WO2011112068A1 - Lateral flow device and method of detection of nucleic acid sequence - Google Patents

Lateral flow device and method of detection of nucleic acid sequence Download PDF

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Publication number
WO2011112068A1
WO2011112068A1 PCT/MY2010/000212 MY2010000212W WO2011112068A1 WO 2011112068 A1 WO2011112068 A1 WO 2011112068A1 MY 2010000212 W MY2010000212 W MY 2010000212W WO 2011112068 A1 WO2011112068 A1 WO 2011112068A1
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WIPO (PCT)
Prior art keywords
region
nucleic acid
acid sequence
sub
internal amplification
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PCT/MY2010/000212
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French (fr)
Inventor
Yean Yean Chan
Ang Lim Chua
Lalitha Pattabiraman
Manickam Ravichandran
Boon Huat Lim
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Universiti Sains Malaysia (U.S.M.)
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Publication of WO2011112068A1 publication Critical patent/WO2011112068A1/en

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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/558Immunoassay; Biospecific binding assay; Materials therefor using diffusion or migration of antigen or antibody
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54366Apparatus specially adapted for solid-phase testing
    • G01N33/54386Analytical elements
    • G01N33/54387Immunochromatographic test strips
    • G01N33/54388Immunochromatographic test strips based on lateral flow
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6816Hybridisation assays characterised by the detection means
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/686Polymerase chain reaction [PCR]

Definitions

  • the present invention relates to a lateral flow device destined for the detection of the presence or absence of a target nucleic acid sequence and to a method of detection of the target nucleic acid sequence using said device.
  • PCR polymerase chain reaction
  • UV spectrometry or radioisotopic detection.
  • Lateral flow tests are simple devices intended to detect the presence or absence of a target analyte in a sample. Most commonly these tests are used for medical diagnostics, for home testing, or laboratory use. They are often produced in a dipstick format, and the test sample flows along a solid substrate via capillary action. After the sample is applied to the test, it encounters a coloured reagent which mixes with the sample and transits the substrate encountering lines or zones which have been pretreated with an antibody or antigen. Depending upon the analytes present in the sample the coloured reagent can become bound at the test line or zone. Lateral flow dipsticks have been well used in the art for detection of antigens or antibodies from a liquid sample. These devices require very little expertise to use and can give results within minutes. The current invention utilizes the principles and advantages of lateral flow dipsticks for detection of amplified nucleic acid analytes in a simple and rapid format.
  • the objective of the present invention is the development of a microsphere based DNA biosensor device which is capable of detecting the amplified DNA by lateral flow technology.
  • the advantage of this new diagnostic device is the reduction of the time taken to analyze the amplified DNA as compared to the conventional agarose gel, which requires skilled workers and use of a carcinogenic substance like ethidium bromide.
  • Object of the present invention is a lateral flow device for detecting the presence or absence of at least one target nucleic acid sequence bearing a first hapten label and a second hapten label, comprising
  • an internal amplification control sub-region containing an internal amplification control capture reagent immobilized in the internal amplification control sub- region, which binds to a first hapten label of an internal amplification control nucleic acid sequence, which is different from the first hapten label of the target nucleic acid sequence, said internal amplification control sub-region preferably being located between the last capture sub-region and a chromatographic control sub-region,
  • chromatographic control sub-region containing an antibody against the detector conjugate, said antibody being immobilized in the chromatographic control sub- region, said chromatographic control sub-region being located between the last capture sub-region and an adsorbent region;
  • a hapten generally is a small molecule that can elicit an immune response only when attached to a large carrier.
  • a hapten label provides a unique tag, which a specific detector agent (e.g., an antibody) can detect and capture.
  • the application, conjugate and detection regions may be made of a single continuous glass fibre membrane, or they may include glass fibre membrane in capillary contact with other membrane types to allow lateral flow as a single whole device.
  • a glass fibre membrane is made of glass fibres bound into a porous matrix.
  • the glass fibre membrane is porous and hydrophilic and as such allows capillary migration of a solution and its solutes from the wicking region to the absorbent region of the device while moving along rehydrated conjugates, without hindrance.
  • the absorbent region is preferably made of cellulose.
  • the device according to the present invention may be provided with a backing.
  • the backing may be a rigid or semi-rigid polymer, e.g., polyester, vinyl, etc.
  • the purpose of the backing is to provide mechanical strength which makes the device easy to handle and use.
  • the backing may be connected with other parts of the device, e.g., by laminating or adhesion.
  • An example of a suitable backing is white vinyl backing with pressure adhesive from G&L Precision Die-cutting (The Netherlands).
  • the detection region may contain one or more capture sub-regions, preferably lines, with each dedicated to the detection of one particular target analyte. Each capture sub-region may contain a different capture reagent, specific to the first hapten label of its target nucleic acid sequence.
  • the capture reagent which is specific to the first hapten label of the polynucleotide analyte, different from the second hapten label recognized by the detector reagent, serves to detect and capture the analyte from the liquid sample.
  • the capture reagent will form a complex with the analyte, which is then detected by the binding of the detector reagent to form a visual signal.
  • the capture reagent may be a monoclonal or polyclonal antibody or a molecule that specifically interacts with the hapten labels of the target polynucleotide analyte, and may be immobilized by coupling to a carrier bead (carrier microparticle).
  • the carrier bead preferably is from material that allows the stable addition of capture reagents to the surface, and allows analyte samples to approach the surface even after prolonged dried storage. Furthermore, the carrier bead should be of similar colour and tint to the chromatographic membrane (e.g., glass fibre membrane) material in which the capture reagents are impregnated. The beads should also be of sufficient size to ensure efficient trapping within the matrix of the membrane and at the same time provide sufficient surface area for the capture reagent to capture the analyte from the liquid sample.
  • the carrier beads may be polystyrene latex beads activated with carboxyl groups. Covalent coupling of the amino groups of the capture reagent to COOH-modified microparticles may be performed through the use of carbodiimide (with or without hydroxysuccinimide ester).
