GB2618578A - Method and consumable for nucleic acid extraction - Google Patents

Method and consumable for nucleic acid extraction Download PDF

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Publication number
GB2618578A
GB2618578A GB2206869.6A GB202206869A GB2618578A GB 2618578 A GB2618578 A GB 2618578A GB 202206869 A GB202206869 A GB 202206869A GB 2618578 A GB2618578 A GB 2618578A
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Prior art keywords
consumable
cavities
magnetic
transfer
cavity
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GB2206869.6A
Inventor
Meyer Andreas
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Stratec SE
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Stratec SE
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Priority to GB2206869.6A priority Critical patent/GB2618578A/en
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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
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5025—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures for parallel transport of multiple samples
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/50273—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by the means or forces applied to move the fluids
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502761—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
    • B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C1/00—Magnetic separation
    • B03C1/005—Pretreatment specially adapted for magnetic separation
    • B03C1/01—Pretreatment specially adapted for magnetic separation by addition of magnetic adjuvants
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C1/00—Magnetic separation
    • B03C1/02—Magnetic separation acting directly on the substance being separated
    • B03C1/28—Magnetic plugs and dipsticks
    • B03C1/288—Magnetic plugs and dipsticks disposed at the outer circumference of a recipient
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C12N15/1013—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by using magnetic beads
    • 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
    • G01N33/54333—Modification of conditions of immunological binding reaction, e.g. use of more than one type of particle, use of chemical agents to improve binding, choice of incubation time or application of magnetic field during binding reaction
    • 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
    • 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
    • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
    • G01N35/026—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations having blocks or racks of reaction cells or cuvettes
    • 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
    • G01N35/1065—Multiple transfer devices
    • G01N35/1074—Multiple transfer devices arranged in a two-dimensional array
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/16—Reagents, handling or storing thereof
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
    • B01L2300/087—Multiple sequential chambers
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C2201/00—Details of magnetic or electrostatic separation
    • B03C2201/18—Magnetic separation whereby the particles are suspended in a liquid
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C2201/00—Details of magnetic or electrostatic separation
    • B03C2201/26—Details of magnetic or electrostatic separation for use in medical applications

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Abstract

A consumable 1 for handling liquids in an automated analyser system for nucleic acid extraction comprises a plurality of cavities 5a-e which are connected by a transfer channel 20, wherein an upper opening of the transfer channel is surrounded by a transport rim 10. The rim may be gripped by gripper arms of the automated analyser system. The consumable may be sealed with a pierceable cover. A system may comprise an external magnet (50, figures 3 and 4) to agitate and mix particles or beads and transfer them between chambers or receptacles (figures 3 and 4). Each cavity may be used for lysis, washing or separation and the volume or size of them may be varied accordingly.

Description

METHOD AND CONSUMABLE FOR NUCLEIC ACID EXTRACTION
DESCRIPTION
Field of the Invention
[0001] The invention relates to a consumable and a system for nucleic acid extraction
Brief description of the related art
[0002] Automated analyser systems for use in clinical diagnostics and life sciences are produced by a number of companies For example, STRATEC' SE, Birkenfeld, Germany, produces a number of devices for specimen handling and detection for use in automated analyser systems and other laboratory instrumentation.
[0003] Nucleic acid extraction (NAE) methods relate to the extraction of both DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) from samples but can be more broadly separated into chemical and mechanical methods. The following descriptions will focus on mechanical solid-phase methods and furthermore address processes which are based on magnetic particles or beads.
[0004] The magnetic beads technology represents a well-established strategy for the extraction of RNA and genomic, plasmid and mitochondria1 DNA. Suitable buffer systems (mainly silica matrices) will be coupled via coating procedures to functionalized magnetic particles or beads. The extraction technique involves the separation of nucleic acids from complex mixtures and provides several advantages compared to other isolation processes: - Binding of target nucleic acids to the coating surface of the magnetic particles.
- Magnetic core facilitates manipulation and handling of the nucleic acid bead complexes.
