Sample processing devices including magnetic and mechanical actuator elements with linear or rotational motion and methods of use thereof

Abstract

To provide a method and a device for simple and low-power automated biological sample processing.SOLUTION: A microfluidic device comprising a microfluidic cartridge comprising one or more cams comprising a cam shaft and a cam lobe, one or more rocker arms, one or more flow channels, one or more reaction chambers, and one or more burst pouches comprising a fluid and a frangible membrane seal, and a cam mechanism configured to rotate the cam shaft, wherein the one or more cams are configured such that rotation of the cam shaft causes the cam lobe to actuate the one or more rocker arms; Wherein the one or more rocker arms are configured such that actuation moves the rocker arms from an open position to a closed position to apply pressure to the one or more burst pouches to break the frangible membrane and release the fluid into the one or more reaction chambers.SELECTED DRAWING: Figure 1

Description

[Technical Field]

[0001] The present invention relates to sample processing devices that include magnetic and mechanical actuator elements that perform linear or rotational motion, and methods for using the same.

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application No. 62 / 196,816, filed July 23, 2015, U.S. Provisional Patent Application No. 62 / 261,577, filed December 1, 2015, and U.S. Provisional Patent Application No. 62 / 331,635, filed May 4, 2016, the entire contents of which are hereby incorporated by reference in their entireties. [Background technology]

[0003] Point-of-care ("POC") devices enable convenient and rapid testing at the point of patient care. Therefore, sample-to-answer lab-on-a-chip ("LOC") systems, a type of POC device incorporating microfluidics technology, are becoming increasingly popular. These LOCs integrate various laboratory functions, such as extraction, amplification, detection, interpretation, and reporting, all onto the same device, which have traditionally been performed manually and / or off-site. Because sample-to-answer LOC tests are performed at the point of patient care rather than in a laboratory, these types of tests present contamination control challenges, especially during processing steps involving human interaction. Therefore, there is a need to automate sample processing within the sample-to-answer LOC to minimize human interaction. Such sample-to-answer LOCs are typically a few square millimeters to a few square centimeters in size and are often microelectromechanical systems ("MEMS"). MEMS capable of detecting and analyzing biological materials, such as those described herein, are commonly referred to as bioMEMS.

[0004] Most commercially available POC diagnostic devices are categorized as moderate to high complexity under the Clinical Laboratory Improvement Amendments (CLIA). These federal guidelines generally apply to human clinical laboratory testing equipment, except for certain conditions under which these guidelines are exempt. One of these conditions is if the device or instrument meets certain risk, error, and complexity requirements. For a POC diagnostic test to be eligible for CLIA exemption, sample preparation and fluid handling steps must be minimized. One way to minimize these steps is to sell reagents contained in sealed mechanisms such as blister pouches or burst pouches. Reagent delivery to microfluidic chips typically involves the use of pumps, such as syringe pumps or peristaltic pumps, and bottles, syringes, or reservoirs filled with external reagents. Such systems are not only difficult to transport but also complex due to the large number of components that must be integrated and the need for a leak-tight fluidic interface with the microfluidic chip. Even the most advanced commercial products have yet to successfully implement a method that allows for automation of fluidic operations while being simple, compact, and low-power. Therefore, this is seen as an obstacle preventing the implementation of POC in the majority of multi-stage bioassay tests still performed in large clinical centers.

[0005] Complex bioassays requiring multiple processing steps, including but not limited to pipetting, heating, cooling, mixing, washing, incubation, labeling, binding, and elution, rely on expensive lab automation equipment to perform sample-to-answer sequencing. Low-cost, low-power, and compact instrumentation for automating sample-to-answer sequencing has yet to be realized, and thus point-of-care microfluidic devices performing sample-to-answer sequencing rely on additional instrumentation in the form of standalone benchtop or portable instruments to run the assays on the microfluidic device. Implementing separate instrumentation capable of automating sample processing steps on microfluidic cartridges is considered one way to keep the cost per test, and therefore the cartridge cost, low. In systems developed for point-of-care applications, this instrumentation can automate sample processing sequences in the form of portable benchtop instruments with solenoid plungers, linear actuators, microcontrollers, and electronics. While this instrumentation gives users control over the sample processing sequence, it requires a controlled environment and a significant amount of power to operate. Such point-of-care systems are not feasible in low-resource environments where the infrastructure to operate the instruments does not exist, or in home or out-of-hospital settings where non-professionals are available who do not understand the need for, cannot afford, or are not trained in operating expensive test instruments. Therefore, developing methods to enable low-power, stand-alone, inexpensive, and disposable instrumentation that can be directly integrated into microfluidic devices and perform automated sample-to-answer sequencing is seen as an obstacle to developing disposable test devices capable of performing complex multi-step nucleic acid, protein, and immunoassays from a sample-to-answer perspective.

[0006] Disposable tests that do not require instrumentation to run them are limited to: 1) simple, single-step assays that require only a liquid sample and no reagents (such tests typically include dipstick tests such as urine test strips or pregnancy tests), and 2) multi-step assays sold in kit form that include vials of reagents and instructions, with the user following the instructions to dispense the reagents into separate areas of a disposable test cartridge (such devices typically run immunoassays that do not require a sample preparation step).

[0007] Some examples of multi-step assay devices include, but are not limited to, Chembio Diagnostic Systems, Inc.'s DPP® HIV 1 / 2 assay, SURE CHECK® HIV 1 / 2, HIV 1 / 2 STAT-PAK®, and HIV 1 / 2 STAT-PAK® DIPSTICK tests. These tests require the user to manually perform a series of steps to complete the sequence. If the user is not trained or does not properly follow the instructions, there is a risk that the test will not be performed correctly, and therefore, results may vary depending on how the test is performed. Furthermore, there is a risk of contamination if the reagents are not fully contained within the device. Some harsh reagents, which are hazardous if not handled with proper lab protocols, gloves, and equipment (e.g., lab infrastructure such as fume hoods and enclosed biosafety facilities), cannot be implemented in such kit tests unless the test is performed by skilled technicians in an enclosed facility.

[0008] Unless a test is simple and automated, there is a risk that non-experts will not be able to perform it correctly. As test complexity increases beyond two or three steps, these manual, kit-based tests no longer achieve their usefulness. Advances in nucleic acid amplification assays (e.g., isothermal assays such as loop-mediated amplification) have reduced the instrumentation burden of heating / cooling thermal cycling by allowing these tests to maintain samples at a single temperature (typically 60–70°C). However, such tests still require users to perform multiple steps to complete the sample-to-answer sequence, which requires either a skilled operator or additional automated instrumentation.

[0009] Sample preparation is essential for many diagnostic assays that require the processing of biological samples. Biological samples typically undergo multiple complex processing steps to become suitable for use in an assay. These steps are necessary to isolate, concentrate, and / or purify the analyte of interest from the raw sample and to remove substances from the sample that may interfere with the desired assay. Sample processing steps often require strict conditions with respect to temperature, reagent volume, and incubation time, and must be performed in a strict sequence and in a tightly controlled environment, such as a laboratory environment. Traditional automated systems for sample processing require highly complex and expensive instrumentation and skilled operators. Because these systems are often located in centralized laboratories, raw samples must frequently be properly stored and transported to a separate laboratory for processing. These factors lead to several limitations, including high costs, slow results, and reduced sample integrity due to shipping and improper storage. Summary of the Invention [Problem to be solved by the invention]

[0010] The present invention provides methods and devices for simple, low-power, automated biological sample processing across multiple sample preparation and assay steps. The methods and devices described herein facilitate point-of-care performance of complex diagnostic assays in resource-poor, non-laboratory settings. [Means for solving the problem]

[0011] In accordance with the present invention, various embodiments of sample-to-answer microfluidic devices having magnetic and mechanical actuator elements with linear or rotary motion automation and methods of their use are disclosed. In one embodiment, a microfluidic device is provided, comprising: one or more cams including a camshaft and a cam lobe; one or more rocker arms; a microfluidic cartridge including one or more flow channels, one or more reaction chambers, and one or more burst pouches containing fluid and a frangible membrane seal; a cam mechanism configured to rotate the camshaft; The one or more cams are configured such that, upon rotation of the camshaft, the cam lobes actuate the one or more rocker arms, the one or more rocker arms being configured such that upon actuation, the rocker arms move from an open position to a closed position, applying pressure to the one or more burst pouches and rupturing the frangible membrane to release fluid into the one or more reaction chambers.

[0012] In some embodiments, the multiple cam lobes and rocker arms are configured such that, upon one complete rotation of the camshaft, the rocker arms apply pressure to the multiple burst pouches in a temporally and spatially controlled manner. In some embodiments, the one or more cam lobes and the one or more rocker arms are configured such that the rocker arms remain in a closed position after a frangible membrane seal of one or more burst pouches is breached. In some embodiments, the cam lobes are configured to remain in a closed position after the rockers rupture the pouches. In some embodiments, the microfluidic device further includes one or more diaphragm valves along one or more flow paths, the one or more cam lobes configured to open and / or close the one or more diaphragm valves as the camshaft rotates. In some embodiments, the camshaft is configured to rotate by a clockwork mechanism. In some embodiments, the microfluidic device further includes a sample preparation chamber, the sample preparation chamber including a DNA capture vehicle. In some embodiments, the rotational speed of the camshaft and the configuration of multiple cam lobes and multiple rocker arms allows multiple burst pouches to burst in a time-controlled manner to perform the wash steps of DNA purification.

[0013] In some embodiments, the microfluidic cartridge further includes an amplification chamber, a heat sink, and a heater, the heat sink and heater configured to intermittently cool or heat the amplification chamber upon actuation of the multiple cam lobes and multiple rocker arms. In some embodiments, the rotational speed of the cam shaft and the configuration of the multiple cam lobes and multiple rocker arms enable the heat sink and heater to intermittently cool or heat the amplification chamber in a time-controlled manner to perform PCR thermal cycling. In some embodiments, the microfluidic cartridge further includes a DNA hybridization chamber containing a DNA capture vehicle.

[0014] In another embodiment, a microfluidic device is provided that includes a microfluidic cartridge, comprising: a plurality of pre-filled reagent pouches; a reaction chamber; a camshaft, The camshaft includes multiple slots at multiple angular positions along the camshaft, whereby when the camshaft rotates to a predetermined position, one or more of the angular slots form a flow path between one or more of the reagent-filled pouches and the reaction chamber.

[0015] In another embodiment, a reagent dispensing device is provided comprising: a reagent pouch containing the reagent and a frangible seal; and an integrated magnetic element configured to collapse the reagent pouch and break the frangible seal when attracted to the magnetic field. In some embodiments, the magnetic element comprises a plunger. In some embodiments, the magnetic element comprises a bead. In some embodiments, the magnetic element comprises a sharp object.

[0016] In another embodiment, a microfluidic device is provided, comprising: a fluid conduit; a reaction chamber; a reagent dispensing device as described elsewhere herein; The reagent dispensing device is bonded to the microfluidic device such that an airtight seal is formed, and the reagent dispensing device is configured to empty the reagent into the reaction chamber via the fluid conduit upon breaching the frangible seal. In some embodiments, the microfluidic device further includes a trap, the trap including a free magnetic material and configured to hold the reagent pouch in a collapsed state.

[0017] In another embodiment, a microfluidic device is provided, comprising: a plurality of fluid chambers fluidly connected to one another via valves; a rotating shaft including permanent magnets arranged axially and radially around the circumference of the rotating shaft with alternating magnetic poles; Each of the fluid chambers contains a trapped permanent magnet whose direction of motion is restricted along a path perpendicular to the axis of the rotating shaft, and the rotating shaft and fluid chambers are configured such that, as the rotating shaft rotates, the permanent magnet moves to mix the fluids in each fluid chamber.

[0018] In another embodiment, a reagent pouch is provided that has a rupture point at a precise location in the frangible portion of the seal, and the reagent pouch includes a magnetic element constrained to a specific location on the reagent pouch that directly overlies the frangible portion of the seal.