  • the detector conjugate which is specific for the second hapten label on the target polynucleotide analyte, serves to provide a visual signal in the presence of the analyte.
  • the specific detector reagent will form a complex with the analyte captured by the capture reagent in the capture sub-region.
  • This detector reagent may be a conjugated polyclonal or monoclonal antibody that could bind specifically to the complementary second hapten labelled to the polynucleotide analyte.
  • the detector reagent employs coloured particulate labels to provide a visual signal.
  • Known labels include coloured latex microparticles, colloidal carbon particles and metallic colloids such as gold and silver.
  • the coloured particulates of detector conjugate reagent in the conjugate region are colloidal gold particles with diameter of 30 to 40 nm, preferably 40 nm diameter particles, coated with monoclonal or polyclonal antibodies.
  • the chromatographic control preferably as a control line, may be made of a species- specific antibody against the detector reagent and may be immobilized by coupling to carrier beads similarly to above-mentioned capture reagent.
  • the formation of complex between the control line reagent and the detector reagent will give rise to a control signal. This enables the user to check whether the device is in working order or not.
  • the device according to this invention is destined for rapid and specific detection of the presence of target nucleic acid products from a molecular amplification assay, particularly from a PCR assay, and for the verification of the amplification cycles.
  • the primers in the particular PCR assay are modified to have a different hapten label at the 5' end of each primer.
  • Molecular amplification using this set of modified primers produces polynucleotide products labelled with two different haptens at different ends. These hapten labelled polynucleotides are detected by specific capture by the capture reagents.
  • the PCR assay to be used for molecular amplification of the target nucleic acid sequence includes an internal amplification control (IC) which verifies the amplification cycles.
  • the primers for both target genetic sequence and IC material share one common hapten label (the second hapten label) for one of the two primers in each pair, while having another two different first hapten labels for the other primer in each pair. This modification of both primer pairs will generate two polynucleotide analyte types - both sharing one common hapten at one end while having two different haptens for the other end.
  • the hapten labelled polynucleotide analyte amplified from the target nucleic acid sequence will be captured by one capture reagent, while the other polynucleotide analyte amplified from IC material will be captured by the internal amplification control capture reagent within the internal amplification control sub-region.
  • the first capture reagent binds to a specific first hapten on the polynucleotide analyte amplified from target genetic sequence, while the second (IC) capture reagent binds to a different specific first hapten on the polynucleotide analyte amplified from IC material.
  • Visual signal is generated for both captured analytes at first capture reagent and second capture reagent when the detector reagent forms complexes with the common second hapten labels present on the other end of both polynucleotide analytes.
  • the internal amplification control capture reagent may be a monoclonal or polyclonal antibody or a molecule that specifically interacts with the hapten labels of the internal amplification control polynucleotide analyte, and may be immobilized by coupling to a carrier bead, similarly to the capture reagent for the target nucleic acid sequence.
  • the capture sub-region, the chromatographic control sub-region and the internal amplification control sub-region all have the shape of lines extending the whole width of the detection region.
  • the present invention further includes a method of detecting the presence or absence of at least one target nucleic acid sequence using the device comprising the internal amplification control sub-region, comprising the steps of:
  • the chromatographic running buffer rehydrates the immobilized and dried detector reagent and releases it from the conjugate pad area, and it ensures the passage of the added sample analyte and the rehydrated detector reagent through the reaction membrane for efficient specific capture of target analytes by capture reagents.
  • the chromatographic running buffer can, for example, consist of a low molarity phosphate buffered saline (PBS) buffer containing pre-determined amounts of a chemical detergent polyoxyethylene (20) sorbitan monolaurate.
  • Said chemical detergent ensures complete rehydration of the dried, impregnated detector reagent and release of the detector reagent from the conjugates region into the detection region.
  • Conventional lateral flow dipsticks are usually based on nitrocellulose membrane which is hydrophobic in nature and requires blocking of unreacted sites to prevent background signals.
  • One embodiment of the current invention overcomes many of these problems by using a glass fibre membrane as the platform for the novel device, thus ensuring hydrophilic properties and requires no complicated blocking strategies.
  • the same glass fibre membrane is also used as the conjugate pad, sample application pad and the reaction pad and this easily avoids contact problems which prevent imperfect flow characteristics of liquid samples within the device.
  • the present invention in a preferred embodiment immobilizes capture reagents that are conjugated to carrier beads within the glass fibre membrane matrix.
  • the device can be modified to detect one target amplicon analyte as well as the internal amplification control (IC) amplicons of the molecular amplification assay. This ensures the validity of the molecular amplification assay.
  • the device further incorporates a chromatographic control to check whether the device is in working order or not.
  • the present invention is aimed to replace the conventional method of detecting amplicons from a molecular amplification assay with a device capable of detecting the amplification products in as little as 5 minutes and requires no special equipment or trained personnel.
  • the disposable device is easy to manufacture and simple to use.
  • Fig. 1 shows the device as desribed in the example 1.
  • Fig. 2 shows a schematic representation of the result of an analysis carried out with a device described in the example 2. Examples of carrying out the Invention
  • Example 1 The invention is herein further described by way of examples, which should not be construed as further limiting.
  • Example 1
  • the device used in this example comprises an application 2, conjugate 3, detection 4 and absorbent 5 regions, the detection region comprising a capture sub-region 6, an internal amplification control sub-region 7 and a chromatographic control sub-region 8, each of the sub-regions having the shape of a line extending the whole width of the detection region 4.
  • the glass fibre membrane chromatographic device that is presented in this example consists of a glass fibre membrane (detail of the membrane structure is shown in a circle in Fig. 1 ), attached to a semi-rigid polymer backing 18, preferably of white vinyl backing with pressure adhesives by G&L Precision Die-cutting (The Netherlands), together with an absorbent area made from cellulose.
  • the glass fibre membrane is used as the application 2, conjugates 3 and detection 4 areas, while the cellulose membrane is used as the absorbent area 5.
