Systems, devices, and methods for performing preparative electrophoresis

Abstract

Embodiments described herein relate to systems, devices, and methods for performing preparative electrophoresis. In some embodiments, a housing defines a plurality of cavities each configured to receive a vertical channel. Each vertical channel may include a hydrogel defining a sample well configured to receive a sample of DNA fragments. The vertical channel may be placed in fluidic communication with at least a first reservoir and a second reservoir. In some embodiments, preparative electrophoresis may be completed for the plurality of vertical channels simultaneously. The embodiments described herein may be integrated into automatic workflows for high-throughput applications. The embodiments described herein may be used for both long-read and short-read sequencing applications.

Description

IN THE UNITED STATES PATENT AND TRADEMARK OFFICEINTERNATIONAL PATENT APPLICATIONSYSTEMS, DEVICES, AND METHODS FOR PERFORMING PREPARATIVE ELECTROPHORESISRelated Applications

[0001] This application claims priority to and benefit of U.S. provisional patent application no. 63 / 602,232, filed November 22, 2023, the entire disclosure of which is incorporated herein by reference in its entiretyTechnical Field

[0002] Embodiments described herein relate to systems, devices, and methods for performing preparative electrophoresis.Statement Concerning Government Support

[0003] This invention was made with government support under Federal Award Identification Number (FAIN) R43HG012531 awarded by the National Human Genome Research Institute. The government has certain rights in the invention.Background

[0004] Many long-read DNA sequencing platforms rely on careful control of DNA library length. In current long-read DNA sequencing technologies, library loading onto read positions in a flow cell is diffusion-limited, and smaller library elements will be over-represented in the sequencing output relative to longer, more informative library elements. Longer reads arecritical to achieving high quality de novo genome assemblies; therefore, size-selection to eliminate shorter library molecules is widely practiced before performing long-read DNA sequencing. Standard size-selection methods used in long-read library preparation include size- selective precipitation, Ampure bead isolation methods, and preparative agarose gel electrophoresis. Size-selection by preparative electrophoresis is far more effective and flexible than precipitation or magnetic bead methods, but it suffers from incompatibility with conventional liquid handling (LH) instrumentation. This incompatibility is a challenge for implementing high quality long-read sequencing in applications including biological research, genetic testing, and liquid biopsy. Therefore, there is a need for systems, devices, and methods for high-resolution preparative electrophoresis that are compatible with conventional LH instrumentation and may be integrated into automated workflows.Summary

[0005] In some embodiments, a preparative electrophoresis apparatus is provided and includes a vertical channel having an open top end portion; a hydrogel disposed in a portion of the vertical channel, a top surface of the hydrogel defining a sample well configured to receive a sample of DNA fragments, and a plurality of electrodes, wherein: the vertical channel is arranged within a housing such that the vertical channel is in fluid communication with a first reservoir and a second reservoir, the vertical channel and each reservoir configured to receive a buffer solution, the first reservoir and the second reservoir at least partially defined by the housing, the vertical channel and the first and second reservoirs are each coupled to at least one specific, respective electrode from the plurality of electrodes; upon application of a first voltage gradient by the plurality of electrodes, the sample received by the well moves in a first direction through the hydrogel such that a portion of the sample exits the vertical channel, and upon application of a second voltage gradient by the plurality of electrodes, the remaining sample moves in a second direction opposite to the first direction through the hydrogel toward; the sample well.

[0006] The above noted embodiments, as well as some other embodiments, may further include one and / or another of the following structures, features, functionality, functions, steps, and clarifications, and in some embodiments, if such structures, features, functionality, functions, steps, and clarifications are not mutually exclusive, a plurality of, a majority of,substantially all of, or all of, the following structures, features, functionality, functions, steps, and clarifications: a bottom end of the vertical channel includes a first opening and a second opening,- the first opening is in fluid communication with the first reservoir, the second opening is in fluid communication with the second reservoir such that the first reservoir and the second reservoir are physically separate from one another;- the vertical channel includes a first opening, a second opening, a third opening, and a fourth opening,- the first opening in fluid communication with the first reservoir, the second opening in fluid communication with the second reservoir, the third opening in fluid communication with the third reservoir, the fourth opening in fluid communication with the fourth reservoir,- the third and fourth reservoir each coupled to at least one specific, respective electrode from the plurality of electrodes;- before application of the second voltage gradient, application of a third voltage gradient by the plurality of electrodes moves the remaining sample in the first direction such that a second portion of the sample exits the vertical channel;- the third opening and the fourth opening are positioned closer to the bottom end of the vertical channel than the first opening and the second opening; an inner surface of the vertical channel tapers inward such that a width of the vertical channel decreases along at least one direction; an inner surface of the vertical channel tapers inward along a first direction and widens along a second direction perpendicular to the first direction such that a cross-sectional area defined by the inner surface remains constant along a length of the vertical channel; a cross-section of the vertical channel is a circle, an oval, a square, or a rectangle;- the hydrogel includes 0.50% to about 5% agarose; and- the housing defines a plurality of cavities, each cavity from the plurality of cavities configured to receive a vertical channel;

[0007] In some embodiments, a preparative electrophoresis system is provided and includes a vertical channel including a hydrogel disposed in at least a portion of the vertical channel and a top end configured to receive a buffer solution, the vertical channel including a first opening and a second opening, wherein the hydrogel includes a top surface defining a sample well for receiving a DNA fragment sample; at least one sample well electrode arranged proximate the top end of the vertical channel, wherein the vertical channel is configured with a size and shape so that the buffer solution at the top end of the vertical channel is in contact with the at least one sample well electrode; a first elution electrode and a second elution electrode; a first reservoir in fluid communication with the first opening of the vertical channel and including a top end, wherein the buffer solution at a top end of the first reservoir is in contact with the first elution electrode; and a second reservoir in fluid communication with the second opening of the vertical channel and including a top end, wherein the buffer solution at a top end of the second reservoir is in contact with the second elution electrode, and the at least one sample well electrode and the first elution electrode are configured to provide a voltage gradient therebetween for a first predetermined period of time so as to move the sample in a first direction through the hydrogel such that a portion of the sample exits vertical channel.

[0008] Each of the above-noted embodiments may further include one and / or another of the following structures, features, functionality, functions, steps, and clarifications, and in some embodiments, if such structures, features, functionality, functions, steps, and clarifications are not mutually exclusive, a plurality of, a majority of, substantially all of, or all of, the following structures, features, functionality, functions, steps, and clarifications: after the portion of the sample exits the vertical channel, the first elution electrode is configured to provide a voltage gradient along a length of the first reservoir to move the portion of the sample in a second direction toward the first elution electrode into the first reservoir during a second predetermined period of time, and / or the at least one sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween during the second predetermined period of time to move the remaining sample in the second direction through the hydrogel toward the sample well;- the vertical channel includes a third opening and a fourth opening; a third elution electrode and a fourth elution electrode;a third reservoir in fluid communication with the third opening of the vertical channel and including a top end, wherein the third reservoir is configured with a size and shape such that the buffer solution at the top end of the third reservoir is in contact with a third elution electrode; a fourth reservoir in fluid communication with the fourth opening of the vertical channel and including a top end, wherein the fourth reservoir is sized and shaped so that the buffer solution at a top end of the fourth reservoir in contact with the fourth elution electrode; the first and second reservoirs are configured as waste reservoirs and the third and fourth reservoirs are configured as clean reservoirs;- the at least one sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween for the first predetermined period of time so as to move the sample in the first direction through the hydrogel such that a first portion of the sample exits the vertical channel into the waste reservoirs,- the at least one sample well electrode and at least one of the third and fourth elution electrodes provide a voltage gradient therebetween for a second predetermined amount of time to continue moving the sample in the first direction through the hydrogel;- the voltage gradient between the at least one sample well electrode and at least one of the first elution electrode and the second elution electrodes cause a second portion of the sample to exit the vertical channel into the waste reservoirs;- the at least one sample well electrode and at least one of the third and fourth elution electrodes provide a voltage gradient therebetween for a third predetermined amount of time to move the sample in a second direction through the hydrogel toward the sample well;- the first portion of the sample has a molecular weight lower than a predetermined range and the second portion of the sample has a molecular weight higher than the predetermined range;- the at least one sample well electrode and the first elution electrode provide a voltage gradient therebetween and the at least on sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween for the first predetermined period of time so as to move the sample in the first direction through thehydrogel such that the portion of the sample exits the vertical channel into the waste reservoirs;- the at least one sample well electrode and the third elution electrode provide a voltage gradient therebetween and the at least one sample well electrode and the fourth elution electrode provide a voltage gradient therebetween for a second predetermined amount of time to continue moving the sample in the first direction through the hydrogel; and- the at least one sample well electrode and the third elution electrode provide a voltage gradient therebetween and the at least one sample well electrode and fourth elution electrode provide a voltage gradient therebetween for a third predetermined amount of time to move the sample in a second direction through the hydrogel toward the sample well.

[0009] In some embodiments, a preparative electrophoresis system is provided and includes a housing defining at least one cavity having an inner surface; a plurality of electrodes comprising at least a first electrode, a second electrode, and a third electrode; a hydrogel having a top surface; a vertical channel disposed in the cavity of the housing and including the hydrogel disposed in at least a portion thereof, a top end, a bottom end, and an outer surface, wherein: the top surface of the hydrogel defines a sample well for receiving a sample, the top end of the vertical channel is configured to receive a buffer solution, and the bottom end of the vertical channel having a first opening and a second opening; the outer surface of the vertical channel and an inner surface of the cavity define a first reservoir including a top end and in fluid communication with the first opening and a second reservoir including a top end and in fluid communication with the second opening, the first electrode is arranged proximate the top end of the vertical channel, and the second electrode from the plurality of electrodes is arranged near the top end of the first reservoir, the third electrode from the plurality of electrodes is arranged near the top end of the second reservoir.

[0010] Each of the above-noted embodiments may further include one and / or another of the following structures, features, functionality, functions, steps, and clarifications, and in some embodiments, if such structures, features, functionality, functions, steps, and clarifications are not mutually exclusive, a plurality of, a majority of, substantially all of, or all of, the following structures, features, functionality, functions, steps, and clarifications:- the at least one cavity includes a plurality of cavities, each cavity of the plurality of cavities configured to receive a vertical channel; a circuit board electrically connected to the plurality of electrodes and configured to control voltage provided to each electrode from the plurality of electrodes;- the electrodes include a material selected from the group consisting of conductive polymer, graphite, carbon fiber, carbon paper, platinum, gold, gold-plated conductive metal, carbon black, and any combination thereof;- the electrodes include an injection moldable conductive polymer;- the plurality of electrodes are coupled to the housing and comprise disposable electrodes,- the circuit board includes a plurality of reusable electrode contacts configured to electrically connect the circuit board to the plurality of electrodes; a power supply;- the power supply is a remote power supply connected to the housing via a cable connector; and- the housing is configured to be Society of Laboratory Automation and Screening Standards (SLAS) compliant.

[0011] In some embodiments, a method for preparative electrophoresis is provided and includes providing a DNA fragment separation apparatus; loading a sample into the sample well from above the vertical channel; generating a first voltage gradient having a first direction for the first predetermined period of time to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel, wherein the first direction is defined along the length of the vertical channel; and generating a second voltage gradient having a second direction after at least the portion is eliminated from the vertical channel so as to move a remainder of the sample upward through the vertical channel toward the sample well, wherein the second direction is defined along the length of the vertical channel.

[0012] These embodiments may further include one and / or another of the following structures, features, functionality, functions, steps, and clarifications, and in some embodiments, if such structures, features, functionality, functions, steps, and clarifications are not mutuallyexclusive, a plurality of, a majority of, substantially all of, or all of, the following structures, features, functionality, functions, steps, and clarifications:- the first voltage gradient having the first direction is generated between the at least one sample well electrode and the first elution electrode to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel;- the second voltage gradient having the second direction is generated between the at least one sample well and the second elution electrode to move the remainder of the sample upward through the vertical channel toward the sample well;- the second voltage gradient having the second direction is generated for the second predetermined period of time after at least the portion of the sample has been eliminated from the vertical channel; generating a third voltage gradient having the first direction between the at least one sample well electrode and the first elution electrode during the second predetermined period of time;- the third voltage gradient is weaker than the first voltage gradient; replacing, after the second predetermined period of time, the buffer solution in the second reservoir with a solution comprising at least one of sucrose and glycerol; generating, after the buffer solution has been replaced, a fourth voltage gradient having the second direction between the at least one sample electrode the second elution electrode for a third predetermined period of time to move the sample back into the sample well; removing the separated sample from the vertical channel after the entirety of the remaining sample is moved into the sample well; concentrating and exchanging the remaining sample into a suitable buffer; concentrating and exchanging the remaining sample into a suitable buffer includes using magnetic bead cleanup; concentrating and exchanging the remaining sample into a suitable buffer is accomplished by binding and eluting the sample from a solid phase purification matrix;concentrating and exchanging the remaining sample into a suitable buffer is accomplished by precipitation and centrifugation;- the first voltage gradient having the first direction is generated between the at least one sample well electrode and at least one of the first elution and the second elution electrode to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel;- the second voltage gradient having the second direction is generated between the at least one sample well and at least one of the third elution electrode and the fourth elution electrode to move the remainder of the sample upward through the vertical channel toward the sample well;- before generating the second voltage gradient, generating a third voltage gradient having the first direction between the at least one sample electrode and at least one of the third elution electrode and the fourth elution electrode during a second predetermined period of time to move the sample down the vertical channel;- before generating the second voltage gradient, generating a fourth voltage gradient having a third direction between the at least one sample electrode and at least one of the first elution electrode and the second elution electrode during a third predetermined period of time to move a second portion of the sample out of the vertical channel and into the first reservoir and the second reservoir;- the second voltage gradient is generated during a fourth predetermined amount of time;- upon the housing defining the plurality of cavities, separation of DNA fragments can be conducted for a plurality of samples simultaneously; and- the sample includes molecules of DNA having different lengths.Brief Description of the Drawings

[0013] FIG. 1A is a schematic block diagram of a device for performing preparative electrophoresis, according to some embodiments. FIG. IB is a schematic block diagram of anassembly including the device of FIG. 1A for performing preparative electrophoresis, according to some embodiments.

[0014] FIG. 2A-2B are flow charts of example methods of performing preparative electrophoresis.

[0015] FIG. 3 is a schematic diagram depicting a process of preparative electrophoresis, according to some embodiments.

[0016] FIG. 4A-5C are schematic diagrams of a device for performing preparative electrophoresis including a vertical channel and one reservoir, according to some embodiments.

[0017] FIG. 5A-5C are schematic diagrams of a device for performing preparative electrophoresis including a tapered vertical channel and one reservoir, according to some embodiments.

[0018] FIG. 6A-6C are schematic diagrams of a device for performing preparative electrophoresis including a tapered vertical channel and two reservoirs, according to some embodiments.

[0019] FIG. 7A is a cross-sectional schematic diagram of a device for performing preparative electrophoresis, according to some embodiments.

[0020] FIG. 7B is a cross-sectional schematic diagram of the device of FIG. 7A depicting a first and second voltage gradient generated by the apparatus, according to some embodiments.

[0021] FIG. 8 shows three different perspectives of a device for performing preparative electrophoresis, according to some embodiments.

[0022] FIG. 9 shows four perspectives of a tapered bottom end of a vertical channel, according to some embodiments.

[0023] FIG. 10A-10B are schematic diagrams of a device for performing preparative electrophoresis including a vertical channel and two reservoirs.

[0024] FIG 11 is a schematic diagram comparing a first sample well with a flat bottom surface and a second sample well with a curved bottom surface.

[0025] FIG. 12 is a schematic diagram depicting an example method of using a device for performing preparative electrophoresis including a vertical channel and four reservoirs, according to some embodiments.

[0026] FIGS. 13A-13B show a first and second isometric view, respectively, of a device for performing preparative electrophoresis, according to an embodiment. FIGS. 13C-13D show an ariel view and an isometric view, respectively, of a device for performing preparative electrophoresis disposed in a portion of a housing, according to some embodiments.

[0027] FIG. 14 shows different cross-sectional views of the device of FIGS. 11 A-l IB disposed in a portion of a housing.

[0028] FIG. 15 shows three partial views of a device for performing preparative electrophoresis and depicts flow of ions, according to some embodiments.

[0029] FIGS. 16 shows a housing configured to receive one or more vertical channels for performing preparative electrophoresis, according to some embodiments.

[0030] FIG. 17 shows an isometric view of a housing including a plurality of vertical channels for performing preparative electrophoresis, according to some embodiments.

[0031] FIG. 18 shows an assembly for performing preparative electrophoresis, according to some embodiments.

[0032] FIG. 19A shows an assembly for performing preparative electrophoresis including reusable components, according to some embodiments.

[0033] FIG. 19B shows an assembly for performing preparative electrophoresis including access holes, according to some embodiments.

[0034] FIG. 20 shows an assembly for performing preparative electrophoresis, according to some embodiments.

[0035] FIG. 21A-21B show example methods of manufacturing an assembly for performing preparative electrophoresis according to some embodiments.