[0005] In general, all semi-and fully-automated nucleic acid extraction systems or instruments perform the following basic process steps of: - Lysis: Disruption / break open of cells to release nucleic acids; - Nucleic acid Separation: Separation of nucleic acids from other cell components: - Binding: Binding of nucleic acids to magnetic particle surface; - Washing: Removal of cellular material (debris) in multiple wash steps.
- Nucleic acid isolation or extraction: Elution of nucleic acids.
[0006] Considering these basic steps in combination with the magnetic particle / bead approach all system-specific nucleic acid isolations come down to the four steps of lysis, binding, washing and elution. The modules or stand-alone instruments mainly differ in the actual implementation of the basic process steps.
[0007] Published US Patent No. US 8,454,825 teaches a rod assembly for the extraction of magnetizable particles from solutions. The rod assembly includes at least one guide element. A rod element that is insertable into the at least one guide element and moveable in a direction substantially parallel to the at least one guide element. A magnet element is moveable to a distal magnet element position; wherein the distal magnet element position is located on a distal end section of the at least one guide element; wherein the at least one guide element includes an opening at a distal end. A method for the extraction of magnetizable particles from solutions is also described, as well as a magnet element for the extraction of magnetizable particles from solutions.
[0008] Other systems known from the prior art transfer the liquids between reaction wells via disposable tips and separate the magnetic beads, with or without bound nucleic acids, inside the cavities. The processing principle includes the following steps: - Introducing the sample to the instrument.
- Sample lysis, inactivation of nucleases, and nucleic acids release.
- Magnetic particle addition, binding of nucleic acids to particles.
- Magnetic separation of nucleic acid particles-complex inside the reaction wells. - Multiple washing steps - Elution of purified nucleic acids from particles [0009] Another alternative is to transfer the liquids between reaction wells via disposable tips, wherein the magnetic particles, with or without bound nucleic acids, are separated inside the tip. The processing principle includes of the following steps: - Introduce sample to the instrument.
- Cell disruption and protein digestion by addition of lysis buffer and enzyme.
- Nucleic acids binding to the surface of magnetic particles.
- Magnetic separation of the nucleic acid-bead complex.
- Removal of cellular debris by extensive washing steps.
- Magnetic separation of the nucleic acid-bead complex - Nucleic acids elution at high temperatures during the removal of the magnetic particles.
[0010] There is also a system known, which performs the extraction in a single reaction cavity. The magnetic particles will be manipulated (separation and resuspensi on) via multiple movable magnetic arrays. Injectors dispense reagents and by the use of disposable aspirator tips the supernatant from each well can be removed. The processing principle includes the following steps.
- During incubation of the lysed samples, all target nucleic acids are captured by magnetic particles - The magnetic device attracts all magnetic beads, enabling the system to purify nucleic acids through several washing steps.
- The heating step releases the nucleic acids form the beads.
- Magnetic particles are separated from the eluate by the magnetic device. [0011] All systems known from the prior art are related to a limited flexibility with respect to liquid components and assay extraction parameters.
[0012] There is a need for a method and a consumable allowing the handling of magnetic particles without requiring additional material like disposable tips for minimizing the risk of introducing contaminations.
Summary of the Invention
[0013] The present invention provides a consumable for handling fluids in an automated analyser system, comprising a plurality of vertically arranged cavities for receiving a fluid which are connected by a horizontally arranged transfer channel, wherein the cavities are arranged next to each other and wherein an upper opening of the transfer channel is surrounded by a transport rim [0014] In a further aspect of the invention, each of the plurality of vertically arranged cavities has a different diameter and/or depth and/or shape.
[0015] Another aspect of the invention relates to a consumable, wherein the cavities of the plurality of vertically arranged cavities are connected in a straight line.
[0016] Another embodiment relates to inner surfaces of the consumable covering the cavities and the transfer channel are made of a material or are coated with a material providing low friction [0017] It may further be intended that the consumable is made of a temperature transferring material to facilitate the transfer of temperature changes [0018] The consumable according to the present invention may have a rectangular shape.