  • the detection area houses two capture reagents 10, 1 1 , the reagent 10 dedicated for the detection of the specific target polynucleotide amplicons, while the reagent JJ . is for detection of the internal amplification control of a PCR assay.
  • the capture reagents 10, 1 1 and the chromatographic control antibody 12 are immobilized within the glass fibre membrane.
  • the chromatographic control antibody J_2 is made from goat anti- mouse IgG antibodies coated onto microparticles.
  • the monoclonal anti-fluorescein antibody conjugated colloidal gold particles are the detector reagents 9 used in this example and are impregnated into the glass fibre membrane.
  • the conjugate pad 3 is impregnated with coloured particles that are coated with monoclonal or polyclonal antibodies or molecules that can specifically bind to their complementary specific hapten attached on polynucleotide analytes.
  • the coloured particles of conjugate reagent 9 in the conjugate region 3 are colloidal gold particles with diameter of 40 nm.
  • the conjugates region is impregnated with the gold conjugate after a dilution step in a specific buffer to provide optimal rehydration with the chromatographic running buffer when the test is running.
  • the gold conjugates is preferably diluted into a final 10 mM phosphate buffer containing 200 mg/ml sucrose, 50 mg/ml trehalose and 10 mg/ml bovine serum albumin before sprayed into the membrane using an air spray dispenser (e.g. Airjet dispenser of the XYZ3050 dispensing system from BioDot) at 10 ⁇ /cm to 40 ⁇ /cm, in this example at 20 ⁇ /cm, with a pressure ranging from 1 to 6 psi.
  • Coupling antibodies to colloidal gold is well known in the art.
  • the detector reagent used here is monoclonal anti- fluorescein antibody.
  • one part of antibodies diluted in borax buffer is mixed with 4 parts of colloidal gold particles at 1.0 OD 53 o for 30 minutes in room temperature for the bioconjugation process. Unreacted sites are later blocked by the addition of bovine serum albumin and the blocking is allowed to proceed for an additional 30 minutes. Excess antibodies are removed by centrifugation followed by resuspension of the conjugates in phosphate buffer supplemented with bovine serum albumin. The gold conjugates are later added with sucrose and trehalose just before spraying onto the conjugates area of the device.
  • the capture reagent J_0 immobilized in the capture sub-region 6 of the detection region 4 of the device, the internal amplification control capture reagent JJ_ located in the IC sub- region 7, as well as the chromatographic control reagents Y2 immobilized in the chromatographic control sub-region 8, are coupled to carrier beads.
  • Polystyrene latex beads activated with carboxyl groups (COOH) are used to couple the capture reagents 1 1 and the chromatographic control reagent 12.
  • Covalent coupling of the amino groups of the capture reagent to COOH-modified microparticles is performed through the use of carbodiimide (with or without hydroxysuccinimide ester).
  • Capture reagent for the target PCR amplified nucleic sequence is streptavidin which binds specifically to the biotin hapten ⁇ A.
  • Capture reagent for internal amplification control of PCR is polyclonal anti- digoxigenin antibody which captures specifically the digoxigenin hapten ⁇ 7.
  • Chromatographic control reagent is polyclonal goat anti-mouse IgG antibody which specifically captures the detector reagent 9. The capture reagents and chromatographic control reagent are covalently coupled to COOH-modified polystyrene latex microparticles of 2.0 ⁇ in diameter using carbodiimide chemistry.
  • This coupling strategy is well known in the art and it is performed here as described by the latex microparticles manufacturer (Polysciences, USA) with modifications. Briefly, the latex beads are washed and resuspended in MES buffer before activation with carbodiimide. The activated beads are washed and resuspended in borate buffer. Covalent coupling with the capture reagents and chromatographic control reagent are performed by mixing the capture reagents and chromatographic control reagent, diluted in the same borate buffer, with the activated beads. The reaction is performed for 15 minutes at room temperature before blocking of unreacted sited on the beads by addition of ethanolamine.
  • the coupled beads are washed to remove excess uncoupled capture reagents and chromatographic control reagent by centrifugation and finally resuspended in 10 mM phosphate buffer.
  • Impregnation of the capture reagents 10, 1 1 and the chromatographic control reagent V2 within the glass fibre membrane matrix is performed by diluting the reagent in an appropriate buffer and dispensing onto the membrane with a contact system (e.g. XYZ3050 from BioDot).
  • Dispensing rate can vary from 2 ⁇ /cm to 8 ⁇ /cm.
  • Reagent concentration varies from 10 mg/ml to 30 mg/ml and preferably at 20 mg/ml.
  • the buffer used for dispensing consisted of 20 itiM phosphate buffer at pH 7.4.
  • the glass fibre membrane is attached by means of pressure adhesive material to a semi- rigid backing card J_8 together with the cellulose absorbent membrane.
  • the backing is made of white vinyl.
  • the membrane is then dried within a vacuum chamber for 30 minutes after impregnation of the capture reagents and the gold conjugates into the membrane matrix.
  • the membrane is then further dried in a desiccating chamber of ⁇ 10% relative humidity overnight.
  • the membrane is later cut into 5 mm width pieces and stored in a sealed pouch together with silica gel.
  • Target DNA sequence ⁇ 3 amplification was performed by PCR with a 5 ' end biotin hapten J_4_labelled forward primer and a 5 ' end fluorescein hapten J_5 labelled reverse primer.
  • the amplification reaction is performed simultaneously with the internal amplification control within the same reaction mixture.
  • the internal amplification control is designed as to show if a negative test result is a true negative, i.e. that the negative result is not due to an amplification inhibitory substance possibly present in the test sample.
  • This internal amplification control is a set of PCR primers with its complementary template DNA that is different from the target DNA sequence.
  • the template for internal amplification control is designed from an unrelated species.
  • the forward primer is modified to be labelled with digoxigenin hapten J_7 at the 5' end while the reverse primer is modified to be labelled with fluorescein hapten J_5 at the 5' end.
