The present invention relates to methods and devices for chemical analysis. More specifically it relates to devices for processing biological specimens. Yet more specifically it relates to devices for extracting biomolecules, for example peptides and/or proteins, from a mixture of molecules in a solution.
Chemical analysis and particularly biomolecular analysis of e.g. proteins in a biological specimen are experiencing an increased demand for speed and accuracy. Different techniques for increasing separation, extraction and preparation of different parts of a specimen have being suggested, but there is still a problem to really increase handling and processing times for large multiple specimens investigations.
WO0138865A1 to Harrison et al., discloses an apparatus and method for trapping bead based reagents within microfluidic analysis systems.
U.S. Pat. No. 6,265,715 to Perreault et al., discloses a non-porous membrane for MALDITOF MS, claiming a method comprising the following steps: providing a non-porous membrane as a sample support; providing a matrix solution; applying the analyte sample directly to the non-porous membrane; allowing the analyte sample to dry; applying the matrix solution to the dried analyte sample; allowing the matrix solution to dry; mounting the non-porous membrane onto a probe body; inserting the probe body and the non-porous membrae into a mass spectrometer; and carrying out MALDI-TOFMS analysis of the analyte sample.
U.S. Pat No. 6,074,725 to Kennedy, (Caliper) discloses a method for fabrication of microfluidic circuits by printing techniques including providing laminates having microfluidic structures disposed between sheets of the laminate.
U.S. Pat. No. 2002/0,039,751 A1 discloses high throughput screening assay systems in microscale fluidic devices.
EP1163052A1, to Burd Mehta et al., identical to WO0050172 discloses manipulation of microparticles in microfluidic systems.
U.S. Pat. No. 5,969,353 to Hsieh discloses a microfluid chip mass spectrometer interface comprising a very fine tube to an outlet port of a microfluid chip, enhancing the sensitivity of mass spectroscopy analysis of materials exiting the outlet port.
WO 0046594 to Dubrow et al., (EuroPCT EP1159605A1) discloses methods, devices and systems for characterizing proteins.
U.S. Pat. No. 5,646,048 discloses an analytical apparatus having a microcolumn and an interface system for controlling the flow from a first microcolumn to a second microcolumn.
WO 01/56771 discloses a manufacturing method for micro structures having different surface properties in a multilayer body using plasma etching.
WO 99/22228 discloses a multichannel system for separation, collection and analysis of samples. The device makes use of a solution permeable gel and capillary columns for separation.
U.S. Pat. No. 4,908,112 discloses a silicon semi-conductor plate (wafer) for analysing biological specimens of micrometer size. Channels sealed with glass plates is arranged together with electrodes to activate fluid motion through the channels using electroosmosis.
U.S. Pat. No. 3,915,652 discloses a transport system for analytical specimens using capillaries sealed between movable nozzles.
U.S. Pat. No. 5,595,653 discloses a micro column for extraction of assays from liquids, comprising an extraction media having a particle size less than 20 microns that is held on place and compressed by two compression layers.
U.S. Pat. No. 5,965,237 discloses a microstructure device comprising a support element and a flat surface and a micro structure element having a microstructure surface with both even surface components and recesses. Material is poly (dimethylsiloxane) glass, silicon, or the like.
U.S. Pat. No. 4,891,120 discloses a chromatographic separation device comprising a body of semiconductor material and having a channel arranged in the surface layer to house liquid or solid phase material for a chromatological test or separation procedure. The channel comprises at least one electrode and may be provided with an electronic or optical system.
Important for all biochemical analysis systems is to keep the dispersion to a minimum. When dealing with detection of low concentration analytes it is also of importance to keep the area of the surfaces in e.g. interconnecting tubings/channels to a minimum in order to avoid unspecific analyte adsorption.
If bead based techniqes are used it is of importance to simplify the loading and unloading of the beads and analytes. Using integrated systems, i.e. the bead trapping unit is integrated in the analysis system, as in WO0138865A1 (Harrison) or EP1163052A1 (Burd) requires special arrangements for the handling of the beads which will reduce the overall throughput.
This invention satiesfies the above mentioned need for increased handling speed of biological specimens. In particular it increases handling speeds for such specimens subjected to analysis involving separation of the specimen into different fractions where each fraction is subjected to subsequent extraction of analytes. Embodiments of the invention also greatly simplifies the loading and unloading of beads in bead based systems.
A typical embodiment of the invention comprises an extraction device for extracting certain biomolecules from a solution, comprising at least one elongated channel for passage of the specimen in fluid phase, said channel having an inlet end and an outlet end and being provided with an adhering unit for the capture of certain biomolecules, each said unit being provided with adhesive means, having affinity for said certain biomolecules. The extraction device further comprises docking means having an array of inlet openings and an array of outlet openings, that enables the extractor to be docked to and undocked from other devices having corresponding docking means, such that said specimen or another fluid can be made to enter through the docking means inlet openings, flow through the at least one channels of the device and to leave the extraction device via the docking means outlet openings.