[0036] FIG. 22 A shows an assembly for performing preparative electrophoresis, according to some embodiments.

[0037] FIG. 22B shows an example method of using the assembly of FIG. 20A, according to some embodiment.

[0038] FIG. 23A shows an example method for performing preparative electrophoresis, according to some embodiments. FIG. 23B shows the results from the example methods for performing preparative electrophoresis.Detailed Description

[0039] Embodiments described herein relate to system, devices, and methods for performing high-resolution preparative electrophoresis for long-read and short-read DNA sequencing applications. Precise selection of DNA library length directly impacts accuracy of the results obtained from popular long-read DNA sequencing platforms (e.g., platforms such as PacBio and Oxford Nanopore (ONT)). Current long-read DNA sequencing technologies depend on diffusion; therefore, smaller library elements will be over-represented in the sequencing output relative to the contribution of longer, more informative library elements. Longer reads are critical to achieving high quality de novo genome assemblies. For this reason, size-selection to eliminate shorter library molecules is widely practiced. For certain sequencing methods such as the HiFi PacBio sequencing method, size-selection is used to generate a narrow distribution of library insert sizes (in the range of 15-20kb). This size limitation enables the sequencing polymerase to read through both insert strands of the circular SMRTbell library element multiple times, thereby increasing read accuracy to greater than Q20 (>99%). Size limitation may also be beneficial in increasing the overall sequence yield of flow cells. For example, the best total sequence output of certain flow cells (e.g., ONT flow cells) is seen with libraries 15- 50 kb in length, whereas “ultra-long” libraries (>100 kb in length) have >4-fold lower sequence yield. Therefore, for optimal high duplex ONT sequence output, it is useful to limit the upper size of the libraries to <70kb.

[0040] Precise gel-based size selection has also been shown to increase sensitivity of liquid biopsy in prenatal testing and oncology. In these assays, cell-free DNA from plasma or serum is isolated and fractions smaller than 160bp are used for short-read library construction (targeted range, approx. 30-150bp). Such libraries are up to 6-fold enriched in fetal or tumor DNA. In such liquid biopsy size-selections, magnetic bead approaches cannot provide the necessary size resolution.

[0041] Standard size-selection methods used in long-read library preparation include size- selective precipitation, customized Ampure bead isolation methods, and automated preparative agarose gel electrophoresis. Size-selection by preparative electrophoresis is far more effective and flexible than precipitation or magnetic bead methods, but some systems can be incompatible with conventional liquid handling instrumentation. This incompatibility is a challenge for implementing high quality long-read sequencing broadly in biological researchand genetic testing. Current gel-based size-selection method may tailor both high and low library size distributions. However, current gel-based consumables are bulky, since they depend on a relatively long gel column to achieve good electrophoretic resolution with long DNAs. In addition, the gel consumables require customized LH equipment to load and unload and have ports that may not be positioned in accord with Society of Laboratory Automation and Screening Standards (SLAS)plate standards.

[0042] The systems, devices, and methods described herein provide a high-throughput, cost- effective gel-based size-selection system that is easy to integrate with standard LH robotics. The embodiments described provide the following benefits: (1) designed to be flexible in physical configuration (capable of operation on or off the deck), (2) capable of accommodating different size-selection needs (e.g., serving size-selection needs of both long-read and shortread sequencing), (3) result in high accuracy separation of DNA samples, (4) compatible with automatic LH workflows, (5) capable of running many gel columns simultaneously, (6) SLAS- compliant, (7) achieve high recovering of target sample DNA, and (8) easy to integrate into automatic workflows, thereby enabling preparative electrophoresis for high through-put applications.

[0043] FIG. 1A is a schematic block diagram of a device 100 for performing preparative electrophoresis, according to an embodiment. As shown, the device 100 includes a vertical channel 120 including a hydrogel 122 disposed in at least a portion of the vertical channel 120. In some embodiments, a top surface of the hydrogel 122 defines a sample well 124 configured to receive a sample 102. In some embodiments, the sample 102 may include DNA fragments. In some embodiments, the device 100 may be configured to separate the DNA fragments based on certain criteria (e.g., size, molecular weight, kb length). In some embodiments, the device 100 may separate DNA fragments based on a predetermined target size range of the DNA fragments, the predetermined target size range having a lower threshold and an upper threshold. For example, DNA fragments having a size below the lower threshold may be removed. In some embodiments, DNA fragments having a size above an upper threshold may be removed. In some embodiments, DNA fragments having a size that falls between the lower threshold and the upper threshold may be collected. In some embodiments, the DNA fragments having the size that falls within the predetermined target range may be referred to as a target portion of the sample 102. In some embodiments, the predetermined size range may depend on a subsequent use of the DNA fragments (e.g., for long-read sequencing, for biopsy, etc.)

[0044] In some embodiments, the hydrogel 122 can include a porous material for electrophoresis. In some embodiments, the hydrogel 122 can include a polyacrylamide or a polysaccharide such as, for example, agarose or starch. In some embodiments, the hydrogel 122 includes agarose with a concentration between about 0.5% to about 5%, inclusive of all ranges and subranges therebetween. In some embodiments, the hydrogel 122 includes agarose with a concentration between about 0.5% to about 1% agarose, inclusive of all ranges and subranges therebetween. In some embodiments, the hydrogel 122 includes agarose with a concentration of at least about 0.5%, at least about 0.55%, at least about 0.60%, at least about 0.65%, at least about 70%, at least about 0.75%, at least about 0.8%, at least about 0.85%, at least about 0.90%, at least about 0.95%. In some embodiments, the hydrogel 122 includes agarose with a concentration of no greater than about 5.0%, no greater than about 4.0%, no greater than about 3.0%, no greater than about 2.0%, no greater than 1.0%, no greater than 0.95%, no greater than 0.90%, no greater than 0.85%, no greater than about 0.80%, no greater than about 0.75%, no greater than about 0.70%, no greater than about 0.65%, no greater than about 0.60%, no greater than about 0.60%, no greater than about 0.55%. In some embodiments, the agarose is porous such that DNA fragments in the sample 102 are separated based on size (e.g., kb length or molecular weight) as the DNA fragments move through the hydrogel 122.

[0045] A top end portion 129 of the vertical channel 120 may be configured to receive a solution 105 such that the top surface of the hydrogel 122 is in fluid communication with the solution 105. The vertical channel 120 may be configured to be placed in fluid communication with a first reservoir 112a and a second reservoir 112b. The first reservoir 112a and the second reservoir 112b may each have a top end configured to receive a solution 106 (e.g., a separation solution) or a solution 104 (e.g., an elution solution), respectively. In some embodiments, each of the solutions 104, 105, 106 may include a buffer solution. In some embodiments, the solutions 104, 105, 106 may include [tris(hydroxymethyl)methylamino]propanesulfonic acid (TAPS), ethylenedi aminetetraacetic acid (EDTA), Tris-TAPS-EDTA (TTE), Tris-acetate- EDTA (TAE), Tris-borate-EDTA (TBE) Tris-TAPS-EDTA, etc. In some embodiments, the solutions 104, 105, 106 may include TTE. In some embodiments, the solutions 104, 105, 106 may include a concentration of Tris base in a range of about 25 millimolar (mM) to about 75 mM, inclusive of all ranges and subranges therebetween. In some embodiments, the solutions 104, 105, 106 may include a concentration of TAPS acid in a range of about 15 mM to about 45 mM, inclusive of all ranges and subranges therebetween. In some embodiments, the solution 104, 105, 106 may include a concentration of EDTA acid in a range of about 0.25 mM to about2 mM, inclusive of all ranges and subranges therebetween. In some embodiments, the solutions 104, 105, 106 may include 50 mM Tris base, 29 mM TAPS acid, and 0.1 mM EDTA acid. In some embodiments, the vertical channel 120 may be configured to receive a first solution for a first amount of time, and then the first solution may be replaced with a second solution different from the first solution for a second amount of time. In some embodiments, the second solution may include a second buffer solution. In some embodiments, the second buffer solution may include an additive. In some embodiments, the second buffer solution may include at least one of sucrose or glycerol. In some embodiments, the second buffer solution may include at least one of sucrose at a high concentration or glycerol at a high concentration. In some embodiments, the second buffer solution may include between about 5 %w / v and about 35 %w / v sucrose, inclusive of all ranges and subranges therebetween. In some embodiments, the second buffer solution may include between about 12 %w / v and about 25 %w / v sucrose, inclusive of all ranges and subranges therebetween. In some embodiments, the second buffer solution may include between about 5 %w / v and about 35 %w / v glycerol, inclusive of all ranges and subranges therebetween. In some embodiments, the second buffer solution may include between about 12 %w / v and about 25 %w / v glycerol, inclusive of all ranges and subranges therebetween. In some embodiments, the second buffer solution may reduce mobility of the target portion of the sample 102, thereby improving recovery of the target portion of the sample 102 from the sample well 124.

[0046] In some embodiments, the vertical channel 120 may be coupled to the first reservoir 112a via a first opening positioned at (or near) a bottom end 121 of the vertical channel 120 and may be coupled to the second reservoir 112b via a second opening positioned at (or near) the bottom end 121 of the vertical channel 120. In some embodiments, the first opening and the second opening may be located on opposite sides of the vertical channel 120. In some embodiments, the first opening may be located on the first side of the vertical channel 120 such that the first reservoir 112a is positioned on the first side of the vertical channel 120, and the second opening may be located on the second side of the vertical channel 120 opposite the first side such that the second reservoir 112b is positioned on the second side of the vertical channel 120. In some embodiments, the first opening may be located at a first height along the length of the vertical channel 120, and the second opening may be located at a second height along the length of the vertical channel 120. In some embodiments, the first height (e.g., the height of the first opening) may be the same as the second height (e.g., the height of the second opening). In some embodiments, the first opening and the second opening may be located onopposite sides of the vertical channel 120 and located at the same height along the length of the vertical channel 120. In some embodiments, the first opening and the second opening may be located on the same side of the vertical channel 120 and the first height may be different from the second height such that both the first reservoir 112a and the second reservoir 112b are positioned on the same side of the vertical channel 120 at different heights. In some embodiments, the bottom end 121 of the vertical channel 120 may split into a first channel coupled to the first reservoir 112a and a second channel coupled to the second reservoir.

[0047] In some embodiments, the vertical channel 120 may additionally be configured to be placed in fluid communication with a third reservoir 112c and a fourth reservoir 112d. The third reservoir 110c and the fourth reservoir HOd may each include a top end configured to receive a solution. In some embodiments, the first reservoir 112a and the second reservoir may be configured to receive the solution 106 (e.g., the separation solution), and the third reservoir 112c and the fourth reservoir 112d may be configured to receive the solution 104 (e.g., the elution solution). In some embodiments, the vertical channel 120 may include a third opening coupled to the third reservoir 112c, and a fourth opening coupled to the fourth reservoir 112d. In some embodiments, the third opening may be located at a third height along the length of the vertical channel 120 and the fourth opening may be located at a fourth height along the length of the vertical channel 120. In some embodiments, the third height (e.g., the height of the third opening) and the fourth height (e.g., the height of the fourth opening) may be the same. In some embodiments, the third opening and the fourth opening may be located on opposite sides of the vertical channel 120 such that the third reservoir 112c and the fourth reservoir 112d are positioned on opposite sides of the vertical channel 120. In some embodiments, the third opening and the fourth opening may be located closer to the bottom end 121 of the vertical channel 120 than the first opening and the second opening. In some embodiments, the bottom end portion 121 of the vertical channel 120 may split into two channels coupled to the third reservoir 112c and the fourth reservoir 112d. In some embodiments, the first and second reservoirs 112a 112b may be coupled to the vertical channel 120 above the third and fourth reservoirs 112c, 112d (e.g., between the sample well 124 and the third and fourth reservoirs 112c, 112d).

[0048] The vertical channel 120 may be coupled to one or more electrodes 111 (hereinafter, “the sample well electrode(s) 111”). In some embodiments, the sample well electrode(s) 111 may be arranged proximate to a top end 129 of the vertical channel 120. The sample wellelectrode(s) 111 may be in contact with the solution 105 disposed in the vertical channel 120 such that when the sample well electrode(s) 111 are activated, a voltage gradient forms along a length of the vertical channel 120. The sample well electrode(s) 111 in combination with one or more elution electrodes 110a-l lOd may be configured to generate a voltage gradient across the length of the vertical channel 120 such that charged particles in the solution 105 move within the vertical channel 120. DNA fragments carry a negative charge; therefore, when the sample well electrode(s) 111 are configured as cathodes (negatively charged) and one or more elution electrodes 110a-l lOd are configured as anodes (positively charged), the sample 102 of DNA fragments are repelled away from the sample well electrode(s) 111 and move through the hydrogel 122 in the vertical channel 120 toward the bottom end portion 121 of the vertical channel 120 (e.g., downward). Conversely, when the sample well electrode(s) 111 are configured as anodes and the one or more elution electrodes HOa-l lOd are configured as cathodes, the sample 102 of DNA fragments move through the hydrogel 122 in the vertical channel 120 toward the top end portion 129 of the vertical channel 120 (e.g., upward). As the DNA fragments move through the hydrogel 122, fragments having a low molecular weight (LMW) move at a speed faster than fragments having a high molecular weight (HMW). In some embodiments, the vertical channel 120 may be coupled to a pair of sample well electrodes 111, with the pair of sample well electrodes 111 symmetrically positioned at the top end portion 129 of the vertical channel 120. For example, a first electrode from the pair of sample well electrodes I l l is positioned on a first side of the top end 129 of the vertical channel 129, and a second electrode from the pair of sample well electrodes I l l is positioned on a second side opposite the first side. The symmetrical positioning of the pair of sample well electrodes 111 may help generate an even voltage gradient across the width of the vertical channel 120. The even voltage gradient along the width of the vertical channel 120 may prevent undesired movement of the DNA fragments along the width of the vertical channel 120.

[0049] Each of the reservoirs 112a, 112b, 112c, 112d may be configured as reservoirs for performing elution to separate the DNA fragments in the sample 102 by size (e.g., kb length, molecular weight, etc.). For example, the reservoirs 112a-l 12d may be configured to draw an unwanted portion of the sample 102 out of the vertical channel 120 (e.g., through one of the openings on the vertical channel 120) and / or move a target portion of the sample 102 toward the sample well 124 for collection. As such, each of the reservoirs 112a-l 12d may be coupled to a respective electrode 110a, 110b, 110c, HOd (hereinafter, “elution electrode 110a, 110b, 110c, HOd”). As shown, the first reservoir 112a may be coupled to a first elution electrode110, and the second reservoir 112b may be coupled to a second elution electrode 110b. In embodiments in which the device 100 includes the third and fourth reservoirs 112c, 112d, the third reservoir 112c may be coupled to a third elution electrode 110c, and the fourth reservoir 112d may be coupled to a fourth elution electrode 1 lOd. Each elution electrode 110a-l lOd may be in contact with the solution 104, 106 disposed in the corresponding reservoir 112a-112d. Activation of sample well electrode(s) 111 and of one or more elution electrodes HOa-l lOd generates a voltage gradient within the vertical column 120. For example, the sample well electrode(s) 111 can be configured as a cathode and the first elution electrode 110a can be configured as an anode to generate a first voltage gradient. Conversely the sample well electrode(s) 111 can be configured as an anode and the one or more elution electrodes 1 Wal l Od can be configured as a cathode to generate a second voltage gradient with an opposite polarity and direction of DNA movement to the first voltage gradient. Any one of the elution electrodes HOa-l lOd and the sample well electrode(s) 111 may be configured to create a voltage gradient to move the sample 102 through the vertical channel 102 and / or the reservoirs 112a-112d.

[0050] In some embodiments, the device 100 may be used to perform preparative electrophoresis using the vertical channel 120, the first reservoir 112a, and the second reservoir 112b. In some embodiments, the first reservoir 112a may be configured as a waste reservoir, and the second reservoir 112b may be configured as a clean reservoir. For example, the sample well electrode(s) 111 and the first elution electrode 112a may be configured to provide a voltage gradient therebetween for a first predetermined period of time to move the sample 102 in a first direction through the hydrogel 122 until a portion of the sample 102 (e.g., a portion with a molecular weight and / or kb length below the lower threshold) exits the vertical channel 120 into the first reservoir 112a. In some embodiments, the first elution electrode 110a may be configured as an anode and the sample well electrode(s) 111 may be configured as a cathode, thereby generating the voltage gradient therebetween to move the sample 102 away from the sample well 124, down the vertical channel 120, and toward the first opening. In some embodiments, the first elution electrode 110a may be configured as an anode during a second predetermined period of time to move the portion of the sample 102 that has exited the vertical channel 120 away from the first opening and toward the first elution electrode 110a. The first elution electrode 110a may create a voltage gradient across a length of the first reservoir 112a to draw the portion of the sample 102 toward the top of the first reservoir 112a, which may be useful to prevent the portion of the sample 102 from traveling back into the vertical channel120 and contaminating the target portion of the sample 102. In some embodiments, the sample well electrode(s) 111 and the second elution electrode 110b may be configured to generate a voltage gradient therebetween during the second predetermined period of time to move the target portion of the sample 102 (e.g., a portion remaining in the vertical channel 120 and having DNA fragments with a kb length and / or molecular weight within the predetermined range) through the hydrogel in a second direction opposite the first direction toward the sample well 124. In some embodiments, the sample well electrode(s) 111 may be configured as an anode and the second elution electrode 110b may be configured as a cathode, thereby creating the voltage gradient therebetween to move the target sample 102 toward the sample well 124. In some embodiments, the voltage gradient between the sample well electrode(s) 111 and the second elution electrode 110b may be paused before the target portion of the sample 102 reaches the sample well 124, and the solution 105 in the sample well may be replaced (e.g., with the second buffer solution described above). In some embodiments, the generation of the voltage gradient between the sample well electrodes(s) 111 and the second elution electrode 110b may be resumed after the solution 105 is replaced with the second solution.