[0019] Another aspect of the present invention relates to a consumable, wherein its upper openings are sealed with a cover.
[0020] It is envisaged that the cover is configured to be pierced by a probe.
[0021] Another object of the present invention relates to a stack of consumables for handling fluids in an automated analyser system, comprising at least two consumables as described above which are arranged next to each other with their flat sides extending in a longitudinal direction.
[0022] Another object of the present invention elates to a system for handling fluids in an automated analyser system, comprising a consumable according as described above or a stack of consumables as described above and at least one external magnet which is configured to be moved in the x-, y-and z-axis and for rotational movements along a fictional vertical axis [0023] Still other aspects, features, and advantages of the present invention are readily apparent from the following detailed description, simply by illustrating preferable embodiments and implementations The present invention is also capable of other and different embodiments and its several details can be modified in various obvious respects, all without departing from the spirit and scope of the present invention. Accordingly, the drawings and descriptions are to be regarded as illustrative in nature, and not as restrictive. Additional objects and advantages of the invention will be set forth in part in the description which follows and in part will be obvious from the description, or may be learned by practice of the invention
Summary of the Figures
[0024] The invention will be described based on figures. It will be understood that the embodiments and aspects of the invention described in the figures are only examples and do not limit the protective scope of the claims in any way. The invention is defined by the claims and their equivalents. It will be understood that features of one aspect or embodiment of the invention can be combined with a feature of a different aspect or aspects of other embodiments of the invention, in which: [0025] FIG. 1 shows a consumable according to the disclosure in a top view.
[0026] FIG. 2 shows a sectional side view of a consumable according to the present disclosure.
[0027] FIG. 3 shows a sidewise view of a consumable along its longitudinal axis.
[0028] FIG. 4 shows a top view onto a consumable arid external magnet.
[0029] FIG. 5 shows a circular embodiment of a consumable.
[0030] FIG. 6 shows a rectangular embodiment of a consumable.
[0031] FIG. 7 shows a conical embodiment of a consumable with a centred transfer channel.
Detailed Description of the Invention and the Figures [0032] The technical problem is solved by the independent claims. The dependent claims cover further specific embodiments of the invention.
[0033] The term consumable refers within the present disclosure to a device which provides cavities, receptacles or recesses for receiving a fluid which can be a liquid patient sample for instance. The term fluid refers to a liquid or gas which both may comprises solids like magnetic particles. A patient sample may be any body liquid like whole blood, plasma, urine, lymph or saliva. The terms magnetic beads and magnetic particles are used synonymously.
[0034] The present invention provides a method and a consumable allowing nucleic acid (NA) extraction without requiring additional consumables or disposable tools despite the primary sample handling equipment which is subject of the present disclosure. All magnetic particle-related processing steps comprising collection, transfer, resuspension, mixing etc. via the application of magnetic forces can be made with a consumable according to the present disclosure. It is advantageous that the magnetic particle handling and manipulation can be done without considering haying the appropriate material at the right time at hand.
[0035] The following disclosure refers to material for use in a fully automated analysis system in the field of molecular diagnostics, which can perform nucleic acid extraction (NAE) as well as polymerase chain reaction (PCR) for a sample according to a given workflow or method. The core of the present disclosure is a design for a consumable and a corresponding method using said consumable for the magnetic particle-based extraction of nucleic acids, with a specific focus on particle handling.
[0036] The consumable according to the present disclosure for nucleic acid extraction comprises multiple cavities or vessels for performing lysis, binding, washing and elution within a single consumable so that there is no need for using multiple consumables. The single cavities are connected to another by a common transfer channel. The inner surfaces of the cavities are configured to allow an efficient magnetic particle transfer. Particle movements along the inner walls are supported by a low binding raw material, raw material additives, appropriate surface roughness and/or additional surface coatings.
