WO1991015768A1 - Process and composition for performing dna assays - Google Patents
Process and composition for performing dna assays Download PDFInfo
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- WO1991015768A1 WO1991015768A1 PCT/US1991/002323 US9102323W WO9115768A1 WO 1991015768 A1 WO1991015768 A1 WO 1991015768A1 US 9102323 W US9102323 W US 9102323W WO 9115768 A1 WO9115768 A1 WO 9115768A1
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- nucleic acid
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- magnetically responsive
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L7/00—Heating or cooling apparatus; Heat insulating devices
- B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING 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
- C12Q1/00—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
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING 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
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
- C12Q1/701—Specific hybridization probes
- C12Q1/702—Specific hybridization probes for retroviruses
- C12Q1/703—Viruses associated with AIDS
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
- G01N33/54313—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals the carrier being characterised by its particulate form
- G01N33/54326—Magnetic particles
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
- G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
- G01N35/1009—Characterised by arrangements for controlling the aspiration or dispense of liquids
- G01N2035/1025—Fluid level sensing
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
- G01N35/0098—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor involving analyte bound to insoluble magnetic carrier, e.g. using magnetic separation
Definitions
- This invention relates generally to nucleic acid hybridization assays and, more particularly, to a fully automated process for performing nucleic acid hybridization assays using magnetically responsive particles.
- Nucleic acids which are the carriers of genetic information between generations, are composed of linearly arranged individual units called nucleotides. Each nucleotide has a sugar phosphate group to which is attached one of the pyrimidine or purine bases, adenine (A) , thymidine (T) , uracil (U) guanine (G) or cytosine
- nucleic acid Single stranded nucleic acids form a double helix through highly specific bonding between bases on two strands; A will bond only with T or U, G will bond only with C. Thus, a double stranded, or hybridized, nucleic acid will form where, and only where, the sequence of the bases in the two strands is sufficiently complementary as to allow such hybridization.
- the nucleic acid is termed either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) .
- Nucleic acid hybridization assays are based on this principle of complementarity. Typically, a single stranded nucleotide sequence complementary to the sequence of interest is combined with a sample under conditions allowing hybridization. The former sequence is termed the "probe;” the latter, the “target.” The presence of double stranded nucleic acid including the probe indicates that the target sequence is present in the sample.
- Such assays have wide applicability, including the testing of biological samples for the presence of a pathogen, such as a bacterium, virus or parasite; the diagnosis of disease associated with a genetic abnormality; the indication of susceptibility to certain genetically mediated conditions; paternity or other relatedness, as for example in forensic analysis; and the biological contamination of food or other product.
- PCR polymerase chain reaction
- ligation-based amplification procedures See, for example, United States Patent Nos. 4,683,195; 4,683,202 and 4,800,159 and the PCT Publication No. W089/12696.
- nucleic acid hybridization assays utilize isotopic detection, primarily 32 P, and are manual processes requiring separation steps.
- the conventional membrane-based assays involve sample pretreatment, denaturation, and fixation of nucleic acids onto solid supports, such as nitrocellulose or nylon filters.
- Such procedures are imprecise, labor intensive, time consuming, and difficult to automate.
- the hybridization probes are usually radiolabeled to high specific activity in order to obtain the required sensitivity. Clinical laboratories are averse to such probes because they are unstable and present significant problems of handling and disposal. Consequently, the few such tests on the market have limited practical application in the clinical laboratory.
- Non-isotopic labels have also been used in nucleic acid hybridization assays.
- biotin labeled probes utilizing alkaline phosphatase-avidin polymeric complexes can be used to detect unique DNA sequences immobilized on filters through the enzymatic production of a colored, precipitatable dye, as described by Ward, et al., U.S. Patent No. 4,711,955.
- These nonisotopic, indirect detection systems however are plagued by intermediate, background-susceptible, binding and washing steps, and are limited to hybridization on membranes.
- Direct capture hybridization supports are synthesized by attaching nucleic acids, usually cloned DNA, by chemical modification, adsorption, or enzymatic processes to a variety of solid phases, including nitrocellulose, cellulose, nylon, polystyrene, teflon- polyacrylamide, polypropylene, agarose, sephacryl and latex.
- the hybridization efficiencies and capacities of immobilized DNA have been described in detail. See, for example, Miller, et al., J. Clin. Microb. July 1988, p. 1271-1276 and Yehle, et al., Molecular and Cellular Probes 1:177-193 (1987), which are incorporated herein by reference.
- the supports described thus far are difficult to make, however, and with the exception of oligonucleotide resins, have relatively poor loading capacities.
- the mixed-phase direct capture hybridizations are also limited kinetically and may be inefficient due to inaccessibility of immobilized DNA.
- the present invention resides in an improved process for performing nucleic acid hybridization assays that is both highly precise, efficient and repeatable and that is fully automated, requiring only minimal involvement by trained personnel.
- the process of the invention includes an initial step of providing a programmable XYZ pipetter and an associated plurality of wells, an associated array of thermally-controlled reaction tube holders, each being adapted to carry a test tube, and means for effecting an alternating or rotating magnetic field about each reaction tube's longitudinal axis.
- the XYZ pipetter is used to transfer nucleic acid samples to separate test tubes carried by the plurality of reaction tube holders, to transfer successively a hybridization solution and a suspension of magnetically responsive particles to the plurality of test tubes at prescribed times, and to effect position of the reaction tubes relative to their associated magnetic fields at prescribed times, such that binding reactions between the target nucleic acid samples, probe and oligonucleotides in the hybridization solution, and magnetically responsive particles can occur and a precise, repeatable automated nucleic acid hybridization assay can be provided.
- the XYZ pipetter is used by initially placing the hybridization solution in a first well, the suspension of magnetically responsive particles in a second well, a wash buffer solution in a third well, a substrate buffer in a fourth well and a quench buffer solution in a fifth well.
- the separate nucleic acid target samples are placed in the plurality of reaction tubes, each carried in a separate reaction tube holder.
- the XYZ pipetter is used initially to transfer the hybridization solution from the first well to the plurality of test tubes, in sequence, whereupon hybridization reactions are allowed to occur.
- the XYZ pipetter transfers the suspension of magnetically responsive particles from the second well to the plurality of reaction tubes, in sequence, and the reaction tubes are then selectively rotated or the magnetic field removed such that the magnetically responsive particles remain in liquid suspension and are allowed to undergo a binding reaction with the separate nucleic acid samples.
- Terminating the step of selectively rotating allows the magnetically responsive particles to be moved by the magnetic fields to selected locations in the reaction tubes, allowing the XYZ pipetter then to remove the unbound nucleic acid sample in the liquid phase and hybridization solution from the plurality of reaction tubes.
- a electromagnetic field may be induced around the stationary tubes to remove the particles from suspension.
