Process for Conducting Electrophoresis and Transfer

This invention relates to processes and apparatus for carrying out horizontal gel electrophoresis for separation and subsequent vacuum assisted transportation of macromolecules to a support membrane to facilitate detection.

The process known as electrophoresis involves the migration of charged molecules through a suitable retarding medium under the influence of an electric field. Generally, the compounds of higher molecular weight migrate at a slower rate through the medium than do the compounds of lower molecular weight. Devices have been provided previously for carrying out electrophoresis. An example of such a device is U.S. Pat. No. 4,415,418 in which a tray is provided with a raised platform at the center. Removable partitions are placed in the tray at opposite ends of the platform, and a conventional electrophoresis gel is poured over the platform to form a thin layer. When the gel has cooled, the partitions are removed. A comb is provided to form wells across the surface of the gel. Substances that are to be subjected to electrophoresis are delivered into each of the wells, and the tray is at least partially filled with an electrolyte buffer. Electrodes are positioned at each end of the tray and a sufficient voltage difference is applied to the electrodes to cause migration of the molecules of the substance in the wells across the length of the gel, separated according to their molecular weight. After electrophoresis, the gel is removed from the original casting tray, and placed in a dish containing depurination solution. Approximately thirty minutes later this solution is poured out by tipping the dish toward one edge while the gel is held with the fingers. It is important to use great care during this procedure to prevent the gel from breaking because there is no gel support structure and subsequent processing is possible only with an integral gel. A denaturation solution is then added to the dish and incubation is continued for approximately thirty minutes. Again, the solution is carefully poured off. Then neutralization buffer is added and incubation is continued for thirty additional minutes.

In accordance with conventional techniques, transfer of the nucleic acids is accomplished by placing a piece of filter paper, which is as wide as and longer than the gel, on a platform which is suspended above a solution of 10X saturated saline citrate buffer (SSC). The ends of the filter paper are long enough to hang off the ends of the platform and dip into the 10X SSC. Thus, the filter paper acts as a wick to absorb the SSC solution. The gel is removed from the dish and placed on top of the filter paper saturated with 10X SSC. Next, a piece of membrane filter paper which is the same size as the gel is saturated with 10X SSC and placed on top of the gel. The nucleic acids are eventually bound to the membrane filter paper. Another piece of saturated filter paper, the same size as the gel, is placed on top of the membrane. The entire layered unit is then smoothed to remove any air bubbles that may exist between the gel and the filter paper. Finally, a stack of paper towels, the same size as the gel, is positioned on top of the layered unit.

Over a period of about 12 to 16 hours, the 1OX SSC solution is drawn up through the gel by capillary action and the nucleic acids are transferred out of the gel into the membrane above. The paper towels absorb the excess buffer and provide the force for capillary action. At the end of the transfer period, the entire layered unit is disassembled and the membrane is removed for hybridization. This technique is described in an article by E. Southern, "Detection of Specific Sequences Among DNA Fragments Separated by Gel Electrophoresis," J. Mol. Biol., 98:503 (1975).

Although the trays such as the one described in U.S. Pat. No. 4,415,418 are convenient for carrying out electrophoresis, they are not suitable for situations where a large number of samples must be tested in a relatively short period of time.

Therefore, the prior art uses a tedious multi-step, multi-apparatus process for preparing nucleic acid fragments for subsequent hybridization. Four steps are generally undertaken to achieve preparation of the sample for hybridization. Electrophoresis was previously described. Depurination removes purine bases from nucleic acids. Denaturation involves separating the strands of nucleic acids and breaks down the depurinated nucleic acids into suitable size to allow eventual transfer of the fragments out of the gel. Transfer involves allowing the fragments to go out of the gel onto the porous membrane.

It is the principal object of the present invention to provide one apparatus wherein the steps of electrophoresis, depurination, denaturation and transfer to a membrane may all be carried out.

It is an object of the present invention to standardize and simplify the electrophoresis and transfer techniques to facilitate applications of molecular biology.

It is a further object of the present invention to develop a process for electrophoresis and transfer which offers considerable time and cost savings.

Another object of the present invention is to avoid the difficulties generally associated with prior art methods with respect to handling the gel and further processing.

