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Title:
DIGITAL MICROFLUIDICS SYSTEMS AND METHODS WITH INTEGRATED PLASMA COLLECTION DEVICE
Document Type and Number:
WIPO Patent Application WO/2019/023133
Kind Code:
A1
Abstract:
A digital microfluidics (DMF) device can be used to extract plasma from whole blood and manipulate the extracted plasma. The device can have a plasma separation membrane disposed between a sample inlet and sample outlet that leads into the DMF device. Once the plasma contacts the actuation electrodes of the DMF device, the plasma can be actively extracted from the whole blood sample by actuating the actuation electrodes to pull the plasma through plasma separation membrane.

Inventors:
JEBRAIL, Mais, J. (458 Brannan Street, San Francisco, CA, 94107, US)
SOTO MORENO, Jorge, Abraham (458 Brannan Street, San Francisco, CA, 94107, US)
LEE, Victor (458 Brannan Street, San Francisco, CA, 94107, US)
Application Number:
US2018/043293
Publication Date:
January 31, 2019
Filing Date:
July 23, 2018
Export Citation:
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Assignee:
MIROCULUS INC. (458 Brannan Street, San Francisco, CA, 94107, US)
International Classes:
G01N27/447
Domestic Patent References:
WO2016197103A12016-12-08
WO2013090889A12013-06-20
Foreign References:
US20130288254A12013-10-31
US20080038810A12008-02-14
US20120085645A12012-04-12
US20110118132A12011-05-19
Other References:
HOU ET AL.: "Microfluidic Devices for Blood Fractionation", MICROMACHINES, vol. 2, no. 4, 20 July 2011 (2011-07-20), pages 310 - 343, XP055355949
Attorney, Agent or Firm:
CHU, Winston, S. et al. (Shay Glenn LLP, 2755 Campus Drive Suite 21, San Mateo CA, 94403, US)
Download PDF:
Claims:
CLAIMS

What is claimed is: 1. An air-matrix digital microfluidic (DMF) apparatus configured to process whole blood and manipulate plasma extracted from the whole blood, the apparatus comprising:

a first plate having a first hydrophobic layer;

a second plate having a first side coated with a second hydrophobic layer, the second plate having a sample outlet;

an air gap formed between the first and second hydrophobic layers;

a plurality of actuation electrodes adjacent to the first hydrophobic layer;

a sample inlet positioned over the sample outlet, the sample inlet configured to receive a sample of whole blood;

a plasma separation membrane positioned between the sample inlet and the sample outlet, the plasma separation membrane configured to extract plasma into the sample outlet from the whole blood in the sample inlet; and

a controller programmed to actuate a subset of the plurality of actuation electrodes that are

activated when the plasma extracted from the whole blood contacts the first plate in order to draw the plasma through the plasma separation membrane.

2. The apparatus of claim 1, wherein the sample inlet has a super-hydrophobic surface.

3. The apparatus of claim 2, wherein the second plate has a second side with a super-hydrophobic surface, wherein the plasma separation membrane is positioned between the super-hydrophobic surface of the second plate and the super-hydrophobic surface of the sample inlet.

4. The apparatus of claim 1, wherein the sample inlet comprises a cover plate with a hole.

5. The apparatus of claim 1, wherein the sample inlet is positioned above the sample outlet such that when the sample of whole blood is placed in the sample inlet, gravity draws the plasma through the plasma separation membrane.

6. The apparatus of claim 1, wherein the plasma separation membrane is porous and has larger pores positioned towards the sample inlet and smaller pores positioned towards the sample outlet.

7 The apparatus of claim 6, wherein the plasma separation membrane is an assembly of a plurality of membranes having different pore sizes. 8 The apparatus of claim 1, wherein the first plate is part of a reusable device and the second plate is part of a disposable cartridge.

9 The apparatus of claim 8, wherein the actuation electrodes are disposed on a removable film.

10. The apparatus of claim 1, wherein the sample outlet is larger than the sample inlet.

11. A method of extracting plasma from whole blood in an air-matrix digital microfluidic (DMF) apparatus, the method comprising:

introducing a sample of whole blood into a sample inlet of the air-matrix DMF apparatus;

extracting plasma from the sample of whole blood in the sample inlet through a plasma separation membrane and into a sample outlet of the air-matrix DMF apparatus;

transporting the extracted plasma from the sample outlet to one or more actuation electrodes of a plurality of actuation electrodes of the air- matrix DMF apparatus; and

actuating the one or more actuation electrodes of the air-matrix DMF apparatus to actively extract plasma from the sample of whole blood.