[0037] All vessels of a single consumable are arranged in a straight line for facilitating the required particle manipulation, respectively the transfer of fluids comprising the magnetic particles. Sizes and shapes of the cavities are tailored to the requirements and needs of the individual process steps (e.g. liquid volumes, interfacing vessel heating etc.). The consumable may provide a "flat" design with respect to its longitudinal extension for allowing a fast and reliable fluid heating and magnetic particle collection (also called magnetic separation).
[0038] The circumferential rim surrounding the upper openings of the cavities represents the Z-reference and allows holding and transfer of the consumable during the extraction process. The hand-like design of the consumable and the thus existing finger gaps can be used for an automated consumable transport and positioning within an automated analyser. Further interfaces for moving or transporting the consumable can be part of the consumable for improving or facilitating the manual as well as robotic handling (e.g. gripper interface).
[0039] A consumable according to the present disclosure can also be sealed via a pierceable cover like a foil for reducing or avoiding the risk of a contamination or the evaporation of sample fluids and reagents like buffer.
[0040] The magnetic particle manipulation as a key functionality of a consumable according to the present disclosure is illustrated and described exemplarily in FIG. 1-4, wherein FIG. 1 shows a consumable 1 according to the present disclosure in a top view. Five cavities 5 are arranged next to another and all cavities S are surrounded by a transport rim 10.
[0041] FIG. 2 shows a sectional side view of a consumable 1 according to the present disclosure. The most left cavity 5a is intended for cell lysis and binding of target molecules to magnetic beads. Consequently, the most left cavity 5a can be designates as a lysis and binding cavity.
[0042] The section below transport rim 10 and the volume of the cavities Sa-e is formed as a bead transfer channel 20 going through or connecting all present channels for transferring the magnetic beads from one cavity to the next, neighbouring cavity. Cavities 5b, Sc, 5d are intended for performing washing steps. Cavity 5e can be used for separating the target molecules from the magnetic beads in an elution step. It is obvious for a skilled person that the volumes of the cavities 5a-e can be adjusted to the required needs of a step depending on the required total liquid volume [0043] FIG. 3 shows a sidewise view of a consumable 1 along its longitudinal axis from the direction of cavity 5a of FIG. 2. An external magnetic field will be applied to the consumable 1 by an external magnet 50 which can be moved in all three dimensions (indicated by the arrows in FIG. 3A-C). The distance of the external magnet 50 to the lateral side of the consumable 1 can also be adjusted so that the magnetic beads can be attracted to the inner surface of the consumable 1 next to the external magnet (FIG. 3B, 3C). The magnetic beads can be moved from one cavity to another cavity by moving the external magnet 50 upwards/downwards and sidewise, respectively. Permanent magnets and/or electromagnets may be used as external magnets depending on the required magnetic forces for particle attraction. The magnetic forces, the particle properties and the consumable design enable the collection, transfer, separation, resuspension and mixing of the magnetic beads.
[0044] FIG. 4 shows a top view onto a consumable 1 and external magnets 50 and indicates by the arrows that the magnets may be rotated for agitation of the magnetic beads in the respective sample or buffer. The upper external magnet is in a position for attracting magnetic beads for their transfer, while the lower external magnet 50 is rotated for agitating the magnetic beads due to the changing polarity of the magnetic field.
[0045] FIG. 5 shows a consumable 1 in a circular embodiment. The left part of FIG. 5 shows a perspective view and the right part a top view onto a consumable 1. The cavities are no longer arranged upwards next to each other but radially next to each other like chambers 65 which do no longer provide an upper opening, wherein the consumable has a disc like shape.
[0046] The disc like consumable 1 has a pi petting port 60 for providing a sample with magnetic beads (not shown) to the first chamber 65a, which may be designated for lysis for instance. Chambers 65b, 65c, 65c are intended for performing washing steps and chamber 65e is the elution chamber. This chambers 65b, 65c, 65d comprise washing ports 62b, 62c, 62d each for applying and aspirating a washing buffer.