- the XYZ pipetter then transfers the wash buffer solution from the third well to the reaction tubes. After resuspension and separation of the magnetically responsive particles, the pipetter then removes the wash buffer solution, to leave behind the magnetically responsive particles with bound DNA sample and hybridization molecules. The pipetter then transfers the substrate buffer from the fourth well to the plurality of reaction tubes whereupon an enzyme probe label catalyzes a detectable reaction. Alternatively, if the label is a luminescent or fluorescent moiety, the probe is dehybridized to allow detection in solution. The pipetter then transfers the quench buffer solution from the fifth well to the plurality of reaction tubes, and then transfers a sample from each of the reaction tubes to a separate well of the microtiter plate. In this fashion, the degree of binding reaction between the hybridization solution and the separate nucleic acid samples can conveniently be measured.
- the XYZ pipetter is further associated with an optical sensor, and the steps of selectively alternating and fixing the magnetic field are accomplished by moving the pipetter's sampling tip to a location where it can be detected by the optical sensor.
- the precise timing of the steps of selectively alternating and fixing the magnetic field, as well as the time delays between the steps of using the pipetter to transfer the hybridization solution and the solution of magnetically responsive particles, are precisely controlled.
- the hybridization solution includes both nucleic acid probes having an attached label and nucleic acid probes having attached biotin or hapten molecules, and the magnetically responsive particles have attached to them avidin, streptavidin or antibody molecules.
- the process thereby effects a sandwich assay.
- the label may be a fluorescent or luminescent moiety, or a labeling enzyme.
- the labeling enzyme advantageously can exhibit fluorescence or luminescence, and the process can further include a step of assaying the samples carried by the microtiter plate using a spectrophotometer, fluorometer, or luminometer.
- the invention utilizes ligand derivatized magnetically responsive particles to separate single stranded target from heterologous nucleic acid in a hybridization assay.
- the magnetically responsive particles can have streptavidin stably attached thereto through a covalent spacer. The length and composition of the attachment to the particles is critical to their performance.
- FIG. 1 is a perspective view of an XYZ pipetter and an associated array of reagent wells and reaction tube holders, for performing a nucleic acid hybridization assay in accordance with the preferred process of the invention.
- FIG. 2 is a plan view of the array of reagent wells and reaction tube holders depicted in FIG. 1.
- FIG. 3 is a generalized flowchart depicting the operational steps performed by the XYZ pipetter of FIG. 1, in performing the nucleic acid hybridization assay of the invention.
- FIG. 4 is a more detailed flowchart of the operational steps performed by the XYZ pipetter in mixing a hybridization buffer with a number of separate nucleic acid samples.
- FIG. 5 is a more detailed flowchart depicting the operational steps performed by the XYZ pipetter in admixing a solution of magnetically responsive particles with the separate nucleic acid samples.
- FIG. 6 is a more detailed flowchart depicting the operational steps performed by the XYZ pipetter in washing the reacted nucleic acid samples.
- FIG. 7 is a more detailed flowchart depicting the operational steps performed by the XYZ pipetter in transferring the reacted nucleic acid samples to a microtiter plate, for subsequent reading.
- Reagents appropriate for use in the process of the invention and methods of preparing them are herein described. It will be appreciated that other reagents and processes, known to those skilled in the art, can alternatively be utilized.
- Oligonucleotide probes can be synthesized using various standard procedures and reagents. Preferably, the probes are chemically synthesized using methods well known in the art. See, for example, Ruth, PCT Publication No. WO84/03285, which is incorporated herein by reference. Capture probes were prepared containing a biotin moiety attached to either an internal base as described in WO84/03285, or to the 5'-terminal nucleotide through a spacer and a C-6 amino modifier. The amino terminated oligomers were synthesized using an automated DNA synthesizer, such as Applied Biosystems, Inc. Model 380 (Foster City, CA) .
- an automated DNA synthesizer such as Applied Biosystems, Inc. Model 380 (Foster City, CA) .
- spacer phosphora idite (O-dimethoxytrityl- diethyleneglycol-0'-(cyanoethyl-N,N-diisopropyl- phosphoramidite) ) and 5'-amino-modifier C6 [3-(4- monomethoxytrity1- amino)hexy1-(2-cyanoethy1)-(N,N- diisopropyl)-phosphoramidite] , (Glen Research Corp., Herndon, VA) were resuspended in anhydrous acetonitrile.
- the spacer phosphoramidite was synthesized as follows. Diethyleneglycol (10 g, 94.2 mole) was rendered anhydrous by repeated evaporation of pyridine under vacuum. 4,4 '-dimethoxytritylchloride (3.19 g, 9.4 mmole) in anhydrous pyridine (20 ml) was added with stirring for 1 hour. After vigorous stirring in ice water (100 ml) , the reaction mixture was extracted with 75 mis methylene chloride, 3 times. Three back extractions with 75 mis water and drying over sodium sulfate were followed by filtration and rctoevaporation to small volume.
- the oligomers were purified by reverse phase HPLC on C-8 silica columns and analyzed by 20% polyacrylamide gel electrophoresis.
- the oligonucleotide- containing reactive amine spacer arm was reacted for 1 hour with a 100 to 1000 fold molar excess of NHS-X-biotin (N-hydroxysuccinimidyl-aminocaproic-biotin; CalBiochem, La Jolla, CA) in 0.2 M sodium bicarbonate, pH 8.5.
- Biotinylated probe was purified from free probe and excess biotin by reverse phase HPLC on C-8 silica columns eluted with an acetonitrile gradient, then desalted and ethanol precipitated. Product purity was determined by analytical gel electrophoresis.
- Direct labeled alkaline phosphate-DNA conjugates can be prepared according to a procedure adapted from the method of Jablonski, et al. Nucl. Acids Res. 14:6115 (1986) , which is incorporated herein by reference.
- the linker arm nucleosides are thymidine analogs modified by replacement of the C-5 methyl with an 11 atom linker arm which terminates in a primary amine.
- Such probes are purified by conventional methodologies and exhibit essentially unaltered behavior with respect to physical characteristics as compared to unmodified probes. More specifically, linker arm nucleoside 3 1 - phosphoramidite was prepare by the method of Ruth, et al.
- the oligomers were purified by reverse phase HPLC on C-8 silica columns and analyzed by 20% polyacrylamide gel electrophoresis. Product purity was determined by analytical gel electrophoresis.
- Linker arm oligomers were first derivatized with disuccinimidylsuberate (DSS) .
- DSS disuccinimidylsuberate
- One volume of oligomer in 0.2 M sodium bicarbonate was combined with a 30 fold excess of DSS in two volumes of DMSO. After 3 minutes at ambient temperature, the reaction was applied to FPLC G- 25 gel filtration column and eluted in 1 mM sodium acetate, pH 5.0. The fractions were monitored by flow- through absorptiometry at 260nm, collected and concentrated by microconcentrator (Centricon 10K; Amicon, Danvers, MA) .
- the invention utilizes ligand derivatized magnetically responsive particles, including those which are magnetic or paramagnetic.
