WO2016058054A1 - Improved nucleic acid quantitation method - Google Patents
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- WO2016058054A1 WO2016058054A1 PCT/AU2015/050637 AU2015050637W WO2016058054A1 WO 2016058054 A1 WO2016058054 A1 WO 2016058054A1 AU 2015050637 W AU2015050637 W AU 2015050637W WO 2016058054 A1 WO2016058054 A1 WO 2016058054A1
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6851—Quantitative amplification
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- C12Q2561/00—Nucleic acid detection characterised by assay method
- C12Q2561/113—Real time assay
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- C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
- C12Q2563/107—Nucleic acid detection characterized by the use of physical, structural and functional properties fluorescence
Definitions
- the present invention relates to methods of quantifying nucleic acid without the need for normalising data to a reference gene or synthetic gene of interest.
- the invention relates to an improved universal method of quantifying nucleic acids for gene expression studies. This method is applicable to diagnostic, forensic and research use.
- PCR technologies for quantification of gene expression have improved through the development of rapid thermocyclers and the introduction of fluorescence monitoring of amplified products after each cycle (real-time PCR).
- Quantification of gene expression occurs through the use of dyes, particularly fluorescent dyes, and the detection of increasing fluorescence during the exponential phase of PCR amplification proportional to the amount of nucleic acids in the sample at the beginning of the reaction. Quantification is based on the threshold cycle, i.e. the first cycle with detectable fluorescence, and can be performed in an absolute manner with external standards (usually a synthetic gene) or in relative manner with a comparative normalizing reference gene serving as an internal calibrator (i.e. reference gene). Control genes or reference genes are used to normalise mRNA levels between different samples.
- GPDH glyceraldehyde-3-phosphate dehydrogenase
- PBGD porphobilinogen deaminase
- B2M beta2-microglobin
- Actb beta-actin
- the present invention relates to a method for quantifying nucleic acids of interest that does not require the use of a reference gene or synthetic gene of interest to normalize nucleic acid expression data. Rather the method of the present invention utilizes a universal reference nucleic acid which can be used to generate a calibration curve from which the level of an amplified target nucleic acid in a sample can be calculated.
- the present invention also relates to kits for use in the method of the invention.
- the present invention provides a method for quantifying a target nucleic acid, the method comprising the steps of: measuring the fluorescence of known quantities of a fluorophore-tagged universal reference nucleic acid to generate a calibration curve;
- steps (a) to (d) are conducted substantially simultaneously.
- the fluorophore-tagged universal reference nucleic acid is single stranded.
- the calibration curve is generated using from about OnM to about 500nM of fluorophore-tagged universal reference nucleic acid.
- the calibration curve is generated using from about OnM to about 200nM of fluorophore-tagged universal reference nucleic acid.
- the calibration curve is generated using at least three known quantities of the fluorophore-tagged universal reference nucleic acid.
- the calibration curve is generated using at least six known quantities of the fluorophore-tagged universal reference nucleic acid.
- the calibration curve is generated using about OnM, about 20nM, about 40nM, about 60nM, about 80nM, about 10OnM and about 120nM of the fluorophore-tagged universal reference nucleic acid.
- the calibration curve is generated using about OnM, about 20nM, about 40nM, about 60nM, about 80nM, about 10OnM, about 120nM, about 140nM, about 160nM and about 200nM of the fluorophore-tagged universal reference nucleic acid.
- the universal reference nucleic acid has a length of less than about 60bp.
- the universal reference nucleic acid has a length of greater than about 170bp. [0023] In another embodiment, the universal reference nucleic acid has a length of about 20bp.
- the universal reference nucleic acid has a GC content of less than about 45%, preferably less than about 40%, preferably less than about 35%, preferably less than about 30%, preferably less than about 25%, preferably less than about 20%, preferably less than about 15%, preferably less than about 10%.
- the universal reference nucleic acid has a GC content of greater than about 60%, preferably greater than about 65%, preferably greater than about 70%, preferably greater than about 75%, preferably greater than about 80%, preferably greater than about 85%, preferably greater than about 90%.
- the universal reference nucleic acid has a GC content of about 30%.
- the universal reference nucleic acid has a GC content of about 40%.
- the universal reference nucleic acid has a GC content of about 60%.
- the universal reference nucleic acid has a GC content of about 80%. In another embodiment, the universal reference nucleic acid has a length of about 21 bp and a GC content of about 62%.