[0051] In some embodiments, the device 100 may begin in a first state in which no voltage gradient is applied by the electrodes 111, HOa-l lOd. The device 100 may transition into a second state in which the sample well electrode(s) 111 and the first elution electrode 110a are configured to generate a voltage gradient therebetween to move the sample 102 through the hydrogel 122 in the first direction. After the portion of the sample 102 (e.g., the unwanted portion) exits the vertical channel 120, the device 100 may transition from the second state to a third state. Alternatively, or additionally, the device 100 may transition from the second state to the third state after the first predetermined period of time. The device 100 in the third state may be configured such that (1) a voltage gradient between the sample well electrode(s) 111 and the second elution electrode 110b moves the sample 102 through the hydrogel in the second direction toward the sample well 124 and (2) a voltage gradient across the length of the first reservoir 112a generated by the first elution electrode draws the unwanted portion of the sample 102 away from the first opening. The device 100 may transition from the third state back to the first state in which no voltage gradient is applied by the electrodes 111, HOa-l lOd after the target portion of the sample 102 is received by the sample well 124. Alternatively, or additionally, the device 100 may transition from the third state back to the first state after the second predetermined amount of time.

[0052] In some embodiments, the first predetermined period of time (e.g., the separation time) and / or the second predetermined period of time (e.g., the elution time) may depend on the separation criteria of the DNA fragments and other factors. For control of electrophoresis separation and elution times, the average electric current in each gel column may be used to accurately estimate DNA mobility. In some embodiments, the period of time for size-selection (e.g., the first period of time) may be in a range of about 5 minutes (min) to about 300 minutes, inclusive of all ranges and subranges therebetween. In some embodiments, the period of time for size-selection may be in a range of about 10 min to about 90 min, inclusive of all ranges and subranges therebetween.

[0053] In some embodiments, period of time for elution (e.g., the second predetermined period of time) may include a first phase and a second phase. In some embodiments, the first phase may correspond to moving the sample 102 toward the sample well 124 using a first buffer solution, and the second phase may correspond to moving the sample 102 toward the sample well 124 using a second buffer solution configured to trap the sample 102 in the sample well 124. In some embodiments, the second phase may begin when the sample 102 is near the sample well 124. In some embodiments, the first phase may take between 5 minutes to about 300 minutes, inclusive of all ranges and subranges therebetween. In some embodiments, the first phase may take about 10 to about 90 minutes. In some embodiments, the second phase may take between 5 minutes and 30 minutes. In some embodiments, the second phase may take about 15 minutes. In some embodiments, a total time for elution may be in a range of about 10 minutes to about 300 minutes, inclusive of all ranges and subranges therebetween. In some embodiments the total time for elution for elution may be in a range of about 20 min to about 70 min, inclusive of all ranges and subranges therebetween.

[0054] In some embodiments, the device 100 may be used to perform preparative electrophoresis using the vertical channel 120, the first reservoir 112a, the second reservoir 112b, the third reservoir 112c, and the fourth reservoir 112d. In some embodiment, using all four reservoirs 112a-l 12d may allow removal of both DNA fragments having a size below the lower threshold (LMW DNA fragments) and DNA fragments having a size above the upper threshold (HMW DNA fragments). In some embodiments, the first reservoir 112a and the second reservoir 112b may be configured as waste reservoirs, and the third reservoir 112cand the fourth reservoir 112d may be configured as a clean reservoirs. Therefore, the first reservoir 112a and the second reservoir 112b may be configured to receive the solution 106 (e.g., theseparation solution), and the third reservoir 112c and the fourth reservoir 112b may be configured to receive the solution 104 (e.g., the elution solution). The sample well electrode(s) 111 and the first elution electrode 110a may be configured to provide a voltage gradient therebetween and / or the sample well electrode(s) 111 and the second election electrode 110b may be configured to provide a voltage gradient therebetween for a first predetermined period of time to move the sample 102 in the first direction through the hydrogel 122 until a first portion of the sample 102 (e.g., a portion with a kb length and / or molecular weight below the lower threshold) exits the vertical channel 120 into the first reservoir 112a and / or the second reservoir 112b. In some embodiments, the sample well electrode(s) 111 and the third elution electrode 110c may be configured to generate a voltage gradient therebetween and / or the sample well electrode(s) 111 and the fourth elution electrode HOd may be configured to generate a voltage gradient therebetween during a second predetermined period of time to move a remaining portion of the sample 102 through the hydrogel 122 further down the vertical column in the first direction. In some embodiments, the first elution electrode 110a and / or the second elution electrode 110b may be configured as anodes during a third predetermined period of time to move a second portion of the sample 102 (e.g., the portion with a kb length and / or molecular weight above the upper threshold) through the first opening and / or second opening and toward the first elution electrode 110a and / or second elution electrode 110b, respectively. In some embodiments, the sample well electrode(s) 111 and the third elution electrode 110c may be configured to generate a voltage gradient therebetween and / or the sample well electrode(s) 111 and the fourth elution electrode 1 lOd may be configured to generate a voltage gradient therebetween during a fourth predetermined period of time to move the target portion of the sample 102 (e.g., the portion remaining in the vertical channel 120 and having DNA fragments with a kb length and / or molecular weight within the predetermined range) through the hydrogel 122 in a second direction opposite the first direction toward the sample well 124. In some embodiments, the voltage gradient between the sample well electrode(s) 111 and the third elution electrode 110c and / or the fourth elution electrode 1 lOd may be paused before the target portion of the sample 102 reaches the sample well 124, and the solution 105 in the sample well may be replaced (e.g., with the second buffer solution described above). In some embodiments, the generation of the voltage gradient between the sample well electrodes(s) 111 and the third and / or fourth elution electrodes 110c, 1 lOd may be resumed after the solution 105 is replaced.

[0055] In some embodiments, the device 100 may begin in a first state in which no voltage gradient is applied by the electrodes 111, HOa-l lOd. The device 100 may transition from the first state to a second state in which the sample well electrode(s) 111 and at least one of the first elution electrode 110a and the second elution electrode 110b are configured to generate a voltage therebetween for a first predetermined period of time to move the sample 102 through the hydrogel 122 in the first direction such that a first portion of the sample exit the vertical channel 120. After the first portion of the sample 102 exits the vertical channel 120, the device 100 may transition from the second state to a third state. Alternative or additionally, the device 100 may transition from the second state to the third state after the first predetermined period of time. The device 100 in the third state is configured such the sample well electrode(s) 111 and at least one of the third elution electrode 110c and the fourth elution electrode HOd generate a voltage gradient therebetween for a second predetermined period of time to move the remaining sample 102 through the hydrogel 122 further in the first direction. After a second portion of the sample 102 is at a height along the length of the vertical channel 120 substantially equivalent to the height of the first and second openings of the vertical channel 120, the device 100 may transition from the third state to a fourth state. Alternatively, or additionally, the device 100 may transition from the third state to the fourth state after the second predetermined period of time. The device 100 in the fourth state is configured such that the sample well electrode(s) 111 and at least one of the first elution electrode 110a and the second elution electrode 110b generate a voltage gradient therebetween for a third predetermined period of time to move the second potion of the sample out of the vertical channel 120, into the first and / or second reservoirs 112a, 112b. After the second portion of the sample 102 exits the vertical channel 120, the device 100 may transition from the fourth state to a fifth state. Alternative or additionally, the device 100 may transition from the fourth state to the fifth state after the third predetermined period of time. The device 100 in the fifth state is configured such that the sample well electrode(s) 111 and at least one of the third elution electrode 110c and the fourth elution electrode 1 lOd generate a voltage gradient therebetween to move the target sample (e.g., the sample with a kb length and / or molecular weight within the predetermined range) toward the sample well 124. The device 100 may transition from the fifth state back to the first state in which no voltage gradient is applied by the electrodes 111, 110a-l lOd after the target portion of the sample 102 is received by the sample well 124. Alternatively, or Additionally, the device 100 may transition from the fifth state back to the first state after the fourth predetermined amount of time.

[0056] In some embodiments, each of the reservoirs 112a-l 12d may each be coupled to more than one electrode. In some embodiments, the device 100 may include a plurality of electrodes distributed across the vertical channel 120 and reservoirs 112a-d, the plurality of electrodes configured to generate at least (1) a first voltage gradient to move the sample 102 in a first direction along the vertical channel 120 until a first portion of the sample 102 exits the vertical channel and (2) a second voltage gradient operable to move a second portion of the sample remaining in the vertical channel 120 in a second direction along the vertical channel 120 toward the sample well 124. In some embodiments, the plurality of electrodes may be configured to generate a third voltage gradient operable to move the portion of the sample 102 (e.g., unwanted DNA fragments) away from the vertical channel to prevent unwanted DNA fragments from traveling into the sample well 124.

[0057] In some embodiments, a bottom surface of the sample well 124 may be a flat surface. In some embodiments the bottom surface of the sample well 124 may be a curved surface. In some embodiments, the curved surface may curve upward (e.g., with an apex toward a center of the sample well 124). In some embodiments, the curved surface may help achieve better separation when the sample 102 reaches the bottom end 121 of the vertical channel 120. In some embodiments, the device 100 (e.g., the sample well 124) is configured to receive a sample 102 including about O.Olmicrogram (pg) to about 20 pg of genomic DNA. In some embodiments, the device 100 (e.g., the sample well 124) is configured to receive a sample 102 including about 1 pg to about 5 pg of genomic DNA. In some embodiments, recovery of the target DNA fragment size is in a range of between about 40% to about 70%. In some embodiments, the device 100 can yield DNA having a tight size range, meaning the device 100 can separate DNA at a high resolution. In some embodiments, the size selected products can have size distributions with upper and lower boundaries differ from the mean products by between 10% to 50% of the mean value. For instance, for embodiments targeting DNA sizes centered on about 20kb, some size selection workflows will allow collection of DNA between about lOkb and 30kb, while other workflows will allow collection of narrower size distributions, such as about 18kb to 22kb. Similarly, for size selections on smaller DNA samples with an average size of about 140 bp, some size selection workflows will product size fractions between about 70bp and 210bp, while others will produce size fractions between about 126 bp to 154 bp.

[0058] In some embodiments, the vertical channel 120 may be any shape suitable for electrophoretic separation of the DNA fragments such as, for example, a cylinder with a circular cross-section, a cylinder with an oval cross-section, a cylinder with a changing crosssection, a prism with a triangle cross-section, a prism with a square cross-section, a prism with a rectangular cross-section, a prism with a changing cross-section, etc. In some embodiments, a bottom end portion 121 of the vertical channel 120 may taper inward such that a width of the vertical channel 120 decreases along at least one direction. In some embodiments, an inner surface of the vertical channel 120 may taper inward such that the width of the vertical channel 120 decreases along the at least one direction. The tapered vertical channel 120 may lead to more precise separation of the DNA fragments. However, tapering the vertical channel 120 may impact the voltage gradient across the vertical channel 120, which may in turn complicate optimization of non-linear electrophoresis techniques such as pulsed field (PF) methods. In some embodiments, the inner surface of the vertical channel 120 may taper inward along a first direction and widen along a second direction perpendicular to the first direction such that a cross-sectional area defined by the inner surface remains constant along the length of the vertical channel 120. Keeping the cross-sectional area constant along the length of the vertical channel 120 may decrease the impact of the taper on the voltage gradient, thereby enabling more convenient implementation of pulse field (PF) methods for separation of DNA fragments. PF electrophoresis may be useful in separation of DNA fragments longer than about 15kb to about 20kb. In some embodiments, the vertical channel 120 may be a cylindrical channel with a circular top end 129 that tapers into an oval shape at the bottom end 121 to minimize positional variations in the electrophoretic field throughout the length of the vertical channel 120.

[0059] FIG. IB is a schematic block diagram of an assembly 1500 configured to receive a plurality of vertical channels 120 to perform preparative electrophoresis. As shown, the assembly 1001 includes a housing 150 including a plurality of cavities 152, each cavity 152 configured to receive a vertical channel 120. The assembly 1001 may include a plurality of electrodes 110, a circuit board 170, a cover 180, and a power supply 190, and may optionally include electrode contacts 115. In some embodiments, the circuit board 170 and / or the cover 180 may optionally include pipette access holes.

[0060] In some embodiments, the housing 150 includes a plurality of cavities 152 arranged an array. In some embodiments, the housing 150 may be formed in a shape compatible withautomatic liquid handlers (LH). For example, the housing 150 may be a rectangle including cavities 152 arranged in m rows and n columns. In some embodiments, the housing 150 may include 4 rows and 6 columns of cavities 152 such that the housing 150 may receive up to 24 vertical channels 120. In some embodiments, the housing 150 may include a range of about 1 row to about 10 rows, inclusive all ranges and subranges therebetween. In some embodiments, the housing 150 may include a range of about 1 column to about 20 columns, inclusive all ranges and subranges therebetween.

[0061] In some embodiments, when the vertical channel 120 is disposed in a cavity 152 of the housing 150, an inner surface of the cavity 152 and an outer surface of the vertical channel 120 form at least a portion of the first reservoir 112a and the second reservoir 112b. In some embodiments, when the vertical channel 120 is disposed in the cavity 152, the first reservoir 112a is formed on a first side of the vertical channel 120, and the second reservoir 112b is formed on a second side of the vertical channel 120 opposite the first side. In some embodiments, a first portion of the vertical channel 120 at least partially defines an inner volume of the first reservoir 112a, and a second portion of the vertical channel 120 at least partially defines an inner volume of the second reservoir 112b. In some embodiments, the first reservoir 112a and the third reservoir 112c are formed on the first side of the vertical channel 120, and the second reservoir 112b and the fourth reservoir 112d are formed on the second side of the vertical channel 120. In some embodiments, the cavity 152 may include one or more projections (e.g., walls, protrusions, ledges, ridges, etc.) extending from the inner surface of the cavity 152, and an outer surface of the vertical channel 120 may include one or more projections extending outward from the vertical channel 120. In some embodiments, when the vertical channel 120 is disposed in the cavity 152, the projections on the outer surface of the vertical channel 120 and the projections extending from the cavity may engage with one another (e.g., via a friction fit) to form one or more barriers defining the reservoirs 112a-l 12b.

[0062] In some embodiments, the electrodes 100 may include conductive polymer, graphite, carbon fiber, carbon paper, platinum, gold, carbon black, and / or any combination thereof. In some embodiments, the conductive polymer may include polypropylene, polyacetylene (PA), polyaniline (PANI), polypyrrole (Ppy), polythiophene (PTH), poly(para-phenylene) PPP, poly(phenylenevinylene) (PPV), polyfuran, and / or any combination thereof. In some embodiments, electrodes 100 may include materials including non-conductive injection- moldable polymers mixed with conductive materials such as graphite, carbon fiber, carbonpaper, platinum, gold, carbon black, PANI, Ppy, PTH, PPP, PPV, polyfuran, and / or any combination thereof In some embodiments, the electrodes 110 may include a conductive polymer that is heat resistant. In some embodiments, the electrodes 110 may include a conductive polymer that is injection moldable. In some embodiments, the electrodes 110 may be configured to be stable during storage in contact with the electrophoresis buffer solution. In some embodiments, the electrodes 110 may be configured to not produce DNA damaging agents during storage and / or during electrophoresis. In some embodiments, the electrodes 110 may include polypropylene and carbon black. In some embodiments, the electrodes may be gold-plated. In some embodiments, the electrodes 110 may be coupled directly to the housing 150. In some embodiments, the electrodes 110 may be coupled to the circuit board 170. In some embodiments, the electrodes 110 may be reusable electrodes such as platinum, gold, or gold-plated conductive metal. In some embodiments, the electrodes 110 may be disposable electrodes. In some embodiments, the electrodes 110 may be disposable to reduce risk of crosscontamination between samples. In some embodiments, the electrodes 110 may include (or couple to) a disposable component to reduce risk of cross-contamination between samples.

