Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
  • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
  • G01N27/416—Systems
  • G01N27/447—Systems using electrophoresis
  • G01N27/44756—Apparatus specially adapted therefor
  • G01N27/44773—Multi-stage electrophoresis, e.g. two-dimensional electrophoresis
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/14—Extraction; Separation; Purification
  • C07K1/24—Extraction; Separation; Purification by electrochemical means
  • C07K1/26—Electrophoresis
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/14—Extraction; Separation; Purification
  • C07K1/24—Extraction; Separation; Purification by electrochemical means
  • C07K1/26—Electrophoresis
  • C07K1/28—Isoelectric focusing
  • C07K1/285—Isoelectric focusing multi dimensional electrophoresis

Definitions

• the invention relates to a method and a device for separating complex protein mixtures with the aid of high-resolution two-dimensional electrophoresis (2D electrophoresis, 2DE) in large gels.
• 2DE forms the basic technology e.g. for proteome analysis, i.e. for the separation and identification of the total protein of a cell type, organ or organism.
• High-resolution 2-dimensional electrophoresis is an established method for the separation of protein mixtures (patents: US 5837116 - California Inst of Technology, US, 1999; Bio-Rad Lab. Inc., US, 1998: US 5773645, EP 877245 and 1990: US 4874490, EP 366897; DE 4244082 - ETC GmbH, DE, 1994; JP 05048421, US 4666581 - Hitachi Ltd., JP, 1986; Aimes, GF, Nikaido, K .: PubMed Abstract: Biochemistry, 1976, Vol. 15, No. 3, pp. 616-623; US 5534121), which are extracted from organ tissues.
• the protein mixture is applied to a polyacrylamide gel, which is located in a glass capillary.
• the proteins are separated in the electric field according to the principle of isoelectric focusing: the freely movable ampholytes form a pH gradient under the electric voltage, into which the proteins are classified according to their isoelectric points.
• the gel is expelled from the capillary tube.
• the Gel is then present as a thin, long, gelatinous thread. This gel thread is picked up and placed in a rectangular, large-area glass cassette which in turn contains polyacrylamide gel (FIG. 1).
• SDS SDS gel electrophoresis
• the CA-2DE was further developed by Klose and Kobalz [6] into a so-called large gel technique: the 1 D gel thread is 41 cm long (diameter 0.9 mm), the 2D gel has the dimensions 46 cm x 30 cm; Thickness 0.75mm (the gel is made in half). With this gel technique, the highest possible resolution is achieved today (more than 10,000 proteins per gel).
• Two solutions are made, one with ampholytes for the low pH range and one for the high pH range. Then, with these two solutions, a gel is poured over a gradient mixer, which contains the finished pH gradient.
• IPG gels IPG - immobilized pH gradients, Immobiline ®
• the gel is dried and cut into strips. The strips are offered commercially. The user swells the strip in a buffer, applies the sample and then carries out the 1-D step. The separation in the 2nd dimension is the same as with the CA technique.
• the gels offered are relatively small, ie a maximum of 23cm x 20cm.
• CA technology Advantages: High resolution due to large gels, clean separation, good reproducibility. Disadvantages: Largely manual in implementation, therefore complex and dependent on
• IPG technology Advantages: The 1 D gels (dried gel strips) are offered ready for use. This means a significant simplification of the method. In addition, there is a very distinctive marketing of the companies Pharmacia and BioRad (manual, sales events, workshops). The method is therefore dominant today. Practically all beginners use it. After the IPG patent expires (Swedish patent 14049-1), the number of manufacturers will increase. Disadvantages: Dissolution and separation are comparatively bad, since only relatively small gels (see above) can be used. The IPG technique was developed with the intention of significantly improving the reproducibility by binding the ampholytes to the gel matrix. The improvement that can theoretically be expected is practically of no consequence (cause: influence of
• the most difficult and time-consuming steps are pouring the 1 D gels in the capillary, ejecting the gel thread from the capillary after the run and transferring the long gel thread to the 2D gel.
• the invention has for its object to develop a method and an apparatus with which the separation of protein mixtures can be simplified considerably.
• the object was achieved according to the invention as follows:
• the separation of the proteins in the first dimension is carried out in protein-permeable materials - porous, capillary tubes, which can also be tubular.