[0019] In another embodiment, a microfluidic device is provided, comprising: one or more linear actuator elements; a microfluidic cassette; The one or more linear actuator elements include a fixed magnetic element for magnetic bead movement, a fixed magnetic element for fluid valve actuation, and / or a fixed magnetic element for reagent pouch rupture, and the microfluidic cassette includes a storage reagent pouch with an integrated magnetic plunger element, a reagent chamber for sample processing, a magnetic orbital rocker valve featuring a non-magnetic plunger that controls the movement of magnetic beads through the valve, and a magnetically controlled valve including a magnetic plunger that includes a fixed magnetic element for magnetic bead movement. In some embodiments, the one or more actuator elements are configured to slide under and / or over the microfluidic device. In some embodiments, the actuator element is moved by a method selected from the group consisting of a motor, a clockwork, a hand crank, a manual push, and a linear solenoid actuator.

[0020] In another embodiment, a microfluidic device is provided, comprising: one or more linear actuator elements; a microfluidic cassette; The one or more linear actuator elements include a combination of fixed and partially trapped magnetic elements, each contained in a respective trap, with each motion restricted to one axis or direction for magnetic bead movement, fluid valve actuation, and / or reagent pouch rupture. The microfluidic cassette includes a storage reagent pouch with an integrated magnetic plunger element, a sample processing reagent chamber, a magnetic orbital rocker valve featuring a non-magnetic plunger that controls magnetic bead movement through the valve, and a magnetically controlled valve including a magnetic plunger that includes a fixed magnetic element for magnetic bead movement. In some embodiments, the one or more actuator elements are configured to slide under and / or over the microfluidic device. In some embodiments, the actuator element is moved by a method selected from the group consisting of a motor, a clockwork, a hand crank, a manual push, and a linear solenoid actuator.

[0021] In another embodiment, a microfluidic device is provided that includes a reagent pouch aligned with a magnetic plunger element integrated into a reaction chamber, the magnetic plunger element configured to, when attracted by a magnetic field, break a frangible seal of the reagent pouch, enter the reagent pouch, and push a reagent within the reagent pouch into the reaction chamber. In some embodiments, the magnetic plunger element is located between the fluid inlet and the reagent pouch, and the magnetic element further includes a notch that acts as a guide to restrict fluid flow into the reaction chamber through the guide notch, the guide notch being configured to close fluid flow into the reaction chamber when the magnetic element plunger reaches its highest position.

[0022] In another embodiment, a microfluidic device is provided, comprising: an actuator element having a plurality of partially trapped magnetic elements housed within a rotatable shaft, the rotatable shaft configured to have a plurality of magnetic traps within a sleeve; a plurality of reagent dispensing devices as described elsewhere herein; a mixing chamber; and a mixing chamber magnet. In some embodiments, the microfluidic device further includes a stationary permanent magnet configured with both magnetic poles on the circumference of the rotatable shaft to attract and repel the mixing chamber magnet at high frequency as the shaft rotates. In some embodiments, the microfluidic device is configured such that as the rotatable shaft rotates, the first reagent dispenser aligns with the first partially trapped magnetic element, causing the first partially trapped magnet to move out of the rotatable shaft and into a first magnetic trap in the sleeve, thereby attracting the magnetic element and enabling it to breach the frangible seal of the pouch of the first reagent dispenser. In some embodiments, the microfluidic device is configured such that as the rotatable shaft continues to rotate, the second reagent dispenser aligns with the second partially trapped magnetic element, causing the second partially trapped magnet to move out of the rotatable shaft and into a second magnetic trap in the sleeve, thereby attracting the magnetic element and enabling it to breach the frangible seal of the pouch of the second reagent dispenser. In some embodiments, the microfluidic device is configured such that after dispensing of the stored reagents is complete, the rotating shaft can rotate at high RPM to effect mixing, by having a fixed permanent magnet within the shaft present alternating magnetic poles at high frequency to the mixing magnet.

[0023] In another embodiment, the system uses a mechanical device to ensure that the magnetic plunger element cannot return to its initial position after actuation, where the sleeve housing the magnetic plunger has at least one cantilevered ratchet element molded into its wall, where the magnet biases the ratchet in this position, but when the magnet is moved, the ratchet returns and prevents the magnetic plunger from returning to its initial position. In some embodiments, a spring-loaded ball is used instead of a ratchet.

[0024] In another embodiment, a sample processing system is provided that uses an actuator element including a magnet that moves on a track, attracting magnetic beads having biomolecules bound to their surface. As the magnet moves along the track, it drags the magnetic beads through the microfluidic chip. The path of the track passes through multiple reagent chambers, and the magnetic beads are moved through all of the reagent chambers at the appropriate time, until the magnet passes through a trap, e.g., a ball trap. In some embodiments, the magnetic element is mounted on a carriage that moves freely along a sliding rail. The entire sliding rail traverses the length of the microfluidic device by moving along a linear screw. In another embodiment of this system, a rack-and-pinion mechanism is used instead of a linear screw. In another embodiment, one or more magnets may be arranged on the track to perform multiple sample processing steps sequentially or simultaneously.

[0025] In another embodiment, a microfluidic device is provided that uses rotary actuator elements to automate sample processing sequences. Additionally, some sample processing device embodiments may use a combination of one or more rotary and linear actuator elements to control the x, y, z, and r axes, depending on the design and sample processing requirements.

[0026] In another embodiment, a magnetic plunger element valve is provided for controlling fluid flow in an exemplary microfluidic device. In some embodiments, a magnetic pivot rocker valve is provided that has a non-magnetic plunger element; for example, in such a valve, a rocker with a magnetic element pivots (or rotates) about its axis. When an external magnetic field enters the vicinity, the magnetic field attracts the magnetic element on the rocker, causing the plunger to push against the diaphragm valve, stopping the flow of fluid through the flow path. When the magnetic field is removed, the rocker returns to its original position, allowing flow through the flow path to resume.

[0027] In another embodiment, a diaphragm or pinch valve is provided on a microfluidic device that can be collapsed using a magnetic plunger element. When an external magnetic field comes into proximity with the magnetic plunger element, the magnetic field attracts the plunger, collapsing the diaphragm valve and stopping flow through the flow channel.

[0028] In another embodiment, permanent magnets are affixed axially and radially around the circumference of a rotating shaft with alternating polarity along the length of the rotating shaft. A fluidic device or fluid vessel has a second permanent magnetic material trapped therein, constraining its motion to one axis. When the rotating shaft is placed near the fluidic device or vessel, it exerts alternating attractive and repulsive forces on the permanent magnetic material within the vessel, resulting in a reciprocating shear motion within the fluidic device or vessel.

[0029] In another embodiment of the system, the magnetic plunger element is restricted to only be able to move in the direction necessary to squeeze the pouch of the reagent dispenser, to break the frangible seal, and to dispense the reagent through the fluid conduit into the microfluidic device.

[0030] In some embodiments, reaction chambers in a microfluidic device are designed to be compressible to move fluid from one reaction chamber to another.

[0031] In another embodiment, a microfluidic device for sample preparation for nucleic acid amplification testing is provided. The fluid wells are connected to one or more reagent dispensers containing miscible reagents by inlet fluid conduits located at the bottom of each fluid well. Each fluid well volume is designed so that it is only partially filled with miscible liquid reagents entering through the inlet fluid conduits. Once the fluid wells are filled, the reagent dispenser containing the immiscible liquid is actuated to dispense its contents through the main fluid conduit into the fluidic device, filling the main fluid conduit and the remaining volume of the fluid wells, forming a fluid pathway and simultaneously forming a barrier between the miscible liquids in the fluid wells, thereby preventing mixing of the miscible liquids.

[0032] In another embodiment, a microfluidic cartridge for magnetic bead sample preparation is provided, comprising fluid wells, fluid conduits, storage liquid reagent reservoirs, and valves. The microfluidic cartridge is sandwiched between upper and lower actuator elements, each containing a permanent magnet and a protrusion or projection. The permanent magnet and projection are spatially arranged to precisely time various steps in an assay automation sequence depending on the position and speed of the actuator elements as the microfluidic cartridge rotates adjacent to them. Possible assay steps include dispensing storage reagents into the fluid wells, opening and closing valves to control the direction of fluid flow, opening and closing vents, and capturing, resuspending, and moving magnetic beads between wells.

[0033] While certain aspects of the presently disclosed subject matter have been described above that are addressed in whole or in part by the presently disclosed subject matter, other aspects will become apparent as the following detailed description proceeds in conjunction with the accompanying examples and drawings.

[0034] Having generally described the subject matter of the present disclosure, reference is now made to the accompanying drawings, which are not necessarily drawn to scale. [Brief explanation of the drawings]

[0035] [Figure 1A] FIG. 1 is a side view of one embodiment of a sample-to-answer microfluidic device prior to actuation of the rocker arms. [Figure 1B] FIG. 10 is a side view of the embodiment of the sample-to-answer microfluidic device after actuation of the rocker arms. [Figure 2] FIG. 1 is a perspective view of an exemplary sample-to-answer microfluidic device. [Figure 3] FIG. 1 is a block diagram of an exemplary microfluidic device with sample analysis capabilities. [Figure 4] FIG. 1 is a top view of one embodiment of an exemplary microfluidic device using a rotating port design. [Figure 5] 5A and 5B are cross-sectional views of a reagent dispensing unit (RDU), where FIG. 5A shows a magnetic disruptive element within a reagent pouch, and FIG. 5B shows a sharp object rupturing a frangible seal within a microfluidic device. [Figure 6] FIG. 10 shows a reagent pouch that is burst by a magnetic element plunger. [Figure 7]