In accordance with the present invention, nucleic acid fragments such as DNA and RNA may be prepared for subsequent hybridization using the process and apparatus of this invention. The process and apparatus are particularly useful for detection of gene rearrangements, restriction fragment polymorphisms and restriction fragment patterns. The process enables rapid screening of tissue specimens and body fluids for the presence of infectious viruses such as Human Papilloma virus, for typing B-cell and T-cell monoclonal populations, and for screening patients for the development of cancer or other disease states.

Thus, the apparatus of the present invention combines in a single unit means for conducting electrophoresis and transfer, and includes a tray having opposite side walls, opposite end walls and a bottom wall. There is a central platform in the tray, with a vacuum chamber between the platform and the bottom wall. The platform surface is pervious to liquid. A liquid reservoir is provided adjacent each of the end walls and electrophoresis electrodes are mounted in the reservoirs. A conduit is provided for transferring liquid into and out of the tray. The tray is covered by a lid. The apparatus is adapted to perform electrophoresis and transfer without removing the gel from the tray.

The process of the present invention is performed by placing the gel on a porous platform in a tray. Samples are deposited in spaced wells in the gel. An electrophoresis buffer is supplied to the tray to cover the gel and the electrodes. An electric potential is applied between the electrodes. After the electrophoresis step, depurination and denaturation are carried out while the gel remains in the tray. During the denaturation step, a transfer membrane is inserted manually between the gel and the platform, and the liquid is drawn through the porous membrane to cause the displaced samples to be transferred from the gel to the membrane. The membrane is then removed from the tray.

A preferred embodiment of the invention is illustrated in the accompanying drawings, in which:

FIG. 1 is a top plan view of the electrophoresis transfer tray in accordance with this invention, with the lid removed;

FIG. 2 is a side elevational view of the cartridge of this invention, partially in cross-section;

FIG. 3 is a detail top plan view of the tray with the perforated plate removed;

FIG. 4 is a cross-sectional view of the tray along the line 4--4 in FIG. 3;

FIG. 5 is a detail view of the plate during the vacuum step showing the membrane and gel superimposed on the plate;

FIG. 6 is a top plan view of the lid for the cartridge;

FIG. 7 is a cross-sectional view of the lid along the line 7--7 in FIG. 6;

FIG. 8 is a cross-sectional view of the lid along the line 8--8 in FIG. 6;

FIG. 9 is a detail plan view of the tray with the bridge installed;

FIG. 10 is a front elevational view of the tray with the bridge installed as in FIG. 9; and

FIG. 11 is a cross-sectional view of the bridge and tray along the line 11--11 in FIG. 9.

Referring to FIGS. 1 and 2, a cartridge 2 is used for carrying out the electrophoresis and transfer processes of this invention. The cartridge 2 includes a tray 4 and a lid 6. Tray 4 is preferably composed of polyvinyl chloride or Delrin, a resin which is a registered trademark of E. I. duPont de Nemours & Co. Inc.; however, any material which has good dimensional stability for fabrication and non-electrically conductive and which is chemically compatible with the intended use is suitable. The tray 4 has opposite side walls 8, end walls 10 and a bottom wall 12. A support surface 14 is provided at the center of the tray. The bottom wall 12 adjacent the end walls 10 slopes downwardly, as shown in FIG. 2 away from the support surface 14. A plurality of webs 16 extend inwardly from the end walls 10. The webs facilitate insertion of the gel without tearing. The webs also align the gel thereby assuring proper orientation of the gel in the electric field.

As shown in FIGS. 2 and 4, a transverse passage 18 is provided in the bottom wall 12 and ports 20 communicate with the passage 18 to allow the circulation of fluid into and out of the tray. A tubing fitting 22 is provided on the side wall 8. An identical passage 18 is provided at the opposite end of the tray (FIG. 1) and has corresponding ports 20 and a tube fitting 22.

Electrodes are provided at each end of the tray. The electrode 24 is in the form of a thin wire, preferably of platinum, which is wrapped on an insulated rod 26. The rod is supported in aligned holes in the webs 16. The electrode 24 extends through the side wall 8 and is connected with an electrical contact element 28 which is adapted to be connected to a source of electric potential.