[0063] In some embodiments, the circuit board 170 is coupled to the housing 150. In some embodiments the circuit board 170 is a printed circuit board (PCB). In some embodiments, the circuit board 170 may include a plurality of openings corresponding to the cavities 152 of the housing 150. In some embodiments, the circuit board 170 may be configured to couple to the housing 150 from underneath the housing 150, and the cavities 152 may be disposed through the openings on the circuit board 170. In some embodiments, the circuit board 170 includes the electrodes 110 disposed on the circuit board 170. In some embodiments, the electrodes 110 are disposed on the circuit board 170 in a predetermined pattern such that when the circuit board 170 is coupled to the housing 150, the electrodes 110 are arranged near the top end of the vertical channel 120 and the top end of each of the reservoirs 112a-l 12d. In some embodiment, the circuit board 170 may instead be coupled to the cover 180. In some embodiments, the circuit board 170 may be coupled to a side of the cover 180 configured to face the top ends of the vertical channels 120 and reservoirs 112a-l 12d such that the electrodes 110 are arranged at the top end 129 of the vertical channel 120 and top ends of the reservoirs when the cover 180 is placed on the housing 150. In some embodiments, the circuit board 170 and / or the cover 180 may include pipette access holes that allow access to the top of the vertical channel 120 after the cover 180 is placed on the housing 150. In some embodiments, the electrodes 110 on the circuit board 170 may protrude from the circuit board 170 such that the electrodes 110 contactthe solution 105, 104, 106 in the vertical channel 120 and reservoirs 112. For example, the circuit board 170 may be configured to couple to the housing 150 from underneath, and the electrodes 110 may protrude upward into the top end 129 of the vertical channels and the reservoirs. In some embodiments, the circuit board 170 may be configured to couple to the cover 180, and the electrodes may protrude downward into the top end 129 of the vertical channels 120 and the reservoirs 112.

[0064] In some embodiments, the circuit board 170 may include electrodes contacts 115, and the housing 150 may include electrodes 120 such that when the circuit board 170 is coupled to the housing 150, the electrodes 110 make contact with the electrode contacts 115 to supply electrical output to the vertical channels 120 and reservoirs 112. In some embodiments, the electrode contacts 115 may be reusable. In some embodiments, the electrodes 110 may be disposable electrodes coupled to the housing 150. In some embodiments the electrode contacts 115 may include a biasing member to ensure adequate contact between the electrode contacts 115 and the electrodes 110. In some embodiments the electrode contacts 115 may be spring loaded. In some embodiments, the electrode contacts 115 may be pogo pins. In some embodiments, when the circuit board 170 is coupled to the housing 150, the electrode contacts 115 electrically connect the disposable electrodes 110 to the circuit board 170. In some embodiments, the housing 150 may be disposable, and the cover 180 including the circuit board 170 and electrode contacts 115 may be reusable.

[0065] In some embodiments, the assembly 1001 is SLAS-compatible system compliant and / or configured to be compatible with automatic liquid handlers (LH). In some embodiments, the assembly 1001 may be a consumable and / or certain pieces of the assembly 1001 may be consumable. In some embodiments, the circuit board 170 includes a port for coupling to a power supply 190. In some embodiments, the housing 150 may include an opening through which the port may be disposed. In some embodiments, the power supply 190 may be a remote power supply 190 which is coupled to the circuit board 170 via a connector (e.g., USB cable). The circuit board 170 may carry all the electrodes 110, all circuits connecting the electrodes 110 to the connector, and a single USB-style plug-in connector to interface with the external power supply 190.

[0066] A remote power supply 190 allows flexible physical configuration and easy maneuvering of the assembly 1001, thereby making it possible to use the assembly 1500 for automatic workflows. Electrophoresis steps can be carried out with the housing 150 on a LHdeck and with the power supply 190 off-deck in a remote position. Alternatively, the housing 150 can be loaded and unloaded on a LH deck but moved off-deck to carry out the electrophoresis steps. For instance, after loading input samples on the LH deck, it may be convenient to run initial size-selection electrophoresis step off-deck since these steps may take a few hours. For final elution and sample collection, the assembly 1001 can be moved back on the LH deck, with the remote power supply 190 located adjacent to the LH. In some embodiments, electrophoresis through a plurality of assemblies 1001 may be completed using an automatic LH. The power supply 190 may be designed to power at least four 24-well assemblies 1001, for a potential throughput of 96 samples per run cycle. Including the remote power supply 190 that can power electrophoresis of at least four 24-well assemblies 1001 enables a straightforward path for integrating gel-based size selection with almost any high- throughput LH platform.

[0067] In some embodiments, the hydrogel 122 may be cast in the vertical channel 120 to create a gel column. In some embodiments, the hydrogel 122 may be cast in the vertical channel 120 outside of the housing 150 such that quality control of the gel column can be accomplished before assembling into the housing 150. After inspection, gel columns may be inserted into the housing 150. In some embodiments the dimensions of the cavity 152 configured to hold the gel column are carefully matched so that a tight friction fit between the reservoirs 112 and the vertical channel 120 is achieved. In some embodiments, the friction fit ensures an amount of current leakage is small enough to not affect the size-selection process.

[0068] In some embodiments, the assembly 150 may be operatively coupled to a processor configured to execute code. In some embodiments, the code may include instructions that when executed by the processor, cause the processor to control the circuit board 170 and therefore the electric output from the electrodes 110, 111. In some embodiments, the code may include instructions to determine separation and elution times. The gel plate system may not use optical detection of markers; therefore, the code may calibrate the mobility of DNA as a function of some property of the electrophoretic current in each gel column. In some embodiments, such calibration may be performed by running marker ladders through many vertical columns and evaluating marker mobility as a function of average lane current. DNA mobility may be calibrated as a function of average current during size separation electrophoresis in the column, evaluated over the entire size selection electrophoresis process, or averaged over some chosen portion of that process. This approach allows the determination of a DNA mobility calibrationcurve specific for each vertical channel 120. This method allows for reproducible size selection across all vertical channels 120 in the housing 150 despite differences in hydrogel 122 temperatures between the inner and outer portions of the housing 150, and small differences in sample salt concentration. Methods, systems, and devices related to determining instructions to control a preparative electrophoresis system are described in U.S. Patent No. 8,361,298, filed October 8, 2009, and titled “Multichannel Preparative Electrophoresis System” and U.S. Patent No. 8,361,299, filed April 14, 2010, and titled “Multichannel Preparative Electrophoresis System,” the disclosure of each of which is hereby incorporated by reference in its entirety.

[0069] FIG. 2 A is a flow chart of a method 200 for using the assembly 1001 for performing preparative electrophoresis, according to an embodiment. While described with respect to the assembly 1001 including circuit board 170, power supply 190, the vertical channel 120, reservoirs 112, an electrodes 110, 111, the method 200 is equally applicable to any preparative electrophoresis assembly described herein. All such variants should be considered to be within the scope of this disclosure. The method 200 includes placing the vertical channel 120 in fluid communication with the first reservoir 112a and the second reservoir 112b, the vertical channel 120 including the hydrogel 122 configured to receive the sample 102 disposed therein, at 201. At 202, a buffer solution is disposed in the first reservoir 112a, the second reservoir 112b, and a top end of the vertical channel 120. At 203, the sample 102 is loaded into a sample well 124 of the vertical channel 120. In some embodiments, a top surface of the hydrogel 122 defines the sample well 124. In some embodiments, the sample 102 includes DNA fragments of different sizes. In some embodiments, a portion of the sample includes DNA fragments having a size below a lower threshold. In some embodiments, the method 200 can be used to separate the portion from the sample.

[0070] At 204, a first voltage gradient having a first direction is generated for a first predetermined period of time to move the sample 102 down the vertical channel 120 such that a portion of the sample is eliminated from the vertical channel 120. In some embodiments, the first predetermined period of time is determined based on a target size range for DNA fragments in a target portion of the sample 102. In some embodiments, the first direction is defined across a length of the vertical channel 120. In some embodiments, the first portion of the sample is eliminated from the vertical channel 120 into the first reservoir 112a. In some embodiments, the sample well electrode(s) 111 and the first elution electrode 110a are activated to generate the first voltage gradient therebetween.

[0071] In some embodiments, after the portion of the sample 102 is eliminated from the vertical channel 120, a second voltage gradient having a second direction is generated for a second predetermined period of time to move a remainder of the sample upward through the vertical channel 120 toward the sample well 124, at 205. In some embodiments, the second direction is defined along a length of the vertical channel 120. In some embodiments, the sample well electrode(s) 111 and the second elution electrode 110b may be activated to generate the second voltage gradient therebetween. In some embodiments, a third voltage gradient having the second direction may be generated during the second period of time to move the first portion of the sample up the first reservoir 112a. In some embodiments, the third voltage gradient may be generated by the first elution electrode 110a. In some embodiments, the third voltage gradient may move the first portion of the sample 102 toward the first elution electrode 110a to reduce likelihood that the first portion of the sample contaminates the remaining portion of the sample 102. In some embodiments, the third voltage gradient is weaker than the first voltage gradient.

[0072] At 207, method 200 optionally includes pausing generation of the second voltage gradient and replacing the buffer solution in the sample well 124 with a second buffer solution containing an additive. In some embodiments, the second buffer solution may ensure the remaining portion of the sample is held in the sample well 124 for collection. In some embodiments, the second buffer solution may reduce a mobility of the remaining sample once the remaining sample has reached the sample well. In some embodiments, the second buffer solution may include at least one of a sucrose and a glycerol. At 207, the method 200 includes continuing the generation of the second voltage gradient for a third predetermined period of time such that the remaining sample reaches the sample well 124. In some embodiments, the remaining sample may be removed from the sample well 124. In some embodiments, the remaining sample may be optionally concentrated and exchanged into a suitable buffer, at 208. In some embodiments, concentrating and exchanging the remaining sample includes using magnetic bead cleanup. In some embodiments, concentrating and exchanging the remaining sample is accomplished by binding and eluting the remaining sample from a solid phase purification matrix. In some embodiments concentrating and exchanging the remaining sample is accomplished by precipitation and centrifugation. In some embodiments, the method 200 may be completed for a plurality of vertical channels 120 simultaneously. For example, 24 vertical channels 120 may be disposed in the housing 150, and the method 200 may be completed for the 24 vertical channels. In some embodiments, at least some of the method 200may be completed by an automatic LH. In some embodiments, method 200 may be completed for four housings 150 simultaneously, meaning that 96 vertical channels 120 may be run simultaneously.

[0073] FIG. 2B is a flow chart of a method 300 for using the assembly 1001 for performing preparative electrophoresis, according to an embodiment. While described with respect to the assembly 1001, the method 300 is equally applicable to any preparative electrophoresis system described herein. All such variants should be considered to be within the scope of this disclosure. The method 300 includes placing the vertical channel 120 in fluid communication with a first reservoir 112a, a second reservoir 112b, a third reservoir 112c, and a fourth reservoir 112d, the vertical channel 120 including the hydrogel 122 disposed therein configured to receive the sample 102, at 301. At 302, a buffer solution is disposed in the first reservoir 112a, the second reservoir 112b, the third reservoir 112c, the fourth reservoir 112d, and a top end of the vertical channel 120. At 303, the sample 102 is loaded into a sample well 124 of the vertical channel 120. In some embodiments, a top surface of the hydrogel 122 defines the sample well 124. In some embodiments, the sample is similar to or the same as the sample as described with respect to FIG. 2 A. In some embodiments, the method 300 can be used to separate a first portion from the sample 102 having a size below the lower threshold. In some embodiments, the method 300 can be used to separate a second portion from the sample 102 having a size above the upper threshold. In some embodiments, the method 300 can be used to separate both the first portion and the second portion from the sample 102.

[0074] At 304, a first voltage gradient having a first direction is generated for a first predetermined period of time to move the sample 102 down the vertical channel 120 such that the first portion of the sample is eliminated from the vertical channel 120. In some embodiments, the first predetermined period of time is determined based on a target size range for DNA fragments in a remaining portion of the sample. In some embodiments, the first direction is defined across a length of the vertical channel 120. In some embodiments, the first portion of the sample is eliminated from the vertical channel 120 into the first reservoir 112a and / or the second reservoir 112b. In some embodiments, the sample well electrode(s) 111 and at least one of the first elution electrode 110a and the second elution electrode 110b are activated to generate the first voltage gradient therebetween.

[0075] In some embodiments, after the first portion is eliminated from the vertical channel 120, a second voltage gradient having the first direction is generated for a second predeterminedperiod of time to move a remaining portion of the sample further downward through the vertical channel 120, at 305. In some embodiments, the sample well electrode(s) 111 and at least one of the third elution electrode 110c and the fourth elution electrode HOd are activated to generate the second voltage gradient therebetween.

[0076] At 306, a third voltage gradient having a second direction may be generated for a third predetermined period of time such that a second portion of the sample 102 is eliminated from the vertical channel 120, leaving the target portion of the sample 102 in the vertical channel 120. In some embodiments, the sample well electrode(s) 111 and at least one of the first elution electrode 110a and the second elution electrode 110b are activated to generate the third voltage gradient therebetween. In some embodiments, the second portion of the sample 102 exits the vertical channel 120 into the first reservoir 112a and / or the second reservoir 112b. In some embodiments, the third voltage gradient moves the second portion of the sample 102 upward through the first reservoir 112a and / or the second reservoir 112b toward the first elution electrode 110a and / or the second elution electrode 110b.

[0077] At 307, a fourth voltage gradient having a third direction is generated for a fourth predetermined period of time such that the target portion of the sample is moved upward through the vertical channel 120 toward the sample well 124. In some embodiments, the third direction is defined across the length of the vertical channel 120. In some embodiments, the third direction is opposite the first direction. In some embodiments, the sample well electrode(s) 111 and at least one of the third elution electrode 110c and the fourth elution electrode 1 lOd are activated to generate the fourth voltage gradient. In some embodiments, the fourth voltage gradient moves the target portion of the sample 102 upward through the vertical column 120 toward the sample well 124. Method 300 optionally includes pausing the fourth voltage gradient and replacing the buffer solution in the sample well with a second buffer solution containing an additive, at 308. In some embodiments, the second buffer solution may ensure the remaining portion of the sample is held in the sample well for collection. In some embodiments, the second buffer solution may reduce a mobility of the remaining sample once the remaining sample has reached the sample well. In some embodiments, the second buffer solution may be similar to or the same as the buffer solution described with respect to FIG. 1 A and FIG. 2 A. At 309, the method 300 includes continuing the generation of the fourth voltage gradient for a fifth predetermined period of time such that the target portion of the sample 102 reaches the sample well 124. In some embodiments, the target portion of the sample 102 maybe removed from the sample well 124. In some embodiments, the target portion of the sample 102 may be optionally concentrated and exchanged into a suitable buffer, at 310. In some embodiments, concentrating and exchanging the remaining sample may be similar to or the same as the concentrating and exchanging as described with respect to FIG. 2A. In some embodiments, the method 300 may be completed for a plurality of vertical channels 120 simultaneously. For example, 24 vertical channels 120 may be disposed in the housing 150, and the method 300 may be completed for the 24 vertical channels. In some embodiments, at least some of the method 300 may be performed by an automatic liquid handler (LH). In some embodiments, method 300 may be completed for four housings 150 simultaneously, meaning that 96 vertical channels may be run simultaneously.

[0078] FIG. 3 is a schematic diagram depicting use of a device for performing preparative electrophoresis. As shown, the device includes a vertical channel with a hydrogel gel disposed in at least a portion of the vertical channel, and the hydrogel forms a sample well configured to receive a sample. The vertical channel is coupled to a first reservoir and a second reservoir. A bottom end of the vertical channel may split into a channel coupled to the first reservoir and a second channel coupled to the second reservoir. The vertical channel is coupled to at least one electrode (not shown) and the first reservoir and the second reservoir are coupled to a first elution electrode and a second elution electrode, respectively (not shown). The arrows indicate the direction that negatively charged ions will travel under the applied field. The arrow length indicates the relative field strength. Relative electrode voltage and polarity is shown with the numbers above each channel. The dark particles represent a portion of the sample with HMW, the light particles represent a portion of the sample that has an intermediate molecular weight, and the medium shade particles represent an unwanted portion of the sample with a molecular weight below the lower threshold (LMW). Here, preparative electrophoresis is carried out to separate the LMW fragments from the sample. Certain aspects of device are functionally and / or structurally similar to device 100, and therefore certain aspects of device are not described again with respect to FIG. 3.

[0079] In some embodiments, the process of electrophoresis may be divided into a sizeselection phase and an elution phase. In embodiments, the size-selection phase may include step A through step C, and the elution phase may include step D through step E. At step A, the apparatus is in a first state in which the electrodes deliver no voltage, and therefore the sample remains at rest in the sample well. At step B, the device transitions to a second state in whichan electric field is applied using the sample well electrode(s) as cathodes and the first elution electrode as an anode, while the second elution electrode remains unpowered. In some embodiments, the negative voltage applied by the sample well electrode(s) has an equivalent magnitude to the positive voltage applied by the first elution electrode. In response to the voltage applied at the sample well electrode and the first elution electrode, a voltage gradient is generated therebetween operable to move the sample down the vertical channel. At step C, the relative voltage applied by the sample well electrode and the first elution electrode remains the same as the portion of the sample with LMW exits the vertical channel through the first opening and begins to move toward the first elution electrode. At step D, the device transitions to a third state in which the sample well electrode(s) serve as anodes with a first electric field potential, and the first and second elution electrodes serve as cathodes wherein the first elution electrode has an electrode potential half as large as the second elution electrode. As shown, the first magnitude may be equivalent to the third magnitude, and the first magnitude and the third magnitude may be larger than the second magnitude. In some embodiments, the second magnitude may be half the strength of the first magnitude and the third magnitude to prevent movement of the target sample in an undesirable direction. In some embodiments, the positive voltage generated by the first elution electrode generates a voltage gradient across the first reservoir that may draw the portion of the sample with LMW away from the first opening and toward the first elution electrode. In some embodiments, the positive voltage generated by the sample well electrode and the negative voltage generated by the second elution electrode may generate a voltage gradient between the sample well electrode and the second elution electrode to move the target portion of the sample (e.g., the portion of the sample with a molecular weight above the lower threshold) toward the sample well using clean solution. At step E, the wanted portion of the sample continues to move upward toward the sample well.