[0033] Figure 7A shows an embodiment of a rotating shaft magnetic mixing element. Figure 7A shows a rotating shaft with permanent magnets arranged axially and radially around the circumference of the rotating shaft with alternating poles. Figure 7B shows a multi-chamber fluid mixing system adjacent to the rotating shaft. [Figure 8] 1A and 1B are top and AA cross-sectional views of an exemplary RDU reagent pouch including a constrained magnetic rupture element for controlling the location of rupture of the frangible seal. [Figure 9] 9A and 9B show an exemplary microfluidic device for sample processing: Figure 9A is a top view of a linear actuator element, Figure 9B is an AA cross-sectional view of the linear actuator element, and Figure 9C is a top view of a microfluidic cassette. [Figure 10A] ~ [Figure 10F]1A-1C illustrate various steps in a sample processing sequence as an actuator element slides beneath a microfluidic cassette. [Figure 11A] ~ [Figure 11F] 1A-1C illustrate various embodiments of a linear actuator element. [Figure 12A] ~ [Figure 12D] FIG. 1 shows an example of a microfluidic sample processing device including an actuator element having a combination of fixed and partially trapped magnetic elements. [Figure 13] 13A and 13B are cross-sectional views of an exemplary microfluidic device, in which FIG. 13A shows a magnetic plunger element incorporated into a reaction chamber, and FIG. 13B shows how the magnetic plunger element is attracted by a magnetic field, breaking a frangible seal and forcing the contents of a reagent pouch into the reaction chamber. [Figure 14] 14A and 14B are cross-sectional views of an exemplary microfluidic device, in which FIG. 14A shows a notched magnetic plunger element incorporated into a reaction chamber, FIG. 14B shows how the notched magnetic plunger element is attracted to a magnetic field, breaking a frangible seal and forcing the contents of a reagent pouch into the reaction chamber, and FIG. 14C shows how the notched magnetic plunger element closes the inlet port of the fluid conduit after the reagent in the reagent pouch has been dispensed, and a ratchet element mechanically holds the magnetic plunger element in a permanently sealed position even when the external magnetic field is removed. [Figure 15] FIG. 1 illustrates an embodiment of a sample processing system including a rotating shaft actuator element with a partially trapped magnetic element and a fixed magnetic element housed within the rotating shaft. [Figure 16A] ~ [Figure 16D] 1A-1C illustrate various steps in a sample processing sequence as a rotating shaft actuator element rotates relative to a microfluidic device. [Figure 17A] ~ [Figure 17B]10A-10C illustrate another non-limiting embodiment of mechanically holding a magnetic plunger element in a permanently sealed position even in the absence of an external magnetic field. [Figure 18A] ~ [Figure 18B] FIG. 1 illustrates an embodiment of a sample processing system that includes an actuator element that includes a magnet that moves on a track. [Figure 19A] ~ [Figure 19C] 1A-1C illustrate various embodiments of a rotary actuator element. [Figure 20] 20A and 20B show an exemplary magnetic swing rocker valve with a non-magnetic plunger element. Figures 20A and 20B are top views of two non-limiting embodiments of swing rocker valve geometries. Figure 20C shows how the rocker is actuated by a magnetic field, causing the non-magnetic plunger to depress the diaphragm valve and stop flow. [Figure 21] 21A and 21B show a diaphragm or pinch valve with an integrated magnetic plunger element, in which Fig. 21A shows the valve in an open state when no magnetic field "M" is in the vicinity of the valve, and Fig. 21B shows the valve in a closed state when a magnetic field "M" is in the vicinity of the valve. [Figure 22] 22A and 22B show an RDU that squeezes reagent from a reagent pouch using the sliding and rolling motion of a magnetic plunger element. 22A shows a sliding planar magnetic element. 22B shows a rolling cylinder magnetic element. 22C and 22D show emptying of the reagent pouch. [Figure 23A] ~ [Figure 23D] 1A and 1B show a top view and an AA cross-sectional view of an actuator element, a top view and a BB cross-sectional view of a microfluidic cassette with a throttle element, and the process in which the throttle element is dragged by a linear actuator element to push fluid into the next reaction chamber. [Figure 24] FIG. 1 shows a schematic diagram of the fluid well configuration and the principle of dispensing stored reagents to form an oil-water fluid circuit. [Figure 25A] ~ [Figure 25C]FIG. 1 shows a schematic of an exemplary microfluidic cartridge for magnetic bead-based sample preparation, including fluid wells, fluid conduits, storage liquid reagent reservoirs, and valves. [Figure 26B] FIG. 1 illustrates the principle of magnetic bead sample preparation in an exemplary microfluidic device that integrates upper and lower rotary actuator elements containing fixed permanent magnets. [Figure 26A] ~ [Figure 26I] 10A-10C show various steps in the position of a microfluidic cartridge relative to an actuator element to demonstrate the principle of magnetic bead capture, resuspension, and transfer between fluidic wells by linear actuation. [Figure 27A] ~ [Figure 27G]

[0023] Figure 1 is a cross-sectional view of a microfluidic device with upper and lower actuator elements, illustrating the principle of sample preparation with magnetic beads in a microfluidic device. The microfluidic device contains fluid wells connected to each other via an oil phase. The upper and lower actuator elements contain electromagnets that can be turned on or off in a predetermined sequence. The microfluidic device moves between the two actuator elements. [Figure 28] 1 is a perspective view of a microfluidic device showing a microfluidic cartridge and an actuator element, the microfluidic cartridge sliding between the actuator element. [Figure 29A] ~ [Figure 29E] FIG. 1 illustrates the principle of using protrusions in fluid wells of a microfluidic device as baffles to constrain magnetic beads to the wells as the magnet continues to move along its motion path. [Figure 30A] ~ [Figure 30B] FIG. 1 illustrates the principle of using an actuated lancet to transfer fluid from a fluid well on a microfluidic device to a lateral flow strip. DETAILED DESCRIPTION OF THE INVENTION

[0036] The presently disclosed subject matter will now be described more particularly with reference to the accompanying drawings, in which some, but not all, embodiments of the presently disclosed subject matter are shown. Like reference numerals refer to like elements throughout. The presently disclosed subject matter may be embodied in a variety of forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Indeed, various modifications and other embodiments of the presently disclosed subject matter described herein will come to mind to one skilled in the art to which the presently disclosed subject matter pertains and having the benefit of the teachings presented in the foregoing descriptions and associated drawings. It is therefore to be understood that the presently disclosed subject matter is not limited to the particular embodiments disclosed, and that modifications and other embodiments are intended to be included within the scope of the appended claims. Sample-to-answer microfluidic device with magnetic and mechanical actuator elements for automating linear or rotational motion and methods of use thereof

[0037] The disclosed inventions include methods and integrated devices for sample-to-answer automation using simple, low-cost, and low-power instrumentation. In one embodiment, a lab-on-a-chip microfluidic system and related methods are provided in which multiple steps are performed in a precise sequence, with all automation integrated within one camshaft revolution. In one exemplary embodiment, pressure is applied to rupture frangible seals in pre-filled reagent pouches stored in a cartridge, enabling a fluid manipulation sequence that includes timed reagent delivery. In one embodiment, temperature management is also possible; for example, during polymerase chain reaction (PCR), a cam mechanism can be used to actuate heat sink contacts to control sample temperature and reduce overall time to results.

[0038] Camshafts operate like clockwork to perform tasks such as operating an engine by opening and closing multiple valves in precise sequences. When applied to an LOC, the present invention allows a single camshaft to perform all of the actuation and automation steps necessary to complete a sample-to-answer diagnostic test.

[0039] Therefore, the only actuation required is one full rotation of the camshaft. Furthermore, the present invention also enables a self-contained microfluidic cartridge that includes pre-PCR and post-PCR modules, or several downstream assay processes, on a single platform in one embodiment.

[0040] Additionally, the rotating camshaft may be self-powered by a mainspring, which allows for completely battery-free automation on, for example, an LOC device.

[0041] Because diagnostic devices in low-resource environments must generally be battery-powered, the present invention allows point-of-care technology to move one step closer to being completely powerless. By incorporating a rotating camshaft, point-of-care diagnostics is improved by several factors, including reduced device size, power consumption, cost, and complexity, to name a few.

[0042] A microfluidic cartridge according to one embodiment of the present invention can utilize the modularity of microfluidics to enable the integration of pre-PCR and post-PCR processing steps on a single platform. The system may also be more versatile because PCR-based DNA amplification and further downstream processing (e.g., DNA hybridization arrays) can be integrated on the same chip. As a result, a single sample can be easily screened for multiple pathogens.

[0043] Various aspects of the present invention may be applicable to a variety of other devices. For example, the present invention may be used to essentially automate sample-to-answer bioassays on lab-on-a-chip devices. Another possible application may be protein assays.

[0044] Other advantages of the present invention over prior existing technology include: 1) Control of all actuation steps for fluidic, thermal, and electrical management on a single camshaft; 2) Extremely simple design, low manufacturing cost, low power, and one motor or spring controlling the actuation sequence; 3) Ability to integrate multiple downstream assay processes on a single self-contained platform using microfluidic cartridge and camshaft technology; and 4) The self-contained cartridge allows for the "Lego" block" addition of additional modules for downstream processing that can operate in lockstep with the rotating camshaft actuator, enabling tight automation on the device.

[0045] Thus, various aspects of the present invention enable a device comprised of a disposable, self-contained microfluidic cartridge featuring a reagent-filled blister pouch and a complementary camshaft that completes all of the individual actuation and automation steps of a sample-to-answer sequence in a single revolution. The camshaft essentially acts as a mechanical "program" for the entire sample-to-answer automation process. When the camshaft is used in conjunction with a rocker arm, the rocker arm can act like an actuation plunger. As the camshaft rotates, the rocker contacts the blister pouch and applies the force necessary to rupture the frangible seal. This concept is illustrated in Figure 1. Using this concept, a single camshaft actuator can perform one or more of the following essential tasks: 1) rupture the frangible seal of an on-chip reagent-filled blister pack to release its contents; 2) actuate on-chip diaphragm valves to control fluid delivery on the microfluidic chip; and 3) release controlled amounts of reagents spatially and temporally into reaction chambers. 4) Actuating cooling elements for rapid thermal cycling on microfluidic chips, 5) Actuating permanent magnets to move magnetic beads from one location to another, and 6) Actuating electrical contacts for readout.

[0046] Alternative non-limiting embodiments include: 1) using a mainspring to power a camshaft; 2) using a camshaft actuator used to automate the movement of the syringe plunger to dispense reagents in an automated sequence; and 3) using a horizontal or vertical design.

[0047] Each of the features described herein may enable 3D spatial and temporal control of fluid manipulation / management, temperature management, and electrical management with a single actuation mechanism, with the motion sequence encoded by the alignment and orientation of the cam lobes.

[0048] Some embodiments may also include rockerless cams, pinned cams, gears, clockwork, springs, piano hammer action, or any other mechanical variation that may be capable of automating the sample-to-answer sequence.

[0049] In one embodiment, a cam mechanism may be used to actuate the functionalized electrodes to move from one sample to another.

[0050] 1A and 1B, side views of an exemplary microfluidic device 101 are shown, respectively, before and after actuation of a rocker arm 109. The microfluidic device 101 includes a cam 102 having a camshaft 103 and a cam lobe 104. A microfluidic cartridge 105 is also shown, which includes at least one on-chip burst pouch or blister pouch 106 and a reaction chamber 107. The burst pouch or blister pouch 107 is filled with a fluid, such as a reagent, and upon rupture, dispenses the fluid. These burst pouches or blister pouches 106 can be manufactured in large batches, thereby reducing manufacturing costs. When manufactured specifically for microfluidic applications, the fluid volumes they contain range from 15 μL to 450 μL. The blister pouches 106 typically include a frangible membrane seal at the pouch's outlet. The frangible membrane generally requires the intentional application of pressure to break the seal and release the contents.

[0051] When the cam mechanism 102 is rotated by the camshaft 103, the cam lobe 104 actuates the rocker 109, which exerts pressure on the burst pouch 107 and ruptures the frangible membrane.

[0052] As shown in FIG. 2 , multiple cams 202 may be mounted on a camshaft 203. Each cam 202 has a cam lobe 204 with a spatial topography that actuates a rocker arm at various times and intervals. As the camshaft 203 rotates, the cam lobe 204 pushes against a rocker arm 209, which in turn exerts pressure on a burst pouch or blister pouch 206, expelling its contents. By arranging multiple cams 202 on the camshaft 203, it is possible to control the reaction spatially and temporally. The rocker arm 209 or rocker mechanism acts like a plunger, depressing the blister pouch 206 with sufficient pressure to rupture its frangible membrane seal. Multiple burst pouches containing various reagents may be spatially assembled on a microfluidic cartridge, for example, as shown in FIG. 2 .

[0053] During one complete rotation of the camshaft 203, each cam lobe 204 lifts and engages with a respective rocker 209, spatially and temporally controlling the release of reagent stored in each blister pouch 206 on the microfluidic cartridge 205. The cam lobes 204 are designed so that the rockers remain in a closed position after the pouch is ruptured. This can act as a check valve to prevent reagent from flowing back into a ruptured pouch. The cam lobes 204 may also be used to achieve fluid flow control in a channel by opening or closing a diaphragm valve along the flow path.

[0054] As generally described above, multiple cam and rocker mechanisms are shown in Figure 2. Each cam 202 and rocker 209 mechanism corresponds to a particular blister pouch 206. When the cam and rocker mechanisms are actuated at appropriate intervals, various reagents are released from each blister pouch, through respective channels 208 formed on the microfluidic cartridge 205, and into respective reaction chambers 207 also formed on the microfluidic cartridge 205.

[0055] The rotating camshaft may be self-powered by a clockwork mechanism. This allows for fully power-free automation on LOC devices, where the user can essentially obtain automated diagnostic results by turning a key. Because diagnostic devices in low-resource environments must be battery-powered, this innovation brings point-of-care technology one step closer to being fully power-free.

[0056] Referring now to FIG. 3, a conceptual block diagram of an exemplary sample-to-answer system 301 for PCR and DNA hybridization is shown. In this example, multiple cams 302 are supported by a camshaft 303. Each cam 302 has a cam lobe 304, which acts to actuate a rocker 309. A microfluidic cartridge 305 is provided with multiple burst pouches 306 (in this example, lysis buffer, wash buffer, and elution buffer), various reaction chambers 307, a waste chamber 313, and various channels 308 connecting each fluid to its respective chamber 307, 313. Additionally, valves 310 are provided between specific chambers 307, 313 and the burst pouches 306 to prevent backflow of fluids and possible contamination.