The support surface 14 is formed of a porous plate 30 (FIG. 11). Any porous plate is suitable, however, a plate made of a porous polyethylene is preferred. The porous plate should be about 30% to 85% open to sufficiently pull water. As shown in FIG. 5, the plate 30 has parallel score lines on each side which are perpendicular, so that small holes through the plate are formed at the inner section of the score lines. Of course, any suitable porous plate could be substituted for the plate 30. A porous membrane 31 has approximately the same dimensions as the plate 30, so that when it is in place, it substantially covers the plate 30. Membrane 31 must have properties such that it is optimum for binding of vacuum assisted transported DNA fragments. Membrane 31 is preferably comprised of nylon or nitrocellulose such as a nylon membrane comprised of about 0.2 to 1.2 micron porosity. However, any fluid-permeable membrane which is sufficient to bind nucleic acids would be suitable.

A gel is cast on a separate tray as in conventional practice. The gel can be agarose, polyacrylamide, mixed agarose/polyacrylamide or any other material suitable for the separation of macromolecules in an electric field. Generally, 0.7% w/v agarose is used. The gel 32 is then transferred to the tray 4 where it is superimposed on the plate 30, as shown in FIG. 2. A vacuum chamber is provided beneath the plate 30, as shown in FIGS. 2 and 3. The chamber includes a pair of ridges 34 extending outwardly from a central channel 36. A tubing fitting 38 extends through the side wall 8 and communicates with the channel 36. The fitting 38 is adapted to be connected by tubing to a suitable vacuum pump. The opposite ends of the gel 32, when placed in the tray 4, abut the ends of the webs 16, as shown in FIG. 11. The side edges of the gel 32 are positioned by engagement with the side walls 8 of the tray.

As shown in FIG. 6, the lid 6 has a shoulder 40 which extends around the perimeter of the lid and engages the inside surface of the side walls 8 and the end walls 10. A sealing gasket 42 is retained within a groove in the shoulder 40. The gasket 42 prevents the leakage of fluid from the interior of the cartridge. A gas bubble channel 44 is formed in the interior of the lid 6 and extends along the end walls and side walls of the tray. The channel portion at the right side of FIG. 6 is more shallow than the groove at the left side of FIG. 6, and the grooves extending along the side walls 8 progressively increase in depth from the right end to the left end as viewed in FIG. 6. This arrangement of the grooves causes the gas bubbles to migrate progressively toward an outlet port 46 through the lid 6. The outlet port has a tube fitting 48 through which the gas bubbles can escape.

The central portion of the lid 6 has a plurality of grooves 50 formed in the top side of the lid. As shown in FIGS. 6 and 8, ports 52 extend from the bottom of the grooves to the lower surface of the lid so that fluid can pass from the grooves 50 into the interior of the cartridge when the lid is in place. A cover plate 54 encloses the grooves 50 and a tube fitting 56 allows liquid to be conducted through the plate 54 into the interior of the grooves 50.

In order to enable samples to be delivered into the wells formed in the gel layer 32, a bridge 58 is provided. The bridge aids in directing the operator to the correct well for sample filling thus making it easier to fill the well. The bridge is received in vertical slots 60 in each of the side walls 80 at a position that is aligned with the wells that are molded in the gel layer. A black strip may be positioned near the wells to aid in visualizing the wells during sample loading. The bridge 58 includes funnel-shaped passages 62 in a shape to receive the tip of a pipette for delivering the samples into the wells formed in the gel. As shown in FIG. 10, arches 64 are formed in the bridge between the passages 62 to allow fluid circulation between opposite sides of the bridge. If additional recirculation is necessary, the bridge can be removed prior to electrophoresis.

