Abstract:
A cassette and electrophoretic gel assembly includes a non-conductive cassette, two solid buffer reservoirs, and an agarose gel. The assembly is disposable, and the sample wells on the gel are in standard microtiter plate format. The configuration is such that the gel is continuously in electrical contact with the electrodes in operation despite the production/migration of water and other exudates.

Description:
FIELD OF THE INVENTION 
     The present invention relates to equipment used in bufferless gel electrophoresis. 
     BACKGROUND OF THE INVENTION 
     The volume of PCR reactions has grown dramatically as new applications are developed for use in many research areas. In many cases, the amplified product is to be used for further analysis, such as sequencing or in micro-array experiments. Because these types of analysis are both time consuming and expensive, it is more efficient to interrogate the PCR reaction results for amplified product before initiating any further analysis. The easiest and least expensive way to check for successful amplification is to run the product on an agarose gel for a few millimeters. 
     Conventional electrophoretic screening uses large format (approximately 15-25 cm by 20-30 cm) horizontal submarine agarose gels with multiple combs to form ranks of wells 4 to 8 centimeters apart. This format is expensive in both labor and materials. Moreover, this method is inconvenient for loading and analysis when the sample handling and reactions are performed in microtiter plates (96 wells on 9 mm centers or less). Because the conventional electrophoresis units are difficult to assemble and use, it is much more efficient to run as many samples as possible per gel. However, it is more convenient to analyze the results if the image of the gel maps directly to the layout of the samples on the microtiter tray. With the larger gels, therefore, there is a tradeoff between loading only twelve samples per row, analogous to standard microtiter plate layout (thereby simplifying analysis but wasting gel space) and filling the gel with as many rows as possible (which is more time efficient but complicates analysis). 
     Furthermore, in agarose gel and buffer strip systems, endosmotic flow of water across fixed anions in the agarose matrix draws water out of the anode and pumps it to the cathode, thus drying and shrinking one end and forming a puddle of liquid on the surface at the other end. In some cases, the gels may also deteriorate at the anode due to hydroxide ions which are generated there. As known by those of skill in the art, it is important that electrical contact be maintained despite potentially deleterious accumulation of water and hydroxide ions. 
     Therefore, there is a need to provide a gel with an array of wells using both the same spacing and format of standard microtiter plates, in which the electrodes successfully maintain electrical contact with the gel. Previous attempts to meet this need have been unsuccessful. A typical electrophoresis unit (such as the GenePhor, by Amersham Pharmacia Biotech, in San Francisco, Calif.) is capable of giving high-resolution analysis of relatively small numbers of samples. Such a unit is ill-fitted for a fast, comparatively crude analysis such as those which would benefit post-PCR analysis. Generally, units such as these are large, complex to use, slow (due to high resolution), and require complex assembly as described hereinabove. 
     Several groups have tried to address the difficulty of retaining electrode contact during electrolysis. In Sarrine et al (U.S. Pat. No. 5,637,203, the contents of which are hereby incorporated by reference as if recited in full herein), the gel is placed over a set of pin-type electrodes that protrude through holes in the gel and a gasketed support sheet, making contact with the gel outside of a moulded buffer strip. The holes provide a vent for the gases produced in electrolysis and a means for maintaining contact despite the endosmotic effects. Sarrine et al specifically teaches that a covered hole with the electrode making contact from below is not desirable because it traps electrolysis gas, causing the gel to float off of its support tray. Earlier patents (e.g. U.S. Pat. Nos. 5,045,164 and 4,975,173 by Tansamrit et al, the contents of which are incoporated by reference as if recited in full herein) address alternative ways to reduce and divert the fluid generated during electrophoresis away from the area of separation, such as multiple layered buffer block structures, and appropriate placement of serrations at the ends of the gel outside the buffer blocks. 
     Other groups (U.S. Pat. Nos. 5,582,702 and 5,865,974 by Cabilly et al, the contents of which are hereby incorporated by reference as if recited in full herein) describe a substantially closed cassette for electrophoresis without liquid buffer in which they must deal with the electrolytic gases produced. Their solutions include adding one or more vents in the cassette, providing or generating unfilled volumes into which the gases can be directed, or creating electrodes composed of material that adsorbs or reacts with either or both of the O 2  and H 2  produced at the electrodes (e.g. aluminum or palladium). 
     The present invention describes a gel with an array of wells in the microtiter array format that is cast in a disposable cassette substantially the same size as a standard microtiter plate (approximately 85 mm×127 mm×21 mm), and that uses solid buffer strips in lieu of liquid buffer effectively as described in commonly-assigned U.S. Pat. No. 4,874,491 to Stalberg et al the contents of which are hereby incorporated by reference as if recited in full herein. The electrodes advantageously contact the buffer strips, providing continual electrical contact, as well as an escape path for accumulated liquids and gases. 
     OBJECTS AND SUMMARY OF THE PRESENT INVENTION 
     In view of the foregoing, it is an object of the present invention to provide an apparatus for basic, inexpensive and convenient agarose gel electrophoresis of many samples. 
