive oligonucleotide (e.g., primary cleavage flap) is considered to be background signal.In some examples, background signal is measured in a "negative control" reaction or test that omits target nucleic acid.

[0136] As used herein, a "channel" of an energy sensor device, such as a device equipped with a light energy sensor, refers to a predetermined wavelength band that can be detected or quantified to the exclusion of other wavelength bands. For example, one detection channel of a fluorometer can detect the light energy emitted by one or more fluorescent labels over a wavelength range as a single event. The light emitted as a result of fluorescence can be quantified as relative fluorescence units (RFU) over a given wavelength or wavelength band. Examples of common fluorescence detection channels include those that detect fluorescence emission wavelengths in the ranges of approximately 510-530 nm (e.g., common to the "FAM" detection channel), approximately 560-580 nm (e.g., common to the "HEX" detection channel), approximately 610-650 nm (e.g., common to the "Texas Red" detection channel), approximately 675-690 nm (e.g., common to the "Cy5" detection channel), and approximately 705-730 nm (e.g., common to the "Quasar 705" detection channel). Cy5 and Alexa Fluor® 647 are examples of two different fluorophores that can be detected in the Cy5 channel of a fluorometer.

[0137] As used herein, " threshold " or " threshold cutoff " refers to the quantitative limit used to interpret experimental results, and results above and below the cutoff lead to different conclusions.For example, a measurement signal below a cutoff can indicate the absence of a specific target, while a measurement signal above the same cutoff can indicate the presence of that target.By convention, results that meet the cutoff (i.e., have the exact cutoff value) are given the same interpretation as results that exceed the cutoff.

[0138] As used herein, "threshold cycle number" refers to an indication of amplification that measures the time or cycle number when a real-time trial curve signal crosses a given value or threshold. Determining "TTime" and "Ct" are examples of threshold-based indications of amplification. Other methods include performing derivative analysis of the real-time trial curve. For purposes of this disclosure, TArc and OTArc can also be used to determine when a real-time trial curve signal crosses a given value (e.g., corresponding to a maximum or minimum angle of curvature, respectively). Methods for determining TTime are disclosed in U.S. Pat. No. 8,615,368, methods for determining Ct are disclosed in European Patent No. 0640828 B1, derivative-based methods are disclosed in U.S. Pat. No. 6,303,305, and methods for determining TArc and OTArc are disclosed in U.S. Pat. No. 7,739,054. Those skilled in the art will recognize variations that can also be used to determine threshold cycle number.

[0139] As used herein, an "internal calibrator" nucleic acid is a nucleic acid that can be amplified in an in vitro nucleic acid amplification reaction and is distinguishable from an analyte nucleic acid (e.g., a target nucleic acid from a test sample) co-amplified in the same reaction. "Internal" means that the calibrator nucleic acid is amplified and detected in the same reaction mixture as the analyte target nucleic acid or a fragment thereof. In some embodiments, the internal calibrator nucleic acid is amplified with the same primers used to amplify the analyte nucleic acid to be quantified. In other embodiments, different primers are used for this purpose. Generally speaking, the analyte nucleic acid and the internal calibrator nucleic acid differ by at least one nucleotide position that can be distinguished by an invasive cleavage reaction. This allows a multiplexed invasive cleavage assay to independently detect the amplified internal calibrator and analyte target nucleic acid.

[0140] As used herein, a "calibration standard" is a composition that contains a known or predetermined amount of an internal calibrator nucleic acid.

[0141] As used herein, a "reaction vessel" or "reaction receptacle" is a container for containing a reaction mixture. Examples include individual wells of a multi-well plate and plastic tubes (including, e.g., individual tubes within a formed linear array of a multi-tube unit). However, it should be understood that any suitable container can be used to contain the reaction mixture.

[0142] As used herein, "allowing" a reaction means that the reaction mixture provides reagents and conditions to test for the presence of a specific nucleic acid (e.g., target DNA or a cleaved 5' flap), which may or may not be present in the reaction mixture. For example, "allowing" a primary reaction of an invasive cleavage assay to occur means that the reaction mixture contains an invasive probe, a primary probe containing a 5' flap sequence, and an FEN enzyme under appropriate buffer and temperature conditions to allow cleavage of the primary probe and release of the cleaved 5' flap, provided that target DNA is also available in the reaction mixture to participate in the primary reaction. Similarly, "allowing" a secondary reaction of an invasive cleavage assay to occur means that the reaction mixture contains a FRET cassette and an FEN enzyme under appropriate buffer and temperature conditions to allow cleavage of the FRET cassette, provided that a cleaved 5' flap specific to the FRET cassette is also available in the reaction mixture to participate in the secondary reaction. Furthermore, temperature conditions that are "permitting" (or "permit" or "permissive") for a reaction to occur are temperature conditions that are conducive to causing or allowing a reaction to proceed.

[0143] "Kit" means a packaged combination of materials intended for use in conjunction with one another. Kits useful in accordance with the disclosed technology may include one or more containers or tubes containing various reagents. Kits may further include instructions or other information in "tangible" form (e.g., printed information, information recorded electronically on a computer-readable medium, or information recorded on a machine-readable medium such as a barcode).

[0144] Detailed Description This specification discloses a multiplexed nucleic acid amplification and detection system that can be used to detect the presence of multiple specific nucleic acid sequences in a temperature-dependent manner using only a single fluorescent detection channel of a nucleic acid analyzer. This technology simplifies the multiplexed detection of nucleic acid analytes, such as single nucleotide polymorphisms (i.e., "SNPs"), so that it can be used in diagnostic applications. Conveniently, this technology can be performed using standard PCR equipment equipped for fluorescent detection or monitoring.

[0145] The disclosed procedure uses a "masking oligo" that hybridizes via complementary base pairing to a fluorescently labeled 5' flap cleaved from a probe or FRET cassette (e.g., a cassette cleavage flap) in an invasive cleavage assay. The masking oligonucleotide includes a fluorescent quenching moiety (sometimes referred to herein as a "quencher") attached thereto. Upon hybridization between the masking oligonucleotide and the labeled cleaved flap, the quenching moiety of the masking oligo comes into close proximity with the fluorophore moiety of the cleaved 5' flap. The fluorescent signal emitted by the fluorophore of the cleaved 5' flap is then quenched. Hybridization of different cleavage products (e.g., cleaved flaps of different lengths and / or different sequences) to the cognate masking oligo at an appropriate temperature allows for the determination of the identity of the secondary reaction that liberated the cassette cleavage flap, and therefore, which target sequence was present in the reaction mixture.

[0146] Invasive cleavage reactions and assays Unlike other invasive cleavage assays in which cleavage of a FRET cassette generates a fluorescent signal indicative of the presence of an analyte nucleic acid, the present technique does not require the persistence of a fluorescent signal to determine whether a particular FRET cassette has been cleaved. In fact, the technique described herein actually requires that cleavage of at least one FRET cassette in a multiplex assay produces a fluorescent signal that is quenched or eliminated as a function of the temperature of the reaction mixture. This is achieved by including in the reaction mixture a masking oligonucleotide that is complementary to the fluorescent cleavage product of at least one FRET cassette. Hybridization to form a duplex containing the fluorescent cleavage product and the complementary masking oligonucleotide occurs at a melting temperature (T m ) is characterized by T m At higher temperatures, the fluorescent cleavage products are in a single-stranded state from which a fluorescent signal can be produced and detected or measured. m At lower temperatures, duplexes form and quench the fluorescence emitted from the fluorophore attached to the 5' flap cleaved from the 5' flap FRET cassette. By including different masking oligos complementary to the different fluorescent 5' flap cleavage products in the reaction mixture, the different duplexes resulting from hybridization of the masking oligonucleotides with the fluorescent cleavage products have different T m When the temperature-dependent difference in fluorescence signal is detected, it is possible to determine which FRET cassette, among multiple FRET cassettes labeled with fluorophores detectable in the same channel of a fluorometer, has been cleaved to generate a signal. This fluorescence quenching ability, or temperature-dependent difference in fluorescence signal, is essential for the function of the disclosed technology.

[0147] The invasive cleavage assay disclosed herein involves the formation of an invasive cleavage structure and enzymatic cleavage of the invasive cleavage structure by a flap endonuclease (e.g., FEN-1) enzyme. In some embodiments, the invasive cleavage structure comprises: (1) a FRET cassette; and (2) an invasive oligonucleotide hybridized to the FRET cassette. In some embodiments, the invasive oligonucleotide hybridized to the FRET cassette is a 5' flap cleaved from a primary probe. In some embodiments, the invasive cleavage assay comprises: (1) a target nucleic acid to be detected; (2) a primary probe having a 5' flap, wherein the target-complementary sequence of the primary probe hybridizes to the target nucleic acid; and (3) an invasive oligonucleotide hybridized to the target nucleic acid adjacent to and upstream of the hybridized primary probe. In some embodiments, the invasive cleavage assay sequentially combines a first and a second invasive cleavage reaction (see Figure 1), such that the 5' flap cleaved from the primary probe (e.g., sometimes the "primary cleavage flap") serves as an invasive oligonucleotide to facilitate enzymatic cleavage of the FRET cassette in the secondary reaction.

[0148] The invasive oligonucleotide upstream of the primary reaction is typically heated to a temperature substantially higher than the assay temperature (e.g., a T m The primary probe oligonucleotides are designed to anneal essentially permanently to the target DNA at a temperature close to the assay temperature, whereas the primary probe oligonucleotides do not. The portion of the primary probe that anneals to the target strand has a T m so that the primary probe oligonucleotides in the reaction mixture always anneal to and dissociate from the target strand at the reaction temperature without temperature cycling. mis within about 4°C, more preferably within 3°C, even more preferably within 2°C, and even more preferably within 1°C of the assay temperature. A cleavage structure is formed upon annealing of the primary probe oligonucleotide adjacent and downstream of the invasive oligonucleotide. This cleavage structure can be cleaved by a flap endonuclease.

[0149] An important feature and operating principle of the invasive cleavage reaction disclosed herein is that the number of cleavage products can increase and accumulate under isothermal conditions (i.e., without temperature cycling). For example, a primary probe oligonucleotide hybridized to a target nucleic acid can repeatedly anneal and dissociate without temperature cycling. A single site on the target DNA can be reused or recycled to hybridize to a series of new uncleaved probes without temperature cycling, generating thousands of cleaved probes for each target molecule. See, for example, Olivier, Mutat Res, 573:103-110 (2005). Similarly, the fluorescent signal resulting from FEN-1 cleavage of the FRET cassette after cycling hybridization from the primary probe to the cleaved 5' flap also increases and accumulates under isothermal conditions.

[0150] Invasive cleavage assays can also be configured to operate in a sequential manner, in which the cleaved flap from the primary invasive cleavage reaction is used to form a second cleavage structure. For example, Hall's SISAR assay uses two sequential signal amplification reactions to increase the total signal generated by the assay (see Hall et al., Proc. Natl. Acad. Sci., USA 97 (2000) 8272-8277). In the SISAR assay shown in Figure 1, cleavage of each primary probe releases a cleaved 5' flap ("primary cleavage flap" in Figure 1). The cleaved flap hybridizes to a hairpin "FRET cassette" oligonucleotide to form a second cleavage structure. Cleavage of the second cleavage structure separates the fluorophore dye from the quenching moiety of the FRET cassette, thereby allowing fluorescence from the fluorophore to be detected.