  • the primers are designed to be specific only for the internal amplification control template and do not hybridize with the target DNA sequence. Amplification of this control template will produce control amplicons labelled with digoxigenin and fluorescein haptens.
  • the internal amplification control capture sub- region 7 houses the anti-digoxigenin antibody coated beads _N and detects the internal amplification control amplicons J_6 via binding of digoxigenin label ⁇ 7 on the control amplicons.
  • the rehydrated gold conjugates 9 are carried to the detection area and form complexes with the captured amplicons of both target and internal amplification control.
  • the accumulation of colloidal gold particles gives a distinct cherry red colour, showing a positive result.
  • the remaining gold conjugates migrate further and are captured by the chromatographic control antibody ⁇ 2 in the chromatographic control area 8, giving rise to a signal.
  • the present invention provides a device for a simple and rapid visual detection of amplified DNA of a target gene using immobilized capture reagents, e.g., polystyrene microparticles coated with capture reagents, and visualized through detector conjugates, e.g., gold nanoparticle-based detector reagent, within a bound glass membrane-based lateral-flow device.
  • the device can be used to detect labelled amplified DNA, commonly from a polymerase chain reaction (PCR) assay, without specialised equipment or trained staff in as little as 5 minutes.
  • PCR polymerase chain reaction
  • the device does away the multiple steps involved in analysis of amplified DNA as in agarose gel electrophoresis in the presence of ethidium bromide and the complexity of fluorescence probes analysis usually done in a real-time PCR. Additionally, the device can validate a PCR assay through the detection of internal amplification control DNA of a PCR assay. Furthermore, with a built-in control for device operational assessment, this system ensures validity of results generated.

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Abstract

The present invention relates to a lateral flow device (1) for detecting the presence or absence of at least one target nucleic acid sequence (13) bearing a first hapten label (14) and a second hapten label (15), comprising a) a conjugates region (3) containing a detector conjugate (9) which binds to the second hapten label (15) of the target nucleic acid sequence (13) and is provided with a signalling label; b) an application region (2) adjacent to said conjugates region (3); c) a detection region (4) adjacent to said application region (2), said detection region (4) containing at least one capture sub-region (6) containing a capture reagent (10) immobilized in the capture sub-region (6), which binds to the first hapten label (14) of the target nucleic acid sequence (13); d) an adsorbent region (5) adjacent to said detection region. Further, it provides a chromatographic control of the workability of the device and for an internal amplification control that verifies a nucleic acid amplification assay. In addition to that, the present invention relates to a method using said device.

Description

Lateral flow device and method of detection of nucleic acid sequence Field of the Invention
The present invention relates to a lateral flow device destined for the detection of the presence or absence of a target nucleic acid sequence and to a method of detection of the target nucleic acid sequence using said device. Background Art
Since the detection of specific DNA or RNA target nucleic acid sequence or segment present in air, food, water, environmental or clinical samples is of great significance in the medical, microbiology, food and water safety-testing, and environmental monitoring fields, a wide variety of molecular diagnostic tools have been developed. The detection for the presence of a specific genetic sequence in a sample can rapidly and correctly identify genetic defects, oncogenic events and bacterial, viral or parasitic agents of concern.
Common methods for molecular detection involve a primary step of molecular amplification of the target genetic sequence, and most regularly employing polymerase chain reaction (PCR) assay. The second step is detection of the amplified products using various optical detection such as intercalating dyes, molecular beacons, or microfluidic biosensors using dye-entrapping liposomes which requires special instruments.
Conventional method for detecting amplification products involves using electrophoretic separations coupled with carcinogenic ethidium bromide staining for visualization under
UV spectrometry, or radioisotopic detection. These techniques are labour-intensive and time consuming, especially for health care concern.
Lateral flow tests are simple devices intended to detect the presence or absence of a target analyte in a sample. Most commonly these tests are used for medical diagnostics, for home testing, or laboratory use. They are often produced in a dipstick format, and the test sample flows along a solid substrate via capillary action. After the sample is applied to the test, it encounters a coloured reagent which mixes with the sample and transits the substrate encountering lines or zones which have been pretreated with an antibody or antigen. Depending upon the analytes present in the sample the coloured reagent can become bound at the test line or zone. Lateral flow dipsticks have been well used in the art for detection of antigens or antibodies from a liquid sample. These devices require very little expertise to use and can give results within minutes. The current invention utilizes the principles and advantages of lateral flow dipsticks for detection of amplified nucleic acid analytes in a simple and rapid format.
Though many immunochromatography lateral flow assays have been developed for the detection of proteins currently not many have been developed to detect the DNA. A device for detection of nested PCR amplified DNA using nitrocellulose membrane as reaction membrane and fibreglass membrane for housing detector reagents was described (Horng et al, 2006). Another known device uses gold labelled probe as detector reagent, and cannot function as a universal DNA detection device (Laurent et al, 2009). These biosensors for the detection of DNA sequences may greatly reduce the assay time and simplify its protocol. Such fast on-site monitoring schemes are required for quick preventive action and early diagnosis. Therefore, analysis of the DNA by various faster methods has recently become an attractive research area. The objective of the present invention is the development of a microsphere based DNA biosensor device which is capable of detecting the amplified DNA by lateral flow technology. The advantage of this new diagnostic device is the reduction of the time taken to analyze the amplified DNA as compared to the conventional agarose gel, which requires skilled workers and use of a carcinogenic substance like ethidium bromide.
Disclosure of the Invention
Object of the present invention is a lateral flow device for detecting the presence or absence of at least one target nucleic acid sequence bearing a first hapten label and a second hapten label, comprising
a) a conjugates region containing a detector conjugate which binds to the second hapten label of the target nucleic acid sequence and is provided with a signalling label;
b) an application region adjacent to said conjugates region; c) a detection region adjacent to said application region, said detection region containing
- at least one capture sub-region containing a capture reagent immobilized in the capture sub-region, which binds to the first hapten label of the target nucleic acid sequence,
- an internal amplification control sub-region, containing an internal amplification control capture reagent immobilized in the internal amplification control sub- region, which binds to a first hapten label of an internal amplification control nucleic acid sequence, which is different from the first hapten label of the target nucleic acid sequence, said internal amplification control sub-region preferably being located between the last capture sub-region and a chromatographic control sub-region,
- a chromatographic control sub-region containing an antibody against the detector conjugate, said antibody being immobilized in the chromatographic control sub- region, said chromatographic control sub-region being located between the last capture sub-region and an adsorbent region;
d) an adsorbent region adjacent to said detection region.