The increased handling speed is achieved when having multiple extraction devices capable of being handled in a pipeline or assembly line fashion. In a typical embodiment one extraction device is docked to a priming device where it is primed with adhesive means, e.g. microbeads with a surface coating of adhesive molecules having affinity to the molecules that are to be extracted. The extractor is subsequently undocked from the priming device and docked into a specimen loading device, where a specimen or preferably a number of fractions of a specimen in fluid phase is loaded, via said docking means, into the channels of the extractor, enabling certain molecules to adhere to the microbeads. Subsequent to said loading of the extractor, said extractor is undocked from the specimen loading device and docked to a washing device that flushes the extractor channels with a washing solution via the docking means. The flow of fluid is kept in the same direction all the time, i.e. from inlet to outlet. The extractor can then be undocked from the washing device. The extractor can now be stored away for some time if this is desirable. In most cases, however, the extractor is docked without delay to an elution device where an eluant is provided to flow through the channels of the extractor and eluate the certain molecules from the microbeads, forming separate eluates passing out from the outlet openings of the docking means. The eluates can then be collected for an immediately following analysis or for further processing. Further processing may include micro dispensing (e.g. piezo electric micro dispensing) of at least parts of said eluates on a target plate suitable for subsequent MALDI-TOF mass spectrometry.
Embodiments of the invention is disclosed in the following description and discribed with the aid of the following figures in which
a shows a combined device comprising a separator, an extractor array according to an embodiment of the invention and a dispenser array
b shows in cross section the dispenser array and the beneath arranged target plate
a, b and c shows a dockable extractor according to an embodiment of the invention.
a and b shows an alternative embodiment of the combined extractor of
a shows a view from above of an embodiment of the dockable microextraction chip of the “2D-Array” type, together with a cross section of the same.
b shows a view from above of an embodiment of the dockable microcxtraction chip of the “Film-strip” type.
a shows a side cross section of an embodiment having a droplet inlet zone
b shows a view from above of the embodiment in
a shows components for performing sample loading, washing, docking, and extracting
In this description the term “virtual flow channel” is intended to mean a microscopic flowing portion of a laminary flowing fluid, said portion having a long axis being parallel to the direction of flow, and said portion having a width and a depth orthogonally to the direction of flow, said portion can be regarded as an entity not mixing with the rest of the flowing fluid because of said laminar flow and small (micro) dimensions, thus constituting a “virtual channel”. Alternative term: “virtual channel flow”, “virtual flow line” and “virtual flow lane”.
The inventive concept of the present invention lies in a dockable and disposable processing module comprising a micro-extractor arranged to facilitate extraction, enrichment, and eluation of certain analyte biomolecules origination from a sample solution.
Extractor
A first embodiment of the invention comprises an extractor having a number of separate channels 101, 111 each devised to contain a porous bed 201, able to adsorb species from the one of the components of a mixture that is brought to pass through it. Said bed can comprise e.g. a bed of microscopic beads. The channels 101, 111 are arranged having microscopic dimensions. The width of a channel is typically less than a few tenth of a millimeter, often even smaller. The depth of a channel is in this magnitude too. The microscopic beads are prevented from escaping from the channels by a restraining means 255, 305, 405. Said restraining means can comprise a mesh, or a number of columns arranged having interspaces smaller than the diameter of the micro beads.
As an alternative, the porous bed can be omitted and the function to adsorb species to be analysed can be carried out by means of modified surfaces forming part of the walls that define the channels. To increase the efficiency the surfaces may be subject to a surface enlarging treatment e.g. forming of a porous layer. Embodiments include surfaces comprising surface modified silicon and porous silicon.
In a methodological step said species is eluted by the aid of an eluant forming an eluate corresponding each component, i.e. a type of solid phase extraction, SPE.
Dockable Extractor
In an alternative embodiment the extractor is designed to be dockable. With this term is meant that said extractor is attachable to, detachable from and re-attachable to other devices. Said dockable extractor 207 comprises a plate or another movable entity that is devised to be manually or automatically detachable from other parts of e.g. an analysis device. Said extractor is also devised to be re-attachable to the same or other parts of the analysis device, such as a washing device or a dispensing device. Specifically such embodiments comprise docking means that enables the docking and the flow of liquid from other parts of the analysis device to the inlets of the extractor, and the flow of liquid from outlets of the extractor to other parts of the analysis device. Such parts may include a feeding device or a washing device, or an elution device, or a combination thereof. Said docking means can also comprise means for preventing species from escaping from the dockable extractor, despite of mechanical handling. Said means can comprise the arranged small dimensions, that will keep the species in the extractor by the aid of capillary forces.