12. The method of claim 11 , further comprising prewetting the plasma separation membrane before introducing the sample of whole blood into the sample inlet. 13. The method of claim 11 , wherein the sample inlet is positioned above the sample outlet such that when the sample of whole blood is introduced into the sample inlet, gravity draws the plasma through the plasma separation membrane.

14. The method of claim 11 , wherein the plasma separation membrane is sandwiched between a pair of super -hydrophobic surfaces.

15. The method of claim 11 , wherein the extracted plasma is transported from the sample outlet to one or more actuation electrodes at least in part by gravity. 16. The method of claim 11 , further comprising detecting when the extracted plasma contacts the one or more actuation electrodes.

17. The method of claim 11 , further comprising actuating the one or more actuation electrodes after the extracted plasma contacts the one or more actuation electrodes.

18. The method of claim 11 , further comprising actuating the one or more actuation electrodes before the extracted plasma contacts the one or more actuation electrodes.

Description:
DIGITAL MICROFLUIDICS SYSTEMS AND METHODS WITH INTEGRATED PLASMA

COLLECTION DEVICE

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Patent Application No. 62/536,419, filed July 24, 2017, titled "DIGITAL MICROFLUIDICS SYSTEMS AND METHODS WITH INTEGRATED PLASMA COLLECTION DEVICE," which is herein incorporated by reference in its entirety for all purposes.

[0002] This patent application may claim priority to International Application No.

PCT/US2016/036015, titled "AIR-MATRIX DIGITAL MICROFLUIDICS APPARATUSES AND METHODS FOR LIMITING EVAPORATION AND SURFACE FOULING," filed on June 6, 2016.

INCORPORATION BY REFERENCE

[0003] All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

FIELD

[0004] Air-matrix digital microfluidic (DMF) apparatuses and methods for manipulating and processing encapsulated droplets are described herein.

BACKGROUND

[0005] Microfluidics-based technologies have proven useful in a wide variety of applications. While microfluidic manipulations are typically carried out using microchannels, an alternative paradigm has recently emerged, called digital microfluidics (DMF). In DMF, discrete nanoliter- (nL) to microliter- (μί) sized droplets of fluid are manipulated on a planar hydrophobic surface by applying a series of electrical potentials to an array of electrode pads. DMF has rapidly become popular for chemical, biological, and medical applications, as it allows straightforward control over multiple reagents, facile handling of both solids and liquids, and compatibility with even troublesome reagents (e.g., organic solvents, corrosive chemicals, etc.) because the hydrophobic surface is typically chemically inert.

[0006] Although DMF devices can handle different types of liquids, manipulating whole blood can cause a variety of difficulties, such as interfering with colorimetric assays and causing fouling. Further, many micro- and nano- fluidic assays are not capable of handling the often necessarily larger volumes of blood needed as the input to the assay directly. Therefore, it would be desirable to provide a DMF device that can extract plasma from a whole blood sample. SUMMARY OF THE DISCLOSURE

[0007] Described herein air-matrix digital microfluidic (DMF) methods for manipulating and processing blood, as well as apparatuses adapted to process blood.

[0008] We have recently developed a module for large-volume (milliliter-scale) sample extraction and concentration into the microliter volume used on the DMF device, utilizing a pre -fabricated cartridge and peristaltic pump to efficiently mix a sample with magnetic capture beads. To date, we have demonstrated microRNA extractions from up to 100 μΐ. of plasma into a 2 μL· droplet, with performance (recovery, quality) comparable to that achieved with bench-scale bead-based microRNA extraction. However, a continuing challenge for DMF is extracting plasma from whole blood for a complete sample- in-answer-out solution. In response to this challenge, we developed the first device architecture combining a plasma separation membrane from whole blood samples and downstream processing with DMF (see, e.g., FIG. 1). For many liquid biopsy applications, acquiring cell free plasma is very important to ensure the detection of the cell free fraction of circulating DNA or RNA. This module is meant to not only separate plasma but also to ensure that not even platelets or white blood cells are carried over or lysed during the separation.

