WO1993025912A2 - Preparation automatique d'acides nucleiques - Google Patents

Preparation automatique d'acides nucleiques Download PDF

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Publication number
WO1993025912A2
WO1993025912A2 PCT/GB1993/001222 GB9301222W WO9325912A2 WO 1993025912 A2 WO1993025912 A2 WO 1993025912A2 GB 9301222 W GB9301222 W GB 9301222W WO 9325912 A2 WO9325912 A2 WO 9325912A2
Authority
WO
WIPO (PCT)
Prior art keywords
assay plate
dna
probe
magnetic
magnetic particles
Prior art date
Application number
PCT/GB1993/001222
Other languages
English (en)
Other versions
WO1993025912A3 (fr
Inventor
Trevor Leonard Hawkins
John Edward Sulston
Andrew Robert Watson
Original Assignee
Medical Research Council
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Medical Research Council filed Critical Medical Research Council
Priority to AU43439/93A priority Critical patent/AU4343993A/en
Publication of WO1993025912A2 publication Critical patent/WO1993025912A2/fr
Publication of WO1993025912A3 publication Critical patent/WO1993025912A3/fr

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Classifications

    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/0099Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor comprising robots or similar manipulators
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00Heating or cooling apparatus; Heat insulating devices
    • B01L7/52Heating 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
    • 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
    • C12Q1/6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/0098Automatic 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
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00497Features relating to the solid phase supports
    • B01J2219/005Beads
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718Type of compounds synthesised
    • B01J2219/0072Organic compounds
    • B01J2219/00722Nucleotides
    • CCHEMISTRY; METALLURGY
    • C40COMBINATORIAL TECHNOLOGY
    • C40BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00Libraries per se, e.g. arrays, mixtures
    • C40B40/04Libraries containing only organic compounds
    • C40B40/06Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/10Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
    • G01N35/1081Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices characterised by the means for relatively moving the transfer device and the containers in an horizontal plane
    • G01N35/109Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices characterised by the means for relatively moving the transfer device and the containers in an horizontal plane with two horizontal degrees of freedom