- the target nucleic acid has a length of less than about 80bp.
- the target nucleic acid has a length of greater than about 150bp.
- the target nucleic acid has a length of greater than about 210bp.
- the target nucleic acid has a length of about 90bp.
- the target nucleic acid has a length of about 500bp.
- the target nucleic acid has a length of about 10OObp.
- the target nucleic acid has a GC content of about 75%.
- the target nucleic acid has a GC content of about 25%.
- amplification of the target nucleic acid is by polymerase chain reaction (PCR).
- the PCR is real-time PCR.
- the real-time PCR is multiplex PCR.
- the fluorophore-tagged universal reference nucleic acid and the fluorophore-tagged probe are detectable in the same emission channel.
- the fluorophore-tagged universal reference nucleic acid and the fluorophore-tagged probe have the same excitation and emission spectra.
- the fluorophore is selected from the group consisting of FAM, HEX, Texas Red, TYE665, Alexa 594 and Cy5.
- the PCR is performed over about 30 to about 45 cycles.
- the present invention provides a kit comprising:
- the present invention provides a kit when used in the method of the first aspect, the kit comprising:
- the universal reference nucleic acid sequence need not have any homology with the target nucleic acid or with any reference gene sequence. However, because of the particular way in which the universal reference nucleic acid is used in the method of the present invention (i.e. to prepare a calibration curve following serial dilution of the universal reference nucleic acid) the universal reference nucleic acid sequence can have a degree of homology or can even be identical with a target nucleic acid sequence or a reference gene, or smaller parts thereof.
- An advantage of the present invention is that the method can make use of the same universal reference nucleic acid to quantify different target nucleic acids.
- the universal reference nucleic acid may be of the same or similar length to the target nucleic acid sequence but this need not be so.
- the universal reference nucleic acid may be longer or shorter than the target nucleic acid.
- the universal reference nucleic acid may be double or single stranded.
- the universal reference nucleic acid may be obtained from a biological source, natural or otherwise, using known techniques, or it may be prepared synthetically.
- the universal reference nucleic acid and the probe are both tagged with a fluorophore.
- Suitable fluorophores would be known to the skilled addressee and include, but are not limited to, FAM, JOE, HEX, Alexa 594, Texas Red, Cy5 and TYE665. When used in real time PCR, the fluorophores should be selected so that they are detectable in the emission channels of the real time PCR device.
- a single calibration curve is prepared with the universal reference nucleic acid and used for multiple target nucleic acid amplifications and quantifications.
- the amplification of the target nucleic acid is performed by Polymerase Chain Reaction (PCR) method.
- PCR Polymerase Chain Reaction
- the target nucleic acid is amplified over 30 to 40 cycles but this is not critical to the method of the present invention.
- Simultaneous amplification of multiple target nucleic acids of interest in one reaction can also be performed (i.e., multiplex PCR).
- Figure 1 Fluorescence measured over 40 PCR cycles for a FAM-tagged reference nucleic acid of 21 bp and 30% GC content, diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM and 120nM (Figure 1 A). Calibration curve created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 1 B). Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment from serial dilutions of a stock lambda DNA using a FAM-tagged hydrolysis probe ( Figure 1 C).
- Figure 2 Fluorescence measured over 40 PCR cycles for a FAM-tagged reference nucleic acid of 21 bp and 40% GC content, diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM and 120nM (Figure 2A). Calibration curve created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 2B). Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment from serial dilutions of a stock lambda DNA using a FAM-tagged hydrolysis probe ( Figure 2C).
- Figure 3 Fluorescence measured over 40 PCR cycles for a FAM-tagged reference nucleic acid of 21 bp and 62% GC content, diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM, 120nM, 140nM, 160nM and 200nM and (Figure 3A). Calibration curve created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 3B). Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment from serial dilutions of a stock lambda DNA using a FAM-tagged hydrolysis probe (Figure 3C).
- Figure 4 Fluorescence measured over 40 PCR cycles for a FAM-tagged reference nucleic acid of 21 bp and 80% GC content, diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM and 120nM (Figure 4A). Calibration curve created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 4B). Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment from serial dilutions of a stock lambda DNA using a FAM-tagged hydrolysis probe ( Figure 4C).
- Figure 5 Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment from serial dilutions of a stock lambda DNA using a FAM-tagged hydrolysis probe (Figure 5A) or the intercalating dye Eva green ( Figure 5B).