[0009] For example, described herein are air-matrix digital microfluidic (DMF) apparatuses configured to process whole blood and manipulate plasma extracted from the whole blood. These apparatuses may include: a first plate having a first hydrophobic layer; a second plate having a first side coated with a second hydrophobic layer, the second plate having a sample outlet; an air gap formed between the first and second hydrophobic layers; a plurality of actuation electrodes adjacent to the first hydrophobic layer; a sample inlet positioned over the sample outlet, the sample inlet configured to receive a sample of whole blood; a plasma separation membrane positioned between the sample inlet and the sample outlet, the plasma separation membrane configured to extract plasma into the sample outlet from the whole blood in the sample inlet; and a controller programmed to actuate a subset of the plurality of actuation electrodes that are activated when the plasma extracted from the whole blood contacts the first plate in order to draw the plasma through the plasma separation membrane.

[0010] The sample inlet may have a hydrophobic or super-hydrophobic surface. The second plate may have a second side with a super-hydrophobic surface, wherein the plasma separation membrane is positioned between the super-hydrophobic surface of the second plate and the super-hydrophobic surface of the sample inlet. For example, the sample inlet may comprise a cover plate with a hole. The sample inlet may be positioned above the sample outlet such that when the sample of whole blood is placed in the sample inlet, gravity draws the plasma through the plasma separation membrane.

[0011] Any appropriate plasma separation membrane may be used. For example, the plasma separation membrane may be porous and has larger pores positioned towards the sample inlet and smaller pores positioned towards the sample outlet. The plasma separation membrane may be an assembly of a plurality of membranes having different pore sizes.

[0012] The first plate may be part of a reusable device and the second plate is part of a disposable cartridge. The actuation electrodes may be disposed on a removable film. [0013] The sample outlet may be larger than the sample inlet.

[0014] Also described herein are methods of extracting plasma from whole blood in an air-matrix digital microfluidic (DMF) apparatus, the method comprising: introducing a sample of whole blood into a sample inlet of the air-matrix DMF apparatus; extracting plasma from the sample of whole blood in the sample inlet through a plasma separation membrane and into a sample outlet of the air-matrix DMF apparatus; transporting the extracted plasma from the sample outlet to one or more actuation electrodes of a plurality of actuation electrodes of the air-matrix DMF apparatus; and actuating the one or more actuation electrodes of the air-matrix DMF apparatus to actively extract plasma from the sample of whole blood.

[0015] The method may also include prewetting the plasma separation membrane before introducing the sample of whole blood into the sample inlet.

[0016] As mentioned, the sample inlet may be positioned above the sample outlet such that when the sample of whole blood is introduced into the sample inlet, gravity draws the plasma through the plasma separation membrane. The plasma separation membrane may be sandwiched between a pair of super - hydrophobic surfaces.

[0017] The extracted plasma may be transported from the sample outlet to one or more actuation electrodes at least in part by gravity.

[0018] The method may also include detecting when the extracted plasma contacts the one or more actuation electrodes. The method may also include actuating the one or more actuation electrodes after the extracted plasma contacts the one or more actuation electrodes.

[0019] The method may also include actuating the one or more actuation electrodes before the extracted plasma contacts the one or more actuation electrodes.

BRIEF DESCRIPTION OF THE DRAWINGS

[0020] The novel features of the invention are set forth with particularity in the claims that follow. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

[0021] FIG. 1 is a top view of an example of a portion of an air-matrix DMF apparatus, showing a plurality of unit cells (defined by the underlying actuating electrodes) and reaction chamber openings (access holes).

[0022] FIG. 2A shows the top view of FIG. 1 and FIGS. 2B-2D show side views of variations of reaction chamber wells that may be used in an air-matrix DMF apparatus. In FIG. 2B the reaction chamber well comprises a centrifuge tube; in FIG. 2C the reaction chamber well comprises a well plate (which may be part of a multi-well plate); and in FIG. 2D the reaction chamber well is formed as part of the pate of the air-matrix DMF apparatus.