[0151] Invasive cleavage assays using FRET cassettes (e.g., sequential invasive cleavage assays) typically involve assays in which the cleaved flap-FRET cassette complex is at a T close to the assay temperature (e.g., within 4°C, more preferably within 3°C, even more preferably within 2°C, and even more preferably within 1°C of the assay temperature). m The cleaved flap is designed to have a constant annealing time, so that the cleaved flap constantly anneals and dissociates from the FRET cassette at the reaction temperature without temperature cycling. Annealing the cleaved flap to the FRET cassette forms a cleavage structure that can be cleaved by a flap endonuclease (e.g., FEN-1 endonuclease). Therefore, the secondary reaction involving cleavage of the FRET cassette generates signal using the same recycling principle as the primary reaction. Each cleaved flap can hybridize to a series of new, uncleaved FRET cassettes without temperature cycling, thereby generating thousands of unquenched fluorophores for each cleaved flap.

[0152] A flap endonuclease (e.g., FEN-1) enzyme present in a reaction mixture further containing a sample nucleic acid, an invasive probe, a primary probe, and a FRET cassette cleaves the 5' flap from the remainder of the primary probe when there is a one-base overlap between the invasive probe and the primary probe when both are hybridized to the sample nucleic acid. This cleavage reaction is referred to as the "primary" reaction. The 5' flap released from the primary probe then undergoes cycling hybridization to a FRET cassette having a complementary sequence, whereupon a FEN-mediated cleavage reaction separates the fluorophore from the quencher moiety present on the same FRET cassette, resulting in detectable fluorescence emission. This cleavage reaction, which generates a fluorescent signal by cleavage of the FRET cassette, is referred to as the "secondary" reaction. As described above, the secondary reaction removes the T fragment of the duplex between the 5' flap cleaved from the primary probe to facilitate cycling hybridization and the FRET cassette. mWhen performed at temperatures close to the melting temperature (i.e., the melting temperature), the same 5' flap is free to interact with a similar cognate FRET cassette to further catalyze the cleavage reaction. This linear amplification, which can occur at a fixed temperature, is detectable by the increase in fluorescence as a function of time. Each of the primary and secondary reactions is essentially isothermal. In fact, the FEN-1-dependent secondary invasive cleavage reaction generates a detectable fluorescent signal without the requirement for polymerization, even under thermal conditions where thermostable DNA polymerases (e.g., Taq DNA polymerase) exhibit significantly impaired polymerization activity. In fact, polymerase-based extension of the cleaved 5' flap using the FRET cassette as a template would impair cycling hybridization, which is beneficial for fluorescent signal accumulation. Therefore, extension of the cleaved 5' flap is contraindicated.

[0153] Useful fluorophores and quenchers In some embodiments, the multiplexed invasive cleavage assay according to the disclosed technology can use only a single detection channel to detect the fluorescent signals generated by the multiplexed invasive cleavage assay, and preferably uses the same chemical species of fluorophore for signal generation from different targets in the multiplexed reaction. In other embodiments, multiple different fluorophores can be combined for signal generation from different targets in the multiplexed reaction.Exemplary fluorophores for use in the FRET cassette systems of the disclosed technology include, but are not limited to, fluorescein, rhodamine, REDMOND RED dye, YAKIMA YELLOW dye, hexachloro-fluorescein, TAMRA dye, ROX dye, Cy3, Cy3.5, Cy5, Cy5.5, and Cy7, 4,4-difluoro-5,7-diphenyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, 4,4-difluoro-5,p-methoxyphenyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, 4,4-difluoro-5,p-methoxyphenyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, 4,4-difluoro-5-styryl-4-bora-3a,4a-di Aza-S-indacene-propionic acid, 6-carboxy-X-rhodamine, N,N,N',N'-tetramethyl-6-carboxyrhodamine, Texas Red, eosin, fluorescein, 4,4-difluoro-5,7-diphenyl-4-bora-3a,4a-diaza-S-indacene-3-propionic acid, 4,4-difluoro-5,p-ethoxyphenyl-4-bora-3a,4a-diaza-S-indacene-3-propionic acid, and 4,4-difluoro -5-Styryl-4-bora-3a,4a-diaza-S-indacene-propionic acid, 6-carboxyfluorescein (6-FAM), 2',4',1,4-tetrachlorofluorescein (TET), 21,4',51,7',1,4-hexachlorofluorescein (HEX), 2',7'-dimethoxy-4',5'-dichloro-6-carboxyrhodamine (JOE), 2'-chloro-5'-fluoro-7',8'-fused phenyl-1,4-dichloro 6-carboxyfluorescein (NED), 2'-chloro-7'-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC), fluorescein isothiocyanate (FITC), 5,6-carboxymethylfluorescein, Texas Red, nitrobenzo-2-oxa-1,3-diazol-4-yl (NBD), coumarin, dansyl chloride, amino-methylcoumarin (AMCA), erythrosine, BODIPY dyes, CASCADE BLUE dyes, OREGON GREEN dyes, pyrene, lissamine, xanthene, acridine, oxazine, phycoerythrin, QUANTUM dyes, thiazole orange-ethidium heterodimer, and the like.

[0154] Exemplary quenchers for use in the FRET cassette system of the present technology include, but are not limited to, cyanine dyes such as Cy3, Cy3.5, Cy5, Cy5.5, and Cy7, rhodamine dyes such as tetramethyl-6-carboxyrhodamine (TAMRA) and tetrapropano-6-carboxyrhodamine (ROX), DABSYL dyes, DABCYL dyes, cyanine dyes, nitrothiazole blue (NTB), anthraquinone, malachite green, nitrothiazole, or nitroimidazole compounds, QSY7 (Molecular Probes, Eugene, OR), ECLIPSE quencher (Epoch Biosciences, Inc., Logan, UT), and the like. Alternative quenchers include Black Hole quencher dyes, particularly BHQ-1, BHQ-2, and BHQ-3 (Biosearch Technologies, Petaluma, Calif.); BLACKBERRY® quencher (Berry & Associates, East Dexter, Mich.); IOWA BLACK® (Integrated DNA Technologies, Coralville, Iowa). Analysis of factors such as the absorbance and emission spectra of various molecules in selecting pairs or groups of moieties for use in a FRET configuration is well known to those of skill in the art.

[0155] One skilled in the art will recognize the wavelength ranges that can be detected by different channels of a fluorometer and can easily select fluorophores for different FRET cassettes such that emissions from different fluorophores can be detected in the same fluorometer channel.

[0156] Characteristics of temperature-dependent multiplexing technology Unlike previous invasive cleavage assays that benefit from the uninterrupted continuation of fluorescent signals, the disclosed technology benefits from selective suppression of fluorescence after FEN-1-mediated cleavage of the FRET cassette. Peterson et al., in their published application 2018 / 0163259 A1, disclosed a method in which different FRET cassettes labeled with the same fluorophore were cleaved at different temperatures, essentially isolating one reaction from the other. Monitoring the accumulated fluorescent signal as a function of time or cycle number allowed resolution of the FRET cassette activity. In this way, multiple nucleic acid targets could be detected in a multiplexed format using only a single channel of a fluorometer, even using only a single type of fluorescent label. As disclosed herein, the technology relies on temperature-dependent fluorescence quenching to effectively remove the contribution of fluorescent signals arising from different FRET cassettes, even when the different FRET cassettes have identical fluorescent labels. Therefore, procedures or events performed after FRET cassette cleavage are beneficial in the disclosed technology.

[0157] This technique uses at least one FRET cassette structured to include a 5' flap portion that retains the fluorophore after cleavage by the FEN-1 enzyme in the secondary reaction. Preferably, the 5' flap length ranges from 8 to 30 nucleotides, more preferably 8 to 25 nucleotides, and even more preferably 8 to 16 nucleotides. Particularly preferred 5' flap lengths are 9, 10, 11, 12, 13, 14, or 15 nucleotides. Figure 1 illustrates a sequential invasive cleavage reaction in which the FRET cassette is a flapless FRET cassette that does not include a 5' flap portion, and cleavage in the secondary reaction releases a fluorescent dye attached to a single nucleotide. In contrast, a 5' flap FRET cassette (see Figure 2A) can hybridize by cycling hybridization to the cleaved flap from the primary probe (see Figure 2B) to generate a structure that can be cleaved by the FEN-1 enzyme. The resulting cassette cleavage flap emits a fluorescent signal when in a single-stranded state, but the signal can be reversibly suppressed or quenched by hybridization of the cassette cleavage flap to a masking oligo containing a quenching moiety (see Figure 2C). The hybrid interaction between the cassette cleavage flap and the masking oligo can be controlled in a temperature-dependent manner. When used in the same reaction mixture, the flapless FRET cassette and the 5' flap FRET cassette can produce a signal that can be resolved by temperature change after the cleavage reaction has occurred.

[0158] In addition to distinguishing the origin of fluorescence from flapless FRET cassettes (without a 5' flap) and 5' flap FRET cassettes, the disclosed technology also allows for the resolution of signals originating from identical fluorescent dyes in different 5' flap FRET cassettes. Figure 3 shows a schematic of how the fluorescent signals produced by three different FRET cassettes (flapless FRET cassette; 5' flap FRET cassette 1; and 5' flap FRET cassette 2), each labeled with a fluorophore (e.g., the same fluorophore) detectable in the same channel of a fluorometer, can be distinguished from one another under different temperature conditions. The top of the figure shows the flapless FRET cassette without a 5' flap. This FRET cassette can be cleaved by FEN-1 endonuclease to release the fluorescent dye after cycling hybridization to the complementary cleavage flap from the primary probe, and the fluorescence emitted from the released dye cannot be quenched by interaction with any masking oligonucleotide used in the reaction. The fluorescence emitted from this unquenched dye is detectable at all temperatures. The center of the diagram in Figure 3 shows the first 5' flap FRET cassette (5' flap FRET cassette 1) that can be cleaved by the FEN-1 enzyme to release a 5' flap ("Cassette Cleavage Flap 1") after cycling hybridization to a complementary cleavage 5' flap from the primary probe. Cassette Cleavage Flap 1 remains attached to the fluorophore after the cleavage reaction, but the fluorescent signal is quenched when Cassette Cleavage Flap 1 hybridizes to a complementary masking oligo. This is the T of the hybrid duplex containing Cassette Cleavage Flap 1 and the complementary masking oligo. m This can occur at temperatures lower than T m ("T mWhen the 5' flap FRET cassette (5' flap FRET cassette 2) is cleaved by the FEN-1 enzyme to release a 5' flap ("Cassette Cleavage Flap 2") after cycling hybridization to a complementary cleavage 5' flap from the primary probe, the fluorescent signal can be quenched. Cassette Cleavage Flap 2 remains attached to the fluorophore after the cleavage reaction, but the fluorescent signal is quenched when Cassette Cleavage Flap 2 hybridizes to a complementary masking oligo. This is the T of the hybrid duplex containing Cassette Cleavage Flap 2 and the complementary masking oligo. m (This can occur at temperatures lower than T m ("T m When the T rises above the T threshold (T 2 ) and cassette cleavage flap 2 becomes single-stranded ("unquenched cassette cleavage flap 2" in the figure), a fluorescent signal can be emitted by the fluorophore of cassette cleavage flap 2. m By designing different 5' flap FRET cassettes to have 5' flap portions with different lengths and / or G:C content, signals resulting from different cleavage flaps can be distinguished from one another. For example, (1) the fluorophore of only one of the cassette cleavage flaps can be designed to emit a signal at a time, or (2) the signals emitted by the fluorophores of different cassette cleavage flaps can be monitored as a function of temperature to determine melting profiles. Both of these alternatives are demonstrated in the working examples herein.