- Figure 6 Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment (Figure 6A), a 501 bp fragment ( Figure 6B) or a 1000bp fragment ( Figure 6C) from serial dilutions of a stock lambda DNA using a FAM-tagged hydrolysis probe.
- Figure 7 Fluorescence measured over 40-45 PCR cycles during amplification of a 90bp fragment with 75% CG composition ( Figure 7A) or 75% AT composition ( Figure 7B) from serial dilutions of a stock synthetic oligonucleotide using a FAM-tagged hydrolysis probe.
- Figure 9 Fluorescence measured over 45 PCR cycles during amplification from dilutions of lambda DNA using FAM-tagged hydrolysis probe (Figure 9A), HEX- (black) or JOE- (grey) tagged hydrolysis probes (FIGURE 9B), Alexa 594- (black) or Texas Red- (grey) tagged hydrolysis probes ( Figure 9C), or Cy5- (black) or TYE665- (grey) tagged hydrolysis probes ( Figure 9D).
- Figure 10 Fluorescence measured over 40 PCR cycles during amplification of a 92bp fragment from serial dilutions of lambda DNA using FAM-, HEX- or Texas Red-tagged hydrolysis probes individually (black) or together (grey), and detected in the green (FAM) channel ( Figure 10A), the yellow (HEX) channel ( Figure 10B) or the orange (Texas Red) channel ( Figure 10C).
- FAM green
- HEX yellow
- Figure 10C the orange (Texas Red) channel
- a nucleic acid in the context of the present invention is a molecule that is composed of chains of nucleotides. As used herein the term is intended to encompass DNA, RNA and their variants and derivatives. A nucleic acid may be double or single stranded.
- a target nucleic acid in the context of the present invention is a nucleic acid of interest.
- Amplification of nucleic acids sequences may be conveniently accomplished by Polymerase Chain Reaction (PCR) but may also be accomplished by another suitable method such as ligase chain reaction.
- PCR Polymerase Chain Reaction
- ligase chain reaction another suitable method
- An amplicon in the context of the present invention is a nucleic acid that is formed by amplification reactions such as those performed by PCR or ligase chain reactions.
- the amplicon may be the amplification product of the "target nucleic acid”.
- Real time PCR in the context of the present invention is a laboratory technique based on PCR, which is used to simultaneously amplify and detect/quantify amplicons.
- Multiplex PCR in the context of the present invention is a laboratory technique based on PCR consisting of multiple primer sets and probes within a single PCR mixture to produce multiple amplicons that are specific to different target nucleic acids.
- a probe in the context of the present invention is a nucleic acid of variable length which is used to detect the presence of a target nucleic acid that is complementary to the sequence in the probe.
- Probes include, but are not limited to hydrolysis probes, molecular beacons and Scorpion probes.
- a primer in the context of the present invention is a nucleic acid capable of acting as a point of initiation of nucleotide synthesis.
- nucleic acid useful in the preparation of a calibration curve for quantification of target nucleic acids, wherein the same universal reference nucleic acid may be used to quantify different target nucleic acids.
- the universal reference nucleic acid may be entirely synthetic or may be obtained from natural sources of nucleic acid.
- a fluorophore in the context of the present invention is a fluorescent chemical molecule that can re-emit light upon light excitation.
- a reference gene in the context of the present invention is typically a constitutive gene that is required for the maintenance of basal cellular function. Such genes are found in all cells. Some reference genes are expressed at relatively constant levels however other reference genes may vary in expression depending on experimental conditions used.
- a calibration curve in the context of the present invention is a plot of fluorescence against quantity of fluorophore-tagged universal reference nucleic acid.
- a standard curve in the context of the present invention is a plot of cycle threshold (Ct or Cq) against serial dilutions of a synthetic gene of interest or input nucleic acid.
- Serial dilution in the context of the present invention refers to any form of dilution necessary to prepare a calibration curve or standard curve covering a range of concentrations of a fluorophore-tagged universal reference nucleic acid or synthetic gene of interest.
- dsDNA refers to double stranded DNA
- bp refers to base pairs
- dNTP deoxynucleotide triphosphate
- RNA refers to ribonucleic acid
- tRNA refers to transfer RNA
- rRNA refers to ribosomal RNA
- siRNA refers to small interfering RNA
- miRNA refers to micro RNA
- mRNA refers to messenger RNA
- cDNA refers to complementary DNA.