[0057] In this example, the sample is first loaded into chamber 307 (sample preparation), which may contain a DNA capture vehicle, such as silica beads, FTA paper, or magnetic beads. During the sample preparation phase, camshaft 303 rotates, causing cam lobes 304 to actuate corresponding rockers into the "closed" position, bursting burst pouches containing (in this example) lysis buffer and releasing the lysis buffer into sample preparation chamber 307. The camshaft rotation speed and lobe size can be varied to control the timing of each reaction phase. Other rockers sequentially enter the closed position, bursting their respective pouches and releasing wash buffer 306 into sample preparation chamber 307, for example, for the wash phase of DNA purification.

[0058] During PCR thermal cycling, a thermal sink or heat sink 311 can be intermittently actuated by its corresponding rocker to contact and cool the amplification chamber. A particularly time-consuming step is lowering the sample temperature during PCR thermal cycling. The use of an actuated heat sink can significantly reduce the time it takes to complete each PCR cycle, since contact occurs only during the cooling phase. Thus, a single rotation of the camshaft, as shown in this example, can achieve full automation of sample-to-answer sequencing.

[0059] A heat sink 311 may also be provided on the microfluidic cartridge, for example, to provide intermittent contact with the reaction chambers 307 in a precise sequence dictated by a cam mechanism and / or rotational speed during PCR cycling. First-order heat and mass transfer calculations estimated that the time required to cool a sample from 95°C to 65°C was approximately 7 times faster. This time reduction was achieved with a 1-inch x 1-inch x 0.5-inch aluminum block heat sink at an ambient temperature of 25°C. For example, if the required cooling time without a heat sink was 30 seconds per cycle and 25 cycles were used, this would result in a time savings of 12.5 minutes over the entire PCR process. This provides a significant advantage, for example, in temperature management during fluidic manipulations. A heater 312 is also shown on the microfluidic cartridge 305 in this illustration.

[0060] Referring now to FIG. 4, a top view of an exemplary sample-to-answer microfluidic device design incorporating a rotating port is shown. As shown in FIG. 4, the exemplary microfluidic device 401 incorporates a camshaft 403 as part of a microfluidic cartridge 405. In this embodiment, the cartridge camshaft 403 is coupled to an actuation mechanism while rotating. This system allows for the design and construction of unique camshafts for each of a variety of assays. An alternative approach is to construct a standard camshaft module mount and develop unique camshaft modules for each of a variety of assays.

[0061] The exemplary system of Figure 4 uses a precision-cut slot 414 located at a predetermined angular position along the shaft 403. When rotated to the predetermined angular position, the slot 414 creates a flow path 408 between the reagent-filled pouch 406 and the reaction chamber 407. Flow pressure can be generated by depressing the reagent-filled pouch 406. The rotating port can also be a simple valve.

[0062] The microfluidic cartridge may be designed without a PCR amplification chamber. In this case, the cartridge may include a DNA hybridization chamber for analyte detection without target amplification. This design may be particularly useful for sample-to-answer high-throughput screening through a DNA hybridization array using powerful single-molecule detectors (e.g., total internal reflection fluorescence (TIRF) microscopes or single-photon avalanche diode (SPAD) array detectors).

[0063] Additionally, in some embodiments, the present invention combines magnetic actuation with mechanical automation to complete sample-to-answer sequences on microfluidic devices. The device actuation methods and various embodiments described herein can be used to dispense reagents from fluid conduits into a fluidic device, open or close valves, cause agitation and mixing within a fluidic chip, turn electrical circuits on or off, or make electrical connections within a fluidic chamber.

[0064] The fluidic device comprises a reagent pouch that dispenses reagents necessary for biological sample processing on the microfluidic device. Examples of pouch reagents include, but are not limited to, buffers, salts, acids, bases, labels, tags, markers, water, alcohols, solvents, waxes, oils, gases, gels, etc. When sufficient pressure is applied to the pouch, it ruptures, thereby dispensing the pouch contents into the fluid conduits leading to their respective intended reaction chambers. The pouches are designed with frangible seals aligned with the inlets of the fluid conduits so that upon rupture, the pouch contents are forced out and into the fluid conduits leading to the reaction chambers.

[0065] The magnet can attract a magnetic element, which can be either another magnet, an electromagnet, or a ferromagnetic material. The following describes a novel method and device for applying a bursting pressure to empty a reagent pouch. This device is called a Reagent Dispensing Unit (RDU). The RDU consists of a reagent pouch containing a stored reagent and an integrated magnetic element, which can be either a permanent magnet or a ferromagnetic material. When the magnetic element is attracted to a magnetic field that comes into its vicinity, it moves toward the field and acts like a plunger that indents the reagent pouch, rupturing it and discharging its contents into the fluidic tip, according to one non-limiting embodiment described herein. The plunger's movement is limited to allow it to efficiently empty the blister, and this limitation is achieved by designing a guide for the plunger's movement.

[0066] 5 shows a cross-sectional view of an RDU on a microfluidic device. In this example, the RDU is adhered to the microfluidic device 511 with adhesive 512 so as to form an airtight seal with the microfluidic device 511. The RDU has an integrated magnetic element plunger 503 on a reagent pouch 505. The reagent pouch contains a stored reagent 514 and is sealed with a frangible sealing layer 506. The magnetic element plunger is held in place by being encased in a sheath 502 such that its movement is restricted.

[0067] In some embodiments, the reagent-filled pouch contains a small bead or sharp object 504 that makes the frangible seal susceptible to breaking under the influence of a magnetic field 509. The object is made of a magnetic material and ruptures the frangible seal when attracted to the magnetic field. In another embodiment, as shown in Figure 5B, a sharp object 513 fixed to the inlet of the fluidic device pushes against the frangible seal of the reagent pouch, causing it to rupture.

[0068] In some embodiments, as seen in FIG. 5 , a trap 510 on the microfluidic device 511 can permanently deploy and hold loose magnetic material in place beneath the reagent pouch, keeping the pouch collapsed. Such a system acts like a one-time valve, keeping the reagent pouch collapsed and completely preventing backflow from the reaction chamber into the reagent pouch. In another embodiment, as seen in FIG. 6 , the frangible seal is designed to burst under a certain pressure. A magnetic plunger is attracted to a magnetic field, providing the burst pressure and deformation necessary to break the frangible seal. A magnetic plunger located above the reagent pouch is simultaneously attracted to this same magnetic field, deforming the ruptured pouch and forcing the stored reagent through fluid conduit 607 and into reaction chamber 608.

[0069] In applications where large sample volumes must be mixed, lysed, or homogenized, the fluid may be divided into multiple, separate, smaller chambers that are fluidly connected to one another, each containing its own trapped permanent magnet. Figure 7A shows a rotating shaft 705 containing permanent magnets arranged axially and radially around the circumference of the rotating shaft with alternating magnetic poles 706. Figure 7B shows a multi-chamber fluid mixing system in which multiple fluid chambers 704 are connected to one another by valves 702 and can handle various sample volumes. Each chamber contains a permanent magnet 703 whose direction of motion is restricted to a path perpendicular to the axis of the rotating shaft.

[0070] 8, the reagent pouch is designed so that the rupture point can occur at a defined location. This is achieved by designing the reagent pouch such that it includes a magnetic element 804 that is constrained to a specific location 805 on the reagent pouch, such that the magnetic element 804 is directly over a frangible portion 806 of the sealant 802.

[0071] Although the sample processing methods described herein are capable of performing multiple processes with a single actuation motion, for purposes of describing actuation control on a microfluidic device, this specification describes a simplified example in which a single linear actuator element controls multiple sample processing steps, specifically three sample processing steps: 1) rupturing a reagent pouch to release stored reagents, 2) moving magnetic beads between chambers, and 3) opening and closing fluidic valves.

[0072] Other processes that can be incorporated into the same actuation control element include, but are not limited to, opening and closing electrical connections within a fluid chamber, pressing a push button switch to control an electrical circuit on and off, puncturing a vacutainer, opening and closing a vent, actuating a heating element or heat sink, etc. A significant advantage of such a system is the ability to add additional steps with minimal system complexity. 9A, 9B, and 9C, a top view and cross section AA of an exemplary microfluidic device 901 for sample processing includes a linear actuator element 903 and a microfluidic cassette 908. The linear actuator element 903 includes a fixed magnetic element 904 for magnetic bead movement, a fixed magnetic element 905 for fluid valve actuation, and a fixed magnetic element 902 for reagent pouch rupture. The microfluidic cassette 908 includes a storage reagent pouch 907 with an integrated magnetic plunger element, a sample processing reagent chamber 906, a magnetic orbital rocker valve 909 featuring a non-magnetic plunger that controls the movement of magnetic beads through the valve, and a magnetically controlled valve 910 that includes a magnetic plunger. The actuator element 903 is in close proximity to the microfluidic cassette 908 and slides relative to the microfluidic cassette 908. In this exemplary embodiment, the actuator element 903 slides underneath the microfluidic cassette 908, however, in another embodiment, the microfluidic device 901 is designed so that the actuator element 903 slides on top.

[0073] Additionally, the actuator element may include an upper element and a lower element that move together in the same direction or move separately in different directions, and whose movement results in multiple actuation steps of sample processing being performed in a predetermined sequence.

[0074] Figures 10A, 10B, 10C, 10D, 10E, and 10F show various stages of the sample processing sequence as the actuator element slides under the microfluidic cassette. Possible methods for actuating the sliding motion include a motor, a spring, a hand crank, a manual push, and a linear solenoid actuator. The shapes of the fixed magnetic elements 1004, 1005, and 1002 on the sliding actuator element 1003 are determined so that the actuation state (on / off, open / closed, up / down) of the fluidic elements on the microfluidic cassette is controlled by the shape of the fixed magnetic elements on the sliding actuator element. In the first stage of Figure 10A, the fixed magnet on the sliding actuator element overlaps and closes the magnetic rotary rocker valve 1009, which features a non-magnetic plunger. As the actuator element continues to slide, in the second stage of Figure 10B, the fixed magnetic element indents the storage reagent pouch, releasing its contents into the reaction chamber. At the same time, the magnetic swing rocker valve 1009, featuring a non-magnetic plunger, remains closed, thereby storing the storage reagent in the reaction chamber. As the actuator element continues to slide, the second fixed magnetic element overlaps the second storage reagent pouch, rupturing it and releasing its contents into the same reaction chamber, in a third step in FIG. 10C. The magnetic swing rocker valve 1009, featuring a non-magnetic plunger, remains closed. In a fourth step in FIG. 10D, the magnetic element overlaps the reaction chamber containing the magnetic beads and begins to attract the magnetic beads through the fluid conduit and into the second reaction chamber. In this same step, the third reagent pouch ruptures, releasing its contents into the second reaction chamber. As the actuator element continues to slide, at step 5 in Figure 10E, the fixed magnetic element no longer overlaps the magnetic rotary rocker valve 1009, which features a non-magnetic plunger, causing that valve to go to the "off" state, opening the fluid conduit and allowing the magnetic beads to pass through to the second reaction chamber. Finally, at step 6 in Figure 10F, the magnetic beads are transferred to the second reaction chamber while the fixed magnetic element overlaps and closes the valves leading to and from the second chamber, thereby storing the magnetic beads in the second reaction chamber.

[0075] This embodiment provides an example of how multiple sample processing steps can be controlled by a single actuator element. This system preferably uses permanent magnets, such as neodymium magnets, to complete the actuation steps, minimizing the actuation control power used in the resulting device. However, it is also possible to automate sample processing steps using a combination of electromagnets and permanent magnets.

[0076] For further control, some embodiments may utilize multiple actuator elements that are actuated in different directions at different speeds. Some non-limiting embodiments of linear actuator elements are shown in Figures 11A-11F.