[0159] In particular, in procedures using multiple different 5' flap FRET cassettes and masking oligos, the T of a hybrid duplex containing the 5' flap cleavage products ("cassette cleavage flaps") and the cognate masking oligos is determined. mPreferably, the T of different hybrid duplexes analyzed in the same multiplex reaction (e.g., real-time nucleic acid amplification reaction or end-point melting / annealing analysis procedure) should be different. m The T of the hybrid duplex containing the cassette cleavage flap and the cognate masking oligo differs by at least 2°C, more preferably at least 3°C, more preferably at least 5°C, more preferably at least 7°C, more preferably at least 10°C, or even at least 15°C. m A preferred difference between the T and C ranges from 2° C. to 20° C., more preferably from 5° C. to 20° C., more preferably from 5° C. to 15° C., or even more preferably from 5° C. to 10° C. In some embodiments, the 5′ flap of the masking oligonucleotide and / or FRET cassette oligonucleotide is greater than the T of the masking oligonucleotide-cassette cleavage flap duplex. m For example, in some embodiments, the one or more nucleotide modifications are selected from the group consisting of locked nucleic acids (LNA), peptide nucleic acids (PNA), bridged nucleic acids (BNA), 2'-O alkyl substitutions, L-enantiomeric nucleotides, or combinations thereof.

[0160] Figure 4 shows a schematic of the identification of different target sequences by detecting FEN-1-mediated cleavage products of different FRET cassettes, each of which has a fluorescent dye that can be detected in the same channel of a fluorometer (e.g., the same HEX fluorophore is shown). The cleavage products and masking oligos shown correspond to those shown in Figure 3. The fluorophore-containing cleavage product from the flapless FRET cassette (top) indicates the presence of Target 1 and remains unquenched at all temperatures. Thus, at temperatures below Temperature 1, where Cassette Cleavage Flap 1 and Cassette Cleavage Flap 2 hybridize to their respective masking oligos, detectable fluorescence indicates the presence of Target 1. The fluorophore-containing cleavage product from the 5' flap FRET cassette 1, indicating the presence of Target 2 (middle), is unquenched at temperatures above Temperature 1. At temperatures above Temperature 1 and below Temperature 2, detectable fluorescence can indicate the presence of Target 1 and Target 2. Because the fluorescence signals measured in the procedure are additive, the difference between the fluorescence signal measured at a temperature higher than Temperature 1 but lower than Temperature 2 (center of Figure 4) and the fluorescence signal measured at a temperature lower than Temperature 1 (top of Figure 4) indicates the signal due to the presence of Target 2. The fluorophore-containing cleavage product from 5' flap FRET cassette 2, indicating the presence of Target 3 (bottom), is not quenched at temperatures higher than Temperature 2. At temperatures higher than Temperature 2, detectable fluorescence can indicate the presence of Target 1, Target 2, and Target 3. Therefore, the difference between the fluorescence signal measured at a temperature higher than Temperature 2 (bottom of Figure 4) and the fluorescence signal measured at a temperature higher than Temperature 1 but lower than Temperature 2 (center of Figure 4) indicates the signal due to the presence of Target 3. In this figure, Temperature 1 < Temperature 2 < Temperature 3. Comparison of the results of fluorescence detection at different temperatures can be used to determine which target was involved in promoting the cleavage reaction(s). In some embodiments, this involves comparing the magnitude of the fluorescent signals, where the signals measured at different temperatures are the additive result of the known detectable fluorescence, as described above. In some embodiments, determining which targets were involved in promoting the cleavage reaction(s) involves performing a melting / annealing curve analysis.

[0161] Result Processing and Equipment The procedures disclosed herein can be performed using conventional laboratory equipment for amplifying nucleic acids and monitoring amplicon production, including equipment with an integrated or stand-alone computer or processor programmed with appropriate software. Included within the meaning of "computer" is an embedded processor controlled by software. The computer can be programmed by either the manufacturer or the end user to perform one or more temperature changes or steps, preferably allowing for monitoring of fluorescence within the reaction mixture as the amplification reaction cycles. Preferably, the reaction mixture is contained within a reaction vessel (e.g., a tube or well of a multiwell plate) held within the nucleic acid amplification device. However, it is also possible to complete analysis of the amplification product after the amplification reaction is complete (e.g., to establish a melting / annealing curve of the amplification product). This latter analysis can even be completed outside the device that amplifies the nucleic acids.

[0162] The computer component of an apparatus useful for implementing the disclosed techniques can be programmed with software instructions that cause the computer to perform specific steps. These steps can include controlling a thermocycler that amplifies nucleic acids; receiving input from a fluorometer that monitors fluorescence emissions in a reaction mixture in which FRET cassette cleavage occurs in an invasive cleavage reaction; or processing the results to determine which of two or more FRET cassettes cleaved to generate a fluorescent signal. In preferred embodiments, the FRET cassettes are cleaved to generate fluorescent cleavage products, and the fluorescence produced by the different cleavage products can be detected or measured in a single channel of a fluorometer. In some embodiments, different FRET cassettes are labeled with the same fluorophore. A computer can also be used to perform mathematical steps (e.g., addition, subtraction, multiplication, and / or division) that lead to a determination of which FRET cassette in a mixture was cleaved to generate a detectable or measurable fluorescent signal.

[0163] The methods disclosed herein can be performed using automated nucleic acid analysis equipment, such as devices that amplify nucleic acids and monitor the production of nucleic acid amplification products. These analysis equipment includes PCR instruments or real-time PCR instruments that can be programmed to perform a series of temperature cycling steps. Preferably, the PCR instrument is equipped with a fluorometer that monitors the progress of the reaction occurring in tubes or wells of a multiwell plate (commonly referred to as reaction "receptacles"). Instruments configured to perform and monitor real-time PCR reactions are particularly preferred for use with the disclosed techniques. One example of a preferred instrument for performing, monitoring, and evaluating results obtained using the disclosed techniques is the Panther Fusion System (Hologic, Inc.; San Diego, CA), which advantageously automates procedural steps. Another preferred instrument is the ABI 7500 Real-Time PCR System (ThermoFisher Scientific; New York).

[0164] One common approach to assessing the state of fluorescent cleavage products in a mixture of a flapless FRET cassette and one or more 5' flap FRET cassettes involves assessing the cleavage of the two FRET cassettes separately. This procedure involves raising the temperature of the reaction mixture to the lowest T for any duplex formed between the masking oligonucleotide and the fluorescent cleavage product of the 5' flap FRET cassette in the mixture. m This may involve reducing the fluorescence signal to less than 100%. As a result, the residual fluorescence signal originates from the unquenched fluorescent cleavage product and therefore exhibits a constant value in a first derivative plot of the change in fluorescence as a function of temperature. Therefore, the presence of an unquenched fluorescent cleavage product can be indicated by measuring or detecting the residual fluorescence signal (e.g., a specific signal above background fluorescence) when the fluorescence from other fluorescent cleavage products is quenched as a result of duplex formation with the masking oligonucleotide. Detection of the fluorescence signal under these conditions indicates the presence of an unquenched fluorescent cleavage product in the reaction mixture and, consequently, cleavage of the corresponding FRET cassette. In a second step, a temperature-dependent melting / annealing curve (sometimes referred to as a "quenching profile") can be generated for the reaction mixture containing the fluorescent cleavage product, from which a derivative plot can be generated. For example, a first derivative plot of the change in fluorescence as a function of temperature contains peaks or maxima corresponding to the different duplexes present in the reaction mixture, and duplex formation quenches the signal from the fluorescent cleavage product contained therein. In this way, it is possible to determine which FRET cassette was cleaved to produce the fluorescent cleavage product.

[0165] Exemplary systems are demonstrated herein using the multiplex detection of either two or three analytes using invasive cleavage of different FRET cassettes, each carrying a fluorescent label that can be detected or monitored in a single channel of a fluorometer or fluorescence monitoring device. In some embodiments, multiple FRET cassettes are used in the multiplex procedure. For example, two different FRET cassettes can be combined in a single reaction mixture, with only one of the FRET cassettes having a 5' flap sequence complementary to a masking oligonucleotide included in the same reaction mixture. The other FRET cassette can be a flapless FRET cassette that does not contain any 5' flap sequence, or alternatively, a 5' flap FRET cassette in a reaction mixture that does not contain a complementary masking oligonucleotide. In such cases, the fluorescent signal resulting from cleavage of only one of the two FRET cassettes will undergo temperature-dependent fluorescence quenching. As described above, the fluorescent signal generated by cleavage of the FRET cassette remains substantially constant when the temperature of the reaction mixture is changed, provided that the fluorescent cleavage product does not interact with any masking oligonucleotide to quench the fluorescence. Detection of the unquenched fluorescent cleavage product can include detecting a fluorescent signal (e.g., a fluorescent signal above background) at a temperature at which the formation of a duplex containing the masking oligonucleotide quenches the fluorescent signals from all other quenched fluorescent cleavage products monitored in the same fluorescent channel in the reaction mixture. Detection of the quenched fluorescent cleavage product in the multiplex reaction mixture can be performed by detecting the T at which fluorescence quenching is maximal. m T for masking oligoduplex formation compared to lower temperatures m This may involve simply establishing that at higher temperatures there is a greater measurable fluorescent signal.

[0166] In a different embodiment, the multiplex reaction mixture contains two different FRET cassettes, each containing a cleavable 5' flap sequence, and the fluorescent signal emitted by each cleaved 5' flap can be quenched by hybridization to a different complementary masking oligonucleotide. Determining which FRET cassette has been cleaved in the reaction mixture can involve derivative analysis, preferably a first derivative plot of the melting / annealing curves described above. This approach allows multiple cleavage products to be resolved and identified in a single procedure.

[0167] In some embodiments, the multiple invasive cleavage reaction comprises three or more different FRET cassettes, each labeled with a fluorescent label (e.g., all fluorescent labels may be the same) detectable in a single channel of a fluorometer. Each FRET cassette may have a different cleavable 5' flap sequence that emits a fluorescent signal after cleavage, and may quench the fluorescent signal in a temperature-dependent manner after hybridization of a complementary masking oligonucleotide. The duplexes formed by hybridization of the different fluorescent cassette cleavage flaps have different T mWhen a duplex is characterized by a specific temperature, its identity can be readily determined by assessing its melting / annealing characteristics (e.g., using derivative analysis). This is shown below using a first derivative plot to detect and identify a duplex containing a fluorescent cleavage product hybridized to a masking oligonucleotide. Furthermore, one of the FRET cassettes used in a multiplex reaction can produce a fluorescent cleavage product that does not quench in the reaction mixture. In this situation, some cleavage products exhibit fluorescence quenching at different temperatures, while others do not, so the sum of the cleavage products still exhibits different temperature-dependent fluorescence quenching profiles. In practical terms, different cleavage products can be distinguished by monitoring the fluorescence signal as the temperature of the reaction mixture is changed. This may involve monitoring the fluorescence signal when the temperature is changed from a high to a low state (e.g., to allow annealing of complementary strands to form a duplex) or from a low to a high state (e.g., to promote melting of a preformed duplex). For this reason, the temperature-dependent fluorescence quenching profile is sometimes referred to as a "melting / annealing" curve or profile.