[0080] FIG. 4A-4C are schematic diagrams of a workflow for preparative electrophoresis using a device including a vertical channel 420 and one reservoir 412. As shown in FIG. 4A, a vertical channel 420 is disposed in a reservoir 412 including a solution 404. The vertical channel includes a hydrogel 422 disposed therein and may include a solution 405 disposed above the hydrogel 422. an axial cross-section of the vertical channel 420 may be a square (or a rectangle), and a reservoir 412 in which the vertical channel is disposed may have an axial cross-section that is a square (or a rectangle). In some embodiments, a top portion of the reservoir 420 may be separated into two portions. As shown in FIG. 4B, an axial cross-section of the vertical channel 520 may be a circle. The vertical channel 520 includes a hydrogel 522with a circular cross-section, and a reservoir 512 with a circular-cross section. The reservoir 512 may include a solution 504. FIG. 4C depicts a workflow using device 400. While FIG. 4C depicts device 400, it should be appreciated that the cross-section may represent that of device 500. As shown, the vertical channel has a constant cross-sectional area along the length of the vertical channel 420.

[0081] At step A, a hydrogel 422 is cast in vertical channel 424 and forms a sample well 424. The vertical channel 420 is disposed in a reservoir 412 including a buffer solution 404, and a buffer solution is added to a top end of the vertical channel. At B, a sample 402 including DNA fragments with different molecular weights can be disposed in the sample well 424. At C, a negative voltage is applied at a top end of the vertical channel, and positive voltage is applied at a top end of the reservoir such that the sample 402 moves down the vertical channel 420. At D, the sample 402 approaches a bottom end of the vertical channel 420 and has separated according to molecular weight. At E, The DNA fragments having a molecular weight below the lower threshold exit the bottom of the vertical channel 420 into the reservoir 412. At F, the buffer in the reservoir 412 is replaced with a clean buffer and the voltage (and therefore the electric field) is inverted, and the target portion of the sample moves upward toward the sample well for collection. At G, a mobility modifying solution is added to the sample well just before the sample reaches the well. At H, the sample gets trapped in the mobility modifying solution as it exits the hydrogel 422. The target portion of the sample can then be collected.

[0082] FIG. 5A is a schematic diagram of a device for performing preparative electrophoresis including a tapered vertical channel and one reservoir, according to an embodiment. As shown in FIG. 5A, a vertical channel 620 is disposed in a reservoir 612 including a solution 604. The vertical channel 620 includes a hydrogel 622 disposed therein and may include a solution disposed above the hydrogel 622. In some embodiments, an axial cross-section of the vertical channel 620 may be a square (or a rectangle), and a reservoir 612 in which the vertical channel is disposed may have an axial cross-section that is a square (or a rectangle). In some embodiments, a top portion of the reservoir 612 may be separated into two portions. As shown in FIG. 5B, an axial cross-section of the vertical channel 720 may be a circle. The vertical channel 720 may include a hydrogel 722 with a circular cross-section, and a reservoir 712 with a circular-cross section. The reservoir 712 may include a solution 704. FIG. 5C depicts a workflow using apparatus 600. While FIG. 5C depicts apparatus 600, it should be appreciated that the cross-section may represent that of apparatus 700. As shown, the vertical channel 620has cross-sectional area that decreases along the length of the vertical channel 620. In some embodiments, the vertical channel including a taper along the length of the vertical channel 620 may help improve separation of the sample 602. The steps of the workflow depicted in FIG. 5C may be the same as or similar to the method depicted in FIG. 4C, and therefore details of the workflow in FIG. 5C are not described in further detail herein.

[0083] FIG. 6A is a schematic diagram of a device for performing preparative electrophoresis including a tapered vertical channel and two reservoirs, according to an embodiment. As shown in FIG. 6A, a vertical channel 820 is disposed in between a first reservoir and a second reservoir. The first reservoir may include a first solution 806, and the second reservoir may include a second solution 804. The vertical channel includes a hydrogel 822 disposed therein and may include a solution disposed above the hydrogel 822. In some embodiments, an axial cross-section of the vertical channel 820 may be a square (or a rectangle), and a reservoir 812 in which the vertical channel is disposed may have an axial cross-section that is a square (or a rectangle). As shown in FIG. 5B, an axial cross-section of the vertical channel 920 may be a circle. The vertical channel 920 includes a hydrogel 922 with a circular cross-section. The vertical channel 920 is disposed between a first reservoir and a second reservoir, which together create a circular cross-section. The first reservoir may include a first solution 906, and the second reservoir may include a second solution 904. FIG. 6C depicts a workflow using apparatus 800. While FIG. 6C depicts apparatus 800, it should be appreciated that the crosssection may represent that of apparatus 900.

[0084] At step A, a hydrogel 822 is cast in vertical channel 824 and forms a sample well 824. The vertical channel 820 has cross-sectional area that decreases along the length of the vertical channel 820. A divider 825 is disposed at a bottom end of the vertical channel 820, such that the first reservoir 812a and the second reservoir 812b are physically isolated from one another. The first buffer solution 806 is disposed in the first reservoir 812a, and the second buffer solution is disposed in the second reservoir 812b. A third buffer solution may be disposed in a top end of the vertical channel above the sample well 824. In some embodiments, the first, second, and third buffer solution may be different. In some embodiments, any one of the first, second, and third buffer solution may be the same. At B, a sample 402 including DNA fragments with different molecular weights can be disposed in the sample well 424. At C, a cathode is applied to the top end of the vertical channel, and an anode is applied is applied at the top end of the first reservoir, and a voltage is applied via those electrodes such that thesample moves down the vertical channel 820. At D, the sample 802 approaches a bottom end of the vertical channel 820 and has separated according to molecular weight. At E, The DNA fragments having a molecular weight below the lower threshold may exit the bottom of the vertical channel 820 into the first reservoir 412a. At F, separation of the DNA fragments is completed. At G, the polarity of the electrode at the top end of the vertical channel is changed so that it serves as an anode, and an electrode at the top of the second reservoir 812b is used as a cathode, so that application of a voltage gradient thereby causes the target portion of the sample to moves upward toward the sample well for collection. In some embodiments, a mobility modifying solution is added to the sample well just before the sample reaches the well. At H, the sample gets trapped in the mobility modifying solution as it exits the hydrogel 822. The target portion of the sample can then be collected.

[0085] FIG. 7A is a schematic diagram depicting a cross-section of a device for performing preparative electrophoresis. As shown, a vertical channel 1020 defines an inner volume and includes hydrogel 1022 disposed in the inner volume. A top surface of the hydrogel 1022 defines a sample well 1024 configured to hold a sample 1002 of DNA fragments. The vertical channel 1020 is configured to receive a solution 1005 above the sample well such that the solution 1005 contacts the top surface of the hydrogel 1022. The bottom end of the vertical channel 1020 splits into a first opening coupled to a first reservoir 1012a via a first channel and a second opening coupled to a second reservoir 1012b via a second channel. Certain aspects of the device 1000 are structurally and / or functionally similar to the device 100, and therefore certain aspects of the device 1000 are not described in further detail with respect to FIG. 7A- 7B. The first reservoir 1012a and the second reservoir 1012b are physically separated from one another at a bottom end by a divider 1025 disposed between the first opening and the second opening. In some embodiments, a cavity including the divider 1025 and defining an inner volume is configured to receive the vertical channel 1020 such that the divider 1025 is disposed between the first opening and the second opening of the vertical channel 1020, and the inner volume of the cavity is divided into the first reservoir 1012a and the second reservoir 1012b. In some embodiments, an inner surface of the vertical channel 1020 tapers inward. As shown, the inner surface of the vertical channel 1020 tapers inward at a position along the length of the vertical channel 1020 lower than the bottom surface of the sample well 1024. The first reservoir 1012a and the second reservoir 1012b are configured to receive a buffer solution 1006, 1004. A first electrode 1010a and a second electrode 1010b extend from a circuit board coupled to the device 1000. The first electrode 1010a extends through an opening proximate atop end of the first reservoir 1012a such that the first electrode 1010a is in contact with the buffer solution 1006 (e.g., the separation solution) disposed in the first reservoir 1012a. The second electrode 1010b extends through an opening proximate a top end of the second reservoir 1012b such that the second electrode 1010b is contact with the buffer solution 1004 (e.g., the elution solution) disposed in the second reservoir. Additionally, at least one sample well electrode is arranged near a top end of the vertical channel 1020 such that the at least one sample well electrode is contact with the buffer solution placed in the top end of the vertical channel 1020 (not shown).

[0086] FIG. 7B is a cross-sectional schematic diagram of the device 1000 depicting the electric field lines due to a first and second voltage gradient generated by the device 1000. As shown on the left, the at least one sample well electrode and the first elution electrode 1010a generate an electric field that exerts a force (e.g., on a negative test charge) in a first direction (e.g., downward) along the vertical channel 1020 and in a second direction opposite the first direction (e.g., upward) along the first reservoir. The electric field generated by the at least one sample well electrode and the first elution electrode 1010a may push negatively charged ions through the hydrogel in the first direction and then through the solution in the first reservoir in the second direction. In some embodiments, the electric field may cause the negatively charged particles to follow a “U” shaped path from the sample well to the first elution electrode. The first electric field is generated during a size-selection phase to cause DNA fragments that travel above a certain speed (e.g., DNA fragments with an LMW) to exit the vertical channel. As shown on the right, the at least one sample well electrode and the second elution electrode 1010b generate an electric field that exerts a force in the first direction (e.g., downward) along the second reservoir and in the second direction (e.g., upward) along the vertical channel 1020. In some embodiments, the electric field generated by the at least one sample well electrode and the second elution electrode 1010b may cause negatively charged ions to follow a “U” shaped path from the second elution electrode 1010b to the sample well. The second electric field is generated during an elution phase to move the DNA fragments with a molecular weight in the predetermined target range toward the sample well using a clean buffer solution in the second reservoir.

[0087] FIG. 8 shows three different 3-dimensional views of a device 1100 for performing preparative electrophoresis. An isometric view of the vertical channel 1120 disposed in a cavity of a housing is shown on the left panel. A partial cross-section view of the vertical channel1120 disposed in the cavity 1152 is shown in the middle panel. A full cross-section view of the vertical channel 1120 disposed in the cavity 1152 is shown on the right panel. As shown, the device 1100 includes a vertical channel 1120 configured to receive hydrogel. In some embodiments, the cavity 1152 may be one cavity from a plurality of cavities defined by a housing. In some embodiments, a top end of the cavity 1152 has a wider cross-sectional area than the remainder of the cavity 1152. In some embodiments, at least one sample well electrode 1111, a first elution electrode 1110a, and a second elution electrode 1110b may be positioned in the top end of the cavity 1152 with the wider cross-section. For example, the cavity 1152 may include a ledge along the top edge of the cavity 1152 along which the electrodes may be arranged. In some embodiments, the top end of the cavity 1152 includes a first wall 1134a and second wall 1135a extending parallel from one another from a first corner of the cavity, and a third wall 1134b and fourth wall 1135b extending parallel from one another from a second corner of the cavity. In some embodiments, a first sample well electrode is disposed between the first wall 1134a and second wall 1135a, and a second sample well electrode is disposed between the third wall 1134b and fourth wall 1135b. In some embodiments, when the vertical channel 1120 is disposed in the cavity 1152, (1) the first wall 1134a, the third wall 1134b, and an outer surface of the vertical channel form a first boarder that physically isolates buffer solution in the top end of the first reservoir 1112a; and (2) the second wall 1135a, the fourth wall 1135b, and an outer surface of the vertical channel form a second boarder that physically isolates buffer solution in the top end of the second reservoir 1112b. In some embodiments, the vertical channel 1120 includes cut-outs at a top end of the vertical channel 1120 so that no vertical barrier exists between the inner volume of the vertical channel 1120 and the first sample well electrode and the second sample well electrode. In some embodiments, a divider 1125 is disposed in a bottom of the vertical channel 1120 to physically isolate the first reservoir 1112a from the second reservoir 1112b. Certain aspects of the device 1000 are functionally and / or structurally similar to the device 100, and therefore certain aspects of the device are not described in further detail with respect to FIG. 8.

[0088] FIG. 9 shows four perspectives of a 3 tapered bottom end 1221 of a vertical channel, according to an embodiment. The top panel depicts the axes A-A and B-B of the cross-sectional views shown in the bottom panels. The bottom left panel shows a cross-section along the A-A axis, the bottom center panel shows a cross-section along the B-B axis, and the bottom right shows an isometric view of the bottom end of the vertical channel. The vertical channel forms a cylinder with a circular cross-section at a top end portion of the vertical channel above abranching point 1238, and an oval cross-section at a bottom end of the vertical channel below the branching point 1238. In some embodiments, the hydrogel 1222 may not extend past the branch point. As shown, the wall of the vertical channel tapers inward along the A-A axis, and the wall of the vertical channel widens along the B-B axis. In some embodiments, the cross- sectional area remains constant along the length of the vertical channel even though the shape of the cross-section changes. The cross-sectional area remains the same to ensure easier implementation of activation of the electrodes in a pulsed pattern.

[0089] FIG. 10A is a schematic diagram of device 1300 for performing preparative electrophoresis including a vertical channel 1320 and two reservoirs 1312a, 1312b. As shown at A, a vertical channel 1320 is cast with hydrogel 1322. A top surface of the hydrogel 1322 defines a sample well 1324 configured to receive a sample. In some embodiments, the vertical channel 1320 is coupled to a first reservoir 1312a via a first opening and coupled to a second reservoir 1312b positioned above the first reservoir 1312a via a second opening. In some embodiments, the second reservoir 1312b may be positioned below the first reservoir 1312a. Both the first reservoir 1312a and the second reservoir 1312b may be positioned on the same side of the vertical channel 1320. A bottom portion of the first reservoir 1312a and bottom portion of the second reservoir 1312b both include hydrogel 1322 disposed therein. In some embodiments, the first reservoir 1312a may be configured as the waste reservoir, and the second reservoir 1312b may be configured as the clean reservoir. A buffer solution may be added to the top of the vertical channel (e.g., above the sample well). Certain aspects of the device are functionally and / or structurally similar to the device 100, and therefore certain aspects of the device are not described in further detail with respect to FIG. 10 A.

[0090] FIG. 10B shows a schematic diagram of device 1400 for performing preparative electrophoresis including a vertical channel 1420 and two reservoirs 1412a, 1412b. As shown at A, a vertical channel 1320 is cast with hydrogel 1422. A top surface of the hydrogel 1422 defines a sample well 1424 configured to receive a sample. In some embodiments, the vertical channel 1420 is coupled to a first reservoir 1412a via a first opening and coupled to a second reservoir 1412b via a second opening. The first reservoir 1412a may be positioned on a first side of the vertical channel 1420, and the second reservoir 1412b may be positioned on a second side of the vertical channel 1420 opposite the first side. The second opening of the second reservoir 1412b may be positioned at a height along the vertical channel 1420 higher than the first opening. The second reservoir 1412b includes a bottom portion that extendsperpendicularly from the vertical channel 1420. In some embodiments, the perpendicular portion creates a sharper cut-off to separate the sample. A bottom portion of the first reservoir 1412a and the vertical channel 1420 may create a “U” shape when coupled to one another. A bottom portion of the first reservoir 1412a and bottom portion of the second reservoir 1412b may both include hydrogel 1422 disposed therein. In some embodiments, the first reservoir 1412a may be configured as the waste reservoir, and the second reservoir 1412b may be configured as the clean reservoir. A buffer solution may be added to the top of the vertical channel 1420 (e.g., above the sample well). Certain aspects of the device 1400 is functionally and / or structurally similar to the device 100, and therefore certain aspects of the device are not described in further detail with respect to FIG. 10B.

[0091] Referring to both FIG. 10A and FIG. 10B, at B, a sample including DNA fragments with different molecular weights can be disposed in the sample well. At C, a negative voltage can be applied at a top end of the vertical channel, and positive voltage can be applied at a top end of the first reservoir to move the sample down the vertical channel 20. At D, the sample has separated according to molecular weight, and a portion of the sample passes the second opening and approaches the first opening. At E, a negative voltage can be applied at the top end of the second reservoir, and a positive voltage can be applied at a top end of the vertical channel to move the wanted portion of the sample toward the sample well. In some embodiments, a mobility modifying solution can be added to the sample well just before the sample reaches the well. At F, the sample may be trapped in the mobility modifying solution as it exits the hydrogel 422. The target portion of the sample can then be collected. In some embodiments, having both reservoirs on one side of the vertical channel allows the sample to be biased towards the split, creating a cleaner cut-off of the sample. In some embodiments, having a portion of the second reservoir extend perpendicularly to the vertical channel can create a cleaner cut-off of the sample.