- a variety of materials can be used, including oxides of iron, chromium and titanium or other metals.
- the particles should be small enough to remain dispersed, having an average settling time of greater than about three minutes. Preferably, they are about .1 - lO ⁇ in diameter, more preferably about 1/x.
- Various ligands, other than nucleo ides or oligonucleotides can be utilized, including, for example, avidin or streptavidin, biotin, haptens (including, for example, dinitrophenol (DNP) or digoxigenin, with a carrier) lectins, or antibodies (such as those against biotin, fluorescein or digoxigenin) .
- the length and composition of the covalent linkage between the magnetically responsive particles and the ligands are important to efficient performance.
- the protein is crosslinked to the solid matrix using nonspecific glutaraldehyde, carbodiimides, or cyanogen bromide crosslinking. Both methods produce the protein coupled to the particle.
- activity is significantly reduced and efficiency and strength of binding in subsequent particle hybridization assays is generally unacceptable.
- Beebe et al. in PCT Publication #WO 88/02785, use avidin linked to cellulose beads using N,N'-carbonyldiimidazole, and require the use of 33 mg of beads per assay to have adequate binding sites.
- the covalent linkage produced as described below contains multiple, alternate hydrocarbon and amide (including urea) residues.
- the linker contains at least three total residues and is preferably less than eight total residues.
- the method described below produces proteins attached to magnetically responsive particles through a relatively long linkage (20-60 atoms) with a mixed hydrophilic/hydrophobic character. After testing many lengths and compositions of linkage, this linkage has proved to be the most preferred.
- linkage of proteins to particles using conventional glutaraldehyde, carbodiimide, or cyanogen bromide crosslinking also gives a hydrolyzable linkage which may not be stable to storage conditions in aqueous solutions or mild acids and bases.
- the present invention provides linkages which are chemically stable to aqueous solutions or mild acids or bases, as, for example between pH 4 and 8 and is additionally stable to many a ine-containing buffers, such as Tris, which are often used in biochemical procedures. The resulting particles can be stored and used much more conveniently.
- Streptavidin derivatized magnetically responsive particles were prepared. Briefly, 10 ml of aqueous suspension of amine derivatized magnetic particles, approximately 1 ⁇ m in diameter (Advanced Magnetics, Inc. , Cambridge, MA) (50 mg/ml) was centrifuged at 12,000 rpm for 30 minutes. The supernatant was discarded and the precipitate was fully resuspended, by vortexing in 20 ml of H 2 0 and recentrifuged. The particles were further washed in 20 ml portions of water, twice in methanol, 10% methanol/triethylamine, twice in methanol, and finally twice in ether. The particles were completely resuspended each time. The particles were thoroughly desiccated over P 2 0-Na0H in a vacuum.
- Precipitated particles were freely suspended in anhydrous dioxane (10 ml) , and then centrifuged off in a corex tube. After removing the supernatant, the particles were resuspended in fresh dioxane (10 ml) , then 1,6-diisocyanatohexane (2 ml) was quickly mixed in and the reaction tube placed on a rotator, overnight. Next day, the magnetic particles were centrifuged, the supernatant removed, and the particles were carefully washed with anhydrous dioxane by vortexing and centrifugation, 3 times.
- the precipitate was resuspended in 10 ml of dioxane, to which a solution of 1 g 1,6-diamino-hexane in 5 ml of dioxane was added.
- the reaction tube was placed on the rotator overnight. Next day, the particles were centrifuged and then washed three times with dioxane (20 ml portions) .
- the dioxane-moist particles were resuspended in a solution of glutaric anhydride (1 g) , p-dimethylaminopyridine (1 g) , anhydrous acetonitrile (15 ml) and anhydrous pyridine (5 ml) .
- the particles were centrifuged and thoroughly washed 6 times with dimethylformamide (10 ml each) . They were then transferred into an eppendorf tube and further washed with anhydrous acetonitrile 3 times. They were finally resuspended in anhydrous acetonitrile (1.5 ml). A 100 ⁇ l aliquot of suspension was dried down in a desiccator in a vacuum to determine weight of particles per volume suspension.
- the activated particles were collected to the side of the test tube by a magnet and the supernatant was decanted.
- a 20 mg/ml solution of streptavidin in 0.1 M sodium bicarbonate, 0.05% azide was added to the moist particles at 0.24 mgs streptavidin per mg particles.
- the particles were rotated overnight.
- the particles were washed four times in 1 X SSC, 0.1% SDS and then brought to 50 mg/ml in storage buffer (1 X SSC, l mg/ml BSA, 0.05% triton X100 and 0.05% azide).
- Protein and 14C- biotin binding assays were performed to determine the streptavidin loading and biotin binding capacity per mg particles, respectively.
- Other ligands such as appropriate antibodies, including those to biotin, fluorescein and digoxigenin, can be attached to magnetic particles in a similar manner.
- sample preparation includes lysis of the cells, if present, followed by some separation of cellular nucleic acids from other cellular material. Cells are typically lysed by osmotic pressure, detergent or heat disruption of the membrane, mechanical shearing, ultra sound, or a combination of these methods.
- Nucleic acids can be purified from other cellular materials using methods of solvent extraction, for example, phenol chloroform, ion exchange, or size exclusion, such as dialysis or gel filtration, centrifugation, or a combination of these methods. For some samples, purification of nucleic acids is unnecessary.
- outer cell membranes are lysed by incubation in buffer containing sucrose and non-ionic detergent. Cytoplasmic debris is then removed by pelleting of the nuclei by centrifugation. Addition of detergents and incubation with proteinase K causes lysis of the nuclear membranes and releasing chromosomal nucleic acid. These procedures can be carried out automatically, as described below.
- amplification procedures may be used to specifically increase the target.
- Amplification is typically achieved using standard procedures such as polymerase chain reaction (PCR) , or ligation amplification or other method of amplification.
- PCR polymerase chain reaction
- ligation amplification or other method of amplification Such methods are well known to those skilled in the art. See, generally PCR TECHNOLOGY, (H. A. Erlich, Ed. Stockton Press, 1989) and United States Patent Nos. 4,683,195; 4,683,202; and 4,800,159, which are incorporated herein by reference.
- PCR primer nucleotide sequences complementary to target sequences on opposite strands flanking the sequence of interest are prepared.
- an appropriate DNA polymerase and nucleotide precursors and under suitable reaction conditions, multiple copies of the particular target sequences defined by the flanking primers is exponentially generated.
- a label such as biotin or enzyme, can be covalently attached to one of the primers, resulting in an amplified labelled oligonucleotide.
- primer can contain long or short linker arms without interference with PCR procedures.
- target DNA free of interfering substances is denatured, as by heating to about 95°C, and hybridized with primer oligonucleotides.
- a polymerase such as taq 1 (Cetus Corp., Emeryville, CA) binds to the hybridized primer sequences and catalyzes the synthesis of new complementary strands in the presence of excess nucleotide triphosphates.