A hapten generally is a small molecule that can elicit an immune response only when attached to a large carrier. In this invention, a hapten label provides a unique tag, which a specific detector agent (e.g., an antibody) can detect and capture.
The application, conjugate and detection regions may be made of a single continuous glass fibre membrane, or they may include glass fibre membrane in capillary contact with other membrane types to allow lateral flow as a single whole device. A glass fibre membrane is made of glass fibres bound into a porous matrix. The glass fibre membrane is porous and hydrophilic and as such allows capillary migration of a solution and its solutes from the wicking region to the absorbent region of the device while moving along rehydrated conjugates, without hindrance.
The absorbent region is preferably made of cellulose.
The device according to the present invention may be provided with a backing. The backing may be a rigid or semi-rigid polymer, e.g., polyester, vinyl, etc. The purpose of the backing is to provide mechanical strength which makes the device easy to handle and use. The backing may be connected with other parts of the device, e.g., by laminating or adhesion. An example of a suitable backing is white vinyl backing with pressure adhesive from G&L Precision Die-cutting (The Netherlands). The detection region may contain one or more capture sub-regions, preferably lines, with each dedicated to the detection of one particular target analyte. Each capture sub-region may contain a different capture reagent, specific to the first hapten label of its target nucleic acid sequence. The capture reagent which is specific to the first hapten label of the polynucleotide analyte, different from the second hapten label recognized by the detector reagent, serves to detect and capture the analyte from the liquid sample. The capture reagent will form a complex with the analyte, which is then detected by the binding of the detector reagent to form a visual signal. The capture reagent may be a monoclonal or polyclonal antibody or a molecule that specifically interacts with the hapten labels of the target polynucleotide analyte, and may be immobilized by coupling to a carrier bead (carrier microparticle). The carrier bead preferably is from material that allows the stable addition of capture reagents to the surface, and allows analyte samples to approach the surface even after prolonged dried storage. Furthermore, the carrier bead should be of similar colour and tint to the chromatographic membrane (e.g., glass fibre membrane) material in which the capture reagents are impregnated. The beads should also be of sufficient size to ensure efficient trapping within the matrix of the membrane and at the same time provide sufficient surface area for the capture reagent to capture the analyte from the liquid sample. Preferably, the carrier beads may be polystyrene latex beads activated with carboxyl groups. Covalent coupling of the amino groups of the capture reagent to COOH-modified microparticles may be performed through the use of carbodiimide (with or without hydroxysuccinimide ester).
The detector conjugate, which is specific for the second hapten label on the target polynucleotide analyte, serves to provide a visual signal in the presence of the analyte. The specific detector reagent will form a complex with the analyte captured by the capture reagent in the capture sub-region. This detector reagent may be a conjugated polyclonal or monoclonal antibody that could bind specifically to the complementary second hapten labelled to the polynucleotide analyte. The detector reagent employs coloured particulate labels to provide a visual signal. Known labels include coloured latex microparticles, colloidal carbon particles and metallic colloids such as gold and silver. In a preferred embodiment, the coloured particulates of detector conjugate reagent in the conjugate region are colloidal gold particles with diameter of 30 to 40 nm, preferably 40 nm diameter particles, coated with monoclonal or polyclonal antibodies.
The chromatographic control, preferably as a control line, may be made of a species- specific antibody against the detector reagent and may be immobilized by coupling to carrier beads similarly to above-mentioned capture reagent. The formation of complex between the control line reagent and the detector reagent will give rise to a control signal. This enables the user to check whether the device is in working order or not.
The device according to this invention is destined for rapid and specific detection of the presence of target nucleic acid products from a molecular amplification assay, particularly from a PCR assay, and for the verification of the amplification cycles. The primers in the particular PCR assay are modified to have a different hapten label at the 5' end of each primer. Molecular amplification using this set of modified primers produces polynucleotide products labelled with two different haptens at different ends. These hapten labelled polynucleotides are detected by specific capture by the capture reagents.
The PCR assay to be used for molecular amplification of the target nucleic acid sequence includes an internal amplification control (IC) which verifies the amplification cycles. The primers for both target genetic sequence and IC material share one common hapten label (the second hapten label) for one of the two primers in each pair, while having another two different first hapten labels for the other primer in each pair. This modification of both primer pairs will generate two polynucleotide analyte types - both sharing one common hapten at one end while having two different haptens for the other end. The hapten labelled polynucleotide analyte amplified from the target nucleic acid sequence will be captured by one capture reagent, while the other polynucleotide analyte amplified from IC material will be captured by the internal amplification control capture reagent within the internal amplification control sub-region. The first capture reagent binds to a specific first hapten on the polynucleotide analyte amplified from target genetic sequence, while the second (IC) capture reagent binds to a different specific first hapten on the polynucleotide analyte amplified from IC material. Visual signal is generated for both captured analytes at first capture reagent and second capture reagent when the detector reagent forms complexes with the common second hapten labels present on the other end of both polynucleotide analytes.
The internal amplification control capture reagent may be a monoclonal or polyclonal antibody or a molecule that specifically interacts with the hapten labels of the internal amplification control polynucleotide analyte, and may be immobilized by coupling to a carrier bead, similarly to the capture reagent for the target nucleic acid sequence.
Preferably, the capture sub-region, the chromatographic control sub-region and the internal amplification control sub-region all have the shape of lines extending the whole width of the detection region.