[0092] FIG 11 is a schematic diagram comparing a first sample well 1024 and a second sample well 1524. On both the left and the right panels, the vertical channel includes a hydrogel disposed therein defining a sample well configured to receive a sample. As shown on the left, the bottom surface 1039 of the sample well 1024 is flat. As the sample 1002 moves through the hydrogel, DNA fragments positioned centrally in the vertical channel travel faster, whereas DNA fragments positioned peripherally travel slower. The sample 1002 begins to curve with the center leading as it travels down the hydrogel, which causes mixing between LMWfragments and HMW fragments at the split 1025. As shown on the left, the bottom surface 1539 of the sample well 1524 is curved. In some embodiments, a central part of the sample 1502 well curves upward. Therefore, the sample 1502 starts curved and flattens as it travels down the hydrogel, which reduces mixing of LMW fragments and HMW fragments at the split 1525.

[0093] FIG. 12 is a schematic diagram depicting an example of using a device 1600 for performing preparative electrophoresis including a vertical channel 1620 and four reservoirs 1612a-1612d, according to an embodiment. As shown, the apparatus 1600 includes a vertical channel 1620 with a hydrogel gel 1622 disposed in at least a portion of the vertical channel 1620, and the hydrogel 1622 forms a sample well 1624 configured to receive a sample 1602. The vertical channel 1620 is coupled to a first reservoir 1612a, a second reservoir 1612b, a third reservoir 1612c, and a fourth reservoir 1612d. The first reservoir 1612a and the second reservoir 1612b are positioned on opposite sides of the vertical channel 1620 at a first height along the length of the vertical channel 1620, and the third reservoir 1612c and the fourth reservoir 1612d are positioned on opposite sides of the vertical channel 1620 at a second height along the length of the vertical channel 1620. In some embodiments, the first height (e.g., the height of the first and second reservoirs) is closer toward a top end of the vertical channel 1620 than the second height (e.g., the height of the third and fourth reservoirs). The vertical channel 1620 is coupled to at least one electrode (not shown) at a top end. The first reservoir 1612a, the second reservoir 1612b, the third reservoir 1612c, and the fourth reservoir 1612d are coupled to a first elution electrode, a second elution electrode, a third elution electrode, and a fourth elution electrode, respectively (not shown). The arrows indicate the direction that negatively charged ions will travel under the applied field. The white rectangle represents a first portion of the sample with fragments having a size below the lower threshold, the grey rectangle represents a target portion of the sample that has an intermediate molecular weight that falls within the predetermined target range, and the black rectangle represent a second portion of the sample with a molecular weight above the higher threshold. Certain aspects of apparatus 1600 are functionally and / or structurally similar to apparatus 100, and therefore certain aspects of apparatus 1600 are not described again with respect to FIG. 12.

[0094] In some embodiments, the process of electrophoresis may be divided into a sizeselection phase and an elution phase. In embodiments, the size-selection phase may include step A through step D, and the elution phase may include step E. The apparatus 1600 is in a first state in which the electrodes deliver no voltage, and therefore the sample 1602 remains atrest in the sample well 1624. At step A, the device 1600 transitions to a second state in which the sample well electrode has a negative polarity and the first elution electrode and / or the second elution electrode has a positive polarity, while the third elution electrode and the fourth elution electrode are not powered. In response to the voltage applied at the sample well electrode and at least one of the first elution electrode and the second elution electrode, a voltage gradient is generated therebetween to move the sample through the hydrogel down the vertical channel 1620. As the sample moves through the hydrogel, the sample is separated by size. At step B, the voltage applied by the sample well electrode and the first elution electrode and / or second elution electrodes remains the same and the first portion of the sample with LMW exits the vertical channel 1620 through the first opening and / or the second opening. In some embodiments the first portion of the sample may be drawn toward the first elution electrode and / or the second elution electrode. At step C, the device 1600 transitions to a third state in which the sample well electrode has a negative polarity and the third elution electrode and / or the fourth elution electrode has a positive polarity. In some embodiments, the first elution electrode and the second elution electrode generate no voltage when the device 1600 is in the third state. This activation of the electrodes generates a voltage gradient between the sample well electrode and at least one of the third elution electrode and the fourth elution electrode to continue moving the sample down the vertical channel 1620 such that the target portion of the sample passes a first opening to the first reservoir and a second opening to the second reservoir. After the target portion of the sample passes the first opening and the second opening, a position of the second portion of the sample in the vertical channel 1620 may align with the first opening and the second opening. At step D, the device 100 transitions from the third state to a fourth state in which the sample well electrode has a negative polarity and the first elution electrode and / or the second elution electrode has a positive polarity. In some embodiments, the third elution electrode and the fourth elution electrode do not generate a voltage when device 1600 is in the fourth state. The sample well electrode and at least one of the first elution electrode and the second elution electrode generate a voltage gradient therebetween to cause the second portion of the sample to exit the vertical channel into the first reservoir and / or the second reservoir. At step E, the device transitions from the fourth state to a fifth state in which the sample well electrode has a positive polarity and the third elution electrode and the fourth elution electrode has a negative polarity. In the fifth state, the voltage gradient between the sample well electrode and the third and / or fourth elution electrodes movesthe target portion of the sample (e.g., the portion of the sample with a molecular weight within the predetermined target range) toward the sample well using clean solution.

[0095] FIGS. 13A-13B show a first and second isometric view, respectively, of an apparatus for performing preparative electrophoresis, according to an embodiment. As shown in FIG. 13A-13B, a vertical channel 1720 defines an inner volume 1723 configured to receive a hydrogel. In some embodiments, an outer surface of the vertical channel 1720 includes projections (protrusions, walls, ledges, overhangs, ridges, etc.) 1732, 1734, 1735, 1736 configured to define a first reservoir 1712a, a second reservoir 1712b, a third reservoir 1712c, and a fourth reservoir 1712d when the vertical channel 1720 is disposed in a cavity of a housing. For example, the projections 1732, 1734, 1736 may be configured to engage a portion of an inner wall of the cavity of the housing to define the first reservoir 1712a and the third reservoir 1712c. Projections 1733, 1735, 1737 may be configured to engage a portion of an inner wall of the cavity of the housing to define the second reservoir 1712b and the fourth reservoir 1712d. In some embodiments, the first reservoir 1712a and the second reservoir 1712b may be configured as waste reservoirs, and the third reservoir 1712c and the fourth reservoir 1712d may be configured as clean reservoirs. In some embodiments, the projections 1734, 1735, may partially define the inner volume of the vertical channel therebetween. For example, the projections 1734, 1735 may define a reservoir configured to receive a buffer solution at a top end 1729 of the vertical channel 1720. As shown, the top end 1729 of the vertical channel 1720 has a circular cross-section, and the bottom end 1721 of the vertical channel 1720 has an oval cross-section. At least an inner wall of the vertical channel 1720 may taper inward along a first direction and widen along a second direction such that the bottom end 1721 of the vertical channel 1720 forms an oval cross-section. In some embodiments, the vertical channel 1720 may be injection molded. In some embodiments, the first half of the vertical channel may be molded and a second half of the vertical channel may be molded separately and then the first half and the second half may be coupled together. In some embodiments, the whole vertical channel 1720 may be molded at one time. In some embodiments, the vertical channel may be formed from materials including injection-moldable polymers such as, for example, polystyrene, polycarbonate, acrylic, acrylonitrile butadiene styrene (ABS), and / or any other suitable material or combination thereof.

[0096] FIGS. 13C-13D show an aerial view and an isometric view, respectively, of a device 1700 for performing preparative electrophoresis disposed in a portion of a housing, accordingto an embodiment. As shown, the projections 1732, 1734, 1736 engage (e.g., by a friction fit, adhesive, etc.) portions of the cavity to define the first reservoir 1712a and the third reservoir 1712c. The projections 1733, 1735, 1737 engage (e.g., by a friction fit) portions of the cavity to define the second reservoir 1712b and the fourth reservoir 1712d. A pair of sample well electrodes 1711 are positioned between the projections 1734, 1735. In some embodiments, the pair of sample well electrodes 1711 may be positioned in the reservoir configured to receive the buffer solution at the top end of the vertical channel such that the pair of sample well electrodes 1711 may be placed in fluid communication with a solution disposed in the vertical channel 1720 above the sample well. A first elution electrode 1710a is arranged at a top of the first reservoir, a second elution electrode 1710b is arranged at a top of the second reservoir 1712b, a third elution electrode is arranged at a top of the third reservoir 1712c, and a fourth elution electrode is arranged at a top of the fourth reservoir 1712d.

[0097] FIG. 14 shows three partial views of an apparatus for performing preparative electrophoresis and depicts field lines, according to an embodiment. As shown, during an initial separation phase (e.g., when LMW DNA are removed from the vertical channel), an electric field follows a path downward through the vertical channel 1720 and upward through the first reservoir 1712a. Although not shown, in some embodiments, the electric field may alternatively or additionally follow a path downward through the vertical channel 1720 and upward through the second reservoir. During a subsequent separation phase when the target portion is moved down the vertical channel prior to the removal of the unwanted HMW DNA from the vertical channel 1720, an electric field follows a path downward through the vertical channel 1720 and upward through the third reservoir 1712c (FIG. 14 center). Although not shown, in some embodiments, the electric field may alternatively or additionally follow a path downward through the vertical channel 1720 and upward through the fourth reservoir. During an elution phase (e.g., when the target DNA is moved into the sample well), an electric field follows a path downward through the third reservoir 1712c and upward through the vertical channel 1720. Although not shown, in some embodiments, the electric field may alternatively or additionally follow a path downward through the fourth reservoir 1714d and upward through the vertical channel 1720.

[0098] FIG. 15 shows different cross-sectional views of the apparatus of FIGS. 11A-11B disposed in a cavity in a housing with electric field lines during the initial separation phase and the product elution phase. As shown, the apparatus includes a vertical channel including ahydrogel 1722 disposed therein. The hydrogel defines a sample well in which a sample 1702 is disposed. A separation buffer solution 1706 disposed in the first reservoir and the second reservoir, and an elution buffer solution 1704 disposed in the third reservoir and the fourth reservoir. The vertical channel includes a sample buffer solution 1705 disposed in a top portion of the vertical channel above the sample well. The following cross-sections are depicted: Section A- A, Section B-B, Section C-C, and Section D-D. The field lines as described in FIG. 14 are shown for each cross-sectional view.

[0099] FIGS. 16 shows a housing 2150 configured to receive one or more vertical channels 2020 for performing preparative electrophoresis, according to an embodiment. As shown, the housing includes 24 cavities organized in 4 rows by 6 columns and each configured to receive a vertical channel. The cavities may have a square (or rectangular) cross-section and include walls protruding toward a center of the cavity 2152 configured to couple to the vertical channel 2120 to divide the cavity into a first reservoir and a second reservoir. When the vertical channel 2120 is disposed in the cavity 2152, the vertical channel 2120 and the cavity define the first reservoir on a first side of the vertical channel and the second reservoir on a second side of the vertical channel opposite the first side. A circuit board 2170 may include a plurality of holes 2172 through which the cavities 2152 of the housing 2150 including the vertical channels 2120 may be disposed when the circuit board is coupled to the housing 2150. In some embodiments, the housing 2150 has a top frame configured to hold the vertical channels 2120 in place in each cavity 2152. In some embodiments, the circuit board 2170 is configured to be glued to an underside of the top frame such that a set of electrodes are correctly positioned within each cavity 2152. For example, when the circuit board 2170 is coupled to the underside of the top frame, for each cavity: an electrode pair may be positioned near a top end of the vertical channel 2120, a first elution electrode may be positioned near a top end of the first reservoir, and a second elution electrode may be positioned near a top end of the second reservoir. A port may be disposed on a side of the housing 2150 and configured to electrically connect the circuit board 2170 to a remote power supply via a connector such as a cable. Use of a remote power supply allows the housing to be easily moved on and off of the LH deck during a workflow.

[0100] FIG. 17 shows an isometric view of a housing 3150 configured to receive a plurality of vertical channels 3120 for performing preparative electrophoresis, according to an embodiment. The housing 3150 includes 24 cavities organized in 4 rows by 6 columns and each configured to receive a vertical channel 3120. Some aspects of the assembly 3001 arestructurally and / or functionally similar to the assembly 1001, and therefore certain details of the assembly 3001 are not described herein again with respect to FIG. 17. The top panel shows the housing 3150 with the vertical channels 3120 disposed in the cavities 3152, and the bottom panel shows the housing 3150 with no vertical channels disposed in the cavities 3152. The cavities 3152 may have a square (or rectangular) cross-section and include walls protruding toward a center of the cavity 3152 and configured to couple to the vertical channel 3120 to divide the cavity 3120 into a first reservoir, a second reservoir, a third reservoir, and a fourth reservoir.

[0101] FIG. 18 shows an assembly 4001 for performing preparative electrophoresis, according to an embodiment. As shown, the housing 4150 includes 24 cavities 4152 organized in 4 rows and 6 columns and each configured to receive a vertical channel. A circuit board 4170 includes a plurality of holes 4172 through which the cavities 4152 are disposed when the circuit board 4170 is coupled to the housing 4150. Some aspects of the assembly 4001 are structurally and / or functionally similar to the assembly 1001, and therefore certain details of the assembly 4001 are not described herein again with respect to FIG. 18. The circuit board 4170 includes a plurality of disposable electrodes 4110 disposed on a top surface of the circuit board 4170. In some embodiments, the housing 4150 has a top frame configured to hold the vertical channels 4120 in place in each cavity 4152. In some embodiments, the circuit board 4170 is configured to be glued to an underside of the top frame such that a set of electrodes 4110 are correctly positioned within each cavity 4152. For example, when the circuit board 4170 is coupled to the underside of the top frame, for each cavity 4152: an electrode pair may be positioned near a top end of the vertical channel 4120, a first elution electrode may be positioned near a top end of the first reservoir, a second elution electrode may be positioned near a top end of the second reservoir, a third elution electrode may be positioned near a top end of the third reservoir, and a fourth elution electrode may be positioned near a top end of the fourth reservoir. In some embodiments, the electrodes 4110 may be pins that protrude upward from the circuit board (e.g., the electrodes may be vertical pins). In some embodiments, the top frame includes holes through which the electrodes 4110 may protrude into the reservoirs. In some embodiments, the electrodes 4110 may be disposable electrodes. The circuit board further includes a port 1475 configured to electrically connect the circuit board to an external power supply. In some embodiments, the circuit board 4170 is connected to the power supply via a cable (e.g., a long cable) such that the assembly 4001 may easily maneuvered onto and off of a LH deck. In some embodiments, the assembly 4001 is disposable after one use.

[0102] FIG. 19A-19B show a system for performing preparative electrophoresis. In some embodiments, a housing includes 24 cavities organized in 4 rows by 6 columns and each configured to receive a vertical column. Some aspects of the assembly 5001 are structurally and / or functionally similar to the system 1001, and therefore certain details of the system 5001 are not described herein again with respect to FIG. 19A. In some embodiments, the housing is configured to be coupled to a cover 5180. In some embodiments, a circuit board 5170 may be mounted onto the cover 5170. In some embodiments, the circuit board 5170 includes electrodes 5110 coupled to the circuit board 5170. In some embodiments, the circuit board 5170 is mounted to a side of the cover 5180 configured to face the cavities in the housing, and the electrodes 5110 protrude downward from the circuit board 5170. In some embodiments, the electrodes 5110 are arranged on the circuit board 5170 such that when the cover 5180 is disposed on the housing, the electrodes 5110 protrude downward into their corresponding reservoirs. For example, when the cover 5170 is disposed on the housing, for each cavity: an electrode pair may be positioned near a top end of the vertical channel, a first elution electrode may be positioned near a top end of the first reservoir, a second elution electrode may be positioned near a top end of the second reservoir, a third elution electrode may be positioned near a top end of the third reservoir, and a fourth elution electrode may be positioned near a top end of the fourth reservoir. In some embodiments, the electrodes 5110 may be configured to be reusable. In some embodiments, the cover 5180 including the circuit board 5170 and the electrodes 5110 may be reusable. In some embodiments, the housing including the cavities and vertical channels may be replaced after a single use, and the cover 5180 including the circuit board and the electrodes 5110 may be reused after each use. As shown in FIG. 19B, a cover 6180 and a circuit board 6170 may include access holes 6175 arranged such that when the cover 6180 is disposed over the housing, each of the vertical channels are accessible from the outside. For example, a user may be able to load a sample or load a buffer fluid into a vertical channel in the system using a pipette even when the cover is placed over the housing. Having easy accessibility for loading may increase efficiency of the workflow.