• the porous capillary tube is then introduced into a glass cassette containing a flat gel without ejecting the gel thread and having to transfer it further as such.
• the proteins then migrate under current through the wall of the tube into the flat gel.
• Plastic fiber braided tubes and capillary tubes made of ceramic have proven to be suitable tube types:
• the gel thread then no longer needs to be ejected after the isoelectric focusing, but the entire capillary tube can be inserted into the glass cassette for further separation of the proteins.
• the proteins then migrate under current through the wall of the tube into the flat gel. After the electrophoresis of the proteins in the second dimension, the capillary tube with the empty gel is thrown away.
• the capillary tube with the ready-to-use gel (gel tube) is offered commercially. This eliminates the need to pour and eject the gels, and the transfer of the 1-D gel to the 2-D gel is easy for the user.
• the tube material used according to the invention is permeable to proteins up to a size of approximately 400 kDa (FIG. 2). By choosing the pore size, certain molecular weight ranges can be preferred, whereby an additional improvement in the resolution can be achieved.
• the device according to the invention for the separation of complex protein mixtures with the aid of high-resolution two-dimensional electrophoresis consists - in addition to standard elements of 1D and 2DE technology - of protein-permeable materials in the form of porous tubes, e.g.
• a capillary tube or capillary tube in particular a plastic fiber braided tube or a ceramic capillary tube or ceramic hollow fibers, also a glass cassette that contains a flat gel, from a gel tube, from tube array and pipetting robot, tube array and buffer chamber, 2D cassettes, 2D cassettes in the buffer chamber, a special 1 D chamber, 2D gels as finished gels, a 2D chamber, possibly IPG gels in tubes and an HTP-2DE apparatus (high-throughput technology).
• the device according to the invention initially consists of standard elements of 1D and 2DE technology (FIGS. 1 and 2) with the glass tube (3), the protein sample (1) in the IEF gel (2) in an isoelectric focusing device (4 ).
• the SDS gel electrophoresis device (5) in the gel cassette (7) contains the IEF gel on the SDS gel (6), which after electrophoresis involves the protein sample (9) in the porous gel tube (11, 12) after removing the plastic cover (10) is placed on the gel cassette (7), which provides protein spots (8).
• the porous capillary tubes (14) are encased (15) by a plastic sleeve (13) which connects several tubes (FIG. 3, in cross section FIG. 4).
• the tube array (17) form capillary tubes, encased and connected by a double-layer plastic film. After tearing open the two layers, the pipes can be removed.
• a cross reinforcement (platform) is used to attach the tube array in the focusing chamber.
• the tube array (17) is provided with a pipetting robot (16) (FIG. 5).
• the tube array (FIG. 6) is fastened in the focusing chamber with the aid of a clamping device (18). It forms a platform (19 - supervision).
• the 2D cassette according to the invention (20 in cross section, 21 in side view, 22 in the buffer chamber in FIG. 8) contains the SDS gel and the IEF gel (FIG. 7). In addition to standard elements of 1D and 2DE technology (FIGS.
• the device according to the invention thus consists of gel tubes (FIG. 3, FIG. 4) and gel tubes bundled to form tube arrays (17, FIG. 5, FIG. 6) (17) and pipetting robot (16), tube array and buffer chamber (22, FIG. 8), 2D cassettes (20, 21), 2D cassettes in the buffer chamber (22), a special 1-D chamber (FIG. 6), 2D -Gels as ready-to-use gels (20, 21), a 2D chamber ( Figures 7 and 8) and an HTP-2DE apparatus.
• the polymer membranes used according to the invention in the form of hollow fibers (diameter up to 0.5 mm), capillaries (diameter up to approx. 3 mm) and tubes are commercially available from various manufacturers: Fresenius GmbH, Gambro Dialysatoren GmbH & Co KG, Akzo Faser AG [14 ] or Reichelt Chemietechnik [11] in Germany, X-Flow BV in Holland and AGT - A / G Technology Corporation in the USA [16] are such manufacturers.
• the artificial kidneys and plasma separators represent a very large market with millions of square meters.
• the main components of these elements are capillary membranes with a defined pore structure.
• the polysulfone tubes mentioned in Example 1 come from the US company. AGT.
• the braided hoses mentioned in the examples go back to the company Erfurter Flechttechnik [15].