The present invention further includes a method of detecting the presence or absence of at least one target nucleic acid sequence using the device comprising the internal amplification control sub-region, comprising the steps of:
a) carrying out a PCR reaction with one of forward and reverse primers specific for the target nucleic acid sequence being modified to have at the 5 ' end the first hapten label for the target nucleic acid sequence and the other of forward and reverse primers specific for the target nucleic acid sequence being modified to have at the 5 ' end the second hapten label for the target nucleic acid sequence, and with an internal amplification control nucleic acid sequence with one of forward and reverse primers specific for the internal amplification control nucleic acid sequence being modified to have at the 5 ' end the first hapten label for the internal amplification control nucleic acid sequence, which is different from the first hapten label for the target nucleic acid sequence, and the other of forward and reverse primers specific for the internal amplification control nucleic acid sequence being modified to have at the 5 ' end the second hapten label for the internal amplification control nucleic acid sequence, which is identical to the second hapten label for the target nucleic acid sequence,
b) applying a sample taken from the PCR reaction mixture after carrying out the PCR reaction to the application region of said device, c) dipping said device into a chromatographic running buffer,
d) detecting the target nucleic acid sequence captured by the capture reagent within the capture sub-region and labelled by the detector conjugate,
e) determining whether the PCR reaction was not inhibited by detecting the internal amplification control nucleic acid sequence captured by the internal amplification control capture reagent within the internal amplification control capture sub-region, and f) determining whether the device works by detecting the detector conjugate within the chromatographic control sub-region. The chromatographic running buffer rehydrates the immobilized and dried detector reagent and releases it from the conjugate pad area, and it ensures the passage of the added sample analyte and the rehydrated detector reagent through the reaction membrane for efficient specific capture of target analytes by capture reagents. The chromatographic running buffer can, for example, consist of a low molarity phosphate buffered saline (PBS) buffer containing pre-determined amounts of a chemical detergent polyoxyethylene (20) sorbitan monolaurate.
Said chemical detergent ensures complete rehydration of the dried, impregnated detector reagent and release of the detector reagent from the conjugates region into the detection region.
Conventional lateral flow dipsticks are usually based on nitrocellulose membrane which is hydrophobic in nature and requires blocking of unreacted sites to prevent background signals. One embodiment of the current invention overcomes many of these problems by using a glass fibre membrane as the platform for the novel device, thus ensuring hydrophilic properties and requires no complicated blocking strategies. The same glass fibre membrane is also used as the conjugate pad, sample application pad and the reaction pad and this easily avoids contact problems which prevent imperfect flow characteristics of liquid samples within the device. This ensures that polynucleotide analytes from a molecular amplification assay can pass unhindered through the membrane and does not bind non-specifically to the membrane -Material incompatibility issues frequently plague lateral flow dipsticks based on nitrocellulose as different components require different material sources, but in contrast the device according to the present invention is free from such matters and thus is easier to manufacture. The present invention in a preferred embodiment immobilizes capture reagents that are conjugated to carrier beads within the glass fibre membrane matrix. The device can be modified to detect one target amplicon analyte as well as the internal amplification control (IC) amplicons of the molecular amplification assay. This ensures the validity of the molecular amplification assay. The device further incorporates a chromatographic control to check whether the device is in working order or not.
The present invention is aimed to replace the conventional method of detecting amplicons from a molecular amplification assay with a device capable of detecting the amplification products in as little as 5 minutes and requires no special equipment or trained personnel. The disposable device is easy to manufacture and simple to use.
Brief description of figures
Fig. 1 shows the device as desribed in the example 1.
Fig. 2 shows a schematic representation of the result of an analysis carried out with a device described in the example 2. Examples of carrying out the Invention
The invention is herein further described by way of examples, which should not be construed as further limiting. Example 1
Construction of device
The device used in this example (Fig. 1 ) comprises an application 2, conjugate 3, detection 4 and absorbent 5 regions, the detection region comprising a capture sub-region 6, an internal amplification control sub-region 7 and a chromatographic control sub-region 8, each of the sub-regions having the shape of a line extending the whole width of the detection region 4. The glass fibre membrane chromatographic device that is presented in this example consists of a glass fibre membrane (detail of the membrane structure is shown in a circle in Fig. 1 ), attached to a semi-rigid polymer backing 18, preferably of white vinyl backing with pressure adhesives by G&L Precision Die-cutting (The Netherlands), together with an absorbent area made from cellulose. The glass fibre membrane is used as the application 2, conjugates 3 and detection 4 areas, while the cellulose membrane is used as the absorbent area 5. The detection area houses two capture reagents 10, 1 1 , the reagent 10 dedicated for the detection of the specific target polynucleotide amplicons, while the reagent JJ. is for detection of the internal amplification control of a PCR assay.
On the detection area 4, the capture reagents 10, 1 1 and the chromatographic control antibody 12 are immobilized within the glass fibre membrane. The first capture reagent J_0, dedicated for detecting target amplicons J_3, comprised of streptavidin coated microparticles, while the second (IC) capture reagent JJ_, dedicated to detecting PCR internal amplification control amplicons J_6, is made up of anti-digoxigenin antibody coated microparticles. The chromatographic control antibody J_2 is made from goat anti- mouse IgG antibodies coated onto microparticles.
On the conjugates area 3, the monoclonal anti-fluorescein antibody conjugated colloidal gold particles are the detector reagents 9 used in this example and are impregnated into the glass fibre membrane.