- AccuCal-P in the context of the present application refers to a universal reference nucleic acid tagged with any appropriate fluorophore.
- AccuCal-D in the context of the present invention refers to a universal reference nucleic acid tagged using any appropriate fluorescent intercalating dye.
- the term "AccuBeacon” in the context of the present invention refers to a universal reference nucleic acid tagged with any appropriate fluorophore, wherein the nucleic acid forms a hairpin structure.
- the present invention has been motivated by the lack of accurate and efficient means for quantifying nucleic acid expression in control and treatment animal/human groups. It has also been motivated by the fact that many of the known reference genes used in gene expression studies, change expression levels in response to experimental conditions or treatments, thus skewing results.
- An advantage of the present invention is that the described methods dispose of the need for reference genes or synthetic reference genes used to normalise data and quantify gene expression.
- known quantities of a fluorophore-tagged universal reference nucleic acid are used to generate a calibration curve.
- the calibration curve is generated by serially diluting the fluorophore-tagged universal reference nucleic acid and plotting the fluorescent levels against the concentration of the fluorophore-tagged reference nucleic acid. No amplification of the universal reference nucleic acid is necessary to produce the calibration curve. This contrasts with current methodologies for assessing gene expression whereby the test sample and the reference gene/synthetic reference gene are both amplified either side by side or combined in one reaction mixture.
- the same calibration curve, once prepared, can be used numerous times if required to quantify more than one target nucleic acid.
- the fluorophore-tagged universal reference nucleic acids used for the preparation of the calibration curve are stable over time, for example over a period of about one month, and repeated freezing and thawing of the solutions. This enables the preparation and storage of fluorophore-tagged universal reference nucleic acid solutions ahead of any experimental requirements.
- the fluorophore-tagged universal reference nucleic acid used in the methods of the present invention is not what is described as a “reference gene” or a “synthetic reference gene", i.e. it does not need to be amplified along with the target nucleic acid.
- the fluorophore-tagged universal reference nucleic acid need not have any homology with the target nucleic acid or with any reference gene sequence. However, because of particular way in which the fluorophore-tagged universal reference nucleic acid is used in the method of the present invention (i.e. to set up a calibration curve following serial dilution of the fluorophore-tagged universal reference nucleic acid), the fluorophore-tagged universal reference nucleic acid can have a degree of homology or can even be identical to a target nucleic acid sequence or a reference gene, or smaller parts thereof.
- Each universal reference nucleic acid is tagged with a defined number of fluorophores, typically numbering one.
- the probe is tagged with a known number of fluorophores, which allows for direct comparison between the fluorescence generated by the fluorophore-tagged universal reference nucleic acid and the fluorescence generated by the fluorophore-tagged probe-bound target nucleic acid.
- the length and/or composition of the fluorophore-tagged universal reference nucleic acid is irrelevant, as long as a defined amount of fluorophore can be determined.
- the fluorophore-tagged reference nucleic acid is 21 bp in length and varies between 30%-80% GC content, but it will be appreciated by those skilled in the art, that any length or GC content of fluorophore-tagged reference nucleic acid will provide similar results.
- a fluorophore-tagged universal reference nucleic acid is obtained from a biological source, natural or otherwise, it may be obtained using restriction enzymes to obtain a suitable fragment.
- Synthetic fluorophore-tagged universal reference nucleic acids may also be conveniently used and may be simply prepared by known techniques such as for example those described in Sambrook et al. Molecular Cloning: A Laboratory Manual, 2nd ed. (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. and Roe et al. DNA Isolation and Sequencing" (Essential Techniques Series) (1996) John Wiley & Sons, Inc., N.Y.
- the same fluorophore-tagged universal reference nucleic acid can be used for numerous nucleic acid targets.
- multiple calibration curves can be generated using differing fluorophore-tagged universal reference nucleic acid and similarly differing fluorophore-tagged probes to quantify nucleic acids in multiplex PCR reactions.
- the method of the present invention is advantageous as it disposes of the need to amplify a reference gene and constantly run assays for reference genes or synthetic reference genes to normalize nucleic acid expression data within each experiment.
- One calibration curve can be prepared and used to quantify more than one target nucleic acid, which can vary in size and sequence, thereby cutting the cost and time when compared to conventional gene expression assays.
- the fluorophore-tagged universal reference nucleic acid is serially diluted at a range of concentrations in duplicate using the same reaction buffer as that used for the target nucleic acid and the same reaction tubes and subjected to the same amplification conditions as the target nucleic acid.