[0168] The results from the differential quenching of the fluorescent cleavage products produced in multiple invasive cleavage reactions can be analyzed by different approaches to determine which alternative FRET cassettes were cleaved to produce a fluorescent signal detectable in a single channel of a fluorometer or fluorescence detection device. Two preferred analytical approaches that can be automated (e.g., by a computer, processor, or controller) include: (1) assessing the difference between fluorescence readings or measurements at temperatures at which different fluorescent cleavage products undergo greater or less fluorescence quenching due to masking oligonucleotide hybridization; (2) assessing the difference between the characteristic melting temperatures (i.e., "T") of the duplex, e.g., the melting temperatures of the duplex. m") to evaluate the fluorescence quenching profile (i.e., fluorescence measured as a function of temperature in the presence of a complementary masking oligonucleotide). In certain preferred embodiments, a combination of these different approaches can be used to elucidate which of multiple different FRET cassettes has been cleaved in a reaction mixture, where the different cleavage products have fluorophores that are detected in the same channel of a fluorometer. In some embodiments, the different FRET cassettes have the same fluorophore. For example, a reaction mixture containing fluorescent cleavage products that do not interact with the masking oligonucleotide to result in quenching, along with one or more fluorescent cleavage products that hybridize to the cognate masking oligonucleotide, preferably includes the T of a duplex comprising the masking oligonucleotide and the complementary fluorescent cleavage product of the 5' flap FRET cassette. m Fluorescence measured at higher temperatures and its T m The fluorescence is analyzed by evaluating the difference from the fluorescence measured at a lower temperature, as well as a derivative plot (eg, a first derivative plot) of the change in fluorescence as a function of temperature.

[0169] Cleavage of a FRET cassette in a multiplex invasive cleavage assay to generate two fluorescent cleavage products, if only one undergoes temperature-dependent quenching, can be determined by assessing fluorescence emission at two temperatures, or alternatively, by using this assessment approach together with curve analysis to determine the T m The duplex can be analyzed by identifying it by: Fluorescent cleavage products that cannot be quenched in the reaction mixture remain uniformly fluorescent over the measured temperature range and therefore have a constant slope (i.e., a slope of zero) on a plot of fluorescence as a function of temperature. A plot of the first derivative of fluorescence as a function of temperature can be used to determine the T of any duplex. m In contrast, the first derivative plot, which indicates the presence of fluorescent cleavage products that have undergone temperature-dependent quenching (i.e., due to masking oligonucleotide hybridization), does not show any maximum indicating T of the duplex containing the fluorescent cleaved 5' flap.m Furthermore, simple evaluation of the fluorescence signal measured at two temperatures can indicate the presence or absence of each of the two fluorescent cleavage products. More specifically, the fluorescence indicates the T of the duplex in the reaction mixture. m One higher temperature (i.e., the temperature at which there is no fluorescence quenching) and the T of the duplex in the reaction mixture m It can be measured or detected at a second, lower temperature (ie, the temperature at which the duplex is formed; complete fluorescence quenching).

[0170] In some instances, a single unquenched fluorescent cleavage product (e.g., resulting from cleavage of a flapless FRET cassette or a cassette cleavage flap in the absence of a complementary masking oligonucleotide) is present in a reaction mixture with one or more quenchable fluorescent cleavage products. A fluorescent cleavage product that is not subject to quenching by masking oligonucleotide hybridization produces a detectable fluorescent signal in a fluorometer channel that is greater than the T of a duplex containing other fluorescent cleavage products that exhibit maximal fluorescence quenching in the fluorometer channel. m If the fluorescence is measured at a lower temperature, it is determined to be present. In other words, measurable fluorescence (i.e., a specific signal above the background signal threshold) at the point where the duplex quenches the fluorescence from other cleavage products in the reaction mixture indicates the presence of a fluorescent cleavage product that is not subject to quenching by masking oligonucleotide hybridization. m The fluorescence signal measured at a higher temperature (e.g., the temperature at which fluorescence quenching is minimal) is T m If the fluorescence signal measured at a lower temperature (ie, the temperature at which fluorescence quenching is complete) exceeds that measured at a lower temperature, it can be determined that a fluorescent cleavage product is present that is quenched by masking oligonucleotide hybridization.

[0171] In some embodiments, it may be desirable to use a combination of both approaches, particularly when multiple distinct fluorescent cleavage products that are quenched by masking oligonucleotide hybridization are combined with one fluorescent cleavage product that is not quenched. In such cases, melting / annealing curves are generated and evaluated by derivative analysis to determine the T of the fluorescence-quenching duplex. m The presence of a quenchable fluorescent cleavage product can be determined by detecting the T of the quenchable fluorescent cleavage product. Similarly, points on the melting / annealing curve corresponding to complete fluorescence quenching and / or the absence of fluorescence quenching can be used for the above evaluation. More specifically, the presence of a fluorescent cleavage product that does not undergo quenching can be evaluated at a low temperature where quenching by masking oligonucleotide hybridization is complete. Detecting a residual fluorescent signal when quenching is complete (i.e., maximum) in the reaction mixture indicates the presence of an unquenched fluorescent cleavage product. A single quenchable fluorescent cleavage product indicates the T of duplex formation. m T of duplex formation compared to fluorescence readings at lower temperatures (e.g., when the duplex is formed and stable) m Higher fluorescence readings at higher temperatures (eg, in the absence of duplexes) indicate the presence of quenchable fluorescent cleavage products.

[0172] A reaction mixture containing more than one different fluorescent cleavage product, each of which is quenched by masking oligonucleotide hybridization, can be used to identify any duplex Ts that may be present in the mixture. m This can be conveniently evaluated by processing the results of the melting / annealing curve using derivative analysis to identify the T of the duplex between the masking oligonucleotide and the complementary fluorescent cleavage product. For example, the melting / annealing curve can be processed to calculate the first derivative, and then a first derivative plot of the change in fluorescence as a function of temperature can be established. Peaks or maxima on the first derivative plot represent the T of the duplex between the masking oligonucleotide and the complementary fluorescent cleavage product. m Each of the duplexes corresponds to a different T mWhen characterized by: , it becomes possible to detect duplexes independently of each other. Higher order derivatives are also contemplated to identify duplexes and determine which of multiple FRET cassettes are cleaved to generate a fluorescent signal. As described elsewhere herein, T for different duplexes can be used to facilitate distinction between one duplex and the other duplex(es). m It is desirable to separate the temperature difference by a minimum of one.

[0173] Software that allows the computer to process the results and determine which FRET cassettes in the mixture of FRET cassettes that produced cleavage products are encompassed by the above description. [Example]

[0174] Example Described herein is a technique for multiplexed detection using at least one 5' flap FRET cassette (i.e., a FRET cassette having a 5' flap portion), wherein the 5' flap portion bears a fluorescent label. The signal emitted from the fluorescent label after cleavage of the 5' flap FRET cassette by FEN-1 endonuclease in an invasive cleavage assay can be selectively quenched based on temperature. In some embodiments, the invasive cleavage assay includes both a primary and a secondary invasive cleavage reaction. In some other embodiments, the invasive cleavage assay includes a secondary invasive cleavage reaction without a primary invasive cleavage reaction. It should be understood that FEN-1-mediated cleavage physically separates the fluorophore and quencher portions of the 5' flap FRET cassette onto different oligonucleotide molecules, thereby alleviating the fluorescence quenching characteristic of intact 5' flap FRET cassettes. The quenching of the fluorescence emitted from the cleaved 5' flap is mediated by the temperature-dependent hybridization of the cleaved 5' flap to a complementary masking oligonucleotide having a quencher moiety.With this approach, the quenchable flap is not part of any probe that hybridizes to the target nucleic acid to be detected.Instead, the quenchable flap can be a product of a linear amplification reaction that occurs under isothermal conditions without polymerization.

[0175] According to the present disclosure, 5' flap FRET cassettes reporting different target molecules can be detected using single-channel fluorescence detection. The fluorescent labels of different FRET cassettes can be the same. In some embodiments, the same fluorescent label is used in FRET cassettes with different 5' flaps. Different fluorescent labels can be used instead of the same label, provided that the different labels can be detected in the same fluorescent channel of an optical detector (e.g., a fluorometer). In all cases, cleavage of the FRET cassette to produce a fluorescent signal was mediated by the FEN-1 enzyme (i.e., non-polymerizing flap endonuclease). The 5' flap cleaved from the primary probe plays a catalytic role in the cleavage of the FRET cassette, meaning that the 5' flap transiently hybridizes to the FRET cassette, promoting cleavage to release the fluorescent signal, and then dehybridizes to allow the cleaved flap to interact with a new FRET cassette. The 5' flap cleaved from the primary probe hybridized to the nucleic acid target to be detected preferably does not have a fluorophore moiety.

[0176] Example 1 demonstrates how two different nucleic acid sequences (analyte A and sample B) were amplified and detected in the same reaction mixture using either single-channel or dual-channel fluorescence detection. Amplification was by polymerase chain reaction (PCR). The products of the PCR reaction were detected using an invasive cleavage reaction using a fluorescently labeled FRET cassette. Sample A was detected using a FRET cassette with a first label (hexachloro-fluorescein or "HEX") that was detectable in the HEX channel of the fluorometer component of a real-time PCR instrument. Sample B was detected using one of two different FRET cassettes in the same reaction mixture, each with a different label. The first 5' flap FRET cassette used to detect sample B had a second label that was also detectable in the HEX channel of the PCR instrument. The signal emitted by the label attached to the 5' flap cleaved from this FRET cassette indicated the presence of analyte B and was subjected to quenching after hybridizing the cleaved 5' flap of the FRET cassette to a complementary masking oligo. The second FRET cassette for detecting analyte B contained a label detectable in the ROX channel of the PCR instrument, and the fluorescent signal emitted after cleavage was not quenched. Notably, the signal detected in the ROX channel of the real-time amplification and detection instrument was substantially undetectable in the HEX channel of the instrument, and vice versa. In other words, the fluorescent HEX signal was substantially undetectable in the ROX channel, and the fluorescent ROX signal was substantially undetectable in the HEX channel. The results established that each of the two analyte nucleic acids could be amplified, and the synthesis of different amplification products could be monitored using fluorophores detected in the same or different optical channels of the PCR instrument.

[0177] Example 1 Single-channel or dual-channel fluorescence detection of two analyte nucleic acids in a single reaction Reaction mixtures were prepared in duplicate, each containing a lyophilized composition incorporated into an aqueous reconstitution buffer. The lyophilized composition contained dNTPs, a thermostable DNA polymerase (e.g., Taq DNA polymerase; Promega Corporation, Madison, Wisconsin), a FEN-1 flap endonuclease enzyme (e.g., Cleavase 2.0; Hologic Inc., Marlborough, Massachusetts), oligonucleotides, and trehalose. The oligonucleotides in the lyophilized composition included a pair of primers for each of the two analyte nucleic acids to be detected, a primary probe with a 5' flap non-complementary to the analyte sequence to be amplified and / or detected, and a FRET cassette that could be cleaved by the FEN-1 enzyme after hybridization of the 5' flap cleaved from the primary probe. In this example, the oligonucleotide that promoted cleavage of the 5' flap from the primary probe also served as a primer in the nucleic acid amplification reaction. In an isothermal cycling hybridization reaction, two different primary cleavage flaps (one from each of the primary probes complementary to analyte A and analyte B) were reversibly hybridized to three different FRET cassettes. FRET cassette 1 (used to detect analyte A) was a flapless FRET cassette labeled with a HEX fluorophore and a BlackBerry quencher moiety (Berry & Associates; Dexter, MI). After cleavage of FRET cassette 1, the emission signal from the HEX fluorophore was detectable in the HEX channel of the instrument used to amplify nucleic acids and monitor the progress of the amplification reaction. FRET cassette 1 did not have a 5' flap sequence. FRET cassette 2, also containing no 5′ flap but a flapless FRET cassette labeled with a CAL Fluor Red 610 fluorophore (Biosearch Technologies, Inc.; Novato, CA) and a BHQ®-2 quencher moiety (Biosearch Technologies, Inc.), was used to detect analyte B.After the cleavage reaction, the emission signal from the CAL Fluor Red 610 fluorophore was detectable in the ROX channel but not the HEX channel of the instrument used to amplify the nucleic acid and monitor the progress of the amplification reaction. FRET cassette 3, which was also used to detect analyte B, contained a BHQ® quenching moiety (Biosearch) attached to the hairpin. The 5' flap FRET cassette 3 was labeled on the 5' flap with a CAL Fluor® Orange 560 fluorophore quenched with Biosearch Technologies, Inc. After the cleavage reaction, the emission signal from the CAL Fluor® Orange 560 fluorophore was detectable in the HEX channel of the instrument used to amplify the nucleic acid and monitor the progress of the amplification reaction. A masking oligonucleotide complementary to the 5' flap of FRET Cassette 3 and containing a BHQ® quenching moiety (Biosearch Technologies, Inc.) was included in the reaction mixture at a 3-fold molar excess relative to FRET Cassette 3.