• the pores are formed by the structure and arrangement of the fibers.
• polyester polycarbonates, polyalkylene terephthalates
• polysulfones polyether sulfones, polyaryl ether sulfones, polyarylsulfones
• polyamides polyurethanes, polyacrylonitrile, polypropylene, polyvinylidene fluoride (PVDF) or polyether ketones for membranes
• natural fibers such as silk or cotton
• Porous hollow fibers are described by Lück and others [13].
• Fibers made from polyalkylene terephthalates have proven to be very suitable for the production of braided tubes, in particular polyethylene terephthalate - in addition to polybutylene terephthalate and poly (1,4-cyclohexanedimethylene) terephthalate.
• the gel tubes according to the invention have pore sizes of 0.2 to 0.005 ⁇ m: 0.2 ⁇ m for proteins smaller than 400 kDa
• the combination consists of known elements (1D and 2DE technology, CA-2DE and IPG-2DE technology) and new solutions (1-DE protein separation in hollow porous protein-permeable materials and their unchanged use in the second dimension, 2D -Gels as ready-to-use gels, HTP-2DE technology), which mutually influence each other and result in an advantage (synergistic effect) and the desired success in their new overall effect, which is that simple handling is now combined with high and clean protein resolution ,
• the use of the new large gel technology according to the invention lies in the separation of complex protein mixtures. Furthermore, the use according to the invention relates to the fact that the hollow porous materials in the form of hollow plastic fibers or plastic braided sleeves, in particular polyester braided sleeves or ceramic capillary tubes / ceramic hollow fibers, are used in 1-D electrophoresis and thereafter unchanged in 2D electrophoresis become.
• the gels are poured into tubes that have the same dimensions as the long, thin gel tubes; the wall of these tubes is made of porous material.
• the material must have a pore size that allows the proteins to migrate freely through the wall. After passing through, the proteins in the SDS gel must form the same round, unlubricated 'spots' as is the case with the usual 'naked' gels. This was by no means to be expected, since experience had shown that even the smallest obstacles in the gel (tiny air bubbles or lumps of gel) lead to spot smearing.
• the porous tubes must be tightly covered with a plastic film to prevent the gel from drying out during storage (as a commercial product) and to prevent buffer contact during the IEF run.
• the film must continue the 'tube' at the top for the sample application.
• the film must be easy to remove after the focusing run so that the porous tube can then be placed on the SDS gel without a cover and the proteins can migrate through.
• the new type of tube represents an essential feature of the invention, which only makes sense in the large gel technology due to the concept according to the invention - high resolution through long, thin capillary tubes.
• the separation of the proteins in the first dimension is carried out in protein-permeable materials - porous tubes, for example in a capillary tube or capillary tube - and the capillary tube / capillary tube for further separation of the proteins into one Glass cassette introduced, which contains a flat gel. The proteins then migrate under current through the wall of the tube into the flat gel.
• the protein-permeable materials consist of plastic [12, 13, 14, 15, 16], ceramic capillary tubes [9, 10, 12], plastic braided sleeves [12, 15] or polymer membranes in the form of hollow fibers made of polyester ( Polycarbonates, polyalkylene terephthalates), polysulfones (polyether sulfones, polyaryl ether sulfones, polyarylsulfones), polyamides, polyurethanes, polyacrylonitrile, polypropylene, PVDF (polyvinylidene fluorides) or polyether ketones, made from natural fibers (such as silk or cotton) or inorganic fibers (besides ceramic fibers and others - so - glass - glass Oxide fibers) and non-oxide fibers.
• polyester Polycarbonates, polyalkylene terephthalates
• polysulfones polyether sulfones, polyaryl ether sulfones, polyarylsulfones
• polyamides poly
• polyalkylene terephthalates have proven to be very suitable, in particular polyethylene terephthalate - in addition to polybutylene terephthalate or
• test sample A self-made protein mixture of known proteins was used as the test sample in the following examples. This test sample contained seven proteins with different molecular weights and isoelectric points.
• Example 1 1 .: plastic pipes
• the 2D gels showed the expected seven protein spots. This finding clearly proves that the proteins in the gel tubes of the "polyester braided tube” type [15] could be focused normally and that they entered the 2D gel through the tube wall.