In operation, a gel layer is formed in accordance with conventional practices of a proper size and shape to fit within the tray 4, so that the ends abut the ends of the webs 16 and the sides of the gel fit between the side walls 8 of the tray. Preferably, the gel is cast in a separate tray and has a series of wells molded in the gel layer adjacent one end. The gel 32 is then removed from the casting tray and placed on the porous plate 30, so that the gel 32 occupies the position shown in FIGS. 2, 9 and 11. The sloping top edge of each web 16 aids in guiding the gel into position in the tray 4. A source of electric potential is connected with the electrical connectors 28 and a system for circulating fluid is connected with the tubing fittings 22. An electrophoresis buffer is added to the tray to a depth that fully covers the electrodes 24 and the gel. The bridge 58 is installed in the slots 60 after the gel layer is positioned on the support surface 14. The samples are then delivered into the passages 62 from which they pass into the individual wells. The bridge remains in place when the lid 6 is applied. The electrophoresis buffer is recirculated through the passages 18 by the use of a conventional pump, to provide a fluid current passing over the gel. At the end of electrophoresis, the electrophoresis buffer is then withdrawn from the tray and a depurination buffer is pumped into the tray. After a predetermined period of time, the depurination buffer is then pumped out of the tray and a denaturation buffer is pumped into the tray. The gel tends to float in the denaturation buffer, and before the vacuum is applied, the membrane 31 is inserted manually into the space between the gel and the plate 30, as shown in FIGS. 5 and 11. The gel is then lightly pressed against the membrane and held in place by appropriate means, such as a band or tube 39, as shown in FIGS. 9 and 11. After a suitable elapse of time, the denaturization buffer is withdrawn through the vacuum fitting 38 at a relatively slow rate, which transfers the displaced samples from the gel onto the permeable membrane 31. As an alternative, water or denaturation liquid may be sprayed onto the surface of the gel through the tube fitting 56 as the liquid is being withdrawn through the tube fitting 38. The lid 6 is then removed and the permeable membrane 31 may be removed from the tray for further processing. The membrane now contains the displaced samples in preparation for hybridization.

The cartridge of this invention has the important advantage that it allows electrophoresis and transfer to occur without having to remove the gel from the tray. At the completion of the operation, the nylon membrane bearing the samples can readily be removed for subsequent treatment.

The electrophoresis apparatus is designed to accommodate either a large number of analytical samples or milligram quantities of fragments for preparative runs. Typically, the number of samples which may be introduced into the cartridge may range from about 5 to 15. Generally, 10 samples plus two controls has been found to be suitable.

The tray 4 and the lid 6 must be compatible with standard electrophoresis and nucleic acid transfer reagents. Typical reagents include up to 3 molar (M) salts, acetic acid, 1 M hydrochloric acid and 0.5 M sodium hydroxide. Many polymers could be suitable for the present invention. Furthermore, in view of the direct current being used during electrophoresis, the tray 4 and lid 6 should not conduct electricity. The lid 6 is preferably plexiglass (acrylic) since a further advantage is obtained with the use of a clear cover since it would allow visual tracking of optional dyes during electrophoresis.

Using one buffer or solution throughout the foregoing procedure is more efficient and economical than using a different buffer or solution during each of the electrophoresis, depurination, denaturation and transfer stages. Alternatively, four separate solutions may be used in the practice of the present invention. For example, during electrophoresis any buffer wellknown in the art is suitable such as any solution of a weak acid or base and its salts, such as acetates, borates, phosphates and phthalates, which behave as buffers. Typical compounds used in preparing buffers include acetic acid, phenylacetic acid, sodium, acetate, ethylene diamine tetraacetic acid (EDTA), phosphoric acid, boric acid, hydrochloric acid, sodium hydroxide, sodium chloride and the like. During electrophoresis, a buffer comprised of 40 mM tris-acetate, pH 8, 12 mM sodium acetate and 2 mM EDTA, pH 8, is preferred.

During depurination, any solution which chemically assists in depurination or depyrimidination would be useful. These solutions are well-known in the art. A buffer comprised of 0.25 M hydrochloric acid is preferred. It was discovered that during depurination, it is important to expose the lower surface of the gel as well as the top and side surfaces to the solution. For this reason, the membrane 31 is not inserted between the gel and the platform until just before applying the vacuum under the porous plate 30 to transfer the cells to the membrane.