[0178] The target analytes, FRET cassette configurations, and detection channels used in this procedure are summarized in Table 1. [Table 1]

[0179] Amplification reactions using the detection system shown in Table 1 contained either the analyte A target alone, the analyte B target alone, or a combination of the analyte A and analyte B targets. A "no target" negative control reaction contained all reagents but no added template. Each reaction contained all three FRET cassettes and masking oligonucleotides. Thermal cycling and fluorescence monitoring were performed using an ABI 7500 Real-Time PCR System instrument (ThermoFisher Scientific; Grand Island, NY). Reaction conditions included 10 cycles of 95°C for 120 seconds, 69°C for 5 seconds, 67°C for 5 seconds, 65°C for 6 seconds, and 72°C for 5 seconds. This was followed by 40 cycles of 95°C for 10 seconds, 69°C for 5 seconds, 67°C for 5 seconds, and 65°C for 25 seconds. Fluorescence emission data were collected for the ROX and HEX channels of a real-time PCR instrument at a temperature at which the masking oligo remained unhybridized to the 5' flap released from FRET cassette 3. Fluorescence signals were measured in the HEX and ROX channels as a function of cycle number for reactions containing both sample B and sample A. The ROX channel signal (data not shown) yielded a sigmoidal curve reflecting the cycle-dependent increase in signal, indicating that sample B was amplified in the PCR reaction. The HEX signal reflected the combined signal from the amplification of sample B and sample A but did not distinguish between one and the other (data not shown). HEX and ROX fluorescence signals were independently detectable in multiplex reactions amplifying sample B and sample A.

[0180] Figures 5A-5C display the signal measured in the HEX channel as a function of cycle number for reactions containing the analytes individually or in combination, as indicated. The graph in Figure 5A confirms that amplified analyte A can be detected without the addition of analyte B template, exhibiting a characteristic sigmoidal curve for signal accumulation for this analyte. Figure 5B displays the signal measured in the HEX channel showing amplification of the analyte B template in the absence of analyte A template. The monotonic signal accumulation curve in this case lacked the sigmoidal characteristics of the curve shown in Figure 5A. Figure 5C shows the signal detected in an amplification reaction containing both analyte A and analyte B templates in a single reaction. Here, the signal measured in the HEX channel increased to produce an elongated sigmoidal curve, representing the combined signal produced by the analyte A and analyte B FRET cassettes measured in a single channel of the fluorometer. In this case, signals produced by non-identical fluorophores were detected in a single (i.e., the same) channel of the fluorometer. As discussed elsewhere herein, melting / annealing curve analysis and analysis of the curve shape (eg, first derivative analysis) can be used to deduce the identity of the analyte giving rise to each different result.

[0181] Example 2 demonstrates a procedure for resolving the identity of different analyte nucleic acids in a multiplex amplification reaction mixture using a masking oligonucleotide to quench the signal from the 5' flap FRET cassette used to detect analyte B. Only the fluorescence emitted from the label of the cleaved 5' flap complementary to the masking oligo was subject to quenching.

[0182] Example 2 Endpoint melting / annealing curve analysis distinguishes amplified targets The post-PCR reaction mixture from Example 1 was subjected to melting / annealing curve analysis on the same real-time PCR instrument used for nucleic acid amplification. This involved monitoring the magnitude of the fluorescent signal in the HEX channel of the real-time PCR instrument as the temperature was varied from 90° C. to 21.4° C.

[0183] The results of post-amplification melting / annealing curve analysis are shown in Figure 6. These data confirm that the cleavage product of the FRET cassette specific for the detection of analyte A, with a HEX channel signal generated from the flapless FRET cassette that cannot be quenched by the masking oligonucleotide, remained uniformly fluorescent as a function of temperature (i.e., across the temperature range shown). In contrast, the HEX channel signal generated after cleavage of the 5' flap FRET cassette 3 specific for the detection of analyte B in the presence of a masking oligonucleotide containing a quenching moiety, exhibited temperature-dependent fluorescence quenching. More specifically, fluorescence in reaction mixtures spiked with only the analyte B template was effectively quenched as the temperature approached 20 °C, resulting in a decrease in the fluorescence signal toward 500,000 RLU. Experimentally, we observed that virtually all of the fluorescence was quenched at temperatures below 40 °C. In reactions containing both analyte A and analyte B templates, the signal in the HEX channel was essentially a combination of the individual temperature profiles. More specifically, the melting / annealing curve profile followed that of the analyte B template reaction, but the addition of unaltered fluorescence due to the presence of analyte A in the template reaction resulted in an overall increase in signal. As the temperature approached 20°C, the signal indicating the presence of analyte B was quenched, and the fluorescence in the mixed reaction approached the signal level observed in the analyte A-only reaction. As shown, fluorescence peaked at approximately 63°C in the reaction mixture containing the analyte B template and decreased above 63°C. While not wishing to be bound by a particular theory of operation, masking oligo hybridization is thought to occur due to the T of the 5' flap masking oligonucleotide duplex. m This decrease in fluorescence above 63 °C may be due to a temperature-dependent buffering effect on the fluorophore, as it should decrease or be completely lost at substantially higher temperatures (e.g., 10 °C-20 °C higher).

[0184] The results obtained using the invasive cleavage system for multiplexed detection of nucleic acid analytes disclosed herein can be processed in different ways to determine the presence or absence of the analytes in a test sample. For example, the fluorescence signal measured at two different temperatures (e.g., 63°C and 30°C) in a single channel (e.g., the HEX channel of the fluorometer in this figure) can be compared to a threshold value to establish the presence or absence of each of the two different analytes. The threshold value can be established in advance (i.e., before performing the assay) or at the time the assay is performed (e.g., using one or more calibration standards with one or more analytes to be detected). This analytical method can be used to determine the presence or absence of 2.2 x 10 6 RFU and 1 × 10 6 An exemplary threshold value in RFU can be shown using the results in Figure 6. Under these parameters, 2.2 x 10 6 A fluorescence reading above RFU indicated the detection of analyte B, while a reading below this threshold indicated the absence of analyte B. 6 RFU and 2.2 × 10 6 A fluorescence reading between RFU indicated the presence of analyte A and the absence of analyte B. Similarly, or alternatively, at 30°C, 1 x 10 6 A fluorescence reading above 1 × 10 RFU indicated the presence of analyte A. Such a reading would not signal the presence of analyte B, since the fluorescence from the cleaved 5' flap, which indicates the presence of that analyte, was virtually completely quenched at that temperature. 6 A fluorescence reading below RFU indicates the absence of analyte A.

[0185] Derivative-based data analysis techniques can be used in place of or in combination with the threshold-based analysis described above. For example, a data plot associated with the presence of analyte A (see FIG. 6) may have a constant slope (e.g., 0 slope) and a slope of approximately 5×10 5The fluorescence magnitude is at least two-fold greater than the background fluorescence in RFUs. This fluorescence magnitude (e.g., measured at the temperature where fluorescence quenching in the reaction mixture is maximized) can be used to indicate the presence of analyte A. A data plot related to the presence of analyte B exhibited a first derivative maximum in the range of approximately 50°C to 58°C and a zero crossing (i.e., an x-axis crossing indicating zero slope) at approximately 63°C. Any data set exhibiting these characteristics can be interpreted as indicating the presence of analyte B. In some embodiments, the fluorescence magnitude at a specific temperature can be used for threshold-based analysis, and the temperature-dependent rate of change in fluorescence can be used for derivative-based data analysis; the two analyses can be combined to determine the presence or absence of each of multiple analytes that may be present in the assay reaction.

[0186] Taken together, the above results and discussion demonstrated that unique profiles characterized the melting / annealing curves for each of the three different starting target conditions (i.e., analyte A only, analyte B only, or a combination of analyte A and analyte B). These data indicate that endpoint melting / annealing curve analysis using a single detection channel readily resolved the presence of one or more targets in the reaction mixture.

[0187] The preceding examples demonstrated the detection of two different amplified nucleic acid target sequences using invasive cleavage reactions in real-time and end-point format nucleic acid analysis. Fluorescent signals for the different amplified targets were detected (e.g., as a function of time or cycle number) in a single optical channel (i.e., the HEX channel) of the fluorometer component of the instrument, which monitored nucleic acid amplification as the reaction occurred. This procedure demonstrated that a hybrid duplex containing a masking oligonucleotide and a cleaved flap containing a fluorescent label was generated at the T of the duplex. m It is stable at lower temperatures and has a duplex T mThis exploited the fact that fluorophores are unstable at higher temperatures. Results established that maximum quenching was observed at approximately 39 °C and minimum quenching at approximately 63 °C. Collectively, the results shown in Figures 5 and 6 demonstrate how multiple different nucleic acid analytes can be detected and resolved from one another in a multiplex reaction mixture using only a single optical channel of a fluorometer. This was achieved using different fluorophore species detected in the same optical channel of a fluorometer, although a single fluorophore species could be used instead (e.g., as demonstrated below). Furthermore, those skilled in the art will understand how different fluorescent labels can be substituted for the exemplary labels above and how instrument channels other than the HEX channel can be used for the detection of those labels.

[0188] Example 3 describes a procedure for detecting the presence or absence of multiple analytes using real-time monitoring and only a single optical channel of a PCR instrument's fluorometer. Here, the cycling procedure included a temperature step in which fluorescence quenching by masking oligonucleotides allowed for the determination of the presence or absence of each of the two analytes. More specifically, fluorescence readings were determined at 63°C and 39°C during the cycles of the PCR procedure. As shown below, this technique distinguished dual signals measured in a single optical channel in a real-time format. This procedure can be advantageously used to quantify each of the detected analytes, following standard procedures for processing real-time amplification trial curves by determining the cycle number at which a threshold level of amplification is achieved (e.g., Ct value). The determined Ct value can then be compared to a calibration plot or formula relating the threshold value and the amount or concentration of the analyte nucleic acid. An alternative real-time procedure can establish whether the analyte nucleic acid is present in a multiplex reaction mixture above or below a specified (e.g., predetermined) amount or concentration level. This can involve determining whether a specific level of reaction progression (e.g., as measured by Ct value) is achieved by a specified number of cycles. In particular, where the previous example used two different fluorophores detected in the same light channel of a fluorometer linked to a PCR instrument, here the same fluorophore is used to detect two different analytes.

[0189] Example 3 Real-time monitoring of multiplex amplification using a single fluorophore species The reaction mixture for the real-time amplification protocol was prepared as follows: Serial dilutions of plasmid DNA containing the target sequence of sample A were prepared from a standard stock solution. Wild-type bacterial genomic DNA containing the target sequence of sample B served as the source of template nucleic acid for amplification of that sample. The lyophilized pellet described in Example 1 was reconstituted with aqueous buffer and then spiked with each of the 5' flap FRET cassettes and corresponding masking oligonucleotides specific for the detection of sample B. Again, cleavage of the FRET cassette in the reaction mixture was catalyzed by the primary cleavage flap from the primary probe.