- the newly formed strands are separated from the template strand by thermal denaturation. As the temperature is lowered, new primers bind to the template and the process is repeated. These repetitive reactions are carried out automatically in the thermocycler, as described below.
- the present invention includes certain novel features which are advantageously exploited in a variety of nucleic acid hybridization formats.
- the use of magnetically responsive particles to which the target DNA can be bound permits the efficiency of solution hybridization of target and probe while providing a effective subsequent vehicle for the separation of hybridized and non-hybridized nucleic acid.
- the use of magnetically responsive particles facilitates the automation of the assay system.
- the direct labeling of probes permit ligand/ligand, such as biotin/avidin or hapten/antibody, affinity to be utilized to immobilize the probe/target complex on the magnetically responsive particles.
- a sandwich type format is used to detect the presence of a particular nucleotide sequence in a sample.
- biotinylated capture probe having a sequence complementary to the target sequence or a sequence in proximity thereto is combined with a sample under conditions which permit hybridization between the capture probe and the target.
- a detection probe comprising a labeled sequence complementary to the target sequence or a sequence in proximity thereto, is also allowed to hybridize with the sample.
- the affinity of biotin for avidin or hapten to antibody is utilized to attach target/capture probe/detector probe complexes to magnetically responsive particles, where their presence can be detected or quantified.
- magnetic or paramagnetic microspheres can be derivatized with other materials, such as biotin, haptens (including, for example, dinitrophenol (DNP) or digoxigenin with an appropriate carrier, such as BSA) , avidin lectins, or antibodies (such as to biotin) .
- the capture probes can, in turn, be derivatized with a non- oligonucleotide moiety complementary to that on the microspheres, such as avidin, antibodies, carbohydrates or haptens.
- various labels can be used on the detection probe, including radioactive, components of an enzymatic reaction, chemiluminescen , bioluminescent and fluorescent moieties.
- the target and the probes are composed of DNA.
- the target and/or the probes can be composed of RNA such that the method utilizes DNA-RNA or RNA-RNA hybridization.
- the apparatus includes an XYZ pipetter 11, a test tube rack 13, a reaction tube array 15, a plurality of optical sensors 17 associated with the reaction array, a plurality of reagent wells 19, a thermal cycler 21, and a microtiter plate 23.
- the XYZ pipetter includes a conventional sampling tip 25 for transporting various DNA samples and reagents from one location to another, to perform the assay.
- the nucleic acid hybridization performed by the apparatus of FIG. 1 uses a sandwich technology, in which a DNA probe, designed to hybridize with the target DNA, is bound to biotin, while its conjugate, avidin, is bound to magnetically responsive particles.
- the DNA samples to be tested are first mixed with the biotin-linked DNA probe and a second proximal DNA probe labeled with a reporter group and allowed to react. Thereafter, the mixture is combined with the magnetically-labeled avidin and allowed to react. The magnetic label is then separated from the unreacted DNA sample and DNA probes, and the reporter labeled DNA probe bound to the DNA sample is then detected, to complete the assay.
- the XYZ pipetter 11 is a conventional apparatus available from several commercial sources. It is operated under the control of an associated personal computer, which allows great flexibility in selecting the processing details.
- the pipetter is equipped with a positive-flow washing station 27 for use in cleaning the sampling tip 25 and a liquid level sensor (not shown) on the tip.
- the apparatus includes a reaction tube array 15 that carries reaction tubes 29 in which the binding reactions are made to occur.
- the array includes 48 temperature-controlled reaction tube wells, in a 6 x 8 arrangement, with permanent magnets positioned adjacent to each well.
- Each well further has associated with it a variable-speed motor capable of alternating clockwise/counterclockwise rotation at 400-to-1000 rpm, through 45-to-1080 degrees of rotation.
- the reaction tube wells are positioned slightly off center on the vertical motor shaft. Control of each bank of six motors is made using the adjacent photoelectric switch 17, which can be controlled using the pipetter tip 25. In this fashion, the motors are controlled by mere movement of the pipetter tip, without the need for a separate computer interface.
- a particle mixer 19a which includes an associated motor (not shown) for providing vortexing motion, is provided for carrying the magnetically responsive particle reagent.
- This particle mixer has an associated photoelectric switch 31, for selectively switching the motor on and off, although other types of switches can be used.
- the magnetic reaction array 15 holds the various reaction tubes 29 at a selected temperature and functions to selectively disperse and collect the magnetically responsive particles.
- the particles remain in liquid suspension so long as the tube carrying it is rotated by its associated motor.
- the oscillating motion terminates, however, the particles are quickly collected to the sides of the reaction tube under the force of the adjacent permanent magnets, allowing an efficient removal of excess liquid by the pipetter tip 25.
- the subsequent addition of further liquid reagents and resumption of the oscillating motion causes an immediate uniform resuspension of the magnetic particles.
- the thermal cycler 21 is a temperature- programmable microfuge test tube holder adapted to carry out a thermocyclic amplification reaction. Temperature control is preferably provided from about 25° to 110° C, with a temperature ramping speed of about 3 seconds per degree. Amplified samples can be obtained from the thermal cycler for transfer directly into the hybridization reaction tubes 29 using the pipetter tip 25.
- an initial step 41 the various nucleic acid samples are manually placed in separate test tubes of the test tube rack 21, a hybridization solution containing a hybridization buffer with oligomers, is placed in a reagent well 19b, and a solution of magnetically responsive particles is placed in the particle mixer well 19a.
- the XYZ pipetter apparatus is in condition to initiate the fully-automated portion of the nucleic acid hybridization assay.
- the aspirating/dispensing tip 25 of the XYZ pipetter 11 sequentially aspirates the hybridization solution from the well 19b and the successive nucleic acid samples from the test tubes of the test tube rack 21 and transfers these combined solutions to separate test reaction tubes of the reaction tube array 15.
- the XYZ pipetter in a subsequent step 45, aspirates the solution of magnetically responsive particles and transfers it sequentially to the reaction tubes in the reaction tube array.
- the liquid portion of each sample is removed at step 47 and the remaining magnetic particles, with bound DNA probe and possible DNA sample, is washed using the wash buffer solution carried in a well 19c.
- the pipetter tip 25 is used to remove the wash solution from the reaction tubes and to transfer to the tubes a substrate buffer solution.
- the pipetter tip 25 transfers a quench buffer solution from the well 19d and a sample from each reaction tube to a separate well of the microtiter plate 23 at step 49.
- the tagged DNA probe in these samples is thereafter read, for example using a fluorometer.
- FIG. 4 is a flowchart depicting, in greater detail, the step 43 from FIG. 3 of combining the hybridization solution with the various nucleic acid samples in the reaction tubes of the reaction tube array 13.
- the pipetter's aspirating/dispensing tip 25 is controllably moved to the well 19b, where it aspirates a prescribed amount of the hybridization solution.