- Example 1 Use of AccuCal-P to quantitate a range of amplified lambda DNA.
- a FAM-tagged reference nucleic acid (21 bp and 30% GC - AccuCal-P) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM and 120nM and fluorescence was measured over 40 PCR cycles ( Figure 1 A).
- a calibration curve was created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 1 B).
- Figure 1 C A range of ten-fold serial dilutions of a stock lambda DNA was amplified over 40 PCR cycles, with a 92bp fragment of amplified lambda DNA detected using a FAM-tagged hydrolysis probe. Each PCR was performed in triplicate.
- the theoretical amount of seeded nucleic acid ranged from 4.5 x 1 0 7 to 4.5 x 10 1 copies/PCR, along with a negative control (NTC).
- NTC negative control
- the initial amount of nucleic acid seeded into each of the amplification reactions was quantitated using the calibration curve and the individual efficiency of each reaction over the exponential portion of the amplification curve using a published algorithm (Tichopad et al. 2003, Nucl. Acids Res., 31 (20): e122).
- Example 2 Use of AccuCal-P to quantitate a range of amplified lambda DNA.
- a FAM-tagged reference nucleic acid (21 bp and 40% GC - AccuCal-P) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 1 00nM and 120nM and fluorescence was measured over 40 PCR cycles (Figure 2A).
- a calibration curve was created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 2B).
- a range of ten-fold serial dilutions of a stock lambda DNA was amplified over 40 PCR cycles, with a 92bp fragment of amplified lambda DNA detected using a FAM-tagged hydrolysis probe ( Figure 2C). Each PCR was performed in triplicate.
- the theoretical amount of seeded nucleic acid ranged from 4.5 x 1 0 7 to 4.5 x 10 1 copies/PCR, along with a negative control (NTC).
- NTC negative control
- the initial amount of nucleic acid seeded into each of the amplification reactions was quantitated using the calibration curve and the individual efficiency of each reaction over the exponential portion of the amplification curve using a published algorithm (Tichopad et al. 2003, Nucl. Acids Res., 31 (20): e122).
- Example 3 Use of AccuCal-P to quantitate a range of amplified lambda DNA.
- a FAM-tagged reference nucleic acid (21 bp and 62% GC - AccuCal-P) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM, 120nM, 140nM, 160nM and 200nM, and fluorescence was measured over 40 PCR cycles (Figure 3A).
- a calibration curve was created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated (Figure 3B).
- a range of ten-fold serial dilutions of a stock lambda DNA was amplified over 40 PCR cycles, with a 92bp fragment of amplified lambda DNA detected using a FAM-tagged hydrolysis probe ( Figure 3C).
- PCR was performed in triplicate.
- the theoretical amount of seeded nucleic acid ranged from 4.5 x 10 7 to 4.5 x 10 1 copies/PCR, along with a negative control (NTC).
- NTC negative control
- the initial amount of nucleic acid seeded into each of the amplification reactions was quantitated using the calibration curve and the individual efficiency of each reaction over the exponential portion of the amplification curve using a published algorithm (Tichopad et al. 2003, Nucl. Acids Res., 31 (20): e122).
- Example 4 Use of AccuCal-P to quantitate a range of amplified lambda DNA.
- a FAM-tagged reference nucleic acid (21 bp and 80% GC - AccuCal-P) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM and 120nM and fluorescence was measured over 40 PCR cycles (Figure 4A).
- a calibration curve was created by plotting the fluorescence value at each cycle against the concentration of reference nucleic acid and the linear regression was calculated ( Figure 4B).
- a range of ten-fold serial dilutions of a stock lambda DNA was amplified over 40 PCR cycles, with a 92bp fragment of amplified lambda DNA detected using a FAM-tagged hydrolysis probe ( Figure 4C). Each PCR was performed in triplicate.
- the theoretical amount of seeded nucleic acid ranged from 4.5 x 10 7 to 4.5 x 10 1 copies/PCR, along with a negative control (NTC).
- NTC negative control
- Example 5 Use of AccuCal-D, AccuCal-P and AccuBeacon to guantitate a range of amplified lambda DNA.
- Three reference nucleic acids were used to independently quantitate a range of lambda DNA: AccuCal-D (21 bp and 62% GC reference nucleic acid tagged with Eva green), AccuCal-P (21 bp and 62% GC reference nucleic acid tagged with FAM) and AccuBeacon (21 bp and 62% GC hairpin reference nucleic acid tagged with FAM).