[0190] Four reaction mixtures were prepared in duplicate using multiwell PCR plates (one plate each to demonstrate high- and low-temperature monitoring). The negative control mixture received no nucleic acid template for either analyte A or analyte B. The second set of mixtures received only bacterial genomic DNA containing the analyte B template, but not the analyte A plasmid. The third set of mixtures received only the analyte A plasmid, but not the bacterial genomic DNA containing the analyte B template. The fourth set of mixtures received both the bacterial genomic DNA containing the analyte B template and the analyte A plasmid. All runs contained a threefold excess of masking oligo relative to the corresponding 5' flap FRET cassette used to detect analyte B. PCR reactions involving monitoring of the fluorescent signal generated by invasive cleavage of the FRET cassette were performed on an ABI 7500 real-time PCR instrument using either the first set of cycling conditions with fluorescence monitoring at 63 °C ("high" temperature monitoring) or the second set of cycling conditions with fluorescence monitoring at 39 °C ("low" temperature monitoring). The cycling conditions used for high-temperature (63°C) fluorescence monitoring were as follows: (1) 95°C for 120 seconds; (2) 95°C for 15 seconds, 69°C for 5 seconds, 67°C for 5 seconds, 65°C for 6 seconds, and 72°C for 25 seconds x 10 cycles (initial Taq optimization stage); (3) 95°C for 10 seconds, 69°C for 5 seconds, 67°C for 5 seconds, 65°C for 5 seconds, and 63°C for 25 seconds x 40 cycles. The cycling conditions used for low-temperature (39°C) fluorescence monitoring were as follows: (1) 95°C for 120 seconds; (2) 95°C for 15 seconds, 69°C for 5 seconds, 67°C for 5 seconds, 65°C for 6 seconds, and 72°C for 25 seconds x 10 cycles (initial Taq optimization stage); (3) 95°C for 10 seconds, 69°C for 5 seconds, 67°C for 5 seconds, 65°C for 5 seconds, and 39°C for 25 seconds x 40 cycles. A total of 50 cycles of fluorescence monitoring at high and low temperatures were performed.

[0191] The results of the procedure are shown in the real-time PCR amplification plots in Figures 7A-7D. The most interesting results were from runs performed using the sample B template alone or in combination with the sample A template. Reactions using the sample A template alone served as controls and are not shown in the figures.

[0192] Figures 7A and 7B show analyte B-specific fluorescence as a function of cycle number; fluorescence was determined in the HEX channel of a PCR instrument at 63°C (no fluorescence quenching) or 39°C (fluorescence quenched by the masking oligonucleotide). An increase in fluorescence above background was evident at 63°C, starting at approximately cycle 12 and continuing through cycle 40, as shown in Figure 7A. As shown in Figure 7B, fluorescence measurements taken at 39°C remained at background levels throughout the procedure. These data confirmed that quenching of the analyte B fluorescence signal was essentially complete at lower temperatures due to hybridization of the cleaved flap to the complementary masking oligonucleotide. The fluorescence observed at lower temperatures (39°C) in the plot of Figure 7B was due to background fluorescence and not a signal indicating the presence of analyte B.

[0193] Figures 7C and 7D show real-time trial curve results obtained by monitoring the fluorescence signal produced in reactions that amplified and detected a combination of analyte B and analyte A template nucleic acids. The curve shown in Figure 7C, in which fluorescence readings were measured during a temperature step at 63 °C, reflects the combined contributions from the fluorescence produced from cleavage of both FRET cassettes. Only cleavage of the FRET cassette, indicating the presence of analyte B, produced a fluorescent flap sequence that could be hybridized with a masking oligonucleotide, which had the effect of quenching the fluorescent signal at 39 °C. As shown in Figure 7C, the fluorescence signal measured during the 63 °C temperature step (i.e., without fluorescence quenching) began to rise above background levels at approximately cycle 11 and entered a log-linear phase by approximately cycle 19. The rate of fluorescence increase began to taper off by approximately cycle 29, although the signal magnitude continued to increase. The curve shown in Figure 7D reflects fluorescence readings measured during a temperature step at 39 °C. The signal from the cleaved flap, indicating the presence of analyte B, was efficiently quenched at this temperature, so the fluorescence measured in Figure 7D was solely from the cleavage reaction, indicating the presence of analyte A.

[0194] Taken together, the results presented in Figures 7A-7D demonstrate that a single reaction mixture can be used to detect multiple target nucleic acids using real-time monitoring of only a single fluorescence detection channel (e.g., monitoring emission from a single fluorophore species), and that each target can be distinguished by monitoring fluorescence emission at different temperatures. When the disclosed technique was performed, one temperature corresponded to the condition of fluorescence quenching (i.e., substantially complete or maximal quenching of fluorescence resulting from the cleaved flap). Detection of analyte B demonstrated this condition. Different temperatures in the procedure did not quench the fluorescence resulting from the cleaved flap.

[0195] Although the reactions used to produce the results shown in Figures 7A-7D were run sequentially on the same instrument (i.e., fluorescence measurements were taken during either the 63 °C step or the 39 °C step), it is preferable to monitor a single reaction mixture for fluorescence at both temperature steps to simplify the detection of multiple analytes in the system. Again, this is possible because detection of analyte B signal was effectively eliminated from double-positive samples (i.e., samples with analyte B and analyte A) by fluorescence quenching, thereby leaving only the signal indicating the presence of analyte A.

[0196] As described above, results from real-time monitoring of a multiplex reaction mixture can be used to quantify the analyte nucleic acid or determine whether the analyte nucleic acid is present in an amount greater than or less than a threshold amount or concentration (which may be, for example, zero concentration). In some embodiments, quantifying the analyte nucleic acid can involve comparing the determined Ct value to a calibration plot or equation relating Ct value and analyte concentration. In other embodiments, determining whether the analyte nucleic acid is present in an amount greater than or less than a threshold amount or concentration can involve determining whether the time-dependent fluorescence value reaches a certain level of reaction progress by a specified time or number of cycles. Using the data from Figures 7A-7D as an example, a qualitative determination of the presence or absence of an analyte can involve determining whether a fluorescence reading of at least 500,000 RFU (relative fluorescence units) is achieved by 30 PCR cycles. The fluorescent signal in Figures 7B and 7D due to detection of analyte B is effectively eliminated by fluorescence quenching. The increase in signal observed in the plot of Figure 7A compared to the plot of Figure 7B indicates a contribution of fluorescence due to detection of analyte B, thereby confirming the presence of that target in the reaction mixture. Thus, comparing the results obtained from Figures 7A and 7B indicates that the reaction mixture contained only analyte B, and no analyte A. The increase in signal observed in the plot of Figure 7C compared to the plot of Figure 7D indicates the contribution of fluorescence from the detection of analyte B in that reaction mixture. Again, the remaining fluorescence plotted in Figure 7D is attributable to the signal resulting from the detection of analyte A. Thus, comparing the results obtained from Figures 7C and 7D indicates that the reaction mixture contained both analyte A and analyte B. A similar process can be used to assess the presence or absence of three different analytes.

[0197] Example 4 describes a procedure for detecting three different analyte nucleic acid sequences in a single reaction mixture using an invasive cleavage reaction, in which three FRET cassettes were labeled with the same fluorophore (i.e., HEX). Of course, other fluorophores that can be detected in the same or different single optical channels of a fluorometer in optical communication with the instrument that amplifies the nucleic acids can be used in place of the HEX fluorophore.

[0198] Example 4 Multiplexed detection of three analyte nucleic acids using a single type of fluorophore Invasive cleavage detection of three PCR-amplified analyte nucleic acids was performed using three different sets of oligonucleotides in the same reaction mixture. Each set of detection oligonucleotides was used to detect a different one of the three analytes (Analyte A, Sample B, and Sample C). Each assay reaction used: (1) a unique primary probe with a target-specific binding sequence and a unique 5' flap that was not complementary to the target amplification product being detected; (2) a unique oligonucleotide (referred to as the "invasive primer") that served as the invasive oligonucleotide to cleave the 5' flap from the primary probe when the primary probe hybridized to its cognate target nucleic acid and further functioned as a primer in the amplification reaction; and (3) a unique FRET cassette. Each of the three different FRET cassettes was labeled with a HEX fluorophore and a quencher moiety. The FRET cassette used to indicate the presence of Sample A did not contain a 5' flap hybridized by any masking oligo in the reaction mixture. More specifically, the invasive primers, primary probe, and flapless FRET cassette of Example 1 were used to detect analyte A. The FRET cassettes for detecting analytes B and C contained 5' flap sequences. The FRET cassettes are shown in Figure 3 along with the associated cleavage flaps from the primary probe and masking oligos used in the procedure above. The FRET cassette systems for detecting analytes A, C, and B appear at the top, middle, and bottom of the figure, respectively.

[0199] The multiplex reaction mixture contained two different masking oligonucleotides, one complementary to the 5' flap of the FRET cassette used to detect analyte B and one complementary to the 5' flap of the FRET cassette used to detect analyte C. Each masking oligonucleotide contained a quenching moiety at its 5' end. The FRET 5' flap masking oligonucleotide duplex for analyte B had a GC content of approximately 60%, and the FRET 5' flap masking oligonucleotide duplex for analyte C had a GC content of approximately 40%. The two duplexes were composed of different T m The cleavage product of the 5' flap FRET cassette and the complementary masking oligonucleotide used to detect analyte B formed a more stable duplex for "high temperature" detection, whereas the cleavage product of the 5' flap FRET cassette and the complementary masking oligonucleotide used to detect analyte C formed a less stable duplex for "low temperature" detection.

[0200] Individual reaction mixtures contained all assay oligonucleotides (including all three FRET cassettes) along with all reagents necessary for PCR amplification of the three analyte nucleic acids, cleavage of the primary probes specific for the different analyte nucleic acids, and cleavage of the corresponding FRET cassettes. Reactions contained either analyte A alone, analyte B alone, analyte C alone, or a combination of analytes A, B, and C. Thermal cycling conditions were as follows: (1) 95°C for 120 s x 1 cycle; (2) 95°C for 15 s, 69°C for 5 s, 67°C for 5 s, 65°C for 6 s, and 72°C for 25 s x 10 cycles (initial Taq optimization stage); and (3) 95°C for 10 s, 69°C for 5 s, 67°C for 5 s, and 65°C for 25 s x 40 cycles. Melting / annealing curve analysis after amplification over a temperature range from 90°C to 20.7°C was performed on an ABI 7500 real-time PCR instrument.

[0201] Figure 8 shows the post-amplification melting / annealing curve results for reactions performed using each of the three analyte polynucleotides individually or in combination with each other. The results confirmed that each of the four reactions yielded a unique melting / annealing curve profile, thereby demonstrating successful single-channel multiplexing of three analytes using a single type of fluorophore.

[0202] The results shown in the two panels of Figure 9 demonstrate the unique melting / annealing curve profiles observed for additional analyte combinations. The left panel of Figure 9 shows the melting / annealing curve results for reactions in which analytes B and C were amplified individually. The results demonstrate how the cleaved 5' flaps from each of the FRET cassettes (where the cleaved 5' flaps hybridized to different masking oligos) can be distinguished using only a single fluorescence monitoring channel of the real-time PCR instrument. The right panel of Figure 9 shows the melting / annealing curve analysis results for reactions in which either analyte B alone, analyte C alone, or the combination of analyte B and analyte C were amplified. Again, the results demonstrate how the cleaved 5' flaps from each of the FRET cassettes (where the cleaved 5' flaps hybridized to different masking oligos) can be distinguished from each other using only a single fluorescence monitoring channel of the real-time PCR instrument.