- the tip is moved immediately to the first test tube in the test tube rack 13, where it aspirates a prescribed amount of the nucleic acid sample carried in that test tube.
- the tip is then moved in step 55 to the first reaction tube in the reaction tube array 15, where it dispenses the combined hybridization solution and nucleic acid sample into the tube.
- the tip is then washed at the wash station 27, in step 57.
- step 59 it is determined whether or not the last of the nucleic acid samples has been aspirated from the test tube rack 13. If not, and the last tube in the current column has not been processed, the sample number (n) is incremented by one at step 61, and the program returns to the initial step 51 of aspirating the hybridization solution from the well 19b. Eventually, it will be determined at step 60 that hybridization solution and sample have been dispensed into the last tube in the current column of tubes. When that happens, the program advances to step 63 in which the pipetter tip 25 is moved to the optical sensor 17 for the reaction tube column just completed, to activate its associated column of motors. At step 65 the tip is washed at the wash station 27.
- step 59 it will be determined at step 59 that the last of the n nucleic acid samples has been aspirated from the test tubes of the test tube rack 13 and transferred to a separate one of the reaction tubes of the reaction tube array 15.
- the program then advances to a step 63, in which the pipetter tip 25 is moved to the optical sensor(s) 17 for the affected column(s) of reaction tubes, to switch on the corresponding motors, to begin agitating the solutions.
- step 65 the tip is washed at the wash station 27.
- FIG. 5 is a flowchart depicting, in greater detail, the step 45 in FIG. 3 of adding the magnetically responsive particle solution to the reaction tubes of the reaction tube array 15.
- the pipetter's aspirating/dispensing tip 25 is moved to the optical sensor 31, to initiate agitation of the particle mixer for the particle mixing well 19a containing the magnetically responsive particle solution.
- the tip is moved to the optical sensor(s) 17 to inactivate the corresponding colum (s) of motors in the reaction tube array 15.
- the tip then returns to the optical sensor 31, at step 71, to terminate agitation of the particle mixer.
- the tip then aspirates a prescribed amount of the magnetically responsive particle solution and, at step 75, switches the optical sensor 31 to again agitate the particle mixer.
- the tip dispenses the magnetically responsive particle solution into the first reaction tube Cl, after which the tip is washed at the wash station 27, at step 79.
- step 81 it is determined whether or not the magnetically responsive particle solution has been dispensed into the last of the reaction tubes carrying nucleic acid samples. If not, the program proceeds to step 83, where it is determined whether or not the solution has been dispensed into the last reaction tube in the current column of tubes. If not, the reaction tube number is incremented by one, at step 83, and the program makes a repeated pass through the subroutine, for the next reaction tube, beginning with the step 71 of terminating agitation of the particle mixer. Eventually, it will be determined at step 83 that the magnetically responsive particle solution has been dispensed into the last reaction tube in the current column of tubes.
- step 87 the pipetter tip 25, switches the optical sensor 17 for the reaction tube column just completed, to activate its associated column of motors.
- the column number is then incremented at step 87, and the program returns to the step 69 of using the pipetter tip to inactive the next column of motors in the reaction tube array 15.
- step 81 it will be determined at step 81 that the magnetically responsive particle solution has been dispensed into the last of the reaction tubes that contains a nucleic acid sample.
- the program proceeds to step 91, where the pipetter tip 25 switches the optical sensor 17 for the last reaction tube column, to activate its associated column of motors in the reaction tube array 15. The tip is washed at the wash station 27, at step 93.
- FIG. 6 is a flowchart depicting, in greater detail, the washing step 47 of FIG. 3.
- the pipetter's aspirating/dispensing tip 25 is moved to the first optical sensor 17 to inactivate the first column of motors in the reaction tube array 15. This column is designated by the reference variable X.
- the motors stop oscillating the reaction tubes, the magnetically responsive particles are attracted to the sides of the reaction tubes by the adjacent permanent magnets. While this is occurring, the tip 25 is washed at the wash station 27, at step 97. Thereafter, at step 99, the tip is moved to the next optical sensor 17, to inactivate the second, or X + 1, column of motors in the reaction tube array.
- the tip 25 aspirates the buffer solution from the middle portion of the first reaction tube C_ and, at step 103, discards the aspirated buffer solution and is washed at the wash station 27.
- step 105 it will be determined at step 105 that the buffer solution has been aspirated from the last of the six reaction tubes of the column X in question, and the program then will proceed to a step 109, in which the tip 25 aspirates a wash buffer solution from the reagent well 19c, and step 111, where the wash buffer solution is dispensed into all six reaction tubes.
- the tip is then washed at the wash station 27, at step 113, and the tip then is moved, at step 115, to the first optical sensor 17 to activate the column X of motors in the reaction tube array 15. This begins agitating the six reaction tubes of the column, to homogenize the contained solutions and enhance the washing being effected.
- step 117 it is determined whether or not the variable X, identifying the column number for the six reaction tubes just operated on, is a maximum. If not, the variable X is incremented by one, at step 119, and the program returns to the step 99 of switching the optical sensor 17 for the X + 1 column of reaction tubes, to inactivate the associated column of motors. By the time this step 99 is again reached, the motors for the previous column X of reaction tubes will have been stopped for sufficient time to allow the magnetically responsive particles and buffer solution to separate from each other. The program then proceeds through the subroutine in the same fashion as described above, for this next column of reaction tubes.
- step 117 it will be determined at step 117 that the final column of reaction tubes has been operated on.
- the program proceeds to a step 121, where it is determined whether or not a reference variable k has reached the number four. If not, the variable X is reset to one and the variable k is incremented by one, at step 123, and the program returns to the initial step 99 of switching the optical sensor 17 to inactivate the first column of motors.
- the program then proceeds through the program subroutine in the same fashion as described above, to effect three wash cycles, until the variable k has reached the numeral 4.
- the step 109 is modified such that the tip aspirates a substrate buffer solution from the well 19d, rather than the wash buffer solution from the well 19c.
- it will be determined at the step 121 that four passes through the program subroutine have been completed, and this program subroutine is then exited.
- FIG. 7 is a flowchart depicting, in greater detail, the step 49 of quenching the substrate buffer reaction and the transfer of reaction samples to the microtiter plate 23.
- the aspirating/dispensing tip 25 of the XYZ pipetter 11 is moved to the first optical sensor 17 to inactivate the first associated column of motors in the reaction tube array 15. This column is designated by the reference variable X.
- the magnetically responsive particles will be attracted to the sides of the reaction tubes by the adjacent permanent magnets. While this is occurring, the tip 25 is washed at the wash station 27, at step 125b.
- the variable X is incremented by one at step 141.
- the tip is moved to the next optical sensor 17 to inactivate the next column in the reaction tube array. This allows the particles to separate from the buffer for this second column while the samples in the first column are transferred to a microtiter plate.