[0077] Another embodiment of the actuator element is shown in Figures 12A, 12B, 12C, and 12D. This would include a combination of fixed and partially trapped magnetic elements 1212, housed in respective traps 1211, thereby restricting their movement to one axis / direction. The partially trapped magnetic elements could function to become irreversibly attached and trapped in the magnetic trap 510 shown in Figure 5A, even as the sliding actuator element continues to advance. This embodiment is useful when it is desirable to permanently close a valve, such as to keep a reagent pouch recessed to prevent backflow during subsequent sample processing steps.

[0078] Figure 12B is cross section AA of the actuator element showing the partially trapped magnetic element 1212 housed in a blind hole, with its motion restricted to a direction perpendicular to the surface of the microfluidic cassette 1208. Figure 12D shows a particular process of sliding the actuator element, in which the partially trapped magnet is detached from the actuator element and permanently attached to the magnetic trap 110 located below the reagent pouch. In this embodiment, the reagent pouch is permanently indented by the partially trapped magnetic element 1212 even as the sliding actuator element continues to advance.

[0079] Another exemplary method of dispensing reagent into a fluid chamber is shown in Figures 13A and 13B, where a magnetic plunger element 1303 is incorporated into a reaction chamber 1304 and aligned with a reagent pouch 1302. When the magnetic plunger element is attracted by a magnetic field 1305, it breaks the frangible seal of the reagent pouch, enters the reagent pouch, and forces the reagent 1306 into the reaction chamber.

[0080] In another embodiment, shown in FIG. 14, the reaction chamber is located away from the fluid inlet, and the magnetic plunger element is located between the inlet and the reagent pouch. There is a notch 1403 on the magnetic element, which acts as a guide to restrict fluid flow into the reaction chamber through the guide notch. The guide notch is designed so that when the magnetic element plunger reaches its highest position, the inlet through the fluid conduit to the reaction chamber is closed, as shown in FIG. 14C. There is a ratchet element 1402 inside the fluidic device, which permanently holds the magnetic element plunger in a sealed position.

[0081] Another embodiment of a sample processing system is shown in Figure 15, which shows an actuator element with a partially trapped magnetic element 1502 housed inside a rotating shaft 1503. The rotating shaft is assembled into a sleeve 1504 with a magnetic trap 1505. The sleeve is assembled to a microfluidic device 1506, which includes an RDU 1507, a mixing chamber 1508, and a mixing chamber magnet 1509. A stationary permanent magnet 1510 is arranged with both poles on the circumference of the rotating shaft, and as the shaft rotates, the mixing chamber magnet is attracted and repelled by this magnet at high frequencies.

[0082] FIG. 16A shows the rotatable shaft assembled into the sleeve. Both partially trapped magnets are offset from the RDUs. FIG. 16B shows the rotatable shaft rotated to an angle where the first RDU overlaps with the first partially trapped magnetic element. This moves the partially trapped magnet out of the rotatable shaft and into the sleeve's magnetic trap. This also attracts the magnetic element on the first RDU, rupturing the pouch's frangible seal and expelling its constituent reagents into the lysis chamber. FIG. 16C shows the next rotation of the shaft where the second partially trapped magnet overlaps with the second RDU, causing this RDU to also expel its constituents into the mixing chamber.

[0083] After dispensing of the stock reagents is complete, the rotating shaft is rotated at high RPM to effect mixing, as shown in Figure 16D. This causes a stationary permanent magnet within the shaft to present alternating magnetic poles to the mixing magnet at a high frequency, thus causing mixing within the mixing chamber by high frequency attraction and repulsion.

[0084] Referring to FIG. 17, another embodiment of the system is shown, in which a mechanical device ensures that the magnetic plunger element cannot return to its initial position after actuation. This embodiment is advantageous when an element, such as a reagent pouch or valve, must remain retracted until the end of the sample processing sequence. FIG. 17A shows the magnet in its initial position. The sleeve housing the magnet has at least one cantilevered ratchet element molded into its wall. The magnet biases the ratchet in this position. When the magnet is moved, as shown in FIG. 17B, the ratchet returns, preventing the magnet from descending back to its initial position. FIG. 17C shows another embodiment of this mechanism, with a spring-loaded ball. This ball works similarly to the ratchet described above; while the magnetic force pulls the magnet toward the ball, it is biased by the side of the magnet. However, when the magnetic field is removed, the edge of the magnet cannot push the spring-loaded ball back.

[0085] Referring to Figure 18, a unique embodiment of a sample processing system is shown that uses an actuator element including a magnet 1802 that moves on a track 1803. The magnet attracts magnetic beads that have biomolecules bound to their surface. As the magnet moves along the track, it drags the magnetic beads through a microfluidic chip 1804. The path of the track passes through reagent chambers R1 to R4 in Figure 18. The magnetic beads are moved through all of the reagent chambers at the appropriate time. Finally, the magnet passes through the end of the trap, i.e., ball trap 1805.

[0086] Figure 18B shows the mechanism by which the magnet moves on the track. The magnetic element is mounted on a carriage 1807, which moves freely along a sliding rail 1806. The entire sliding rail traverses the length of the microfluidic device by moving along a linear screw 1808. In another embodiment of this system, a rack and pinion mechanism is used instead of the linear screw. As the sliding rail traverses the length of the chip, the magnet on the carriage rides on the track.

[0087] In another embodiment, one or more magnets may be arranged on a track to perform multiple sample processing steps sequentially or simultaneously. In this embodiment, the magnets are shown sliding on the track, but it is also possible for the magnets to be fixed on the track path of a moving conveyor belt.

[0088] While the above-described embodiments demonstrate the automation of sample processing using linear actuator elements, rotary elements also have their advantages. Figures 19A, 19B, and 19C show embodiments of microfluidic devices that use rotary actuator elements to automate sample processing sequences.

[0089] Additionally, some sample processing device embodiments may use a combination of one or more rotary and linear actuator elements depending on the design and sample processing requirements for controlling the x, y, z, and r axes.

[0090] The following describes an embodiment of a magnetic plunger element valve for controlling fluid flow in an exemplary microfluidic device. In this embodiment, an exemplary magnetic swing rocker valve with a non-magnetic plunger element is described. FIGS. 20A and 20B show top views of two non-limiting embodiments of swing rocker valve geometries that can be used as valves in microfluidic devices. In such valves, a rocker 2003 with a magnetic element 2005 swings (or rotates) about its axis 2006. When an external magnetic field 2004 enters the vicinity, the field attracts the magnetic element on the rocker. This causes the plunger 2002 to push against the diaphragm valve from above, stopping the flow of fluid through the flow channel. In the process shown in FIG. 20C, the rocker is actuated by the magnetic field, causing the non-magnetic plunger to depress the diaphragm valve, stopping the flow. When the magnetic field is removed, the rocker returns to its original position, allowing flow through the flow channel to resume.

[0091] Referring to Figure 21, on a microfluidic device, a magnetic plunger element, designated 2101, can be used to depress a diaphragm or pinch valve. In the process shown in Figure 21A, the flow path is open. The magnetic plunger element 2102 can be seen above the diaphragm 2103. When an external magnetic field comes into proximity with the magnetic plunger element, the field attracts the plunger, causing the diaphragm valve to depress and stop flow in the flow path. This is shown in Figure 21B.

[0092] The application of permanent magnets affixed to a rotating shaft enables the mixing, homogenization, and / or mechanical disruption of biological samples, such as, but not limited to, cells and viruses. In one exemplary embodiment, permanent magnets are affixed axially and radially around the circumference of the rotating shaft, alternating polarity along the length of the rotating shaft. A fluidic device or fluid container has a second permanent magnetic material trapped therein, significantly restricting its motion to one axis. When the rotating shaft is placed near the fluidic device or fluid container, it exerts alternating attractive and repulsive forces on the permanent magnetic material within the container, resulting in a reciprocating shear motion within the fluidic device or fluid container. This effect can be used to mix, homogenize, and lyse biological samples, such as cells and viruses. In this embodiment, the fluid container houses at least one permanent magnet, the motion of which is restricted to a direction perpendicular to the shaft's rotational axis. The frequency of the alternating magnetic field is determined by the rotational speed of the shaft and the radial spatial distribution of the permanent magnet's magnetic poles.

[0093] In other embodiments, the magnet in the fluidic device / fluid vessel may be restricted to reciprocating motion in another direction (e.g., parallel to the axis of the rotating shaft). Furthermore, it may be advantageous to not restrict the magnet's motion at all. In some embodiments, particles (e.g., beads made of glass, silica, polymer, metal, or a combination thereof) may be disposed inside the vessel, and these particles will assist in the mechanical disruption of the biological sample (e.g., cells, viruses, etc.) within the fluid vessel. In one embodiment, the permanent magnet may be in direct contact with the fluid within the fluid chamber, while in another embodiment, the permanent magnet may be in close proximity to the fluid chamber, separated by an impermeable layer within a separate chamber that is close enough to induce vibrations or forced vortices within the fluid chamber. The advantage of such a system compared to using electromagnets with alternating / switching polarity is that it allows a single actuator rotating element (motor shaft) to induce lysis, homogenization, and mixing in multiple fluid chambers or vessels spaced along the length of the rotating shaft.

[0094] In another embodiment of the system, it would be ideal to squeeze the reagent from the reagent pouch on the RDU. This would be particularly advantageous if more control over the reagent flow rate is needed. FIG. 22 shows a cross-sectional view of such an embodiment. In this embodiment, the magnetic plunger element 2203 is constrained to move only in the direction necessary to squeeze the pouch, rupture the frangible seal 2202, and dispense the reagent through the fluid conduit into the microfluidic device. In some embodiments, the magnetic plunger element can be a flat-bottomed plane, as shown in FIG. 22A. In other embodiments, the magnetic plunger element can be a cylinder that provides a rolling action. FIGS. 22B, 22C, and 22D show the magnetic plunger element 2203 on the RDU actuated by a partially trapped cylinder magnet on an actuator element of the microfluidic device, resulting in squeezing the reagent pouch and rupturing the frangible seal, allowing a steady flow of reagent into a chamber on the microfluidic device.

[0095] Fluids can be moved from one reaction chamber of a microfluidic device to another by using an air-filled pouch to force the fluid. In some embodiments, if the reaction chambers of a microfluidic device are designed to be compressible, the embodiment shown in FIG. 22 can be used to move fluid from one reaction chamber to another. As in the reagent-filled case, the air-filled pouch can be ruptured to force the reagent out of the chamber, but in some embodiments, this step can be performed using the squeezing mechanism shown in FIG. 22. FIG. 23 shows the microfluidic device described above, but now the reaction chambers are designed to be squeezed and compressed to a flat, planar state. FIG. 23A shows a top view and cross-section AA of an actuator element including a partially immobilized magnetic roller for squeezing reagent out of the pouch. FIG. 23B shows a top view and cross-section BB of a reaction pouch with a partially trapped magnetic roller adjacent to the reaction chamber. FIGS. 23C and 23D show how, as the linear actuator element moves, the reaction chamber is squeezed by the magnetic roll element to dispense its fluid into the next chamber.

[0096] Another aspect of the invention is a fluidic device for preparing samples for nucleic acid amplification testing. The fluidic device includes two or more fluid wells configured to be connected to one another via a main fluid conduit. The fluid wells may be individually filled with liquid reagents from respective inlet fluid conduits. In some aspects of the invention, the inlet fluid conduits lead to respective exterior openings in the fluidic device, allowing each fluid well to be filled by dispensing or injecting reagents from the inlet fluid conduits into the wells.

[0097] A self-contained system is advantageous in a point-of-care environment because it eliminates any complicated dispensing or injection procedures required by the user. Thus, in another aspect of the present invention, reagents may be stored in a reagent pouch on the fluidic device. When sufficient pressure is applied to the pouch, the pouch ruptures, dispensing its contents into the fluid conduits leading to their intended reaction chambers. The pouches are designed with frangible seals aligned with the inlet fluid conduits, so that upon rupture, the pouch's contents are forced out and into the inlet fluid conduits, filling the fluid wells. Reagents in the pouches may include, but are not limited to, buffers, salts, acids, bases, labels, tags, markers, water, alcohol, solvents, waxes, oils, gases, gels, and the like.