The conjugate pad 3 is impregnated with coloured particles that are coated with monoclonal or polyclonal antibodies or molecules that can specifically bind to their complementary specific hapten attached on polynucleotide analytes. The coloured particles of conjugate reagent 9 in the conjugate region 3 are colloidal gold particles with diameter of 40 nm. The conjugates region is impregnated with the gold conjugate after a dilution step in a specific buffer to provide optimal rehydration with the chromatographic running buffer when the test is running. The gold conjugates is preferably diluted into a final 10 mM phosphate buffer containing 200 mg/ml sucrose, 50 mg/ml trehalose and 10 mg/ml bovine serum albumin before sprayed into the membrane using an air spray dispenser (e.g. Airjet dispenser of the XYZ3050 dispensing system from BioDot) at 10 μΐ/cm to 40 μΙ/cm, in this example at 20 μΐ/cm, with a pressure ranging from 1 to 6 psi. Coupling antibodies to colloidal gold is well known in the art. The detector reagent used here is monoclonal anti- fluorescein antibody. Briefly, one part of antibodies diluted in borax buffer is mixed with 4 parts of colloidal gold particles at 1.0 OD53o for 30 minutes in room temperature for the bioconjugation process. Unreacted sites are later blocked by the addition of bovine serum albumin and the blocking is allowed to proceed for an additional 30 minutes. Excess antibodies are removed by centrifugation followed by resuspension of the conjugates in phosphate buffer supplemented with bovine serum albumin. The gold conjugates are later added with sucrose and trehalose just before spraying onto the conjugates area of the device.
The capture reagent J_0 immobilized in the capture sub-region 6 of the detection region 4 of the device, the internal amplification control capture reagent JJ_ located in the IC sub- region 7, as well as the chromatographic control reagents Y2 immobilized in the chromatographic control sub-region 8, are coupled to carrier beads. Polystyrene latex beads activated with carboxyl groups (COOH) are used to couple the capture reagents 1 1 and the chromatographic control reagent 12. Covalent coupling of the amino groups of the capture reagent to COOH-modified microparticles is performed through the use of carbodiimide (with or without hydroxysuccinimide ester). Capture reagent for the target PCR amplified nucleic sequence is streptavidin which binds specifically to the biotin hapten \ A. Capture reagent for internal amplification control of PCR is polyclonal anti- digoxigenin antibody which captures specifically the digoxigenin hapten Γ7. Chromatographic control reagent is polyclonal goat anti-mouse IgG antibody which specifically captures the detector reagent 9. The capture reagents and chromatographic control reagent are covalently coupled to COOH-modified polystyrene latex microparticles of 2.0 μιη in diameter using carbodiimide chemistry. This coupling strategy is well known in the art and it is performed here as described by the latex microparticles manufacturer (Polysciences, USA) with modifications. Briefly, the latex beads are washed and resuspended in MES buffer before activation with carbodiimide. The activated beads are washed and resuspended in borate buffer. Covalent coupling with the capture reagents and chromatographic control reagent are performed by mixing the capture reagents and chromatographic control reagent, diluted in the same borate buffer, with the activated beads. The reaction is performed for 15 minutes at room temperature before blocking of unreacted sited on the beads by addition of ethanolamine. The coupled beads are washed to remove excess uncoupled capture reagents and chromatographic control reagent by centrifugation and finally resuspended in 10 mM phosphate buffer. Impregnation of the capture reagents 10, 1 1 and the chromatographic control reagent V2 within the glass fibre membrane matrix is performed by diluting the reagent in an appropriate buffer and dispensing onto the membrane with a contact system (e.g. XYZ3050 from BioDot). Dispensing rate can vary from 2 μΐ/cm to 8 μΐ/cm. Reagent concentration varies from 10 mg/ml to 30 mg/ml and preferably at 20 mg/ml. In this example, the buffer used for dispensing consisted of 20 itiM phosphate buffer at pH 7.4.
The glass fibre membrane is attached by means of pressure adhesive material to a semi- rigid backing card J_8 together with the cellulose absorbent membrane. The backing is made of white vinyl. The membrane is then dried within a vacuum chamber for 30 minutes after impregnation of the capture reagents and the gold conjugates into the membrane matrix. The membrane is then further dried in a desiccating chamber of <10% relative humidity overnight. The membrane is later cut into 5 mm width pieces and stored in a sealed pouch together with silica gel.
Example 2
Detection of specific DNA sequences The DNA detection procedure is described herein with reference to Fig. 2, which schematically shows the analysis and its result.
Amplification of target DNA
Target DNA sequence \ 3 amplification was performed by PCR with a 5 ' end biotin hapten J_4_labelled forward primer and a 5 ' end fluorescein hapten J_5 labelled reverse primer. The amplification reaction is performed simultaneously with the internal amplification control within the same reaction mixture.
Internal amplification control of PCR
The internal amplification control is designed as to show if a negative test result is a true negative, i.e. that the negative result is not due to an amplification inhibitory substance possibly present in the test sample. This internal amplification control is a set of PCR primers with its complementary template DNA that is different from the target DNA sequence. The template for internal amplification control is designed from an unrelated species. The forward primer is modified to be labelled with digoxigenin hapten J_7 at the 5' end while the reverse primer is modified to be labelled with fluorescein hapten J_5 at the 5' end. The primers are designed to be specific only for the internal amplification control template and do not hybridize with the target DNA sequence. Amplification of this control template will produce control amplicons labelled with digoxigenin and fluorescein haptens.
Target DNA sequence detection
10 μΐ of the PC reaction was pipetted onto the application region 2 of the dipstick device 1. The dipstick device is then immediately dipped into a microplate well containing 140 μΐ of chromatographic running buffer and the detection is allowed to proceed for 5 minutes. The chromatographic running buffer migrates in the dipstick, rehydrates the gold conjugates 9 from the conjugates area 3 and then pushes the amplicons previously applied onto the application area 2 out to the detection area 4. The target DNA sequence amplicons are captured by the streptavidin coated beads J_0 on the capture sub-region 6 through the biotin hapten 14 labelled on the amplicons. The internal amplification control capture sub- region 7 houses the anti-digoxigenin antibody coated beads _N and detects the internal amplification control amplicons J_6 via binding of digoxigenin label Γ7 on the control amplicons. The rehydrated gold conjugates 9 are carried to the detection area and form complexes with the captured amplicons of both target and internal amplification control. The accumulation of colloidal gold particles gives a distinct cherry red colour, showing a positive result. The remaining gold conjugates migrate further and are captured by the chromatographic control antibody \2 in the chromatographic control area 8, giving rise to a signal.