In a preferred embodiment the extractor part of the docking means comprises a flat surface with a number of holes, each hole being provided with a sealant mechanism slightly protruding from the surface. The sealant mechanism may be formed by patterning a polymer using lithographic technique. In an alternative embodiment the sealant mechanism comprises a hydrophobic break formed using surface modifying technology. In further alternative embodiments the hydrophobic break is achieved by arranging a polymer film surrounding the hole. Still other embodiments comprise sealant layers comprising miniature gaskets or o-rings.
The docking means also comprises a fastening system of notches and protruding parts keeping the dockable extractor in determined position so that the holes of the extractor part of the docking means connect to and align with the corresponding holes of the part it is docked to. The fastening system also exerts a certain mechanical pressure to assure tightness of the connection. The fastening system is also devised to enable appropriate attachment and detachment of the dockable extractor.
Droplet Capillary Loading, Filter Paper Drainage
Referring to
Typically a droplet of 50 microlitres is pipetted in a droplet inlet zone 3 by 3 millimetres and 300 micrometres deep.
Multiple Microextractor Assemblies
In alternative embodiments of the dockable extractor, see
Straight Linked Chain
In one of these alternative embodiments of the dockable extractor, see
Orthogonally Linked Chain (Film-Strip)
In
Disk Unit (Circular Arrangement)
In
Storage Function
The embodiments of the microextractor described above can also, with no, or just minor modification be used as a storage unit, capable of retaining protein samples on the dockable microchip for long term storing e.g. at minus 20 degrees Celcius.
Dispenser
In another preferred embodiment, a processing module comprises an extractor portion 302 with functionality as described above and a dispenser portion 301. A first portion of the module comprises the extractor and a second portion, totally integrated with the first one, comprises an array of dispenser nozzle openings 501-506, (seen from “above” in
In an alternative embodiment the separate flows of eluate is passing through a common basin 510 where the separating walls 521, 525, separating the different fractions is omitted downstream the restraining means 255 (not shown in
In another embodiment the dispenser 301 comprises outlets or an outlet 322 enabling the fluid to flow through the dispenser without having to be dispensed through the dispenser nozzle. This facilitates priming and washing of the device.
Electrospray
Referring to
Isoelectric Focusing Means
In alternative embodiments the module is provided with isoelectric focusing means integrated together with the above described extraction means.
Said focusing means comprises a pair of electrodes 132, 134, 332, 334 integrated in the walls of a isoelectric focusing compartment 135 in the isoelectric focusing portion 130 of the module 100. Alternatively they are arranged within side compartments to the focusing compartment 135, said side compartments standing in fluid connection to said isolelectric focusing compartment 135, to reduce or inhibit gas production.
Material
The device is preferably manufactured in polymer or silicon. A master for mass production of polymer devices is preferably made from metal or from a ceramic material. Silicon is essentially inert when dealing with protein mixtures at room- or near room temperature. The material is also very suitable for micro-machining techniques, e.g. for etching away parts of the material with established etching techniques.
Another advantage using silicon, is that with said etching techniques the dimensions becomes very precise and it is possible to etch surface with far better than micrometer precision.
Structure
The device is preferably manufactured in a plate structure, where said channels are formed in a surface layer of a first plate. Said channels are subsequently sealed by bonding a second plate to the first plate.
Method
The above disclosed extraction device is used in a method for processing biological specimens with increased speed comprising the following steps; docking the extractor to a priming device for loading microbeads into the extractor and flushing the extractor with a priming solution, undocking the extractor from the priming device, flowing a biological specimen in fluid phase through the dockable microextraction device, letting certain biomolecules adhere to said microbeads inside said extractor, docking the extractor to a washing device, flushing the extractor, undocking the extractor from the washing device, docking the extractor to an elution device, eluting the certain biomolecules from the extractor. The biomolecules can be eluted directly to a dispensing device for being dispensed on a target plate for further processing using MALDI-TOF MS.
In a preferred embodiment a dispensing devision is arranged as a part of the extraction device, and in the corresponding method there is no need to dock the device to a special dispensing device, as would be realised by those skilled in the art.
Processing Steps
A preferred embodiment of a method according to the present invention comprises the following steps:
Preferably, in a second process station, the following steps are performed:
In this context it is possible to use the device to perform both global expression studies and focussed expression studies.
Robotic Components
In
Number | Date | Country | Kind |
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0104125-0 | Dec 2001 | SE | national |
0202222-6 | Jul 2002 | SE | national |
0202415-6 | Aug 2002 | SE | national |
Filing Document | Filing Date | Country | Kind |
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PCT/SE02/02285 | 12/11/2002 | WO |