- Each reference nucleic acid (AccuCal-D, AccuCal-P and AccuBeacon) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM, 140nM and 200nM.
- a 92bp fragment was amplified from ten-fold serial dilutions of lambda DNA, ranging from 4.5 x 10 6 to 4.5 x 10 2 and an NTC, and detected using a FAM- tagged hydrolysis probe (Figure 5A) or the intercalating dye Eva green ( Figure 5B).
- the amount of starting nucleic acid input was calculated using AccuCal-D, AccuCal-P or
- Example 6 Use of AccuCal-D or AccuCal-P to quantify a range of amplicon sizes.
- Example 7 Use of AccuCal-P to quantitate nucleic acids of varying composition.
- Synthetic target nucleic acids were designed from which a 90bp amplicon could be amplified that was either 75% CG composition (Figure 7A) or 75% AT composition ( Figure 7B).
- the synthetic templates were diluted ten-fold so that a known amount of template, ranging from 1 x 10 7 to 1 x 10 3 plus NTC, was seeded per PCR.
- AccuCAL-P (21 bp and 62% GC reference nucleic acid tagged with FAM) was diluted to OnM, 20nM, 40nM, 80nM, 100nM and 120nM.
- the amount of starting nucleic acid input was calculated using AccuCAL-P as a calibrator for both GC rich template (Table 7A) and AT rich template (Table 7B).
- Example 8 Fluorescence of various amounts of four reference nucleic acids, each tagged with a different fluorophore, may be detected simultaneously in the same well
- Reference nucleic acids (21 bp and 62% GC) were tagged with FAM (Figure 8A), HEX ( Figure 8B), Texas Red ( Figure 8C) and TYE665 ( Figure 8D) and are detected in the green, yellow, orange and red filter channels, respectively.
- the fluorophore- tagged reference nucleic acids were diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM and 160nM and the fluorescence was measured at the end of each annealing step of the PCR amplification cycle.
- Three reference nucleic acids (21 bp and 62% GC), diluted at OnM, 20nM, 40nM, 60nM, 80nM, 10OnM, 120nM, 140nM, 160nM and 200nM, and tagged with either FAM, HEX or Texas Red were used to quantitate a range of lambda PCRs (Table 8).
- the FAM-tagged reference nucleic acid was used to quantitate lambda PCRs detected with a FAM-tagged hydrolysis probe.
- the HEX-tagged reference nucleic acid was used to quantitate lambda PCRs detected with either a HEX-tagged hydrolysis probe or a JOE-tagged hydrolysis probe.
- the Texas Red-tagged reference nucleic acid was used to quantitate lambda PCRs detected with either a Texas Red-tagged hydrolysis probe or an Alexa 594-tagged hydrolysis probe.
- Example 9 Use of a reference nucleic acid tagged with one fluorophore for quantitatinq amplifications detected using a different fluorophore.
- a FAM-tagged reference nucleic acid (21 bp and 62% GC) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM, 120nM and 140nM and used to quantitate all the amplifications (Table 9).
- Example 10 Both AccuCal-P and samples can be multiplexed.
- Example 1 1 AccuCal-P can be used to quantitate miRNA.
- Hsa-miR-34a was amplified from rat brain RNA using a miRNA kit that utilises a FAM-tagged hydrolysis probe (Applied Biosystems). Following reverse transcription, the RNA was diluted one in three and a half, and both the neat (dark grey in Figure 1 1 ) and the diluted (black in Figure 1 1 ) cDNA were amplified in triplicate, along with a no-RT control (input RNA; light grey in Figure 1 1 ) and a NTC (no cDNA, but all other reagents; light grey in figure 1 1 ).
- FAM-tagged reference nucleic acid (AccuCal-P) was diluted to OnM, 20nM, 40nM, 60nM, 80nM, 100nM, 120nM, 140nM, 1 60nM and 200nM and used to determine the amount of input nucleic acid (Table 1 1 ).
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CA2964410A1 (en) | 2016-04-21 |
BR112017007733A2 (en) | 2018-01-30 |
CA2964410C (en) | 2023-03-14 |
CN107002152A (en) | 2017-08-01 |
KR20170083053A (en) | 2017-07-17 |
KR102360612B1 (en) | 2022-02-09 |
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