- the tip is then washed at the wash station 27, at step 127, and then moved, at step 129, to the reagent well 19e, where it aspirates a prescribed amount of the quench buffer solution.
- the tip then moves to the first reaction tube of the column of tubes, at step 131, where it aspirates a sample from the tube, which is then dispensed by the tip, at step 133, into a first well in the microtiter plate 23, at step 117.
- the program then proceeds to a step 135, where it is determined whether or not a sample has been aspirated from the last of the six reaction tubes in the column. If not, the number n is incremented by one, at step 137, and the program returns to the step 127 of washing the tip 11 at the wash station 27.
- step 135 it will be determined at step 135 that samples have been aspirated from all n reaction tubes in the column of tubes.
- the program proceeds to step 139, where it is determined whether or not the last column of reaction tubes has been operated upon. If not, the column number X is incremented by one, at step 141, and the program returns to the initial step 125, where the aspirating/dispensing tip 25 switches the optical sensor 17 for the next column, i.e., column X, in the reaction tube assay 15. The program then proceeds through the same subroutine as described above, this time for the next column of reaction tubes.
- step 139 it will be determined at step 139 that samples have been aspirated from all of the columns of reaction tubes in the assay 15. When this occurs, the fully automated portion of the nucleic acid hybridization assay process will have been completed.
- the microtiter plate 23, which then will carry n reaction samples, is then transported, in step 143, to a suitable fluorimeter, to provide an accurate and precise measure of the degree of reaction for each DNA sample.
- the sequential operation of the XYZ pipetter 11, as described above with reference to the flowcharts of FIGS. 3-7, can be accomplished using a computer program appropriately written to interface with the particular XYZ pipetter being used.
- An accompanying appendix is a printout of the source code for one suitable program written to operate on an IBM PS-2 Model 30-286 personal computer, or equivalent.
- the program is written in C, for use with a conventional Packard XYZ pipetter.
- Additional operations can also be performed by appropriate programming of the XYZ pipetter. As indicated an amplification procedure can be performed prior to placing the samples in the test tubes. Similarly, samples requiring preparation prior to hybridization, as for example cell lysis, can be placed directly in the reaction tubes and appropriate solutions added and removed therefrom.
- a model system was constructed in which a human immunodeficiency virus (HIV) fragment was inserted into a cloning vector.
- HIV human immunodeficiency virus
- pBH10-R3 SP6-HIV vector
- the vector was constructed by cloning a 9 Kb of HIV genomic insert into the Sst-1 restriction site of PSP-64.
- the plasmid pMBI107 was constructed by restriction of pBH10-R3 with Bam-Hl and then religation which resulted in the deletion of the 3'-LTR region. Cells were transformed and selected for ampicillan resistance.
- Plasmid was purified by CsCl gradient centrifugation (Maniatis, et al.. Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor, New York (1989), which is incorporated herein by reference) .
- pMBI107 was linearized by restriction with Bam- Hl.
- a dilution series of Bam Hl-pMBI107 was made in 10 mM Tris, pH 7.5, 1 mM EDTA (TE) .
- Ten ⁇ l of each target dilution was added to 10 ⁇ l of 0.01 mg/ml human placenta (HP) DNA in TE. Controls contained equal volumes of TE and HP DNA. Samples were denatured at 95°C for 10 minutes, chilled in an ice water bath for 1 minute and centrifuged briefly to collect condensate. The samples were placed in tubes in the magnetic sample rack on the worktable.
- Biotinylated and acid phosphatase labelled oligonucleotides were prepared as described above, using sequences listed in Table I.
- a processing program for the XYZ pipetter was iniated and prompted for assay variables, such as a sample number, replicate number, etc.
- the XYZ pipetter automatically combined 102 ⁇ l of hybridization buffer (6XSSC, pH 8.0, 10% formamide, 0.1% SDS, 0.1 mg/ml BSA) 3 nM bi ⁇ tin-N231, -N226, -N224,
- the XYZ pipetter then automatically added 15 ⁇ l of a 1 mg/ml streptavidin-particles (SA-particles) , prepared as described above, in 6XSSC, pH 8.0, 10% formamide, 0.1% SDS, 0.1 mg/ml BSA to each reaction tube.
- SA-particles posses a biotin binding capacity of approximately 60 pinoles.
- biotin binding sites there is a 35 fold molar excess of biotin binding sites over biotin probe.
- Capture of the ternary hybrid complex onto the particles proceeds at 37°C with rotation for 30 minutes.
- the XYZ pipetter automatically stopped the rotation of the reaction tubes by tripping a photoswitch with the sampling tip. Upon cessation of rotation the particles were quickly cleared from solution by the integral side mounted permanent magnets.
- the XYZ pipetter automatically aspirated the buffer from each reaction tube, washing the tip between each sample, in a given row.
- the XYZ pipetter automatically aspirated and dispensed 200 ⁇ l wash buffer (4 X SSC, 0.1% SDS) into each reaction tube, washing the tip between each sample.
- the XYZ pipetter then tripped the photoswitch to commence rotation of the tubes in a given row.
- the XYZ pipetter proceeded to wash the next row of tubes as described above until all the samples have been processed. This process was repeated 2 more times for a total of 3 washes, each at 37°C for 5 minutes.
- the sampling tip pipetter automatically tripped a photoswitch to stop the rotation of the reaction tubes in a given row, allowing the particles to clear from solution.
- the XYZ pipetter aspirated 40 ⁇ l of 100 mM EDTA from a reagent rack and 110 ⁇ l of substrate buffer from the reaction tubes and dispensed the liquid into a well in a microtiter plate.
- the XYZ pipetter performed a tip wash between each sample.
- the XYZ pipetter proceeded to quench/transfer the next row of tubes until all the samples were processed.
- microtiter plate was used on a fluorescent plate reader (Pandex FCA, Baxter Healthcare, Pandex Division, Mundelein, IL) which automatically scanned each well.
- a single well fluorometer can be used manually. The plate can be read immediately or up to 16 hours after completion. The results are presented in Table II.
- the results indicate that the minimum extrapolated detection limit based on a signal to noise ratio of 2.0 is 4 X 10 5 copies pMBI107 plasmid target.
- the results are linear with respect to target level over three orders of magnitude. Multiple capture/reporter probe pairs increase signal without a proportional increase in noises resulting in better sensitivity overall.
- Amplification reactions were set up in a clean (i.e. no exposure to amplification products) biosafety hood in a room separate from the XYZ pipetter.
- Clean positive displacement pipettes PDP
- disposable pistons and capillaries Rosin, Woburn, MA
- sterile tissue grade water Sigma Chemical Co. , St.
- Fresh Taq 1 heat stable, recombinant DNA polymerase (3.1 units AmpliTaq Cetus Corp., Emeryville, CA) was added to 80 ⁇ l amplification buffer (62.5 mM KCl, 12.5 mM Tris-HCl, pH 8.3, 1.88 mM MgCl 2 , 0.13% (w/v) gelatin, 250 ⁇ M dNTP, 0.31 ⁇ M biotin-A105 and 1.25 ⁇ M A214) .