[0047] Bead transfer channel 20 surrounds a central axis of consumable 1 and thus connects the radially arranged cavities or chambers 65. The central axis may provide an element that allows the movement 64 of the consumable 1, for instance by a gripper (not shown). The final 8 cavity or chamber 65e provides an elution port 61 for obtaining the washed eluate from the process that was performed using the disc like shaped consumable [0048] FIG. 6 shows a consumable with a rectangular shape. The left part of FIG. 6 shows a perspective view and the right part a top view onto a consumable I. Like the embodiment shown in FIG. 5, the cavities of the rectangular shaped embodiment in FIG. 6 are no longer arranged upwards next to each other but next to each other like chambers 65a, 65b, 65c, 65d, 65e which do no longer provide an upper opening. Pipetting port 60 allows to apply a sample to the first chamber 65a, which can be designated as lysis chamber if the consumable is used for nucleic acid extraction. Chambers 65b, 65c, 65c are intended for performing washing steps and chamber 65e is the elution chamber. This chambers 65b, 65c, 65d comprise washing ports 62b, 62c, 62d each for applying and aspirating a washing buffer.
[0049] The chambers of the rectangular shaped consumable are connected by bead transfer channel 20 which is located on one side of the consumable I. Elution port 61 is located at the end of the final chamber 65e. The rectangular shaped consumable 1 may also have a handling interface 64.
[0050] FIG. 7 shows an embodiment of a consumable I according to the present invention with conically shaped cavities 5. Rim 10 surrounds the opening of each cavity and the bead transfer channel 20.
[0051] The consumable may be made of a material which allows a rapid heating and cooling of liquids in terms of facilitating the transfer temperature changes. It is further intended that the inner surfaces of the cavities and the transfer channel are made of a material with a low sticking friction for facilitating the movement of the magnetic beads.
[0052] These basic steps of a method for magnetic particle manipulation are: Collection: A magnetic field is positioned at the outer side of the consumable for promoting the formation of a magnetic bead pellet on the inner wall surfaces of a cavity. Pellet density, size, shape and the number of pellets can be controlled and changed by the number of magnets, the magnetic field design and its properties.
- Transfer and positioning: A relative movement between the consumable and the external magnet, respectively the applied magnetic field can be used to move and/or position the magnetic particles inside or outside the liquid containing cavities along the inner consumable wall surfaces.
- Separation: The collection and transfer capabilities can be used to separate magnetic particles and liquids. The moving or changing of the magnetic field "draws" the collected beads out of the surrounding liquid into the dry bead transfer channel. Further movements allow the transfer of the pellets into the former or other liquids and cavities, respectively.
- Resuspension and mixing: Further relative movements of the consumable and/or external magnets varying the magnetic force variations (e.g. consecutive increase and decrease of distance between magnet and outer wall of consumable or different currents for electromagnets) allow to resuspend collected pellets in order to move much smaller pellets and/or individual magnetic particles through sample material and reagents ("mixing"). Resuspension and mixing is essential because it significantly improves the quality of the following steps: i Binding of target sample material or molecules to magnetic particles coated with synthetic or biological moieties for binding of the target sample material or molecules; Washing and removal of unwanted sample material or molecules like cellular debri s; iii. Elution of the target sample material or molecules or separation of them form the magnetic beads for further analysis.
[0053] These basic steps can also be carried out with multiple individual fields and pellets as well as different types of magnetic force variations. This outlined method is not limited to nucleic acids extraction only. It is also suitable for other magnetic particle-based assay workflows. Consumable and method can be used in track-based systems and discrete processing positions.
[0054] The principle operation method and the available system functionalities comprise the following steps. All assay parameters, for example, processing orders, volumes, temperatures, repetition numbers, durations etc are adaptable, but the functional principle remains unchanged: 1. Introduction of empty consumable to lysis and purification device.
2. Addition of lysis buffer and enzyme into lysis cavity (addition order variable).
3. Optional addition of carrier RNA and / or internal control(s) into lysis cavity.
4. Addition of washing buffer into the respective separate cavities S. Addition (pipetting) of primary sample to lysis cavity.
6. Heat up of liquid mixture in lysis cavity to lysis target temperature and incubate volume for defined time period (for cell break up and release of nucleic acids).