[0103] FIG. 20 shows an assembly 7001 for performing preparative electrophoresis, according to an embodiment. In some embodiments, a housing 7150 includes 24 cavities organized in 4 rows by 6 columns and each configured to receive a vertical column. Some aspects of the assembly 7001 are structurally and / or functionally similar to the assemblies described above, and therefore certain details of the assembly 7001 are not described herein again with respect to FIG. 20. In some embodiments, the circuit board 7170 includes electrode contacts 7115coupled to the circuit board 7170. In some embodiments, the electrode contacts 7115 are reusable. In some embodiments, the housing 7150 includes a plurality of electrodes 7110. In some embodiments, the housing 7150 has a top frame 7155 configured to hold the vertical channels in place in each cavity. In some embodiments the top frame 7155 of the housing includes a plurality of electrodes 7110. In some embodiments, the plurality of electrodes 7110 coupled to the top frame 7155 are disposable electrodes. In some embodiments, the electrodes 7110 may include any of the electrode materials described with respect to FIG. 1. In some embodiments, the electrodes 7110 may include conductive materials or polymers molded into the top frame 7155. In some embodiments, the electrodes 7110 may include carbon. For example, the electrodes may be carbon pads molded into the top frame 7155. In some embodiments, the plurality of electrodes 7110 are arranged on the top frame 7155 such that each cavity has: an electrode pair positioned near a top end of the vertical channel, a first elution electrode positioned near a top end of the first reservoir, a second elution electrode positioned near a top end of the second reservoir, a third elution electrode positioned near a top end of the third reservoir, and a fourth elution electrode positioned near a top end of the fourth reservoir. In some embodiments, the electrodes contacts 7115 are arranged on the circuit board 7170 such that when the circuit board 7170 is coupled to the housing 7150 underneath the top frame 7155, the electrodes contacts 7115 protrude upward and contact the electrodes 7110 on the top frame, thereby electrically connecting the electrodes 7110 to the circuit board 7170. In some embodiments, the electrode contacts 7115 include a biasing member to improve contact with the electrodes 7110. For example, the electrode contacts 7115 may be a spring-loaded contact (e.g., pogo pin).

[0104] FIG. 21 A shows a method for manufacturing the assembly 7001 performing preparative electrophoresis, according to an embodiment. As shown, the housing 7150 may be manufactured by molding the housing 7150 with voids in locations corresponding to the electrodes (e.g., conductive pads). Next, pads may be molded robotically one by one. For example, a conductive glue may be used to fill the voids. In some embodiments, an injection moldable conductive polymer may be used to fill the voids. In some embodiments polypropylene may be used to fille the voids. FIG. 2 IB shows a method for manufacturing the system performing preparative electrophoresis, according to an embodiment. In some embodiments, an electrode mold 7113 can first be created by creating a mold of the electrodes 7113 (e.g., conductive pads) connected by a runner. Then, the electrode mold 7113 including the runner may be disposed in the housing mold 7150, and the housing 7150 may be moldedaround the electrodes (e.g., the conductive pads). Therefore, the housing 7150 is formed around the electrodes (e.g., the conductive pads). In some embodiments, the runner may be trimmed off after the housing is molded.

[0105] FIG. 22A shows a system including a U shape channel 8120 for performing preparative electrophoresis, according to an embodiment. As shown, a housing 8150a includes a first portion and a second portion 8150b configured to be coupled together. The housing 8150 includes a plurality of cavities 8152 each defining an inner volume. In some embodiments, the housing 8150 may include cavities 8152 organized in 2 rows and 6 columns. Each cavity 8152 may be configured to receive a divider 8125 such that the inner volume forms a U shape channel 8120. In some embodiments, a hydrogel 8122 is disposed in the U shape channel 8120. The hydrogel 8122 may define a first sample well 8124a at a first end of the U shape channel 8120 and a second sample well 8124b at a second end of the U shape channel 8120. The first end of the U shape channel 8120 and the second end of the U shape channel 8120 are each configured to receive a buffer solution. In some embodiments, a circuit board 8170 may include a plurality of electrodes 8110 arranged such that when the circuit board 8170 is coupled to the housing 8150, a first electrode is positioned near a top of the first end of the U shape channel, and the second electrode is positioned near a top of the second end of the U shape channel. In some embodiments, a first pair of electrodes may be positioned near a top of the first end of the U shape channel, and a second pair of electrodes may be positioned near a top of the second end of the U shape channel. In some embodiments, the electrodes may protrude upward from the circuit board 8170, such that when the circuit board 8170 is coupled to the housing 8150, the electrodes 8110 protrude upward and contact the buffer solution disposed above each sample well.

[0106] FIG. 22B shows a process of using the system including the U shape channel 8120. At step A, a sample 8102 of DNA fragments is disposed in the first sample well 8124a. At step B, a voltage gradient is generated between the first electrode (or first pair of electrodes) and the second electrode (or second pair of electrodes) to move the sample in a first direction (e.g., downward) along a first portion of the U shape channel 8120. In some embodiments, the voltage gradient is created by the first electrode (or first pair of electrodes) generating a negative voltage. In some embodiments, the voltage gradient is generated by the second electrode (or second pair of electrodes) generating a positive voltage. In some embodiments, the voltage gradient is generated by both the first electrode (or first pair of electrodes)generating a negative voltage, and the second electrode (or pair of electrodes) generating a negative voltage. As the sample 8102 moves in the first direction, the DNA fragments begin to separate according to size. At step C, the electrodes continue to generate the voltage gradient, and the sample further separates. At step D, the electrodes continue to generate the voltage gradient, and the sample begins to move in a second direction (e.g., upwards) along a second portion of the U shape channel 8120 toward the second sample well. At step E, a portion of the sample reaches the second sample well 8124b and may be collected. In some embodiments, the U shape channel 8120 may be used to collect DNA with a size below a threshold. In some embodiments, DNA fragments with LMW may reach the second sample 8120 well be collected for subsequent use.

[0107] FIG. 23A shows an example method for performing preparative electrophoresis, according to an embodiment. The vertical channel is compatible with an SLAS -compatible 24-well plate footprint, with a height of about 4-5 cm. The vertical channel is configured to be loaded from the top, perform electrophoresis vertically to get rid of unwanted DNA size fractions and then to elute the product DNA back into the sample well. In this workflow standard liquid handling robots can load and unload the columns from the top side of the cassette. Four gel columns were loaded with equal amounts of a DNA marker with bands ranging in size from 500bp to 48kb in size. The samples were electrophoresed down for 33 min (“a” step) so that some smaller fragments were lost into the lower buffer chamber. Gel column 4 was stained and photographed to show the retained marker bands near the bottom of the gel column. The lower buffer - along with the unwanted DNA fragments - was discarded and the lower reservoir was refilled with fresh buffer. The voltage was then reversed (“b” step) for 25 min, and gel column 3 was stained and photographed to reveal the position of the retained DNA bands, which have returned to a position near the sample well. The buffer in the sample wells was replaced with electrophoresis buffer containing 12% sucrose, and electrophoresis in the upward direction was resumed for up to 25 min. The sample well contents were removed, DNA was concentrated using Ampure magnetic particles, and run on agarose gels as shown on the right. Under the conditions used, fragments less than 3 kb were removed by the selection. Recovery of DNA >3kb was 55% as measured by Qubit assay.

[0108] FIG. 23B shows the results from example methods for performing preparative electrophoresis. DNA was sheared using a g-Tube (Covaris) to modal sizes of 12kb (left) and 22kb (right). Input loads representative of common long-read library methods were used (3 to4.5 ug). Using the programs shown, size selections with low cutoffs at lOkb (right, modal size of product 15.4kb) and 17kb (left, modal product size 32kb). Total run time for the 15kb product was 2.75 hrs. (right), and 5.5 hrs. for the 32kb products (left). LMW fragment rejection below the low cutoff was good in both runs (reduction of DNA <10kb was ~59-fold on the right, and reduction of DNA <17kb was ~11-fold on the left). Additional improvement in rejection of LMW fragments in the 17-20kb range should be possible with pulsed field programs, which were not used in these experiments. Overall recovery of size-selected product was quite good, about 50-55%, in rough agreement with the overlap between the size distributions of inputs and size-selected outputs.

[0109] The use of electrophoresis buffers with high concentrations of sucrose or glycerol (12- 25% w / v) during elution is important in order to confine the eluted DNA within the sample well. This confinement is important for preventing the eluted DNA from reaching the sample well electrode where it might be damaged by exposure to electrolysis products.Additional Examples:Example 1: A preparative electrophoresis apparatus including a vertical channel having an open top end portion, a hydrogel disposed in a portion of the vertical channel, a top surface of the hydrogel defining a sample well configured to receive a sample of DNA fragments, and a plurality of electrodes. The vertical channel is arranged within a housing such that the vertical channel is in fluid communication with a first reservoir and a second reservoir, the vertical channel and each reservoir configured to receive a buffer solution, the first reservoir and the second reservoir at least partially defined by the housing, and the vertical channel and the first and second reservoirs are each coupled to at least one specific, respective electrode from the plurality of electrodes. Upon application of a first voltage gradient by the plurality of electrodes, the sample received by the well moves in a first direction through the hydrogel such that a portion of the sample exits the vertical channel, and upon application of a second voltage gradient by the plurality of electrodes, the remaining sample moves in a second direction opposite to the first direction through the hydrogel toward; the sample well.Example 2: The apparatus of example 1, where the sample well is configured to receive the buffer solution, and the top surface of the hydrogel is in fluid communication with the sample well.Example 3: The apparatus of examples 1 or 2, where a bottom end of the vertical channel includes a first opening and a second opening, the first opening is in fluid communication with the first reservoir, and the second opening is in fluid communication with the second reservoir such that the first reservoir and the second reservoir are physically separate from one another. Example 4: The apparatus of any of examples 1-3, where the vertical channel includes a first opening, a second opening, a third opening and a fourth opening, the first opening in fluid communication with the first reservoir, the second opening in fluid communication with the second reservoir, the third opening in fluid communication with a third reservoir, the fourth opening in fluid communication with a fourth reservoir, and the third and fourth reservoir each coupled to at least one specific, respective electrode from the plurality of electrodes.Example 5: The apparatus of any of examples 1-4, where before application of the second voltage gradient, application of a third voltage gradient by the plurality of electrodes moves the remaining sample in the first direction such that a second portion of the sample exits the vertical channel.Example 6: The apparatus of any of examples 1-5, where the third opening and the fourth opening are positioned closer to the bottom end of the vertical channel than the first opening and the second opening.Example 7: The apparatus of any of examples 1-6, where an inner surface of the vertical channel tapers inward such that a width of the vertical channel decreases along at least one direction.Example 8: The apparatus of any of examples 1-7, where an inner surface of the vertical channel tapers inward along a first direction and widens along a second direction perpendicular to the first direction such that a cross-sectional area defined by the inner surface remains constant along a length of the vertical channel.Example 9: The apparatus of any of examples 1-8, where a cross-section of the vertical channel is a circle, an oval, a square, or a rectangle.Example 10: The apparatus of any of examples 1-9, where the hydrogel includes 0.50% to about 5% agarose.Example 11: The apparatus of any of examples 1-10, where the housing defines a plurality of cavities, each cavity from the plurality of cavities configured to receive a vertical channel.Example 12: A preparative electrophoresis system including a vertical channel including a hydrogel disposed in at least a portion of the vertical channel and a top end configured to receive a buffer solution, the vertical channel including a first opening and a second opening,wherein the hydrogel includes a top surface defining a sample well for receiving a DNA fragment sample, at least one sample well electrode arranged proximate the top end of the vertical channel, wherein the vertical channel is configured with a size and shape so that the buffer solution at the top end of the vertical channel is in contact with the at least one sample well electrode, a first elution electrode and a second elution electrode, and a first reservoir in fluid communication with the first opening of the vertical channel and including a top end. The buffer solution at a top end of the first reservoir is in contact with the first elution electrode and a second reservoir in fluid communication with the second opening of the vertical channel and including a top end, wherein the buffer solution at a top end of the second reservoir is in contact with the second elution electrode. The at least one sample well electrode and the first elution electrode are configured to provide a voltage gradient therebetween for a first predetermined period of time so as to move the sample in a first direction through the hydrogel such that a portion of the sample exits vertical channel.Example 13: The system of example 12, where after the portion of the sample exits the vertical channel the first elution electrode is configured to provide a voltage gradient along a length of the first reservoir to move the portion of the sample in a second direction toward the first elution electrode into the first reservoir during a second predetermined period of time, and the at least one sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween during the second predetermined period of time to move the remaining sample in the second direction through the hydrogel toward the sample well.Example 14: The system of examples 12 or 13, where the vertical channel includes a third opening and a fourth opening, and the system further includes a third elution electrode and a fourth elution electrode, a third reservoir in fluid communication with the third opening of the vertical channel and including a top end, wherein the third reservoir is configured with a size and shape such that the buffer solution at the top end of the third reservoir is in contact with a third elution electrode, and a fourth reservoir in fluid communication with the fourth opening of the vertical channel and including a top end, wherein the fourth reservoir is sized and shaped so that the buffer solution at a top end of the fourth reservoir in contact with the fourth elution electrode. The first and second reservoirs are configured as waste reservoirs and the third and fourth reservoirs are configured as clean reservoirs.Example 15: The system of any of examples 12-14, where the at least one sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween for the first predetermined period of time so as to move the sample in the firstdirection through the hydrogel such that a first portion of the sample exits the vertical channel into the waste reservoirs, and the at least one sample well electrode and at least one of the third and fourth elution electrodes provide a voltage gradient therebetween for a second predetermined amount of time to continue moving the sample in the first direction d through the hydrogel.Example 16: The system of any of examples 12-15, where the voltage gradient between the at least one sample well electrode and at least one of the first elution electrode and the second elution electrodes cause a second portion of the sample to exit the vertical channel into the waste reservoirs.Example 17: The system of any of examples 12-16, where the at least one sample well electrode and at least one of the third and fourth elution electrodes provide a voltage gradient therebetween for a third predetermined amount of time to move the sample in a second direction through the hydrogel toward the sample well.Example 18: The system of any of examples 12-16, wherein the first portion of the sample has a molecular weight lower than a predetermined range and the second portion of the sample has a molecular weight higher than the predetermined range.Example 19: The system of any of examples 12-14, where the at least one sample well electrode and the first elution electrode provide a voltage gradient therebetween and the at least on sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween for the first predetermined period of time so as to move the sample in the first direction through the hydrogel such that the portion of the sample exits the vertical channel into the waste reservoirs, and the at least one sample well electrode and the third elution electrode provide a voltage gradient therebetween and the at least one sample well electrode and the fourth elution electrode provide a voltage gradient therebetween for a second predetermined amount of time to continue moving the sample in the first direction through the hydrogel.Example 20: The system of any of examples 12-19, where the at least one sample well electrode and the third elution electrode provide a voltage gradient therebetween and the at least one sample well electrode and fourth elution electrode provide a voltage gradient therebetween for a third predetermined amount of time to move the sample in a second direction through the hydrogel toward the sample well.Example 21: A preparative electrophoresis system including a housing defining at least one cavity having an inner surface, a plurality of electrodes comprising at least a first electrode, asecond electrode, and a third electrode, a hydrogel having a top surface, and a vertical channel disposed in the cavity of the housing and including the hydrogel disposed in at least a portion thereof, a top end, a bottom end, and an outer surface. The top surface of the hydrogel defines a sample well for receiving a sample, the top end of the vertical channel is configured to receive a buffer solution, and the bottom end of the vertical channel having a first opening and a second opening. The outer surface of the vertical channel and an inner surface of the cavity define a first reservoir including a top end and in fluid communication with the first opening and a second reservoir including a top end and in fluid communication with the second opening, and the first electrode is arranged proximate the top end of the vertical channel, the second electrode from the plurality of electrodes is arranged near the top end of the first reservoir, the third electrode from the plurality of electrodes is arranged near the top end of the second reservoir. Example 22: The system of example 21, where the at least one cavity comprises a plurality of cavities, each cavity of the plurality of cavities configured to receive a vertical channel.Example 23: The system of example 21 or 22, further including a circuit board electrically connected to the plurality of electrodes and configured to control voltage provided to each electrode from the plurality of electrodes.Example 24: The system of any of examples 21-23, where the electrodes include a material selected from the group consisting of: conductive polymer, graphite, carbon fiber, carbon paper, platinum, gold-plated, carbon black, and any combination thereof.Example 25: The system of any of examples 21-24, where the electrodes include an injection moldable conductive polymer.Example 26: The system of any of examples 21-25, where the plurality of electrodes are coupled to the housing and comprise disposable electrodes, and the circuit board includes a plurality of reusable electrode contacts configured to electrically connect the circuit board to the plurality of electrodes.Example 27: The system of any of examples 21-26, where the system further comprises a power supply.Example 28: The system of any of examples 21-27, where the power supply is a remote power supply connected to the housing via a cable connector.Example 29: The system of any of examples 21-28, where the housing is configured to be Society of Laboratory Automation and Screening Standards (SLAS) compliant.Example 30: A method for preparative electrophoresis including providing a DNA fragment separation apparatus according to any of examples 1-8 and examples 12-20, loading a sampleinto the sample well from above the vertical channel, generating a first voltage gradient having a first direction for the first predetermined period of time to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel, wherein the first direction is defined along the length of the vertical channel, and generating a second voltage gradient having a second direction after at least the portion is eliminated from the vertical channel so as to move a remainder of the sample upward through the vertical channel toward the sample well, where the second direction is defined along the length of the vertical channel.Example 31: The method of example 30, where the first voltage gradient having the first direction is generated between the at least one sample well electrode and the first elution electrode to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel, and the second voltage gradient having the second direction is generated between the at least one sample well and the second elution electrode to move the remainder of the sample upward through the vertical channel toward the sample well. Example 32: The method of any of examples 30 and 31, where the second voltage gradient having the second direction is generated for the second predetermined period of time after at least the portion of the sample has been eliminated from the vertical channel, and the method further comprises generating a third voltage gradient having the first direction between the at least one sample well electrode and the first elution electrode during the second predetermined period of time.Example 33: The method of any of examples 30-32, where the third voltage gradient is weaker than the first voltage gradient.Example 34: The method of any of examples 30-33, further including replacing, after the second predetermined period of time, the buffer solution in the second reservoir with a solution comprising at least one of a sucrose and glycerol, and generating, after the buffer solution has been replaced, a fourth voltage gradient having the second direction between the at least one sample electrode the second elution electrode for a third predetermined period of time to move the sample back into the sample well.Example 35: The method of any of examples 30-34, further including removing the separated sample from the vertical channel after the entirety of the remaining sample is moved into the sample well and concentrating and exchanging the remaining sample into a suitable buffer. Example 36: The method of any of examples 30-35, where concentrating and exchanging the remaining sample into a suitable buffer includes using magnetic bead cleanup.Example 37: The method of any of examples 30-36, where concentrating and exchanging the remaining sample into a suitable buffer is accomplished by binding and eluting the sample from a solid phase purification matrix.Example 38: The method of any of examples 30-37, where concentrating and exchanging the remaining sample into a suitable buffer is accomplished by precipitation and centrifugation.Example 39: The method of any of examples 30-38, where the first voltage gradient having the first direction is generated between the at least one sample well electrode and at least one of the first elution and the second elution electrode to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel, and the second voltage gradient having the second direction is generated between the at least one sample well and at least one of the third elution electrode and the fourth elution electrode to move the remainder of the sample upward through the vertical channel toward the sample well.Example 40: The method of any of examples 30-39, further including before generating the second voltage gradient, generating a third voltage gradient having the first direction between the at least one sample electrode and at least one of the third elution electrode and the fourth elution electrode during a second predetermined period of time to move the sample down the vertical channel, and generating a fourth voltage gradient having a third direction between the at least one sample electrode and at least one of the first elution electrode and the second elution electrode during a third predetermined period of time to move a second portion of the sample out of the vertical channel and into the first reservoir and the second reservoir. The second voltage gradient is generated during a fourth predetermined amount of time.Example 41: The method of any of examples 30-40, where upon the housing defining the plurality of cavities, separation of DNA fragments can be conducted for a plurality of samples simultaneously.Example 42: The method of any of examples 30-41, where the sample includes molecules of DNA having different lengths.