[0203] Figure 10 presents first derivative plots of the measured fluorescence data shown in the two panels of Figure 9. The left panel of Figure 10 shows the first derivative plot of the melting / annealing curve shown in the left panel of Figure 9. The maximum value of the first derivative plot of fluorescence as a function of temperature corresponds to the melting temperature (T m ) is shown. In this case, the T mThe melting / annealing curves were separated from each other by approximately 10°C (i.e., approximately 46°C for the detection of analyte C and approximately 56°C for the detection of analyte B). This distinction between the two melting / annealing curves made it possible to resolve which of the two analytes was present in the reaction mixture being analyzed. A single maximum observed or detected at approximately 46°C indicates the presence of analyte C, and a single maximum at approximately 56°C indicates the detection of analyte B. The right panel of Figure 10 shows the first derivative of the melting plot that appears in the right panel of Figure 9. Each of the different curves had unique features that allowed us to distinguish reaction mixtures containing analyte B, analyte C, or a combination of analytes B and C. Because the fluorescent signal resulting from the presence of analyte A is not quenchable as a function of temperature (i.e., there is no masking oligo complementary to the FRET cassette cleavage product), there is no effect on the first derivative (i.e., a constant first derivative is 0).

[0204] In the above example, a test sample was analyzed for the presence of two different analytes using derivative analysis of melting / annealing curves. First-order derivative calculations were used here for illustrative purposes. However, second-order or even higher-order derivative analysis is contemplated for this purpose. This procedure involved detecting or monitoring fluorescent signals in an amplification reaction mixture using only a single channel of the fluorometer component of a real-time nucleic acid amplification device. The plot can represent the first derivative of raw data, but alternatively, it can represent the first derivative of processed data (e.g., smoothed, normalized to a constant maximum reading, etc.). Detection of a peak or maximum in the first derivative plot at 46°C indicated the presence of analyte C or its amplification product. Detection of a peak or maximum in the first derivative plot at 56°C indicated the presence of analyte B or its amplification product. Detection of peaks at both 46°C and 56°C (e.g., high-level signals at both of these temperatures) indicated the presence of both analyte C and analyte B, or their amplification products. In some embodiments, the analysis can include identifying signals greater than a threshold (e.g., a pre-established threshold, or a threshold based on a fraction or percentage of the normalized maximum). While the examples show the use of first-derivative analysis, second-derivative analysis can be used instead. Here, the maximum on the first-derivative plot corresponds to the zero-crossing point on the second-derivative plot. Detecting the presence of analyte A did not rely on derivative analysis because the FRET cassette used to detect this analyte did not contain a 5' flap sequence complementary to any masking oligo. Cleavage of this FRET cassette resulted in a fluorescent signal that remained stable over the temperature range used for melting / annealing curve analysis. The presence of analyte A in the test sample was reflected by the magnitude of fluorescence at the temperature at which the signal resulting from cleavage of other FRET cassettes (e.g., for detecting analyte B and / or analyte C) was quenched (e.g., approximately 30°C in the plot of Figure 10).

[0205] All literature and similar materials cited in this application, including but not limited to patents, patent applications, papers, books, articles, and Internet web pages, are expressly incorporated by reference in their entirety for any purpose. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which the various embodiments described herein belong. If the definition of a term in an incorporated reference appears to be different from the definition provided in the present teachings, the definition provided in the present teachings shall prevail.