7. Removal of heater or transfer of consumable to separate position for passive cool down or optional active cooling of liquid volume.
8. Addition of magnetic beads and binding buffer into lysis cavity (addition order variable).
9. Magnetic mixing / agitation of particles in sample and reagent mixture within lysis cavity (binding of target nucleic acids to beads).
10. Collection of magnetic particles at inner cavity wall.
11. Relative movement between consumable and magnetic field to draw beads with bound nucleic acids out of lysis cavity for transfer into a first wash buffer and according cavity, respectively (separation step).
12. Magnetic mixing / agitation of particles with bound target nucleic acids in wash buffer (cavity) for resuspensi on and to remove cellular debris.
13. Repeat steps 8 to 10 to perform further washing steps with fresh wash buffer in related consumable cavities (including collection, transfer, separation and mixing).
14. Addition of elution buffer into the according cavity (this step can also be carried out in parallel or directly after the wash buffer addition).
15. Collection of magnetic particles at inner cavity wall.
16. Draw / transfer beads out of the respective washing buffer and hold pellet in a transfer area for a defined drying or incubation time for the evaporation of alcohols to avoid inhibition of subsequent steps for instance.
17. Heat up of elution buffer (cavity) to elution target temperature (optional addition of preheated elution buffer).
18. Transfer of particles after hold time into (heated) elution buffer.
19. Incubation of nucleic acids, bead and buffer mixture for a defined time.
20. Magnetic mixing / agitation of particles in elution buffer (cavity) to separate target nucleic acids from the magnetic beads 21. Final collection of magnetic particles at inner cavity wall (prepare eluate pick-up without magnetic particles to avoid disturbance of next steps).
22. Pick-up (pipetting) of eluate for intermediate storage or PCR setup 23. Aspiration of lysis and wash cavities and transfer into liquid waste.
24. Discarding of empty extraction consumable into solid waste.
[0055] Alternative approaches relate to additional directly integrated interfaces for automated and/or manual handling. The cavities may further be differently arranged, so that the consumable has a disc shaped circular form instead of an arrangement in a straight line (comp. FIG. 5).
[0056] The lysis can be performed in a separate consumable so that a bigger liquid volume can be used. The shape of a cavity may be adapted to the respective step for which it is used like a shape supporting mixing and resuspension of magnetic beads by mechanical shaking (orbital, linear etc) [0057] The consumable may further be adapted to support a bead resuspension process via disposable tip-based intermediate mixing by repeating aspirate and dispense cycles for problematic nucleic acid bead complexes. A method according to the present disclosure may further employ multiple washing steps in the same cavity. It is an advantage that the number of cavities for washing can be adapted to the number of washing steps.
[0058] The method may also relate to dispensing and injecting buffers directly onto a magnetic bead pellet resting in a cavity for supporting resuspension of the bead pellet.
[0059] It is further conceivable to use an array of electromagnets for a defined bead pellet manipulation [0060] The consumable can further have elements so that it s stackable. It may comprise snap-fit features for fixing stacked consumables to another.
[0061] The consumable according to the present invention can be packed in a cardboard box or blister for a pre-orientated or aligned handling like arranging the consumable in a row to easy a batchwise loading of multiple consumables at a time.
[0062] Consumables which are arranged next to another may be sealed with a single foil which is pierceable and can optionally be perforated.
[0063] The foregoing description of the preferred embodiment of the invention has been presented for purposes of illustration and description. It is not intended to be exhaustive or to limit the invention to the precise form disclosed, and modifications and variations are possible in light of the above teachings or may be acquired from practice of the invention. The embodiment was chosen and described in order to explain the principles of the invention and its practical application to enable one skilled in the art to utilize the invention in various embodiments as are suited to the particular use contemplated. It is intended that the scope of the invention be defined by the claims appended hereto, and their equivalents. The entirety of each of the aforementioned documents is incorporated by reference herein.