- Twenty ⁇ l water and 20 ⁇ l template (1 X 104 copies pHSV106 (Bethesda Research Laboratories, Gaithersburg, MD) ) was added to negative and positive samples, respectively.
- the final reaction mix contained 50 mM KCl, 10 mM Tris-Cl, pH 8.3, 1.5 mM MgC12, 0.1% (w/v) gelatin, 200 ⁇ M each dNTP (Pharmacia, Piscataway, NJ) , 0.25 ⁇ M biotin-A105 forward primer and 1.0 ⁇ M A214 reverse primer and 2.5 units AmpliTaq). Samples were overlaid with 100 ⁇ l light mineral oil. Amplification control tubes were capped whereas experimental tubes were left uncapped and placed on a thermal cycler (Ericomp,
- the XYZ pipetter automatically inverted the aqueous and oil phases by dispensing 200 ⁇ l chloroform, equilbrated in 10 mM Tris- Cl, pH 7.5, 1 mM EDTA. The oil/chloroform layer sank to the bottom and the aqueous layer floated to the top.
- the XYZ pipetter then combined 102 ⁇ l hybridization buffer (6 X SSC, pH 8.0, 10% FAM, 0.1% SDS, 0.1 mg/ml BSA) containing 3 nM AP-A209 and 20 ⁇ l of amplification products from the thermal cycler.
- the automated sandwich assay proceeded as described in Example I.
- biotin free biotin primer and biotinylated amplification product
- the total amount of biotin (free biotin primer and biotinylated amplification product) in the sandwich assay does not exceed the binding capacity of the SA-particles.
- Twenty ⁇ l of a 0.25 ⁇ M biotin primer solution is equivalent to 5 pmoles of total biotin which is 12 times less than the 60 pmoles binding capacity of the particles.
- the phase inversion process allowed the sampling tip to aspirate the sample without contacting the oil layer which markedly reduced the carryover frequency.
- the contamination frequency (cf) was defined as the number of open negative samples that gave relative fluorescent units (rfu) greater than twice the rfu from closed negative samples.
- C # open negative rfu > 2 X closed negative rfu total # open negative
- HIV infected CEM-CM3 cells (ATCC Accession No. TIB 195) containing approximately 1 to 20 copies of HIV virus/cell were harvested and prepared for PCR as described below.
- reverse transcriptase could be used to form cDNA from RNA which could then be used in PCR.
- CEM-CM3 cells were cultured in 75 cc flasks in
- RMPI 1640 culture media (M.A. Bioproducts, Walkersville, MD) , 10% fetal calf serum, 1% penicillin-streptomycin, 1% Fungizone (M.A. Bioproducts) and 1% L-glutamine at 37°C in 5% C0 2 .
- Cells were passed 1:6 every 5 to 6 days.
- Control cells were passed as follows: 5 mis CEM-CM3:30 mis RMPI media.
- HIV infected CEM-CM3 cells were passed as follows: 5 mis HIV infected CEM-CM3 cells: 10 mis CEM-CM3 and 20 mis RMPI media. Uninfected CEM-CM3 cells were added to infected cells to increase th viral titer.
- HIV infected CEM- CM3 cells to 30 is RMPI media.
- Cells were harvested after 4 to 5 days when titer was maximum. Cells were pelleted in a clinical centrifuge at 1000 rp for 15 minutes. The supernatant was discarded and the pellet was resuspended in 5 mis 1 X PBS. Cell concentration was quantitated by hemacytometry, usually 2-5 X 10 6 cells/ml. Concentration was adjusted to suit.
- a dilution series from 1 X 10 1 to 1 X 10 5 HIV infected CEM-CM3 cells were spiked into 1 X 10 A uninfected CEM-CM3 cells.
- the pellet was resuspended in 50 ⁇ l nuclear membrane lysis buffer (50 mM KCl, 10 mM Tris-Cl, pH 8.3, 2.5 mM MgCl 2 , 0.1% (w/v) gelatin, 0.05 mg/ml proteinase K, 20 mM DDT and 1.7 ⁇ M SDS) and incubated at 55°C for one hour. The samples were boiled for 20 minutes to inactivate the proteinase K and centrifuged to collect the condensate.
- nuclear membrane lysis buffer 50 mM KCl, 10 mM Tris-Cl, pH 8.3, 2.5 mM MgCl 2 , 0.1% (w/v) gelatin, 0.05 mg/ml proteinase K, 20 mM DDT and 1.7 ⁇ M SDS
- amplification buffer (67 mM KCl, 13 mM Tris-Cl, pH 8.3, 2.0 mM MgCl 2 , 0.13% gelatin, 267 ⁇ M each dNTP, 0.33 ⁇ M biotin-N174, 1.3 ⁇ M N224 and 3.3 units freshly added AmpliTaq; Cetus Corp., Emmeryville, CA) for a final concentration of 50 mM KCl, 10 mM Tris-Cl, pH 8.3, 1.5 mM MgCl 2 , 0.1% (w/v) gelatin, 200 ⁇ M each dNTP, 0.25 ⁇ M biotin-N174 forward primer and 1.0 ⁇ M N224 reverse primer and 2.5 units freshly added heat stable recombinant DNA polymerase (AmpliTaq; Cetus Corp., Emeryville, CA) .
- amplification buffer 67 mM KCl, 13 mM Tris-Cl, pH 8.3, 2.0 mM MgCl 2 ,
- sample tubes were placed on a thermal cycler and amplified as follows: 1 minute denaturation at 94°C; 30 amplification cycles of 1 minute at 55°C and then 1 minute at 94°C; 5 minute extension at 72°C.
- a 20 ⁇ l aliquot of the amplified product was assayed in sandwich using detector probe AP-N227 as described in Example I and II.
- Blood was collected from the donor by withdrawal into a 10.0 ml heparinized or EDTA-treated vacutainer. The samples were stored at room temperature up to 24 hours after withdrawal.
- the blood vacutainer was inverted several times to mix well. Approximately 7.0 ml whole blood was removed by volumetric pipette. The blood was transferred to a cell separation tube (LeukoPrep Cat. No. 2750-2752, manufactured by Becton-Dickinson, Rutherford, NJ) and capped with rubber stopper provided by manufacturer. An additional 2.0 ml of 1 X PBS (120mM NaCl, 2.7mM KCl, lO M phosphate buffered salts) was added to bring the total volume to 9.0 ml. The LeukoPrep tube was centrifuged at 1600 X g for 20 minutes at room temperature in rotor and centrifuge designed for containment of infectious material.