Definitions

  • This invention relates to the automated preparation of nucleic acids and concerns an automated method of nucleic acid preparation and automated apparatus therefor.
  • M13 phage is used to obtain single stranded DNA for sequencing templates.
  • the traditional methods for M13 DNA purification such as polyethylene glycol (PEG)/phenol procedures (Bankier et al ., [1988], in Wu, R. [ed.]. Methods Enz. 155, 52-93) allow icrogram quantities of template to be produced from millilitre volumes.
  • thermally cycled sequencing procedures utilising Taq polymerase (Craxton, [1991], Methods: A Companion to Methods in Enzymology 3., 20-26) only require 200-500ng of template DNA per reaction. Therefore traditional methods produce an excess of template for most purposes, which wastes both time and money.
  • the invention provides apparatus for preparing a DNA sequence of interest from a complex sample comprising use of magnetic particles in an assay plate, said apparatus comprising:
  • means for moving an assay plate in three-dimensional space means for supplying liquids to the assay plate; means for removing liquids from the assay plate; thermal regulation means for controlling the temperature of the assay plate; magnetic separation means for manipulating magnetic particles in the assay plate; and computer control means for controlling and co-ordinating operation of all the above means.
  • the assay plate is of a synthetic plastics material which is suitable for use at temperatures above 50°C, (more preferably at temperatures up to 80°C). It is also preferred that the assay plate comprises a microtitre assay plate, typically with 96 wells.
  • the apparatus of the invention conveniently comprises a robotic head capable of movement in all three dimensions (thus known as an "X, Y, Z robot") with position sensing means, such that the location of the head in three- dimensional space is known relative to a fixed point.
  • a robotic head capable of movement in all three dimensions (thus known as an "X, Y, Z robot") with position sensing means, such that the location of the head in three- dimensional space is known relative to a fixed point.
  • the head is preferably capable of pipetting and dispensing liquids.
  • Convenient pipetting devices are known (e.g. those manufactured by Hook and Tucker) and may be attached to the robot head by tubing.
  • Aspiration means are typically provided b a vacuum pump (such as that available from Charles Austen) connected to the robot head by valves and tubing.
  • a vacuum pump such as that available from Charles Austen
  • liquids are dispensed by a plurality of disposable tips, such as well known to those skilled in the art.
  • the apparatus comprises a store of disposable sterile tips ready for use and a receptacle for the collection of used tips.
  • the apparatus should preferably include tip-sensing means such that the number of tips located on the robot head is known, as it is possible that tips may not become properly attached to the head.
  • any magnetic particles to which are attached an appropriate probe are suitable for use with the apparatus defined above, including those already known in the art. However, it is preferred that the particles used are those described in GB 9212164.9 (co-pending International Patent application No. PCT/GB93/ ).
  • the magnetic separation means conveniently comprise two separate workstations.
  • One such workstation may comprise bar magnets of a size and number such that a typical microtitre plate may rest on the magnets such that each row of wells in the plate aligns with a bar magnet.
  • Such a station may be termed the "separation" station, which may be used to separate magnetic particles from mixtures by attracting said particles to the magnets.
  • the other magnetic workstation may comprise bar magnets of a size and number such that two rows of wells may be positioned between each bar magnet, allowing for movement of the plate relative to the magnets, such that the magnets may be situated between different rows of wells on the microtitre plate.
  • This station may be termed the "washing" station.
  • Washing can be effected by adding washing medium to the wells of the microtitre plate and drawing the magnetic particles to one side of the wells. After a suitable period (for example, 5 seconds), the plate is moved relative to the magnets so that the magnet is on the other side of the wells, thereby dragging the magnetic particles through the washing medium.
  • a suitable period for example, 5 seconds
  • the magnetic workstation ⁇ may comprise "dot" magnets instead of bar magnets.
  • dot magnets Preferably an array of dot magnets is employed, each magnet being approximately the diameter of one of the wells of the assay plate.
  • the dot magnets are rare earth magnets and are arrayed in a matrix 8 x 12 (i.e. that of a typical 96 well microtitre plate) having dimensions 130mm x 85mm, the array being such that each magnet is separated from its nearest neighbours by the same spacing as that between adjacent wells of the microtitre plate (typically about 9mm) such that a rare earth dot magnet may be positioned substantially directly beneath each well of the assay plate.
  • the thermal regulation means conveniently comprises three heating blocks each set at a constant desired temperature, with the microtitre plate being transferred from one to another to alter the temperature of the plate.
  • the thermal regulation means conveniently comprises three heating blocks each set at a constant desired temperature, with the microtitre plate being transferred from one to another to alter the temperature of the plate.
  • a single heating block with a controlled variable temperature may be employed.
  • the apparatus includes a static baseplate, upon which various accessories may be located (for example, a store of microtitre plates awaiting processing) .
  • the overall operation of the apparatus is controlled by computer means, typically a personal computer.
  • a computer would control, for example, the movement of the robot head and microtitre plates, the pipetting/dispensing of liquids and the temperature of the thermal regulation means, typically via an RS232 computer interface.
  • the invention provides an automated method of preparing a DNA sequence of interest from a complex sample, comprising: use of automated means for the steps of causing lysis of DNA-containing entities by the action of heat in the presence of a suitable detergent; adding magnetic particles attached to a probe together with hybridisation buffer containing a polymer to cause an increase in the effective nucleic acid concentration; allowing the sequence of interest to hybridise to the complementary probe and then separating the particle/probe complex and any sequences hybridised thereto from the rest of the sample by magnetic attraction.
  • a suitable detergent is SDS.
  • the steps of the method are performed in the wells of a microtitre assay plate.
  • the DNA-containing entities are generally phages, typically M13.
  • a suitable polymer is PEG.
  • the use of a polymer to increase the effective concentration of nucleic acid allows smaller volumes of reagents to be used than previously, which in turn enables the method to be performed in a microtitre plate or tray, similarly, the method is particularly simple and efficient as it employs a target sequence-specific purification step.
  • Figure 1 is a schematic representation of one embodiment of the apparatus of the invention
  • Figure 2 shows the base sequence of a suitable probe which may be used in the method of the invention
  • Figure 3 shows a photograph of gel electrophoresis which may be performed on DNA prepared using the method of the invention.
  • Figure 4 shows a portion of a sequencing trace which may be obtained using DNA prepared using the method of the invention.
  • Figure 1 is a schematic representation of automated apparatus in accordance with the invention, suitable for performing the DNA preparation method of the invention.
  • the apparatus includes a number of standard, commercially available components, which, in the interests of clarity, are not shown in the figure.
  • the illustrated apparatus comprises an X-Y-z robot 10, e.g. as produced by Burger Lahr, Aerotech or Linear Technology.
  • Robot 10 comprises a base plate (not shown) supporting a rectilinear framework, including rails 12, 14 and 16, 18 extending in the 'X' direction and rails 20 and 22, 24 extending in the ⁇ 1 direction.
  • Rails 22, 24 are mounted on rails 12, 14 and 16, 18 via respective support blocks 26 and 28, permitting sliding movement of the Y rails in the X direction under the action of drive means 29.
  • a support block 30 is carried on rails 22, 24, arranged for sliding movement thereon in the Y direction under the action of drive means 31.
  • Block 30 has fixed thereto a further support block 32, through which extend a pair of rails 34, 36 arranged for movement relative to block 32 in the Z direction under the action of drive means 37.