[0098] Each fluid-well space is designed to be only partially filled with miscible liquid reagents to prevent the miscible liquids in each fluid well from spilling into the main fluid conduit connecting the fluid wells and intermixing with each other. The surfaces of each fluid well may include hydrophilic and hydrophobic surfaces, or may be modified to be hydrophilic or hydrophobic (e.g., by a hydrophilic or hydrophobic coating). Hydrophilic modification may be performed to increase wettability and more easily allow liquid reagents to fill the wells uniformly, while hydrophobic modification may be performed to decrease wettability and facilitate smooth movement of solid particles between fluid-filled fluid wells.

[0099] A reagent pouch containing an immiscible liquid, such as mineral oil, is connected to the main fluid conduit connecting each well. Upon actuation, 1) the contents of the reagent pouch containing the immiscible liquid are released, forming an immiscible oil phase on top of the liquid filling the fluid wells, and 2) all the miscible liquids in the fluid wells are connected in series to form a fluidic circuit, but are separated from each other by the oil phase and do not mix with each other. The main fluid conduit is connected to an external reservoir that collects excess oil. Each miscible reagent can be dispensed into each well sequentially or simultaneously, depending on the assay requirements. After the reagent wells are filled, the immiscible liquid is dispensed, thereby completely filling the main fluid conduit and the vacant space in the partially filled wells with the immiscible oil phase, completing the fluidic circuit.

[0100] While it is possible to pre-fill fluid wells with buffers separated by an oil phase and then seal and store the fluid wells in a cartridge for later use, some reagents (including, but not limited to, enzymes, oligos, dNTPs, buffers, etc.) are not stable in their respective liquid forms at room temperature or over long periods of time and must be stored in lyophilized form or hydrated prior to use. Additionally, sample loading into such pre-filled systems presents challenges. The disclosed invention provides methods and devices that address these challenges associated with sample loading, reagent delivery, and assay automation for sample processing on microfluidic devices.

[0101] FIG. 24 shows a schematic block diagram of the fluid chamber configuration. Fluid wells 2407 are connected to one or more RDUs 2402 (RDU1, RDU2, RDU3) containing miscible reagents by inlet fluid conduits 2403 entering the bottom of each fluid well. Each fluid well volume is designed to be only partially filled with miscible liquid reagent 2404 entering through the inlet fluid conduit. Once the fluid well is fully filled, RDU4 containing the immiscible liquid is actuated to dispense its contents into the fluidic device through main fluid conduit 2401. One non-limiting example of an immiscible liquid is oil 2406, which fills the main fluid conduit and the open volume of the fluid wells to form a fluidic pathway and simultaneously form a barrier between the miscible liquids in the fluid wells, preventing them from mixing. The immiscible liquid used to close the fluid circuit is selected to have minimal or no reactivity with the miscible liquid reagents. Excess oil collects in reservoir 2405. This oil also acts as a vapor barrier to prevent evaporation during nucleic acid amplification or other assay steps that may require heating.

[0102] The formed fluidic circuit is advantageous for automating sample preparation steps using magnetic beads for solid-phase capture because the beads can be moved by a magnet to penetrate the oil phase and enter fluidic wells containing various sample processing reagents. As an example, each fluidic well may be filled with a lysis buffer, binding buffer, wash buffer, and elution buffer for nucleic acid purification, separated by an oil phase. The magnetic beads may be moved through the oil phase to enter various fluidic wells in a predetermined sequence to complete the sample preparation steps for nucleic acid purification. This allows for easy automation of sample processing steps on a microfluidic device.

[0103] In another embodiment, each fluid well and main fluid conduit on the microfluidic cartridge may be completely pre-filled with oil. During use of the microfluidic device, miscible liquid reagents stored in reagent pouches are dispensed into desired fluid wells on the microfluidic cartridge, displacing excess oil, which is collected in excess oil reservoir 105.

[0104] Magnetic beads are commonly used in biological sample preparation to extract, isolate, and purify nucleic acids, proteins, biomolecules, and cells from biological samples. A major advantage of solid-phase extraction with magnetic beads is that it is easily automated because centrifugation or vacuum manifolds are not required. Under optimized conditions, DNA selectively binds to the functionalized surface of the magnetic beads, while other contaminants remain in solution. The beads can be captured in place by an external magnetic field, and the contaminants can be removed by pipetting out the contaminant-containing solution and washing the beads with a wash buffer. The purified DNA can then be eluted in a desired volume and used directly in molecular biology applications.

[0105] The disclosed invention provides a method and device for magnetic bead sample preparation, including a fluidic chip containing a series of fluidic wells with miscible liquid reagents for sample preparation separated by an immiscible oil phase, and upper and lower actuator elements having one or more spatially oriented permanent magnets fixed thereto depending on the number of fluidic wells and resuspension steps required. The permanent magnets on the upper and lower actuators are arranged to 1) resuspend the magnetic beads and 2) move the magnetic beads between the fluidic wells in a predetermined sequence, in a single continuous motion.

[0106] The fluid well is designed with spaced apart upper and lower baffles or obstacles that act as physical barriers to restrain the beads in fixed positions at the top or bottom of the well and prevent further movement of the beads in the direction of the permanent magnet on the actuator element.

[0107] In some embodiments, the walls of the fluid well may act as baffles or physical barriers, restricting the movement of the beads to a predetermined path. When a magnet on the opposing side of the well is brought into proximity with the beads, the beads are attracted to the magnet and resuspended through the liquid reagent or buffer present in the fluid well. The immiscible oil phase serves to complete the fluid path to complete the sample-to-answer sequence, allowing the beads to be resuspended and move through the various reagents in the series of wells via the oil-filled main fluid conduit. The present invention advantageously allows the sample-to-answer sequence to be completed using only a single continuous motion and permanent magnets, thereby reducing the complexity and power load of sample-to-answer automation. In some embodiments, a servo motor or stepper motor may be used to move the actuator element or microfluidic device. In some embodiments, a mechanical spring mechanism may be used to generate the motion. A mechanical spring mechanism is particularly advantageous in that it is completely powerless, requiring no electrical energy to automate the sequence. In some embodiments, the actuator element may be manually actuated by a user's finger.

[0108] Referring to Figure 25A, a schematic diagram of an exemplary microfluidic cartridge for magnetic bead sample preparation is shown, which includes fluid wells, fluid conduits, storage liquid reagent reservoirs, and valves. The microfluidic cartridge is sandwiched between upper and lower actuator elements, each containing a permanent magnet and a protrusion or projection. The permanent magnet and projection are spatially arranged to precisely time various steps in an assay automation sequence depending on the position and speed of the actuator elements as the microfluidic cartridge rotates near them. Possible assay steps include dispensing storage reagents into fluid wells, opening and closing valves to control the direction of fluid flow, opening and closing vents, and capturing, resuspending, and moving magnetic beads between wells. 25B and 25C, magnetic beads can pass sequentially through oil-filled fluid conduits 2505 into multiple reagent-filled fluid wells 2506 on the microfluidic device, the oil-filled fluid conduits 2505 being offset from one another so that the well walls act as physical barriers to confine the beads to the desired wells. The permanent magnets on the rotary actuator element are also offset to capture and resuspend beads in the multiple reagent-filled fluid wells along the rotary path.

[0109] As an example, isothermal nucleic acid amplification tests (NAATs), such as loop-mediated isothermal amplification (LAMP), may be performed on a microfluidic device using built-in heaters. Fluidic wells may be filled with buffers for binding, washing, and elution. ChargeSwitch magnetic beads may be used for nucleic acid extraction and purification. Microfluidic cartridges in fluidic wells designated for amplification may store lyophilized reagents for LAMP. Microfluidic cartridges in wells designated for binding may store magnetic beads.

[0110] As the microfluidic cartridge rotates between the upper and lower actuator elements, the sequence of operations to perform NAAT may be as follows: 1) Lysate is loaded into the first ("Bind") well by opening a valve; 2) "Bind," "Wash 1," "Wash 2," and "Elute" buffers are dispensed into the first, second, third, and fourth wells, respectively, on the microfluidic cartridge; 3) Mineral oil is filled and overlays the reagents in the wells, forming a continuous fluidic circuit through which magnetic beads can travel between wells; 4) Magnetic beads are sequentially captured, resuspended, and deposited into the four wells through the top oil conduit; 5) Eluted DNA from the elution well may be dispensed into the fifth (LAMP amplification) well containing the lyophilized master mix by opening a valve, hydrating the reagents; and 6) A heater on one actuator element contacts the LAMP amplification chamber and heats it to a desired temperature for a desired time.

[0111] 25B and 25C illustrate in more detail the principle of capturing, resuspending, and transferring magnetic beads between fluid wells to achieve sample preparation in the disclosed invention. Upper actuator element 2502 has spatially oriented permanent magnets 2507 labeled 1, 3, and 5, and lower actuator element 2504 has spatially oriented permanent magnets labeled 2, 4, and 6. In this embodiment, microfluidic cartridge 2503 rotates counterclockwise between fixed upper actuator element 2502 and lower actuator element 2504. When the microfluidic cartridge rotates to a position where the "binding" well is under upper permanent magnet "1," the magnetic beads are attracted to upper permanent magnet "1" and captured above the "binding" well. The microfluidic cartridge continues to rotate, displacing the beads into the next well, labeled "wash," via a connecting oil-filled fluid conduit. The sidewalls of the "wash" wells act as a physical barrier along the path of the magnetic beads, constraining the beads in oil above the wash wells. This occurs because permanent magnet "1" has moved away and is no longer exerting its force on the beads. As the microfluidic cartridge continues to rotate, it reaches a position where the first "wash" well is above the permanent magnet labeled "2" on the lower actuator element. This causes the beads above the first wash well to be attracted to permanent magnet "2," where they are resuspended and captured in the wash buffer at the bottom of the "wash" well. Similarly, the magnetic beads are resuspended, captured, and moved by magnets 3, 4, 5, and 6, before reaching the "elution" well, where the nucleic acid on the beads is eluted into the buffer at the bottom of the "elution" well.

[0112] Referring to Figures 26A through 26I, various stages of the position of a microfluidic cartridge relative to an actuator element are shown to illustrate the principle of capturing, resuspending, and transferring magnetic beads between fluid wells using linear actuation. The actuator element includes an upper permanent magnet and a lower permanent magnet. Figure 26A shows the starting position, where none of the wells are within range of the magnetic field. In Figure 26B, the first upper permanent magnet comes into proximity with a first well and captures magnetic beads in oil in the main fluid conduit. The captured magnetic beads are then moved through the main fluid conduit to a second well, as seen in Figure 26C.

[0113] Here, the wall of the second fluid well blocks the path of the magnetic beads, leaving them confined within the second fluid well. In the position shown in Figure 26D, the first lower permanent magnet approaches the second fluid well, drawing the beads to the bottom of the fluid well, where they are resuspended in the buffer reagent in the fluid well. In the position shown in Figure 26E, the second upper permanent magnet approaches the second well, dragging the beads through the main fluid conduit into the third fluid well. Figure 26F shows the beads confined in the third fluid well because the sidewall of the third fluid well acts as a baffle. In Figure 26G, the second lower permanent magnet approaches the third well, drawing the beads to the bottom of the well, where they are resuspended in the buffer reagent in the bottom. In Figure 26H, the beads are drawn to the top by the third upper permanent magnet, moving them through the main fluid conduit to the fourth fluid well. In Figure 26I, a third lower permanent magnet attracts the beads to the bottom of the fourth fluid well, resuspending the beads in the buffer solution in the fourth fluid well.