- Lysis Buffer 50mM KCl, lOmM Tris-Cl, pH 8.3 (25°C), 2.5mM MgCl 2 , O.lmg/ml gelatin, 0.45% NP40, 0.45% Tween-20, and 60 ⁇ g/ml proteinase K added just before use
- the nuclei were resuspended by vortexing and/or disruption by pipette mixing.
- Optimal proteinase K activity was promoted by incubation at 55°C for one hour. Proteinase K was inactivated and genomic DNA fully denatured by boiling the samples for 20 minutes. The sample was collected by brief centrifugation.
- Amplification of target DNA was performed as follows: Seventy-five microliters of amplification buffer as described in Example III was added to a 0.6ml eppendorf tube (Robbins Scientific) . Twenty-five microliters of cell lysate (approximately 10 5 cells or lug genomic DNA) was added and pipette mixed. The final reaction mix contained lOmM Tris-Cl, pH 8.3 (25°C), 50mM KCl, 1.5mM MgCl 2 , 0.1% (w/v) gelatin, 200 ⁇ M each dNTP (Pharmacia), 0.25 ⁇ M biotin-N178 forward primer, 1 ⁇ M N279 reverse primer and 2.5 units AmpliTaq (Cetus). The sample was overlayed with lOOul oil (Sigma light) . The samples were amplified in an Ericomp Programmable Cyclic Reactor (San Diego, CA) as described in Example III.
- Amplified product for assay in the automated sandwich hybridization system was prepared as follows: Twenty-five microliters of HIV amplified product was added to 25 ⁇ l 10 mM Tris, pH 8.0 in a 2.0 ml microfuge tube. This dilution provides an analysis of 1/10 of the PCR reaction. Sandwich proceeded as described in Example I using AP-N280 as the detector probe. The results are presented in Table IV.
- campylobacter infected stool samples were analyzed using conventional dot-blot analysis.
- the membrane was transferred to a hybridization bag and pre-hybridized for 15 minutes at 50°C in 2 mis hybridization buffer (0.75 M sodium citrate, 1% sarcosine, 0.5% BSA, 0.6% Kathon (Rohm and Haas,
- Hybridization Buffer containing 2.5 nM AP-C103b. Hybridization was allowed to proceed for 15 minutes at 50°C. The product was washed for 20 minutes at 50°C in prewarmed working membrane wash buffer 1 (2 X SSC, pH 7.0, 0.5% sarcosine, 0.12% Kathon) and washed 10 minutes at room temperature in working membrane buffer 2 (1 X SSC, pH 7.0, 0.5% triton X100 0.12% Kathon). The membrane was placed in a plastic bag and developed colorimetrically with freshly added (Nitro Blue
- a conventional manual column and a semi- automated bulk affinity chromatography purification method were compared by an automated magnetic sandwich assay.
- 200 ⁇ l of sample, 800 ⁇ l diluent reagent (10% formalin, 0.1 M sodium phosphate, pH 7.0) and 2000 ⁇ l lysis reagent (8 M urea, 0.25% SDS, 0.25% sarcosine, 0.05 M EDTA) were combined and incubated 30 minutes at 50°C.
- the sample was applied to a pre-equilibrated extractor column containing 1 ml of anion exchange resin.
- the column was washed with 15 is Wash Reagent 1 (40% ethanol, 0.2 M NaCl, 0.02 M Tris-Cl, pH 7.5), 5 mis Wash Reagent 2 (0.25 M NaCl, 0.02 M tris- Cl, pH 7.5, 0.05% NaN 3 ) and eluted in 2 mis Elution Reagent (0.5 M NaCl, 0.02 M Tris-Cl, pH 7.5, 0.05% NaN,) .
- the eluent was concentrated to 330 ⁇ l by lyophilization.
- the sample was adjusted to the following final concentrations: 10% formamide, 0.1% SDS, 3.75 nM biotin- C204b in a final volume of 400 ⁇ l.
- the sample was denatured 10 minutes at 95"C, chilled in ice water, spun briefly to collect condensate and placed in the XYZ pipetter test tube rack.
- the XYZ pipetter program was loaded and prompted variables were keyed in by the operator.
- the sampling tip automatically combined 100 ⁇ l hybridization buffer, containing 15 nM AP-C103b, and 400 ⁇ l into reaction tubes. The remainder of the assay proceeds as described in Example I with the variation that 2 X SSC was substituted for 1 X SSC in the wash buffer.
- the sample preparation and concentration was achieved using the automated system and an affinity capture method.
- the advantages of the method include target enrichment, which can obviate the need for amplification, and compatibility with automation.
- the example described below detects HIV DNA in blood.
- Leucoprep tubes and centrifuged as described in Example IV.
- the caps were removed and the tubes were placed in a sample rack on the worktable of the XYZ pipetter, which was properly programmed to perform the following steps.
- the sampling tip transfered 1 ml of mononuclear cells from the "buffy coat" to a reaction tube in the magnetic rack.
- the cells were lysed and the nucleic acid denatured by adding 1 ml 4.0 M guanidinium thiocyanate, 10 mM EDTA, pH 8.0 and incubated for 10 minutes at 37°C with agitation.
- Biotin capture probe in hybridization buffer (15 X SSC, 25% formamide, 0.125% SDS, 0.125% sarcosin, 0.25 mg/ml BSA and 7.5 nM biotin-N178) is added and the tubes were agitated for 30 minutes at 37°C. Thirty ⁇ g paramagnetic streptavidin derivatized Fe 3 0 » particles (Advanced Magnetics) were added and agitated for 30 minutes at 37°C. Upon cessation of agitation, the particles containing bound biotin capture probe hybridized to target nucleic acid were collected to the sides of the tubes. The supernatant containing heterologous nucleic acids and cellular debris was aspirated.
- the particles were washed twice for 5 minutes each in 200 ⁇ l of 20 mM Tris, pH 8.3, 250 mM KCl with agitation.
- the target nucleic acid was released from the particles by denaturing the capture probe:target hybrid with 20 ⁇ l 0.25 M KOH, followed by neutralization with 20 ⁇ l 0.25 M HCL, 150 mM Tris, pH 8.3 for 5 minutes each with agitation.
- the addition of base and acid was reversed if RNA was the target of interest.
- the supernatant (40 ⁇ l) was transferred to a fresh tube for subsequent use with amplification followed by sandwich assay, as described in Example IV.
- This procedure effectively concentrated the amount of target approximately 200 fold in an automated format.
- the method is compatible with many types of samples and sample preparation treatments.
Abstract
Description
Claims
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JP91507650A JPH05507613A (en) | 1990-04-06 | 1991-04-03 | Methods and compositions for performing DNA assays |
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US50590490A | 1990-04-06 | 1990-04-06 | |
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JP (1) | JPH05507613A (en) |
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Also Published As
Publication number | Publication date |
---|---|
CA2080019A1 (en) | 1991-10-07 |
JPH05507613A (en) | 1993-11-04 |
AU7575291A (en) | 1991-10-30 |
EP0523171A1 (en) | 1993-01-20 |
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