• Example 1 1.1 .: polyethylene terephthalate
• Example 1 1.2 .: polycarbonate
• Example 1 1.3 .: polysulfone
• Example 1 2. Ceramic capillary tube [9, 10, 12] A ceramic capillary tube (AI203)
• Gel tubes with different pore sizes are produced in order to be able to separate a different molecular weight class from a cell extract depending on the selected pore size.
• the gel concentration of the 2D gel is adjusted accordingly. In this way, the highly complex and densely packed protein patterns of tissue extracts can be fractionated into several clear patterns. Benefits:
• the gels are dried in the tubes by air drying. This is possible with the gel tubes designed here because they are porous.
• Drying is of great advantage for the storage and distribution of the gels in the gel tubes.
• the gel tubes are welded in plastic and bundled together - preferably in sets of 10 (tube array figures 3 and 4).
• the plastic cover has the following tasks:
• the plastic envelope forms a platform in a central area or at the upper end of the gel tube, with which the entire tube array is clamped in the 1-D chamber (FIG. 5)
• the plastic cover consists of two parts that are torn apart after the 1-D run to remove the gel tubes (the plastic cover is thrown away).
• Example 5 Special 1-D chamber A special 1-D chamber is designed in such a way that the tube array is clamped into it with a simple movement ( Figure 5). The clamping ensures a complete seal against the buffer solution in the 1 D chamber, since the gel tubes must pass through the bottom of the 1 D chamber.
• a pipetting robot specially designed for the inventive purposes is able to fill capillary tubes with liquid (FIG. 4). It fulfills the following functions:
• the sample is applied when the tube array is already inserted in the chamber.
• the 2D gels are also offered to prospective customers / consumers as ready-made gels. They are supplied ready for use in a plastic cassette (Figure 6).
• the plastic cassette has the following properties:
• the cassette (b) it ends in a platform with which it can be easily clamped into the 2D chamber (see example 4 (d)) (c) the cassette can be torn open after the run and then releases the gel (the used cassette is thrown away; the particularly complex cleaning of the plates is not necessary) (d)
• the cassette has a simple mark at the bottom - 0.5 cm before the end - with which the current can be recognized.
• Example 8 2D chamber A 2D chamber is designed in such a way that up to 10 gel cassettes can be hung in it (Figure 7). Sealing takes place with the help of the cassette platform (see example 7 (b) above).
• Example 9 IPG gels in tubes Analog to Examples 2 and 4, IPG gels are produced in tubes.
• the filling, emptying and rinsing of the chambers is automated to such an extent that only storage vessels have to be filled with buffer.
• FIGS 1 to 8 show:
• a transverse reinforcement is used to fasten the tube array in the focusing chamber 18.
• the platform mentioned in FIG. 17 is shown in plan view
• 20 2D cassette in cross-section contains the SDS gel and the lEF gel
• HTP-2DE high-throughput technology lEF gels Isoelectric focusing gels IPG Immobilized pH Gradients, Immobiline ®
• IPG-2DE IPG-2-dimensional electrophoresis kDa kilodalton (measure of molecular weight)

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• Chemical Kinetics & Catalysis (AREA)
• Electrochemistry (AREA)
• Health & Medical Sciences (AREA)
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• Organic Chemistry (AREA)
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• Proteomics, Peptides & Aminoacids (AREA)
• General Chemical & Material Sciences (AREA)
• Physics & Mathematics (AREA)
• General Physics & Mathematics (AREA)
• Immunology (AREA)
• Pathology (AREA)
• Peptides Or Proteins (AREA)
• Other Investigation Or Analysis Of Materials By Electrical Means (AREA)

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• 2000
  • 2000-10-05 DE DE10050838A patent/DE10050838A1/de not_active Withdrawn
• 2001
  • 2001-10-04 US US10/398,408 patent/US20040069631A1/en not_active Abandoned
  • 2001-10-04 EP EP01986344A patent/EP1322950A2/de not_active Withdrawn
  • 2001-10-04 WO PCT/DE2001/003869 patent/WO2002029396A2/de not_active Application Discontinuation
  • 2001-10-04 CA CA002424298A patent/CA2424298A1/en not_active Abandoned
  • 2001-10-04 AU AU2002220491A patent/AU2002220491A1/en not_active Abandoned
  • 2001-10-04 JP JP2002532919A patent/JP2004510978A/ja not_active Withdrawn

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