     It is a further object of the present invention to provide a disposable apparatus for gel electrophoresis which corresponds to standard microtiter plates to facilitate loading and analysis. 
     It is an additional object of the present invention to provide a bufferless system to run electrophoresis on agarose gels. 
     An additional object of the present invention is to provide a cassette and gel assembly which enables the user to analyze the results of the run within the cassette. 
     It is a further object of the present invention to provide an electrophoretic gel system which has electrode-contact surfaces substantially on the bottom yet allows potentially deleterious by-products of electrophoresis to escape. 
     These and other objects are satisfied by the present invention which is directed to a bufferless gel electrophoresis system which is configured to successfully run electrophoresis gels in standard microtiter plates. In particular, a first aspect of the present invention is directed toward a cassette and gel assembly for electrophoresis including a non conductive cassette, two solid buffer reservoirs, and a gel which contains a plurality of wells adapted to contain a plurality of samples, wherein the cassette is adapted to position the gel and reservoirs such that the electrodes of an electrophoretic device will contact the bottom surface of the gel to permit an electrophoretic procedure to be run. A variety of arrangements of the wells are contemplated, as well as a variety of geometries for the cassette. 
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS 
     FIG. 1 is a top view of a preferred embodiment according to the present invention. 
     FIG. 2 is a cutoff side view of a preferred embodiment according to the present invention. 
     FIG. 3 is a cutoff perspective view of a cassette embodiment according to the present invention. 
     FIG. 4A is an enlarged cutoff view of the electrode-gel contact surface on the cathode according to one embodiment of the present invention. 
     FIG. 4B is an enlarged cutoff view of the electrode-gel contact surface on the anode after electrophoresis has commenced, according to the present invention. 
     FIG. 5 depicts the results of an electrophoresis run performed by one embodiment of the present invention. 
    
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS 
     The present invention will now be described more fully hereinafter with reference to the accompanying figures, in which preferred embodiments of the invention are shown. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Like numbers refer to like elements throughout. Layers and regions may be exaggerated for clarity. 
     Referring to the drawings, the cassette and gel assembly  100  of the present invention is shown in FIG.  1 . As shown, the cassette and gel assembly  100  comprises a cassette  110 , two solid buffer reservoirs  120 , and an agarose gel  130 . As FIG. 1 shows, the agarose gel  130  preferably contains 96 sample wells  140 , in an 8×12 matrix, plus one or two additional row(s) of 8 wells in which to place electrophoresis standards. The additional row(s) of wells advantageously allow(s) the user to run standards without using up wells in the original microtiter reaction plate. More preferably, the rows of 8 wells  140  are spaced between 1 and 10 mm apart. Most preferably, the rows of 8 wells  140  are spaced 4.5 or 9 mm apart, which corresponds to the spacing on standard microtiter plates. The columns are similarly preferably spaced between 1 and 10 mm apart, and more preferably 4.5 or 9 mm apart. This spacing advantageously allows automated equipment designed to load and manipulate microtiter plates to additionally load and handle the gels. The wells themselves  140  at the gel-air interface (top) are preferably substantially rectangular in shape as shown in FIGS. 1 and 2, to provide a sizeable target for the pipette tips when loading the gel yet provide a substantial surface area on the “starting line” of the gel. Suitable shapes and sizes of wells  140  are well known in the art. 
     The gel cassette  110  preferably comprises a contiguous arrangement of four laterally extending outer sides  150 A- 150 D which form a frame  150  as shown in FIG.  3 . Preferably, the sides of the frame  150  are situated and oriented such that they are in opposing pairs  150 A,  150 B and  150 C,  150 D, thereby defining a substantially rectangular geometry. Preferably, the rectangular frame  150  is sized to be approximately substantially that of a standard microtiter plate (commonly approximately 85 mm×127 mm×21 mm). 
     In one preferred embodiment, a gel support platform  200  horizontally extends from one outer side to its opposing outer side (between one pair of opposing sides). More preferably, the gel support platform  200  extends between the two shorter sides  150 A,  150 B thereby providing a shelf supported by two walls of the frame  150 A,  150 B at its ends. Preferably, the gel support platform  200  is additionally supported by two vertically extending shelf supports  210 A,  210 B. These shelf supports  210 A,  210 B preferably extend between one opposing pair of sides  150 A,  150 B parallel to and a distance “w 1 ,” and “w 2 ” from the other opposing pair of sides of the frame  150 C,  150 D as shown in FIGS. 2 and 3. Also as shown in FIG. 3, the gel support platform  200  preferably is positioned vertically below the top edge of the cassette  110  “t” such that the gel support platform  200  is recessed. More preferably, the gel support platform  200  is recessed from the top of the cassette “t” at least approximately 4 mm, such that when an agarose gel  130  is placed on top of the gel support platform  200 , the gel  130  does not protrude beyond the top “t.” Agarose gels  130  as known in the art, are generally between 3 and 4 mm high. 