Reference Numerals 1 Consumable 5, 5a, 5b, Sc, 5d, Se Cavity transport rim transfer channel External magnet Pipetting port 61 Elution port 62, 62b, 62c, 62d Washing port 64 Handling interface 65, 65a, 65b, 65c, 65d, 65e Chamber

Claims (1)

  1. CLAIMSA consumable for handling fluids in an automated analyser system, comprising a plurality of vertically arranged cavities for receiving a fluid which are connected by a horizontally arranged transfer channel, wherein the cavities are arranged next to each other and wherein an upper opening of the transfer channel is surrounded by a transport rim.The consumable of claim 1, wherein each of the plurality of vertically arranged cavities has a different diameter and/or depth and/or shape 3. The consumable of claim 1 or 2, wherein the cavities of the plurality of vertically arranged cavities are connected in a straight line.The consumable of claim 1 or 3, wherein the inner surfaces of the consumable covering the cavities and the transfer channel are made of a material or are coated with a material providing low friction.The consumable of any one of claims 1 to 4, wherein the consumable is made of a temperature transferring material to facilitate the transfer of temperature changes.The consumable of any one of claims 1 to 5, wherein the consumable has a rectangular shape.The consumable of any one of claims 1 to 6, wherein the upper openings of the consumable are sealed with a cover.The consumable of claim 7, wherein the cover is configured to be pierced by a probe A stack of consumables for handling fluids in an automated analyser system, comprising at least two consumables according to any one of claims 1 to 8 which are arranged next to each other with their flat sides extending in a longitudinal direction.10. A system for handling fluids in an automated analyser system, comprising a consumable according to any one of claims 1 to 8 or a stack of consumables according to claim 9 and at least one external magnet which is configured to be moved in the x-, y-and z-axis and for rotational movements along a fictional vertical axis.
GB2206869.6A 2022-05-11 2022-05-11 Method and consumable for nucleic acid extraction Pending GB2618578A (en)

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Application Number Priority Date Filing Date Title
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Application Number Priority Date Filing Date Title
GB2206869.6A GB2618578A (en) 2022-05-11 2022-05-11 Method and consumable for nucleic acid extraction

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Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1994026414A1 (en) * 1993-05-17 1994-11-24 Syntex (U.S.A.) Inc. Reaction container for specific binding assays and method for its use
US5912129A (en) * 1998-03-05 1999-06-15 Vinayagamoorthy; Thuraiayah Multi-zone polymerase/ligase chain reaction
EP1890157A1 (en) * 2005-06-07 2008-02-20 Arkray, Inc. Method for replacing liquid, method for extracting component by using it, composite container and automatic analyzer
US20130034845A1 (en) * 2008-02-29 2013-02-07 Northwestern University Barriers for facilitating biological reactions
WO2015113047A2 (en) * 2014-01-27 2015-07-30 Brevitest Technologies, Llc Discontinuous fluidic systems for point-of-care analyte measurement
WO2021184033A1 (en) * 2020-03-13 2021-09-16 Siemens Healthcare Diagnostics Inc. Improved vortex generator for agitation of fluids during sample preparation

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1994026414A1 (en) * 1993-05-17 1994-11-24 Syntex (U.S.A.) Inc. Reaction container for specific binding assays and method for its use
US5912129A (en) * 1998-03-05 1999-06-15 Vinayagamoorthy; Thuraiayah Multi-zone polymerase/ligase chain reaction
EP1890157A1 (en) * 2005-06-07 2008-02-20 Arkray, Inc. Method for replacing liquid, method for extracting component by using it, composite container and automatic analyzer
US20130034845A1 (en) * 2008-02-29 2013-02-07 Northwestern University Barriers for facilitating biological reactions
WO2015113047A2 (en) * 2014-01-27 2015-07-30 Brevitest Technologies, Llc Discontinuous fluidic systems for point-of-care analyte measurement
WO2021184033A1 (en) * 2020-03-13 2021-09-16 Siemens Healthcare Diagnostics Inc. Improved vortex generator for agitation of fluids during sample preparation

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