[0114] As shown in FIG. 27, electromagnets may be used instead of permanent magnets. The microfluidic cartridge moves between actuator elements containing electromagnets. The upper or lower electromagnets may be turned on and off in a sequence to facilitate the movement and resuspension of the magnetic beads between different fluid wells 2703. FIG. 27 illustrates various steps in magnetic bead movement throughout a sample processing sequence. In the step shown in FIG. 27A, electromagnet EM1 2701 is turned on to capture beads in oil phase 2702. As seen in the step shown in FIG. 27B, EM1 remains on, causing the beads to move through the oil phase. In the step shown in FIG. 27C, EM1 is turned off and EM2 2704 is turned on. This attracts the beads to EM2, which then enters reagent 2703 and resuspends them in that fluid well. Once the beads are ready to move to the next fluid well, EM1 is turned on again to attract the beads into the oil phase. In the process shown in Figure 27D, the beads are moved to the next reagent-filled fluidic well. Next, EM1 is turned off and EM2 is turned on, causing the beads to resuspend through the reagent loaded into the fluidic well and then be captured by EM2, as shown in Figure 27E. Finally, in Figures 27F and 27G, EM1 or EM2 are selectively turned on and off in a desired timing sequence, causing the beads to be moved and resuspended into the last fluidic well. To achieve bead mixing and resuspension within the reaction well, the upper and lower electromagnets may be driven with alternating pulses. While electromagnets may be used instead of permanent magnets and baffles, they require a power source and electronic control for on-off switching, complicating instrumentation requirements. Therefore, the use of electromagnets is less appealing than the use of permanent magnets, especially in point-of-care and low-resource environments.

[0115] The disclosed invention provides a method and device for fluid manipulation on a microfluidic cartridge, the microfluidic device including one or more storage reagent-filled pouches having frangible seals and an actuator element including one or more protrusions that are spatially oriented to dispense reagents into the wells of the fluidic cartridge in a predetermined sequence as the cartridge slides between the actuator elements.

[0116] Referring to FIG. 28 , a perspective view of a microfluidic cartridge and actuator element for sequential reagent delivery using magnetic beads for sample preparation is shown. The microfluidic cartridge contains onboard reagent storage in reagent pouches 2803 sealed with a frangible seal; when force is applied, the seal breaks, releasing the reagents through fluid conduits into wells on the microfluidic cartridge. The pouches are spatially oriented so that when the microfluidic cartridge engages and slides between the actuator element from one end to the other, the pouches are squeezed to sequentially deliver the reagents. The fluid wells have one or more upper and lower baffles 2804 and 2802, which act to constrain the beads within the wells. The actuator element has one or more mechanical elements (e.g., protrusions, plungers, etc.) 2806 thereon, which are arranged to squeeze the reagent pouches and dispense the reagents into the wells on the microfluidic cartridge. These mechanical elements are designed to keep the reagent pouches squeezed until the end of the sample-to-answer sequence to prevent backflow. In some embodiments, the mechanical element may act to open and close pinch valves on the microfluidic cartridge in a predetermined sequence to control the direction of fluid flow through the microfluidic cartridge or to open and close vents. The actuator element may have one or more stationary magnets thereon. As seen in FIG. 28 , the actuator element has an upper magnet 2805 and a lower magnet 2807, which are spatially arranged to capture, resuspend, and move magnetic beads into various fluidic wells to complete a sample preparation sequence.

[0117] In some embodiments, the beads may be transferred directly into a LAMP or other NAAT amplification system and eluted directly within that system. This allows all captured nucleic acids to be input into the NAAT amplification system. Figure 29 illustrates the principle of using protrusions in a fluid well as baffles to constrain beads to the well as the magnet continues to move along its motion path. The fluid well has protrusions 2902 at its top, which act to constrain the beads as the magnet continues to move along its motion path. In the schematic cross-sectional view of the microfluidic device shown in Figure 29, reagent 2908 is separated by immiscible oil phase 2904. Upper and lower fixed magnets 2905 and 2907 are located on the upper and lower actuator elements of the microfluidic device, respectively. As shown in Figure 29A, when upper fixed magnet 2905 comes into proximity with the first fluid well, the magnetic beads therein are attracted to the magnet and captured at the top of the oil phase. As the microfluidic cartridge continues to move between the actuator elements, the beads move through the fluid conduit and enter the second fluid well, as seen in FIG. 29B. Here, as the microfluidic device continues to move out of the magnetic field of the upper magnet, protrusions 2902 act to constrain the beads to the second well, as seen in FIG. 29C. The magnetic beads, constrained within the oil phase, can then move through the miscible reagent at the bottom of the well when the lower magnet comes into proximity with the fluid well, as seen in FIG. 29D. Here, the magnetic beads captured at the top are attracted to the lower magnet 2907, where they are resuspended and moved within the reagent at the bottom of the fluid well. In FIG. 29E, the magnetic beads are captured at the bottom of the well, and the sidewalls act as baffles to prevent the beads from exiting the well. In this manner, spatially oriented baffles and permanent magnets can be used to move magnetic beads between chambers or wells on a microfluidic device for sample processing.

[0118] In one embodiment, a lancet, or needle, with a hollow channel can be actuated by an actuator element to puncture the wall of the amplification chamber, allowing fluid to flow to the lateral flow strip for detection. Figure 30 illustrates the principle of transferring a liquid product containing the analyte to be detected from a fluidic well 3002 to a lateral flow strip 3003. Figure 30A shows a lancet 3005 with a hollow channel 3004 before actuation. Figure 30B shows the hollow lancet after actuation, where the lancet penetrates the lateral flow strip and the bottom of the fluidic well, forming a conduit for fluid to flow to the lateral flow strip.

[0119] Depending on the application and user requirements, the sample processing system may integrate motors, actuators, heating elements, thermocouples, fans, cooling devices, microcontrollers, photodetectors, electrodes, filters, light sources, battery packs, wireless modules, and electronic circuitry to form a single, self-contained, and self-sufficient integrated system for performing biological sample processing. The volumes of the reagent pouches, reservoirs, and reaction chambers may vary depending on the bioassay and user needs. Typical volumes may range from 1 μl to 10 ml, or from 5 μl to 1 ml. Various materials are suitable for microfluidic devices, such as glass, polycarbonate, PMMA, COC, silicon, or a combination of one or more of these materials. Microfluidic devices may be polymer injection molded with integrated silicon or glass MEMS-functionalized electrode arrays or microarrays or lateral flow strips for detection. Materials may be selected based on the user's requirements, the requirements of the assay to be performed on the material, and its biocompatibility and chemical compatibility. The footprint of a microfluidic device can range from a few square millimeters to tens of square centimeters, depending on user requirements and sample processing applications. In some embodiments, multiple microfluidic devices can be stacked or arrayed and processed simultaneously. The magnetic attraction, shape, and size of the sample processing system are selected depending on the sample processing needs, the shape, size, volume, material properties, and burst pressure of the frangible sealant. The frangible sealant material can be aluminum foil, polymer, rubber, metal, adhesive tape, metal oxide, or a combination of these materials. general definition

[0120] Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation. All technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the subject matter described herein belongs, unless defined otherwise.

[0121] "Nucleic acid," as used herein, refers to a polymeric compound comprising covalently linked subunits called nucleotides. A "nucleotide" is a molecule (or individual unit within a larger nucleic acid molecule) that contains a nucleoside (i.e., a compound containing a purine or pyrimidine base linked to a sugar, usually ribose or deoxyribose) linked to a phosphate group.

[0122] The terms "polynucleotide" or "oligonucleotide" or "nucleic acid molecule" are used interchangeably herein to refer to single- or double-stranded phosphate polymeric forms of ribonucleosides (adenosine, guanosine, uridine, or cytidine; "RNA molecule" or simply "RNA") or deoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, or deoxycytidine; "DNA molecule" or simply "DNA"), or any of their phosphate analogs (e.g., phosphorothioates or thioesters). Polynucleotides can be of any length and contain RNA, DNA, or RNA / DNA hybrid sequences. Polynucleotides used in the present invention can be natural, synthetic, recombinant, in vitro-produced, or a combination thereof, and can be purified using any purification method known in the art. Thus, the term "DNA" includes, but is not limited to, genomic DNA, plasmid DNA, synthetic DNA, semi-synthetic DNA, complementary DNA ("cDNA"; DNA synthesized from a messenger RNA template), and recombinant DNA (DNA that has been artificially designed and, therefore, has undergone molecular biological manipulation from its naturally occurring nucleotide sequence).

[0123] "Amplify," "amplification," "nucleic acid amplification," and the like refer to generating multiple copies of a nucleic acid template (e.g., a template DNA molecule) or generating multiple copies of a nucleic acid sequence complementary to a nucleic acid template (e.g., a template DNA molecule).

[0124] The terms "top," "bottom," "up," "bottom," and "up" are used throughout this specification to refer to the relative positions of components of the devices described above (e.g., the relative positions of the top and bottom substrates within the device). It should be understood that the functionality of the device is independent of the orientation of the device in space.

[0125] "Bead," with respect to beads on a droplet actuator, refers to any bead or particle capable of interacting with a droplet in the vicinity of the droplet actuator. Beads may be any of a variety of shapes, such as spherical, approximately spherical, ovoid, disc-shaped, cubic, amorphous, and other three-dimensional shapes. Beads may be capable of undergoing droplet operations within a droplet on the droplet actuator or otherwise configured relative to the droplet actuator, for example, to allow a droplet on the droplet actuator to be brought into contact with beads on the droplet actuator and / or beads not on the droplet actuator. Beads may be provided within a droplet, within a droplet operations gap, or on a droplet operations surface. Beads may be provided in a reservoir outside the droplet operations gap or in a reservoir located away from the droplet operations surface, and the reservoir may be associated with a flow path that allows droplets containing the beads to enter the droplet operations gap or be brought into contact with the droplet operations surface. Beads may be made of a variety of materials, such as resins or polymers. The beads may be of any suitable size, such as microbeads, microparticles, nanobeads, nanoparticles, etc. In some cases, the beads are magnetically responsive, and in other cases, the beads are not very magnetically responsive. In the case of magnetically responsive beads, the magnetically responsive material may constitute substantially the entire bead, may constitute only a portion of the bead, or may constitute only one component of the bead. Other portions of the bead may include, among other things, polymeric materials, coatings, and portions that allow for adsorption of assay reagents.Examples of suitable beads include flow cytometry microbeads, polystyrene microparticles and nanoparticles, functionalized polystyrene microparticles and nanoparticles, coated polystyrene microparticles and nanoparticles, silica microbeads, fluorescent microspheres and nanospheres, functionalized fluorescent microspheres and nanospheres, coated fluorescent microspheres and nanospheres, dyed microparticles and nanoparticles, magnetic microparticles and nanoparticles, superparamagnetic microparticles and nanoparticles (e.g., DYNABEADS® particles available from Invitrogen Group, Carlsbad, Calif.), fluorescent microparticles and nanoparticles, coated magnetic microparticles and nanoparticles, ferromagnetic microparticles and nanoparticles, and coated ferromagnetic microparticles and nanoparticles. Beads may be pre-coupled with biomolecules or other substances capable of binding and forming complexes with biomolecules. Beads may be pre-coupled with antibodies, proteins or antigens, DNA / RNA probes, or any other molecules with affinity for the desired target.

[0126] "Immobilizing," with respect to magnetically responsive beads, means substantially positionally constraining the beads within a droplet or within filler fluid on a droplet actuator. For example, in one embodiment, the immobilized beads are positionally constrained within the droplet sufficiently to perform a droplet splitting operation that generates one droplet with substantially all the beads and one droplet with substantially no beads. "Magnetic responsive" means responsive to a magnetic field.

[0127] "Magnetic responsive beads" include or consist of a magnetically responsive material. Examples of magnetically responsive materials include paramagnetic materials, ferromagnetic materials, ferrimagnetic materials, and metamagnetic materials. Examples of suitable paramagnetic materials include iron, nickel, and cobalt, as well as metal oxides such as Fe3O4, BaFel2O19, CoO, NiO, Mn2O3, Cr2O3, and CoMnP.