  • a robot head 38 is carried at the lower end of rails 34, 36. Robot head 38 is movable relative to the base plate in 3 dimensional space under the control of computer control means (not shown) acting to cause appropriate movement of blocks 26, 28, block 30 and rails 34, 36 by the associated drive means.
  • the robot head is designed to transport a standard 96 well microtitre plate (not shown) between different locations within the framework. To this end the head has fixed thereto vacuum pads (from Kos a) and associated vacuum control means (not shown) for suitable attachment to a microtitre plate.
  • the robot head is also designed to perform pipetting and aspirating functions.
  • the apparatus thus includes a pipetting device manufactured by Hook and Tucker (not shown) linked to the robot head by means of suitable tubing (not shown).
  • the apparatus also includes a vacuum pump (from Charles Austen) and associated valves and reagent lines (not shown) leading to the robot head.
  • the base plate supports a number of different components required for performing the method.
  • the plate supports three heat blocks from Techne, one of which is shown schematically at 40 in tne figure. Each heat block is adapted to be heated to a different fixed temperature under the computer control means.
  • the base plate also carries two magnetic separation stations, e.g. from Techne, one of which is illustrated schematically at 42 in the figure. Each magnetic separation station comprises an array of bar magnets arranged in parallel spaced relationship.
  • One magnetic separation station is designed to retain magnetic beads in the base at the microtitre plate wells while liquid is aspirated off, thus separating the beads.
  • This station comprises an array of eight bar magnets separated by 9mm gaps so as to be located beneath adjacent rows of wells in a microtitre plate.
  • the other magnetic separation station is designed to perform a washing function and comprises four bar magnets at a separation so as to be located beneath the spaces between alternate rows of wells in a microtitre plate, in use, a microtitre plate is positioned over the magnetic separation station with the bar magnets aligned beneath a first set of gaps between alternate rows of wells so that magnetic beads are attracted to one side of the bottom of the wells. After a short period of time, such as 5 seconds, the plate is moved laterally the distance of the spacing between rows of wells so that the magnets are aligned beneath a second set of gaps between alternate rows of wells. In this position the magnetic beads are attracted to the opposed side of the bottom of the wells. The process is repeated a number of times, so that the magnetic beads are moved from side to side within liquid in the wells, performing a washing function.
  • the base plate also supports a supply of disposable sterile pipette tips, illustrated schematically at 44, with an associated sensor 46 for determining whether a tip has been properly picked up by the robot head.
  • the base plate also includes a tip disposal station, illustrated schematically at 48, comprising an opening with a tip-receiving receptacle (not shown) therebelow.
  • the apparatus also includes regions for storage of microtitre plates awaiting processing and that have been processed.
  • the apparatus also includes a receptacle for temporary storage of beads which may then be recycled for further use, possibly after rejuvenation.
  • the apparatus further includes computer control means such as a PC (not shown) for controlling and co-ordinating movement of the robot head and associated functions in a manner that will be apparent to those skilled in the art.
  • computer control means such as a PC (not shown) for controlling and co-ordinating movement of the robot head and associated functions in a manner that will be apparent to those skilled in the art.
  • a microtitre plate with samples to be processed is picked up by the robot head 28 and is transported between appropriate locations with suitable addition and removal of reagents to perform the desired process.
  • the following example concerns an automated method of preparing DNA which may be carried out in the apparatus of Figure 1.
  • the example involves an oligonucleotide probe which has been synthesised with a biotin group at the 3' end.
  • the biotinylated probe is attached to a streptavidin-coated magnetic bead to form a magnetic bead/probe complex.
  • the probe is designed to be complementary to a region upstream from the M13 -21 Universal priming site.
  • single plaques may be grown up in culture, the cells harvested and the supernatant collected and lysed to yield free single strands.
  • the bead/probe complex is then added, and the probe allowed to anneal to the target DNA. Once bound, the bead/probe/template complex can be separated from the rest of the sample using magnetic attraction and then washed.
  • the template may then be freed from the bead/probe complex by heating.
  • All the post-growth steps can be carried out in microtitre plates with no centrifugation or ethanol precipitations required. In this example, 250 random M13 sub-clones were prepared and sequenced using the method outlined below.
  • the amount of template recovered depends directly on the design of the probe.
  • the probe must be specific to the target but must not act as a secondary sequencing primer if free probe is left in solution. Consequently, the probe (shown in Figure 2) is 41bp in length and binds to a region upstream from the M13 -21 Universal primer site.
  • the probe has a run of several 'A's at the 3' end together with the biotin group. This acts as a linker arm to prevent steric hindrance between the large streptavidin- coated beads and the binding of the probe to the target. Also the high degree of non-complementarity at the 3 ' end would prevent the free probe from acting as a sequencing primer should it shear from the beads.
  • the probe THM13.3 was synthesised on an ABI 380B DNA synthesiser on a luMole scale. Biotin phosphora idite was obtained from Amersha UK. The sequence of the probe was:
  • Promega nucleotide quality beads were used in this example. 1.2ml of Promega beads are used per 12 samples. The beads were washed in O.lM NaCl three times using a neodymium-iron-boron permanent magnet to separate the beads from the washing solution. 200ul O.lM NaCl and lOnmol THM13.3 oligonucleotide were then added to 1.2ml (1.2mg) dry beads and incubated at room temperature for 10 minutes. The beads were then washed 10 times in O.lM NaCl to remove unbound oligonucleotide. Bead/probe complex was finally taken up in 1.2ml water. Beads may be bound to probe in bulk and stored in storage buffer at 4°C.
  • Random M13 sub-clones with l-2kb inserts were grown up in 2ml 2xTy medium (16g bacto tryptone, lOg yeast extract, 5g NaCl in 11 water) for 5 hours at 37°C. Cells were spun down at 14,000g for 5 minutes and the supernatant transferred to microtitre plates. 400ul supernatant was used from each sample, using two wells, each containing 200ul supernatant (Falcon 3911 MicroTest Flexible Assay Plate. )
  • hybridisation buffer (20% PEG 8000/2.5M NaCl) was added to each well with a multidispensing pipette; no mixing is required so the same tip may be used for all wells. Also, 20ul bead/probe complex were added to each well, and the dish was incubated at 45°C for 30 minutes.
  • the microtitre plate was removed from the cycler and placed on a Dynal MPC-96 magnetic separator. After 30 seconds the supernatant was aspirated, lOOul wash buffer (0.1X SSC) were added to each well and the beads were moved through the wash buffer by repositioning the plate over the magnetic separator three times at intervals of five seconds. This step was repeated a total of three times. Finally, the beads were eluted in lOul water; using the magnet, beads may be dispersed into this small volume.
  • lOOul wash buffer 0.1X SSC
  • the templates were released from the probe by heating the' plate to 80°C for 3 minutes. After heating, the beads were concentrated using the magnet and the supernatant was removed to a fresh microtitre plate. Due to evaporation the final total volume was approximately 8ul from each well, or approximately 16ul per DNA template sample.
  • beads may be re-used as outlined below.
  • Beads were collected and pooled in a 1.5ml eppendorf tube. The supernatant was removed and the beads were resuspended in 1ml reuse buffer (0.15M NaOH, 0.001% Tween 20) for 1 minute. The supernatant was removed and the procedure repeated. Finally the beads were washed once in storage buffer and taken up in half the original volume of storage buffer (PBS pH 7.5, 0.1% BSA) . Beads were then stored at 4°C.
  • NAME Medical Research Council STREET: 20 Park Crescent CITY: London COUNTRY: United Kingdom POSTAL CODE (ZIP): WIN 4AL TELEPHONE: (071) 636 5422 TELEFAX: (071) 323 1331
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO (111)
  • ANTI-SENSE NO