[0110] While various inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and / or structures for performing the function and / or obtaining the results and / or one or more of the advantages described herein, and each of such variations and / or modifications is deemed to be within the scope of the inventive embodiments described herein. More generally, those skilled in the art will readily appreciate that any and all parameters, dimensions, materials, and configurationsdescribed herein are meant to be an example and that the actual parameters, dimensions, materials, and / or configurations will depend upon the specific application or applications for which the inventive teachings disclosed herein is / are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the claims supported by the disclosure, and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present disclosure are also directed to each individual feature, system, article, material, kit, and / or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and / or methods, if such features, systems, articles, materials, kits, and / or methods are not mutually inconsistent, is included within the inventive scope of the present disclosure.[OHl] Embodiments disclosed herein may also be combined with one or more features, as well as complete systems, devices and / or methods, to yield yet other embodiments and inventions. Moreover, some embodiments, may be distinguishable from the prior art by specifically lacking one and / or another feature disclosed in the particular prior art reference(s); i.e., claims to such embodiments are distinguishable from the prior art by including one or more negative limitations.

[0112] Also, various inventive concepts may be embodied as one or more methods, of which examples has been provided. The acts performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated, which may include performing some acts simultaneously.

[0113] The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.” The terms “can” and “may” are used interchangeably in the present disclosure, and indicate that the referred to element, component, structure, function, functionality, objective, advantage, operation, step, process, apparatus, system, device, result, or clarification, has the ability to be used, included, or produced, or otherwise stand for the proposition indicated in the statement for which the term is used (or referred to) for a particular embodiment(s).

[0114] The phrase “and / or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that areconjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and / or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and / or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and / or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

[0115] As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and / or” as defined above. For example, when separating items in a list, “or” or “and / or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of’ or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e., “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.

[0116] As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “at least one of A and B” (or, equivalently, “at least one of A or B,” or, equivalently “at least one of A and / or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally includingelements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.

[0117] In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of’ and “consisting essentially of’ shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.

Claims

What is currently claimed:

1. A preparative electrophoresis apparatus comprising: a vertical channel having an open top end portion; a hydrogel disposed in a portion of the vertical channel, a top surface of the hydrogel defining a sample well configured to receive a sample of DNA fragments, and a plurality of electrodes, wherein: the vertical channel is arranged within a housing such that the vertical channel is in fluid communication with a first reservoir and a second reservoir, the vertical channel and each reservoir configured to receive a buffer solution, the first reservoir and the second reservoir at least partially defined by the housing, the vertical channel and the first and second reservoirs are each coupled to at least one specific, respective electrode from the plurality of electrodes; upon application of a first voltage gradient by the plurality of electrodes, the sample received by the well moves in a first direction through the hydrogel such that a portion of the sample exits the vertical channel, and upon application of a second voltage gradient by the plurality of electrodes, the remaining sample moves in a second direction opposite to the first direction through the hydrogel toward; the sample well.

2. The apparatus of claim 1, wherein the sample well is configured to receive the buffer solution, and the top surface of the hydrogel is in fluid communication with the sample well.

3. The apparatus of claim 1, wherein: a bottom end of the vertical channel includes a first opening and a second opening,the first opening is in fluid communication with the first reservoir, and the second opening is in fluid communication with the second reservoir such that the first reservoir and the second reservoir are physically separate from one another.

4. The apparatus of claim 1, wherein: the vertical channel includes a first opening, a second opening, a third opening and a fourth opening, the first opening in fluid communication with the first reservoir, the second opening in fluid communication with the second reservoir, the third opening in fluid communication with a third reservoir, the fourth opening in fluid communication with a fourth reservoir, and the third and fourth reservoir each coupled to at least one specific, respective electrode from the plurality of electrodes.

5. The apparatus of claim 4, wherein before application of the second voltage gradient, application of a third voltage gradient by the plurality of electrodes moves the remaining sample in the first direction such that a second portion of the sample exits the vertical channel.

6. The apparatus of claim 4, wherein the third opening and the fourth opening are positioned closer to the bottom end of the vertical channel than the first opening and the second opening.

7. The apparatus of claim 1, wherein an inner surface of the vertical channel tapers inward such that a width of the vertical channel decreases along at least one direction.

8. The apparatus of claim 7, wherein an inner surface of the vertical channel tapers inward along a first direction and widens along a second direction perpendicular to the first direction such that a cross-sectional area defined by the inner surface remains constant along a length of the vertical channel.

9. The apparatus of claim 1, wherein a cross-section of the vertical channel is a circle, an oval, a square, or a rectangle.

10. The apparatus of claim 1, wherein the hydrogel includes 0.50% to about 5% agarose.

11. The apparatus of claim 1, wherein the housing defines a plurality of cavities, each cavity from the plurality of cavities configured to receive a vertical channel.

12. A preparative electrophoresis system, comprising: a vertical channel including a hydrogel disposed in at least a portion of the vertical channel and a top end configured to receive a buffer solution, the vertical channel including a first opening and a second opening, wherein the hydrogel includes a top surface defining a sample well for receiving a DNA fragment sample; at least one sample well electrode arranged proximate the top end of the vertical channel, wherein the vertical channel is configured with a size and shape so that the buffer solution at the top end of the vertical channel is in contact with the at least one sample well electrode; a first elution electrode and a second elution electrode; a first reservoir in fluid communication with the first opening of the vertical channel and including a top end, wherein the buffer solution at a top end of the first reservoir is in contact with the first elution electrode; anda second reservoir in fluid communication with the second opening of the vertical channel and including a top end, wherein the buffer solution at a top end of the second reservoir is in contact with the second elution electrode, wherein: the at least one sample well electrode and the first elution electrode are configured to provide a voltage gradient therebetween for a first predetermined period of time so as to move the sample in a first direction through the hydrogel such that a portion of the sample exits vertical channel.

13. The system of claim 12, wherein after the portion of the sample exits the vertical channel: the first elution electrode is configured to provide a voltage gradient along a length of the first reservoir to move the portion of the sample in a second direction toward the first elution electrode into the first reservoir during a second predetermined period of time, and the at least one sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween during the second predetermined period of time to move the remaining sample in the second direction through the hydrogel toward the sample well.

14. The system of claim 12, wherein: the vertical channel includes a third opening and a fourth opening, the system further comprises: a third elution electrode and a fourth elution electrode; a third reservoir in fluid communication with the third opening of the vertical channel and including a top end, wherein the third reservoir is configured with a size and shape such that the buffer solution at the top end of the third reservoir is in contact with a third elution electrode; anda fourth reservoir in fluid communication with the fourth opening of the vertical channel and including a top end, wherein the fourth reservoir is sized and shaped so that the buffer solution at a top end of the fourth reservoir in contact with the fourth elution electrode, and the first and second reservoirs are configured as waste reservoirs and the third and fourth reservoirs are configured as clean reservoirs.

15. The system of claim 14, wherein: the at least one sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween for the first predetermined period of time so as to move the sample in the first direction through the hydrogel such that a first portion of the sample exits the vertical channel into the waste reservoirs, and the at least one sample well electrode and at least one of the third and fourth elution electrodes provide a voltage gradient therebetween for a second predetermined amount of time to continue moving the sample in the first direction d through the hydrogel.

16. The system of claim 15, wherein the voltage gradient between the at least one sample well electrode and at least one of the first elution electrode and the second elution electrodes cause a second portion of the sample to exit the vertical channel into the waste reservoirs.

17. The system of claim 16, wherein the at least one sample well electrode and at least one of the third and fourth elution electrodes provide a voltage gradient therebetween for a third predetermined amount of time to move the sample in a second direction through the hydrogel toward the sample well.

18. The system of claim 16, wherein the first portion of the sample has a molecular weight lower than a predetermined range and the second portion of the sample has a molecular weight higher than the predetermined range.

19. The system of claim 14, wherein: the at least one sample well electrode and the first elution electrode provide a voltage gradient therebetween and the at least on sample well electrode and the second elution electrode are configured to provide a voltage gradient therebetween for the first predetermined period of time so as to move the sample in the first direction through the hydrogel such that the portion of the sample exits the vertical channel into the waste reservoirs, and the at least one sample well electrode and the third elution electrode provide a voltage gradient therebetween and the at least one sample well electrode and the fourth elution electrode provide a voltage gradient therebetween for a second predetermined amount of time to continue moving the sample in the first direction through the hydrogel.

20. The system of claim 19, wherein the at least one sample well electrode and the third elution electrode provide a voltage gradient therebetween and the at least one sample well electrode and fourth elution electrode provide a voltage gradient therebetween for a third predetermined amount of time to move the sample in a second direction through the hydrogel toward the sample well.

21. A preparative electrophoresis system, comprising: a housing defining at least one cavity having an inner surface; a plurality of electrodes comprising at least a first electrode, a second electrode, and a third electrode;a hydrogel having a top surface; a vertical channel disposed in the cavity of the housing and including the hydrogel disposed in at least a portion thereof, a top end, a bottom end, and an outer surface, wherein: the top surface of the hydrogel defines a sample well for receiving a sample, the top end of the vertical channel is configured to receive a buffer solution, the bottom end of the vertical channel having a first opening and a second opening; the outer surface of the vertical channel and an inner surface of the cavity define a first reservoir including a top end and in fluid communication with the first opening and a second reservoir including a top end and in fluid communication with the second opening, the first electrode is arranged proximate the top end of the vertical channel, and the second electrode from the plurality of electrodes is arranged near the top end of the first reservoir, the third electrode from the plurality of electrodes is arranged near the top end of the second reservoir.

22. The system of claim 21, wherein the at least one cavity comprises a plurality of cavities, each cavity of the plurality of cavities configured to receive a vertical channel.

23. The system of claim 22, further comprising: a circuit board electrically connected to the plurality of electrodes and configured to control voltage provided to each electrode from the plurality of electrodes.

24. The system of claim 22, wherein the electrodes include a material selected from the group consisting of: conductive polymer, graphite, carbon fiber, carbon paper, platinum, gold-plated, carbon black, and any combination thereof.

25. The system of claim 24, wherein the electrodes include an injection moldable conductive polymer.

26. The system of claim 24, wherein: the plurality of electrodes are coupled to the housing and comprise disposable electrodes, and the circuit board includes a plurality of reusable electrode contacts configured to electrically connect the circuit board to the plurality of electrodes.

27. The system of claim 21, wherein the system further comprises a power supply.

28. The system of claim 27, wherein the power supply is a remote power supply connected to the housing via a cable connector.

29. The system of claim 21, wherein the housing is configured to be Society of Laboratory Automation and Screening Standards (SLAS) compliant.

30. A method for preparative electrophoresis, comprising: providing a DNA fragment separation apparatus according to any of claims 1-8 and claims 12-20; loading a sample into the sample well from above the vertical channel; generating a first voltage gradient having a first direction for the first predetermined period of time to move the sample down the vertical channel such that a portionof the sample is eliminated from the vertical channel, wherein the first direction is defined along the length of the vertical channel; and generating a second voltage gradient having a second direction after at least the portion is eliminated from the vertical channel so as to move a remainder of the sample upward through the vertical channel toward the sample well, wherein the second direction is defined along the length of the vertical channel.

31. The method of claim 30, wherein: the first voltage gradient having the first direction is generated between the at least one sample well electrode and the first elution electrode to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel, and the second voltage gradient having the second direction is generated between the at least one sample well and the second elution electrode to move the remainder of the sample upward through the vertical channel toward the sample well.

32. The method of claim 31, wherein: the second voltage gradient having the second direction is generated for the second predetermined period of time after at least the portion of the sample has been eliminated from the vertical channel, and the method further comprises generating a third voltage gradient having the first direction between the at least one sample well electrode and the first elution electrode during the second predetermined period of time.

33. The method of claim 31, wherein the third voltage gradient is weaker than the first voltage gradient.

34. The method of claim 33, further comprising: replacing, after the second predetermined period of time, the buffer solution in the second reservoir with a solution comprising at least one of a sucrose and glycerol; and generating, after the buffer solution has been replaced, a fourth voltage gradient having the second direction between the at least one sample electrode the second elution electrode for a third predetermined period of time to move the sample back into the sample well.

35. The method of claim 34, further comprising: removing the separated sample from the vertical channel after the entirety of the remaining sample is moved into the sample well; and concentrating and exchanging the remaining sample into a suitable buffer.

36. The method of claim 35, wherein concentrating and exchanging the remaining sample into a suitable buffer includes using magnetic bead cleanup.

37. The method of claim 35, wherein concentrating and exchanging the remaining sample into a suitable buffer is accomplished by binding and eluting the sample from a solid phase purification matrix.

38. The method of claim 35, wherein concentrating and exchanging the remaining sample into a suitable buffer is accomplished by precipitation and centrifugation.

39. The method of claim 30, wherein:the first voltage gradient having the first direction is generated between the at least one sample well electrode and at least one of the first elution and the second elution electrode to move the sample down the vertical channel such that a portion of the sample is eliminated from the vertical channel, and the second voltage gradient having the second direction is generated between the at least one sample well and at least one of the third elution electrode and the fourth elution electrode to move the remainder of the sample upward through the vertical channel toward the sample well.

40. The method of claim 39, further comprising, before generating the second voltage gradient: generating a third voltage gradient having the first direction between the at least one sample electrode and at least one of the third elution electrode and the fourth elution electrode during a second predetermined period of time to move the sample down the vertical channel; and generating a fourth voltage gradient having a third direction between the at least one sample electrode and at least one of the first elution electrode and the second elution electrode during a third predetermined period of time to move a second portion of the sample out of the vertical channel and into the first reservoir and the second reservoir, wherein the second voltage gradient is generated during a fourth predetermined amount of time.

41. The method of claim 30, wherein upon the housing defining the plurality of cavities, separation of DNA fragments can be conducted for a plurality of samples simultaneously.

42. The method of 30, wherein the sample includes molecules of DNA having different lengths.

43. A system, apparatus, device or method according to any of the disclosed embodiments.

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