     Preferably the shelf supports  210 A,  210 B extend exactly from the plane defined by the bottom of the frame “P” up to the gel support platform  200 . Advantageously, as shown in FIG. 2, in this configuration, the shelf supports  210 A,  210 B and an opposing pair of outer walls  150 C,  150 D define two channels  220  into which solid buffer reservoirs  120  can be placed. Additionally, the solid buffer reservoir  120  is preferably substantially large enough to hold a sufficient volume of buffer for an electrophoresis run. Preferably, this volume is at least about 1 mL. More preferably, the volume of the solid buffer reservoir is between 2 and 10 mL, and most preferably it is between 4 to 7 mL. Notably, the solid buffer reservoirs  120  on a single cassette do not have to be the same volume, and it is advantageous that the solid buffer reservoir  120  on the anode be of larger volume than that on the cathode due to endosmosis. The dimensions of the solid buffer reservoir can be changed such that it may hold more or less buffer, depending on the length of time that the gel is to run. Both the widths “w 1 ,” “w 2 ” and height “h” of the solid buffer reservoir may be changed to alter the resulting volume of the solid buffer reservoir while remaining within the scope of the present invention. However, it may be advantageous to keep the widths “w 1 ,” “w 2 ” of the solid buffer reservoirs between 2 mm and 4 mm to maximize the resulting field of view yet provide sufficient solid buffer volume to complete the run. More preferably, the solid buffer reservoirs are dimensioned such that when the cassette and gel assembly is placed on an electrode  230 /electrode support  240  assembly, there is a gap in the horizontal plane as shown in FIG. 2 between the electrode  230  and the sides of the channel  220 . This gap advantageously allows water  400  and hydroxide ions to preferably exit the system without disturbing the electrical contact between the electrodes  230  and the agarose gel  130  as shown in FIG.  4 A and discussed herein below. 
     The agarose gel  130  preferably can be placed in the cassette  110  such that it is substantially supported by the gel support platform  200  in the cassette  110 , as shown in FIG.  2 . More preferably, as shown in FIG. 2, the agarose gel  130  is in fluid communication with the two solid buffer reservoirs  120 . In a more preferred embodiment, the agarose gel  130  contacts the solid buffer reservoirs  120  substantially from the top as shown in FIG. 2 such that the gravitational force on the agarose gel  130  continually forces the gel  130  to contact the solid buffer reservoirs  120 . Advantageously, therefore, as water is pumped out of the anode due to electroendosmosis, thereby causing the solid buffer reservoir  120  to shrink, the gel  130  settles and therefore maintains contact with the solid buffer reservoir  120 . 
     Preferably, the cassette and gel assembly  100  promote ease of use. To further facilitate ease of use, the cassette  110  preferably comprises a UV-transmitting non-conductive material. This advantageously allows the end user to view the results, after the gel electrophoresis is complete, without removing the agarose gel  130  from the cassette and gel assembly  100 . For example, a UV-transmitting acrylic or any other UV-transmitting plastic can be used as cassette material. More preferably, the cassette  110  comprises a relatively inexpensive UV-transmitting non-conductive material, such that the entire gel and cassette assembly  100  can be discarded after the agarose gel has been run. Since the user does not have to re-use the cassette  110 , the user can also advantageously minimize setup (cassette and gel assemblies can be provided preassembled) and cleanup before and after each run. 
     An embodiment of the present invention has been used to successfully run agarose gel electrophoresis on commercial DNA molecular size standards ranging from 100 bp to greater than 3000 bp. As shown in FIG. 5, the cassette and gel assembly  100  according to the present invention enables a user to successfully determine in a short amount of time (the run illustrated in FIG. 5 took 6 minutes at 100V) the presence of product in each of the wells  140 . 
     In operation, the wells  140  in the gel  130  are filled with samples to be analyzed. The entire gel and cassette assembly  100  is then placed on an electrophoresis device such that the electrodes  230  are in contact with the agarose gel  130  as shown in FIG.  4 A. As the run proceeds, the solid buffer reservoir  120  shrinks at the anode as water is endosmotically pumped to the cathode. Because the electrode  230  preferably makes contact with the solid buffer reservoir  120  from the bottom, the weight of the gel and cassette assembly  100  forces the electrode  230  to maintain contact with the solid buffer reservoir  120 . Preferably the electrode support  240  has a substantially vertically recessed portion (with respect to the electrode) as shown in FIGS. 2 and 4B, to form a vertical upstanding portion  410  and a horizontal portion  420  of the electrode support  240 . Preferably, the walls of the channel  220  are preferably configured such that its widths “w 1 ,” “w 2 ” are larger than the width of the electrode  230  and vertical upstanding portion of the electrode support  410 . In this configuration, as the solid buffer reservoir  120  shrinks at the anode, the entire gel and cassette assembly  100  is not impeded from vertically dropping. Furthermore, this configuration advantageously allows excess water  400  and gases to escape out the bottom of the gel and cassette assembly  100  between the walls of the channel  220  and the electrode  230 /vertical upstanding portion of the electrode support  410  as shown in FIG.  4 A. 
     It is apparent that many modifications and variations of the invention as hereinabove set forth may be made without departing from the spirit and scope thereof. The specific embodiments described are given by way of example only, and the invention is limited only by the terms of the appended claims.