During denaturation, any solution which assists in breaking the hydrogen bonds between the nucleic acid strands is suitable. These solutions are also well-known in the art. For example, water and heat may provide satisfactory results, also formamide or any alkali such as sodium hydroxide or potassium hydroxide. In the present invention a solution of 0.5 M sodium hydroxide is preferred.

As the transfer solution, any solution which allows transfer and binding of the nucleic acid strands to the membrane would be suitable. These solutions are also well-known in the art. Advantageously, in the practice of the present invention the transfer solution is preferably 0.5 M sodium hydroxide, the same as the denaturation solution.

The time periods used in each of the above-described stages may vary over a wide range depending on the processing conditions. For instance, each of electrophoresis, denaturation and depurination may require from about 10 minutes to 5 hours. Useful techniques to decrease the amount of time required for processing include increasing the voltage, using larger ports, selecting the optimum thickness of the gel, different sizes of membranes and the support plate, and the like. A particular advantage of the present process is that the time required for electrophoresis is approximately 40-65% of the typical time required for electrophoresis using prior art apparatus and techniques. A significant time savings is offered by the present invention because of the circulation of fluids, i.e., buffers, through the electrophoresis transfer cartridge, thereby allowing a constant pH and temperature to be maintained during the process. In addition, the geometry of the cartridge results in concentrating the electric field within the gel which also speeds the process.

Furthermore, by maintaining a relatively frequent circulation of the buffer, a smaller volume of buffer is suitable in contrast to the buffer requirements of prior art electrophoresis processes.

The transfer step may require from about 10 minutes to two hours. Generally, about 60 minutes produces adequate results. This step also offers a considerable time savings over prior art transfer techniques. Capillary transfer, for instance, requires about 12 hours, squash blot transfer requires about 3 hours and standard electrotransfer requires about four hours.

A further advantage of the present invention is the time and labor savings that results since the apparatus is a cartridge. The decrease in the number of mechanical steps to be performed by a technician or operator assists in maintaining the accuracy of the procedure since a decrease in the number of necessary steps to be performed also minimizes error.

Other components are useful to achieve the objects of the present invention in addition to the above-described electrophoresis transfer cartridge. For instance, a microprocessor controller may be used to automate electrophoresis and DNA/RNA transfer. Such a controller would control the voltage and time for electrophoresis, the valves for reagents, the pumps to add and remove reagents and the vacuum system for DNA transfer. The electrophoresis transfer cartridge may be connected to a variety of standard laboratory equipment including peristaltic pumps.

The following example is intended to demonstrate one method that may be used to practice the present invention. The following is not intended to limit the invention in any way.

A 14 cm long .times.11 cm wide .times.0.65 cm deep 0.7% w/v agarose gel was placed and aligned in a polyvinyl chloride electrophoresis transfer tray having inside dimensions of 20 cm long .times.11 cm wide .times.2 cm deep. The gel rests on a liquid pervious platform or support plate made of porous polyethylene. Approximately 200 ml of an electrophoresis buffer comprised of 40 mM tris-acetate, 12 mM sodium acetate and 2 mM EDTA was added by hand.

Restriction enzyme digested human genomic DNA samples were loaded into the wells and a plexiglass top was placed over the polyvinyl chloride tray. The unit was then plugged into a power supply which was set at 90 volts. The power was turned on. Electrophoresis was allowed to continue for approximately ten minutes. Then the buffer was recirculated at a rate of approximately 25 ml/min for the duration of electrophoresis. Electrophoresis continued for approximately two hours. The power was turned off and the electrophoresis buffer was pumped out.

Approximately 200 ml of a depurination solution comprising 0.25 M hydrochloric acid was pumped into the polyvinyl chloride tray. The solution was allowed to stand for approximately 15 minutes and then the solution was pumped out. Next, approximately 200 ml of a denaturation solution was added to the polyvinyl chloride tray. A nylon membrane was inserted between the gel and the porous plate. A vacuum pump was turned on to withdraw fluid through the porous polyethylene plate at about 2 ml/min. This was continued for 60 minutes to allow the DNA to transfer from the gel to the nylon membrane below the gel. The unit was turned off.

While this invention has been illustrated and described in accordance with a preferred embodiment, it is recognized that variations and changes may be made therein without departing from the invention as set forth in the claims.