[0206] Various modifications and variations of the described compositions, methods, and uses of the present technology will be apparent to those skilled in the art without departing from the scope and spirit of the described technology. Although the present technology has been described in connection with specific exemplary embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in biochemistry, molecular biology, or related fields are intended to be within the scope of the following claims. In certain embodiments, for example, the following are provided: (Item 1) 1. A composition comprising a FRET cassette reporter system, said composition comprising: (i) a 5' flap FRET cassette oligonucleotide, a 5' flap portion comprising a first fluorophore moiety; and a stem-loop portion comprising a first quencher moiety; a 3' portion comprising a cleaved flap hybridizing sequence, hybridization of a cassette-specific invasive oligonucleotide complementary to the cleaved flap hybridizing sequence of the 5' flap FRET cassette oligonucleotide forms an invasive cleavage structure cleavable by a FEN-1 endonuclease at a cleavage site between the first fluorophore moiety and the first quencher moiety; a 5' flap FRET cassette oligonucleotide, wherein cleavage of the 5' flap FRET cassette oligonucleotide at the cleavage site produces a cassette cleavage flap comprising the 5' flap portion and the first fluorophore moiety; and (ii) a masking oligonucleotide comprising a second quencher moiety, at least a portion of the masking oligonucleotide is capable of specifically hybridizing to the 5' flap portion of the FRET cassette oligonucleotide; hybridization of the masking oligonucleotide to the cassette cleavage flap forms a duplex having a first melting temperature exhibiting a first melting peak; a masking oligonucleotide, wherein the fluorescent emission from the first fluorophore moiety in the duplex is quenched by the second quencher moiety; and A composition comprising: (Item 2) 2. The composition of claim 1, wherein the first quencher moiety and the second quencher moiety are the same as each other. (Item 3) 3. The composition of either item 1 or item 2, further comprising a FEN-1 endonuclease. (Item 4) 4. The composition of claim 3, wherein the FEN-1 endonuclease is a thermostable FEN-1 endonuclease. (Item 5) 5. The composition of claim 4, wherein the thermostable FEN-1 endonuclease is derived from an archaeal organism. (Item 6) further comprising a first target-specific invasive oligonucleotide and a first target-specific primary probe oligonucleotide; each of the first target-specific invasive oligonucleotide and the first target-specific primary probe oligonucleotide comprises a sequence configured to hybridize to a target nucleic acid to form an invasive cleavage structure cleavable by a FEN-1 endonuclease to produce a primary cleavage flap; 6. The composition of any one of items 1 to 5, wherein the primary cleavage flap is a cassette-specific invasive oligonucleotide configured to hybridize to the cleaved flap hybridizing sequence of the 5' flap FRET cassette oligonucleotide to form an invasive cleavage structure cleavable by the FEN-1 endonuclease. (Item 7) 7. The composition of claim 6, further comprising the target nucleic acid. (Item 8) 8. The composition of claim 7, further comprising deoxynucleoside triphosphates (dNTPs), a thermostable DNA polymerase, and a primer having a 3' end extendable by the thermostable DNA polymerase in a template-dependent nucleic acid amplification reaction using the target nucleic acid as a template. (Item 9) (iii) Below: a 5' portion comprising a second fluorophore moiety; a stem-loop portion comprising a third quencher moiety; a 3' portion containing a second cleaved flap hybridizing sequence; and a second FRET cassette oligonucleotide comprising: hybridization of a second cassette-specific invasive oligonucleotide to the second cleaved flap hybridizing sequence of the second FRET cassette oligonucleotide forms an invasive cleavage structure cleavable by a FEN-1 endonuclease at a cleavage site between the second fluorophore moiety and the third quencher moiety; cleavage of the second FRET cassette oligonucleotide at the cleavage site produces a cassette cleavage product comprising the second fluorophore moiety. The composition according to any one of items 1 to 8. (Item 10) the second FRET cassette oligonucleotide is a second 5' flap FRET cassette comprising a 5' flap portion, the cassette cleavage product is a second cassette cleavage flap comprising the second fluorophore, and the composition comprises: (iv) a second masking oligonucleotide comprising a fourth quencher moiety, at least a portion of the second masking oligonucleotide is capable of specifically hybridizing to the 5' flap portion of the second FRET cassette oligonucleotide; hybridization of the second masking oligonucleotide to the second cassette cleavage flap forms a second duplex having a second melting temperature higher than the first melting temperature; 10. The composition of claim 9, further comprising a second masking oligonucleotide, wherein the fluorescent emission from the second fluorophore moiety in the second duplex is quenched by the fourth quencher moiety. (Item 11) 10. The composition of claim 9, wherein the second cassette cleavage product comprises 5 or less, preferably 4 or less, preferably 3 or less, preferably 2 or less nucleotides. (Item 12) 12. The composition of any one of items 9 to 11, wherein the emission signals from the first fluorophore moiety and the second fluorophore moiety are detectable in the same fluorescence detection channel of a fluorescence monitoring device. (Item 13) 13. The composition according to any one of items 9 to 12, wherein the first fluorophore moiety and the second fluorophore moiety are the same as each other. (Item 14) 13. The composition of any one of items 9 to 12, wherein the first fluorophore moiety and the second fluorophore moiety are not the same as each other. (Item 15) 15. The composition of any one of items 10 and 12-14, wherein the third quencher moiety and the fourth quencher moiety are the same as each other. (Item 16) 1. A method for determining which of two different FRET cassettes in a reaction mixture has been cleaved to produce a fluorescent signal, the method comprising: (a) performing a multiple invasive cleavage reaction in the reaction mixture to cleave one or both of the first FRET cassette and the second FRET cassette to produce two different fluorescent cleavage products, if cleavage occurs; the first FRET cassette comprises a first 5' flap portion having a fluorophore attached thereto, the attachment of the fluorophore being arranged such that cleavage of the first FRET cassette by a FEN-1 endonuclease in the multiple invasive cleavage reaction produces a first cassette cleavage flap comprising the fluorophore; the reaction mixture comprises a first masking oligonucleotide that stably hybridizes to the first cassette cleavage flap to form a first duplex at a temperature below a first Tm but not above the first Tm, wherein fluorescence emission from the fluorophore of the first cassette cleavage flap of the first duplex is quenched; wherein each of the two different fluorescent cleavage products produced in the multiple invasive cleavage reaction is characterized by a different temperature-dependent fluorescence quenching profile in the reaction mixture; (b) measuring the fluorescent signals produced in the reaction mixture using a single channel of a fluorescence monitoring device under temperature conditions that differentially quench the fluorescence produced by the different fluorescent cleavage products of the multiple invasive cleavage reactions; (c) determining, from the result of step (b), which of the different FRET cassettes was cleaved in the multiple invasive cleavage reaction; A method comprising: (Item 17) Item 17. The method of item 16, wherein the second FRET cassette in step (a), when cleaved, produces a fluorescent cleavage product that does not hybridize to any masking oligo in the reaction mixture, resulting in fluorescence quenching. (Item 18) Item 18. The method of item 17, wherein step (c) comprises comparing the fluorescence signals measured at a temperature below the first Tm and a temperature above the first Tm. (Item 19) Item 19. The method according to item 18, wherein step (c) comprises comparing the fluorescent signals by calculating the difference between the measured fluorescent signals. (Item 20) step (b) comprises measuring any of the fluorescent signals at a temperature below the first Tm, wherein fluorescent emission from the fluorophore of the first cassette cleavage flap of the first duplex is quenched; step (c) comprising determining that the second FRET cassette has been cleaved in the reaction mixture if measurable fluorescence is detected in step (b); Item 17. The method according to item 17. (Item 21) step (b) comprises measuring any of the fluorescent signals at a temperature below the first Tm and a temperature above the first Tm; Item 18. The method of item 17, wherein step (c) comprises determining that the first FRET cassette has been cleaved in the reaction mixture if the fluorescent signal measured at a temperature higher than the first Tm is greater than the fluorescent signal measured at a temperature lower than the first Tm. (Item 22) 22. The method of any one of items 16 to 21, wherein step (b) comprises measuring any of the fluorescent signals produced in the reaction mixture as a function of temperature to generate a melting / annealing curve. (Item 23) 23. The method of claim 22, wherein step (c) comprises calculating a derivative of the melting / annealing curve and then determining from the calculated derivative whether the reaction mixture contains the first duplex characterized by the first Tm as an indication that the first FRET cassette has been cleaved in the reaction mixture. (Item 24) the second FRET cassette comprises a second 5' flap sequence having a fluorophore attached thereto, the attachment of the fluorophore being arranged such that cleavage of the second FRET cassette by the FEN-1 endonuclease in the multiple invasive cleavage reaction produces a second cassette cleavage flap comprising the fluorophore; the reaction mixture comprises a second masking oligo that hybridizes to the second cassette cleavage flap to form a second duplex at a temperature below a second Tm but does not hybridize at a temperature above the second Tm, and wherein fluorescence emission from the fluorophore of the second cassette cleavage flap of the second duplex is quenched; 17. The method of claim 16, wherein the first Tm and the second Tm differ by at least 5°C. (Item 25) the first Tm is greater than the second Tm; step (b) comprises measuring any of the fluorescent signals at a temperature below the second Tm and above the first Tm; 25. The method of claim 24, wherein step (c) comprises determining that at least one of the first FRET cassette and the second FRET cassette has been cleaved in the reaction mixture if the fluorescent signal measured at a temperature higher than the first Tm is greater than the fluorescent signal measured at a temperature lower than the second Tm. (Item 26) 26. The method of either item 24 or 25, wherein step (b) comprises measuring any of the fluorescent signals produced in the reaction mixture as a function of temperature to generate a melting / annealing curve. (Item 27) 27. The method of claim 26, wherein step (c) comprises calculating a derivative of the melting / annealing curve and then determining from the calculated derivative whether the reaction mixture contains the first duplex characterized by the first Tm as an indication that the first FRET cassette has been cleaved in the reaction mixture. (Item 28) 27. The method of claim 26, wherein step (c) comprises calculating a derivative of the melting / annealing curve and then determining from the calculated derivative whether the reaction mixture contains the second duplex characterized by the second Tm as an indication that the second FRET cassette has been cleaved in the reaction mixture. (Item 29) 29. The method of any one of items 16 to 28, wherein the first and second FRET cassettes are labeled with the same fluorophore. (Item 30) 29. The method of any one of items 16 to 28, wherein the first and second FRET cassettes are not labeled with the same fluorophore. (Item 31) 31. The method of any one of items 16 to 30, wherein the FEN-1 endonuclease of the multiply invasive cleavage reaction in step (a) comprises a thermostable FEN-1 endonuclease. (Item 32) 32. The method of any one of items 16 to 31, wherein step (c) comprises determining using a computer programmed with software. (Item 33) 1. A method for analyzing a sample containing a target nucleic acid, comprising: (a) contacting any of the first target nucleic acids of the sample with a first primary probe oligonucleotide comprising a sequence complementary thereto and a FEN-1 endonuclease in a reaction mixture under conditions such that, when the first primary probe oligonucleotide hybridizes to the first target nucleic acid, the first primary probe is cleaved by the FEN-1 endonuclease to generate a first primary cleavage flap; the first primary cleavage flap hybridizes to a cleaved flap hybridizing sequence of a first FRET cassette oligonucleotide included in the reaction mixture and forms an invasive cleavage structure that is cleaved by the FEN-1 endonuclease at a cleavage site between a first fluorophore moiety and a first quencher moiety of the first FRET cassette oligonucleotide to release a first cassette cleavage flap comprising the first fluorophore moiety; a first masking oligonucleotide comprising a second quencher moiety hybridizes to the first cassette cleavage flap to form a duplex at a temperature below a first Tm of the first masking oligonucleotide and the first cassette cleavage flap; the fluorescence emission from the first fluorophore moiety of the duplex is quenched by the second quencher moiety; at a second temperature higher than the first Tm, the first masking oligonucleotide and the first cassette cleavage flap do not form a stable duplex; (b) detecting any fluorescence emitted from the first fluorophore moiety at the second temperature; (c) Below: if fluorescence emitted from the first fluorophore moiety is detected in step (b), then the sample contains the first target nucleic acid; or If no fluorescence emitted from the first fluorophore moiety is detected in step (b), the sample does not contain the first target nucleic acid. determining whether the A method comprising: (Item 34) step (a) further comprises contacting in the reaction mixture any of the second target nucleic acids of the sample with a second primary probe oligonucleotide comprising a sequence complementary thereto and the FEN-1 endonuclease under conditions such that when the second primary probe oligonucleotide hybridizes to the second target nucleic acid, the second primary probe is cleaved by the FEN-1 endonuclease to generate a second primary cleavage flap that is different from the first primary cleavage flap; the second primary cleavage flap hybridizes to a cleaved flap hybridizing sequence of a second FRET cassette oligonucleotide included in the reaction mixture and forms an invasive cleavage structure that is cleaved by the FEN-1 endonuclease at a cleavage site between the second fluorophore moiety and the third quencher moiety of the second FRET cassette oligonucleotide to release a second cassette cleavage flap comprising the second fluorophore moiety; at a third temperature lower than the second Tm, a second masking oligonucleotide comprising a fourth quencher moiety hybridizes to the second cassette cleavage flap to form a duplex; the fluorescence emission from the second fluorophore moiety of the duplex is quenched by the fourth quencher moiety; at a fourth temperature higher than the second Tm, the second masking oligonucleotide and the second cassette cleavage flap do not form a stable duplex; the first Tm and the second Tm differ from each other by at least 5°C; step (b) further comprises detecting any fluorescence emitted from said second fluorophore moiety at said fourth temperature; Step (c) if fluorescence emitted from the second fluorophore moiety of the 5' flap cleavage product of the second FRET cassette oligonucleotide is detected in step (b), the sample contains the second target nucleic acid; or If fluorescence emitted from the second fluorophore moiety of the 5' flap cleavage product of the second FRET cassette oligonucleotide is not detected in step (b), the sample does not contain the first target nucleic acid. 34. The method of claim 33, further comprising determining whether the (Item 35) step (a) further comprises contacting in the reaction mixture any of the second target nucleic acids of the sample with a second primary probe oligonucleotide comprising a sequence complementary thereto and the FEN-1 endonuclease under conditions such that when the second primary probe oligonucleotide hybridizes to the second target nucleic acid, the second primary probe is cleaved by the FEN-1 endonuclease to generate a second primary cleavage flap; the second primary cleavage flap hybridizes to a cleaved flap hybridizing sequence of a second FRET cassette oligonucleotide included in the reaction mixture and forms an invasive cleavage structure that is cleaved by the FEN-1 endonuclease at a cleavage site between the second fluorophore moiety and the third quencher moiety of the second FRET cassette oligonucleotide to release a cleavage product comprising the second fluorophore moiety; the cleavage products do not hybridize to any masking oligonucleotides in the reaction mixture, resulting in fluorescence quenching; step (b) further comprises detecting any fluorescence emitted from the second fluorophore moiety of the cleavage product; Step (c) if fluorescence emitted from the second fluorophore moiety is detected in step (b), the sample contains the second target nucleic acid; or if no fluorescence emitted from the second fluorophore moiety is detected in step (b), the sample does not contain the first target nucleic acid; 34. The method of claim 33, further comprising determining whether the (Item 36) 36. The method of claim 34, wherein step (b) comprises detecting any fluorescence emitted from the first and second fluorophore moieties using a single channel of a fluorescence monitoring device. (Item 37) 37. The method of claim 36, wherein step (b) is carried out while a nucleic acid amplification reaction is occurring in the reaction mixture, and the product of the nucleic acid amplification reaction comprises the first target nucleic acid and the second target nucleic acid. (Item 38) 38. The method of claim 37, wherein the nucleic acid amplification reaction comprises a step for thermal cycling and the reaction mixture further comprises a thermostable DNA polymerase. (Item 39) 37. The method of any one of items 33 to 36, wherein step (b) is performed when the temperature of the reaction mixture is reduced to allow annealing of the masking oligonucleotide and the complementary cassette cleavage flap. (Item 40) 37. The method of claim 36, wherein the first and second fluorophore moieties are the same as each other. (Item 41) 37. The method of claim 36, wherein the step (b) of detecting any fluorescence comprises measuring any fluorescence. (Item 42) 42. The method of claim 41, further comprising either detecting or measuring fluorescence at the first temperature. (Item 43) 36. The method of any one of items 34 or 35, wherein both the first fluorophore moiety and the second fluorophore moiety are detectable in the same fluorescence detection channel of an energy sensor device. (Item 44) Item 44. The method of item 43, wherein the second fluorophore moiety is the same as the first fluorophore moiety. (Item 45) Item 44. The method of item 43, wherein the second fluorophore moiety is not the same as the first fluorophore moiety. (Item 46) 44. The method of any one of items 33 to 43, wherein fluorescence from the second fluorophore is detected and / or measured at the first temperature. (Item 47) 45. The method of any one of items 33 to 44, wherein the third quencher moiety is the same as the first quencher moiety and / or the second quencher moiety. (Item 48) 48. The method of any one of items 33 to 47, wherein the reaction mixture comprises primer oligonucleotides that amplify a target nucleic acid, and at least one primer oligonucleotide acts as an invasive oligonucleotide in the presence of primary probe oligonucleotides and the target nucleic acid and / or target amplicon to form an invasive cleavage structure that is cleaved by the thermostable FEN-1 endonuclease. (Item 49) 49. The method of any one of items 33 to 48, wherein step (c) comprises determining using a computer programmed with software. (Item 50) 1. A system for determining which of a plurality of target nucleic acid analytes are present in a reaction mixture, wherein each target nucleic acid analyte of the plurality of target nucleic acid analytes is detectable by a fluorescent signal, the system comprising: A thermocycler and a fluorometer in optical communication with the thermocycler, a fluorometer that measures a fluorescent signal indicative of production of nucleic acid amplification products by the thermocycler in a single optical channel; a computer in communication with the fluorometer; The computer, (a) obtaining a melting / annealing curve dataset generated from measurements performed by said fluorometer; (b) determining the presence of a first target nucleic acid in the reaction mixture by detecting a fluorescent signal from a first fluorescent cleavage product in the melting / annealing curve data set at a temperature at which fluorescence in the reaction mixture is maximally quenched; (c) generating a derivative plot from the melting / annealing curve dataset; and (d) determining that a second target nucleic acid is present in the reaction mixture if the derivative plot contains a feature characteristic of a first duplex; said computer being programmed with software instructions; wherein the first duplex comprises a first masking oligonucleotide and a second fluorescent cleavage product produced in the reaction mixture when the second target nucleic acid is present. system. (Item 51) The computer, (e) determining that a third target nucleic acid is present in the reaction mixture if the derivative plot contains a feature characteristic of a second duplex; said computer being programmed with software instructions; wherein the second duplex comprises a second masking oligonucleotide and a third fluorescent cleavage product produced in the reaction mixture when the third target nucleic acid is present. Item 51. The system according to item 50. (Item 52) 52. The system of either item 50 or item 51, wherein the characteristic feature of the first duplex comprises a maximum, minimum, or zero crossing point of a calculated derivative. (Item 53) the calculated derivatives include calculated first derivatives; the characteristic features of the first duplex include, as a first melt peak, a first maximum of a calculated first derivative of the melting / annealing curve data set; the characteristic feature of the second duplex comprises, as a second melting peak, a second maximum of the calculated first derivative of the melting / annealing curve dataset; Item 53. The system of item 52. (Item 54) 54. The system of any one of items 50 to 53, wherein the thermocycler, the fluorometer, and the computer are all components of a real-time PCR instrument. (Item 55) 51. The system of claim 50, wherein the computer-generated melting / annealing curve dataset comprises data points showing fluorescence as a function of temperature.

Claims

[Claim 1] The invention described in this specification.

Images