[0128] When any form of liquid (e.g., a droplet or a continuum, whether moving or stationary) is described as being "on," "at," or "above" an electrode, array, matrix, or surface, such liquid may be in direct contact with the electrode / array / matrix / surface, or may be in contact with one or more layers or thin films interposed between the liquid and the electrode / array / matrix / surface. In one example, a filler fluid may be considered a thin film between such liquid and the electrode / array / matrix / surface.

[0129] Following long-standing patent law convention, the words "a," "an," and "the" mean "one or more" when used in this application, including the claims. Thus, for example, a reference to "a subject" includes a plurality of subjects unless the context clearly dictates otherwise (e.g., a plurality of subjects), etc.

[0130] Throughout this specification and claims, the words "comprise," "comprises," and "comprising" are used in a non-exclusive sense unless the context otherwise requires. Similarly, the word "include," as well as grammatical variations thereof, is intended to be open-ended, whereby the recitation of items in the form of a list does not exclude other similar items that may be substituted for or added to the listed items.

[0131] For purposes of this specification and the appended claims, unless otherwise indicated, all numbers expressing quantities, sizes, dimensions, ratios, shapes, formulations, parameters, percentages, parameters, amounts, properties, and other numerical values ​​used in the specification and claims are to be understood as being modified in all instances by the word "about," even if the word "about" does not explicitly appear in conjunction with a value, amount, or range. Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and appended claims are not, and need not be, exact, but may be approximate and / or larger or smaller, as needed, reflecting tolerances, conversion factors, rounding, measurement error, and the like, as well as other factors known to those skilled in the art depending upon the desired properties sought to be obtained by the presently disclosed subject matter. For example, the term "about," when referring to a value, can be meant to encompass variations of, in some embodiments, ±100%, in some embodiments, ±50%, in some embodiments, ±20%, in some embodiments, ±10%, in some embodiments, ±5%, in some embodiments, ±1%, in some embodiments, ±0.5%, and in some embodiments, ±0.1% from the specified amount, because such variations are reasonable in practicing the present disclosure and using the compositions of the present disclosure.

[0132] Furthermore, the term "about," when used in connection with one or more numerical values ​​or numerical ranges, should be understood to refer to all such numbers, including all numbers within that range, modifying that range by extending the boundaries above and below the stated numerical values. The recitation of numerical ranges by endpoints includes all numbers subsumed within that range, e.g., whole integers, including fractions (e.g., a recitation of 1 to 5 includes 1, 2, 3, 4, 5, and fractions thereof, e.g., 1.5, 2.25, 3.75, 4.1, etc.), and any range subsumed within that range.

[0133] All publications, patent applications, patents, and other documents mentioned in this specification are indicative of the level of ordinary skill in the art to which the disclosed subject matter pertains. All publications, patent applications, patents, and other documents are incorporated herein by reference to the same extent as if each individual publication, patent application, patent, and other document was specifically and individually indicated to be incorporated by reference. Although various patent applications, patents, and other documents are referenced herein, it should be understood that such reference does not constitute an admission that any of these documents form part of the common general knowledge in the art.

[0134] Although the foregoing subject matter has been described in some detail by way of illustration and example for purposes of clarity of understanding, those skilled in the art will recognize that certain changes and modifications may be made without departing from the scope of the appended claims.

Claims

1. one or more cams including a camshaft and a cam lobe; one or more rocker arms; a microfluidic cartridge including one or more fluid channels, one or more reaction chambers, and one or more burst pouches containing fluid and a frangible membrane seal; a cam mechanism configured to rotate the camshaft, the one or more cams are configured such that, when the camshaft rotates, the cam lobes actuate the one or more rocker arms, the one or more rocker arms being configured such that actuation moves the rocker arms from an open position to a closed position, applying pressure to the one or more burst pouches and rupturing the frangible membrane to release the fluid into the one or more reaction chambers; Microfluidic devices.

2. 10. The microfluidic device of claim 1, wherein a plurality of cam lobes and rocker arms are configured such that, as the camshaft rotates one full revolution, the rocker arms apply pressure to a plurality of burst pouches in a temporally and spatially controlled manner.

3. 3. The microfluidic device of claim 1, wherein the one or more cam lobes and the one or more rocker arms are configured such that the rocker arms remain in the closed position after the frangible membrane seal of the one or more burst pouches is broken.

4. The microfluidic device of any one of claims 1 to 3, wherein the cam lobe is configured to remain in the closed position after the rocker ruptures the pouch.

5. 5. The microfluidic device of claim 1, further comprising one or more diaphragm valves along the one or more flow paths, the one or more cam lobes configured to open and / or close the one or more diaphragm valves as the cam shaft rotates.

6. The microfluidic device according to any one of claims 1 to 5, wherein the camshaft is configured to rotate by a power spring mechanism.

7. The microfluidic device of any one of claims 2 to 6, further comprising a sample preparation chamber, said sample preparation chamber containing a vehicle for DNA capture.

8. 8. The microfluidic device of claim 7, further comprising: a rotational speed of the camshaft and the configuration of the plurality of cam lobes and the plurality of rocker arms, which further enables the plurality of burst pouches to burst in a time-controlled manner to perform a wash step of DNA purification.

9. 10. The microfluidic device of claim 8, wherein the microfluidic cartridge further comprises an amplification chamber, a heat sink, and a heater, the heat sink and the heater configured to intermittently cool or heat the amplification chamber after actuation of the plurality of cam lobes and the plurality of rocker arms.

10. 10. The microfluidic device of claim 9, further comprising: a rotational speed of the camshaft and the configuration of the plurality of cam lobes and the plurality of rocker arms that enables the heat sink and the heater to intermittently cool or heat the amplification chamber in a time-controlled manner to perform PCR thermal cycling.

11. The microfluidic device of claim 8 , wherein the microfluidic cartridge further comprises a DNA hybridization chamber containing a vehicle for DNA capture.

12. 1. A microfluidic device comprising a microfluidic cartridge, a plurality of pre-filled reagent pouches; a reaction chamber; a camshaft, the camshaft includes a plurality of slots at a plurality of angular positions along the camshaft, whereby, when the camshaft rotates to a predetermined position, one or more of the angular slots form a flow path between one or more of the reagent-filled pouches and the reaction chamber. Microfluidic devices.

13. a reagent pouch containing the reagent and a frangible seal; an integrated magnetic element configured to collapse the reagent pouch and breach the frangible seal when attracted to a magnetic field; A reagent dispenser including:

14. 14. The reagent dispensing apparatus of claim 13, wherein the magnetic element comprises a plunger.

15. 14. The reagent dispensing apparatus of claim 13, wherein the magnetic element comprises a bead.

16. 14. The reagent dispensing apparatus of claim 13, wherein the magnetic element comprises a sharp object.

17. a fluid conduit; a reaction chamber; A microfluidic device comprising the reagent constant rate supplying device according to any one of claims 13 to 16, the reagent dispensing apparatus is bonded to the microfluidic device such that an airtight seal is formed, and the reagent dispensing apparatus is configured to empty the reagent into the reaction chamber via the fluid conduit upon breaching the frangible seal. Microfluidic devices.

18. 20. The microfluidic device of claim 17, further comprising a trap, the trap comprising a loose magnetic material and configured to hold the reagent pouch in a collapsed state.

19. a plurality of fluid chambers fluidly connected to one another via valves; a rotating shaft including permanent magnets arranged axially and radially around the circumference of the rotating shaft with alternating magnetic poles; each of the fluid chambers includes a trapped permanent magnet constrained to move along a path perpendicular to the axis of the rotatable shaft, the rotatable shaft and the fluid chambers being configured such that rotation of the rotatable shaft moves the permanent magnet to mix the fluids in each of the fluid chambers; Microfluidic devices.

20. A reagent pouch having a rupture point at a precise location in a frangible portion of a seal, the reagent pouch including a magnetic element constrained to a specific location on the reagent pouch directly overlying the frangible portion of the seal.

21. one or more linear actuator elements; a microfluidic cassette, the one or more linear actuator elements include a fixed magnetic element for magnetic bead movement, a fixed magnetic element for fluid valve actuation, and / or a fixed magnetic element for reagent pouch rupture, and the microfluidic cassette includes a storage reagent pouch with an integrated magnetic plunger element, a sample processing reagent chamber, a magnetic orbital rocker valve featuring a non-magnetic plunger that controls the movement of magnetic beads through the valve, and a magnetically controlled valve including a magnetic plunger that includes a fixed magnetic element for magnetic bead movement; Microfluidic devices.

22. 22. The microfluidic device of claim 21, wherein the one or more actuator elements are configured to slide under and / or over the microfluidic device.

23. 23. The microfluidic device of any one of claims 21 to 22, wherein the actuator element is moved by a method selected from the group consisting of a motor, a spring, a hand crank, a manual push, and a linear solenoid actuator.

24. one or more linear actuator elements; a microfluidic cassette, the one or more linear actuator elements include a combination of fixed and partially trapped magnetic elements, the partially trapped magnetic elements contained in respective traps such that their respective motions are restricted to one axis or direction for magnetic bead movement, fluid valve actuation, and / or reagent pouch rupture; and the microfluidic cassette includes a storage reagent pouch with an integrated magnetic plunger element, a sample processing reagent chamber, a magnetic orbital rocker valve featuring a non-magnetic plunger that controls the movement of magnetic beads through the valve, and a magnetically controlled valve including a magnetic plunger that includes a fixed magnetic element for magnetic bead movement. Microfluidic devices.

25. 25. The microfluidic device of claim 24, wherein the one or more actuator elements are configured to slide under and / or over the microfluidic device.

26. 26. The microfluidic device of any one of claims 24 to 25, wherein the actuator element is moved by a method selected from the group consisting of a motor, a spring, a hand crank, a manual push, and a linear solenoid actuator.

27. 1. A microfluidic device comprising: a reagent pouch aligned with a magnetic plunger element integrated into a reaction chamber, the magnetic plunger element configured, when attracted by a magnetic field, to break a frangible seal of the reagent pouch, enter the reagent pouch, and force a reagent within the reagent pouch into the reaction chamber.

28. 28. The microfluidic device of claim 27, wherein the magnetic plunger element is located between a fluid inlet and the reagent pouch, and further wherein the magnetic element has a notch that acts as a guide and restricts fluid flow into the reaction chamber through the guide notch, and the guide notch is configured such that fluid flow into the reaction chamber is closed when the magnetic element plunger reaches its highest position.

29. an actuator element having a plurality of partially trapped magnetic elements housed within a rotatable shaft, the rotatable shaft configured with a plurality of magnetic traps within a sleeve; A plurality of reagent constant-rate supply devices according to any one of claims 13 to 16; a mixing chamber; a mixing chamber magnet; A microfluidic device comprising:

30. 30. The microfluidic device of claim 29, further comprising a stationary permanent magnet configured with both poles on the circumference of the rotating shaft to attract and repel the mixing chamber magnet at high frequency as the shaft rotates.

31. 31. The microfluidic device of claim 29, wherein the device is configured such that as the rotatable shaft rotates, a first reagent dispensing device aligns with a first partially trapped magnetic element, thereby causing the first partially trapped magnet to move out of the rotatable shaft and into a first magnetic trap in the sleeve, thereby attracting the magnetic element and allowing the frangible seal of the pouch of the first reagent dispensing device to be breached.

32. 32. The microfluidic device of claim 31 , wherein as the rotatable shaft continues to rotate, a second reagent dispensing device aligns with a second partially trapped magnetic element, thereby causing the second partially trapped magnet to move out of the rotatable shaft and into a second magnetic trap in the sleeve, thereby attracting the magnetic element and allowing the frangible seal of the pouch of the second reagent dispensing device to be breached.

33. 33. The microfluidic device of claim 32, wherein the rotating shaft is configured to rotate at high RPM to effect mixing after dispensing of stored reagents is complete by having the fixed permanent magnet within the shaft present alternating magnetic poles at a high frequency to the mixing magnet.

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