Abstract

L'invention se rapporte à un appareil permettant de préparer une séquence d'ADN à étudier à partir d'un échantillon complexe, et consistant à utiliser des particules magnétiques dans une plaque de dosage, cet appareil comprenant: un élément permettant de déplacer une plaque de dosage dans un espace tridimensionnel; un élément permettant d'alimenter la plaque en liquides; un élément de régulation thermique servant à réguler la température de la plaque de dosage; un élément de séparation magnétique permettant de manipuler les particules magnétiques dans la plaque; et un élément de gestion par ordinateur servant à commander et à coordonner le fonctionnement de tous les éléments ci-dessus. Un procédé de préparation automatique d'ADN à partir d'un échantillon complexe est également décrit.
PCT/GB1993/001222 1992-06-09 1993-06-09 Preparation automatique d'acides nucleiques WO1993025912A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU43439/93A AU4343993A (en) 1992-06-09 1993-06-09 Automated preparation of nucleic acids

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB9212164.9 1992-06-09
GB929212164A GB9212164D0 (en) 1992-06-09 1992-06-09 Preparation of nucleic acids

Publications (2)

Publication Number Publication Date
WO1993025912A2 true WO1993025912A2 (fr) 1993-12-23
WO1993025912A3 WO1993025912A3 (fr) 1994-03-17

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PCT/GB1993/001223 WO1993025709A1 (fr) 1992-06-09 1993-06-09 Preparation d'acides nucleiques

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Application Number Title Priority Date Filing Date
PCT/GB1993/001223 WO1993025709A1 (fr) 1992-06-09 1993-06-09 Preparation d'acides nucleiques

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AU (2) AU4344093A (fr)
GB (1) GB9212164D0 (fr)
WO (2) WO1993025912A2 (fr)

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AU4344093A (en) 1994-01-04

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