Industrial Applicability
The present invention provides a device for a simple and rapid visual detection of amplified DNA of a target gene using immobilized capture reagents, e.g., polystyrene microparticles coated with capture reagents, and visualized through detector conjugates, e.g., gold nanoparticle-based detector reagent, within a bound glass membrane-based lateral-flow device. The device can be used to detect labelled amplified DNA, commonly from a polymerase chain reaction (PCR) assay, without specialised equipment or trained staff in as little as 5 minutes. The device does away the multiple steps involved in analysis of amplified DNA as in agarose gel electrophoresis in the presence of ethidium bromide and the complexity of fluorescence probes analysis usually done in a real-time PCR. Additionally, the device can validate a PCR assay through the detection of internal amplification control DNA of a PCR assay. Furthermore, with a built-in control for device operational assessment, this system ensures validity of results generated.
) References
Horng, Y. T., Soo, P. C, Shen, B. J., Hung, Y. L., Lo, . Y., Su, H. P., Wei, J, R., Hsieh, S. C, Hsueh, P. R. & Lai, H. C. (2006). Development of an improved PCR- ICT hybrid assay for direct detection of Legionellae and Legionella pneumophila from cooling tower water specimens. Water Res, 40 (1 1 ), 2221 -9.
Laurent, T., Van der Auwera, G., Hide, M., Mertens, P., Quispe-Tintaya, W., Deborggraeve, S., De Doncker, S., Leclipteux, T., Banuls, A. L., Buscher, P. & Dujardin, J. C. (2009). Identification of Old World Leishmania spp. by specific polymerase chain reaction amplification of cysteine proteinase B genes and rapid dipstick detection. Diagn Microbiol Infect Dis, 63 (2), 173-81.

Claims

1. A lateral flow device for detecting the presence or absence of at least one target nucleic acid sequence (13) bearing a first hapten label (14) and a second hapten label ( 15), comprising
a) a conjugates region (3) containing a detector conjugate (9) which binds to the second hapten label (15) of the target nucleic acid sequence (13) and is provided with a signalling label;
b) an application region (2) adjacent to said conjugates region (3);
c) a detection region (4) adjacent to said application region (2), said detection region (4) containing
- at least one capture sub-region (6) containing a capture reagent (10) immobilized in the capture sub-region (6), which binds to the first hapten label (14) of the target nucleic acid sequence (13),
- an internal amplification control sub-region (7), containing an internal amplification control capture reagent (1 1 ) immobilized in the internal amplification control sub-region (7), which binds to a first hapten label (17) of an internal amplification control nucleic acid sequence (16), which is different from the first hapten label (14) of the target nucleic acid sequence (13), said internal amplification control sub-region (7) preferably being located between the last capture sub-region (6) and a chromatographic control sub-region (8),
- a chromatographic control sub-region (8) containing an antibody against the detector conjugate (9), said antibody being immobilized in the chromatographic control sub- region (8), said chromatographic control sub-region being located between the last capture sub-region (6) and an adsorbent region (5);
d) an adsorbent region (5) adjacent to said detection region (4).
2. The device according to claim 1 , wherein the capture sub-region (6), the chromatographic control sub-region (8) and the internal amplification control sub-region (7) each have the shape of a line extending the whole width of the detection region (4).
3. The device according to any of preceding claims, wherein a backing (18) is provided.
4. The device according to any of preceding claims, wherein the application (2), conjugate (3) and detection (4) regions are made of a single continuous, or two-piece overlapped glass fibre membrane and the absorbent region (5) is made of cellulose.
5. The device according to any of claims 1 to 3, wherein the application (2), conjugate (3) and detection (4) regions are made of glass fibre membrane in capillary contact with other membrane types, and the absorbent region (5) is made of cellulose.
6. The device according to any of preceding claims, wherein the detector conjugate (9) is a polyclonal or monoclonal antibody, conjugated with a signalling label selected from the group comprising coloured latex microparticles, colloidal carbon particles and metallic colloidal particles, preferably colloidal gold particles and colloidal silver particles.
7. The device according to any of preceding claims, wherein at least one of the capture reagent (10), the internal amplification control capture reagent (1 1 ) and the antibody (12) for chromatographic control is immobilized by coupling to carrier beads, preferably, the carrier beads are polystyrene latex beads activated with carboxyl groups.
8. A method of detecting the presence or absence of at least one target nucleic acid sequence (13) using the device (1 ) according to claim 1 , comprising the steps of:
a) carrying out a PCR reaction with one of forward and reverse primers specific for the target nucleic acid sequence being modified to have at the 5' end the first hapten label (14) for the target nucleic acid sequence and the other of forward and reverse primers specific for the target nucleic acid sequence being modified to have at the 5 ' end the second hapten label (15) for the target nucleic acid sequence, and with an internal amplification control nucleic acid sequence with one of forward and reverse primers specific for the internal amplification control nucleic acid sequence being modified to have at the 5 ' end the first hapten label (17) for the internal amplification control nucleic acid sequence, which is different from the first hapten label (14) for the target nucleic acid sequence, and the other of forward and reverse primers specific for the internal amplification control nucleic acid sequence being modified to have at the 5 ' end the second hapten label (15) for the internal amplification control nucleic acid sequence, which is identical to the second hapten label for the target nucleic acid sequence,
b) applying a sample taken from the PCR reaction mixture after carrying out the PCR reaction to the application region (2) of said device (1 ),
c) dipping said device (1 ) into a chromatographic running buffer,
d) detecting the target nucleic acid sequence (13) captured by the capture reagent ( 10) within the capture sub-region (6) and labelled by the detector conjugate (9),
e) determining whether the PCR reaction was not inhibited by detecting the internal amplification control nucleic acid sequence (16) captured by the internal amplification control capture reagent (1 1 ) within the internal amplification control capture sub-region (7), and
f) determining whether the device (1 ) works by detecting the detector conjugate (9) within the chromatographic control sub-region (8).
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