[0023] FIGS. 3A-3E illustrate movement (e.g., controlled by a controller of an air-matrix DMF apparatus) into and then out of a reaction chamber, as described herein. In this example, the reaction chamber well is shown in a side view of the air-matrix DMF apparatus and the reaction chamber is integrally formed into a plate (e.g., a first or lower plate) of the air-matrix DMF apparatus which includes actuation electrodes (reaction well actuation electrodes) therein.

[0024] FIG. 4A shows a time series of photos of an air matrix DMF apparatus including a wax (in this example, paraffin) body which is melted and covers a reaction droplet.

[0025] FIG. 4B is an example of a time series similar to that shown in FIGS. 4A(3) and 4A(4), without using a wax body to cover the reaction droplet, showing significant evaporation.

[0026] FIG. 5 is a graph comparing an amplification reaction by LAMP with and without a wax covering as described herein, protecting the reaction droplet from evaporation.

[0027] FIG. 6A show graphical results of LAMP using paraffin-mediated methods; this may be qualitatively compared to the graph of FIG. 6B shows graphical results of LAMP using conventional methods.

[0028] FIGS. 7A and 7B show the encapsulation of a droplet within wax in a thermal zone and the subsequent separation of the droplet from the liquid wax.

[0029] FIGS. 8A-8C show the merging of a carrier droplet with beads with the droplet from FIGS. 7A and 7B and the subsequent separation and re-suspension of the beads.

[0030] FIGS. 9A-9E illustrate a DMF apparatus with an integrated plasma separation device.

[0031] FIG. 10 is a schematic depicting a removable film or sheet with electrodes and/or pre-loaded with reagents that can be attached to one of the plates.

[0032] FIG. 11 is a removable film with electrodes that can be attached to one of the plates.

DETAILED DESCRIPTION

[0033] Described herein are air-matrix digital microfluidics (DMF) methods and apparatuses that may be used with a fresh or stored (e.g., frozen) blood same, including blood samples taken directly from a patient. An air-matrix DMF apparatus as described herein may be particularly useful for use with immediately processing blood samples as part of the DMF process.

[0034] In particular, described herein are air-matrix DMF apparatuses including a plasma separation membrane as part of the apparatus, including as part of a cartridge that may be applied to a DMF driving apparatus. The plasma separation membrane may be formed as part of the top (e.g., top surface, or top plate) of the DMF apparatus. The apparatus may be configured to enhance the capillary forces drawing plasma through the plasma separation membrane and into the air gap of the DMF apparatus. Without the enhancements described herein, the rate of flow of plasma through a typically membrane (e.g., filter, separation membrane, etc.) would be rate limiting and slow, and would further limit the usefulness of the apparatus for directly processing blood without the need for separation or other pre-treatments.

[0035] For example, in any of the apparatuses described herein, a plasma separation membrane may be included on the top plate of the digital microfluidic (DMF) apparatus. The apparatus may be configured to pre-wet the separation membrane and/or a method of using the apparatus may include pre- wetting the separation membrane, to enhanced capillary forces and achieve faster flow through membrane. The apparatus may be configured so that, upon contact of plasma with DMF surface, the electrode(s) is/are actuated to pull the plasma to the DMF device using electro wetting forces. For example, the apparatus may be configured to detect plasma contacting the one or more electrodes within a plasma loading region of the air gap, for example, by electrical detection (e.g., change of an electrical property of the electrode(s)), optical detection (e.g., an optical sensor aimed at the air gap region at or near the plasma loading region), etc. Once fluid, e.g., plasma, is detected within this region, the DM apparatus may electrically modify the electrowetting forces and move the droplet. Pulling the droplet away by adjusting the electrowetting force may increase the flow of plasma through the membrane and into the air gap.

[0036] In any of the apparatuses and methods described herein, the plasma separation membrane may be sandwiched between super hydrophobic surfaces. The loading region on the outward-facing side of the apparatus may be a super-hydrophobic surface (e.g., including super hydrophobic coatings). The super hydrophobic environment surrounding the membrane may prevent a blood sample from overflowing the edges of the separation membrane, and may help achieve a a maximum volume flow through membrane.

[0037] Any of the methods (including user interfaces) described herein may be implemented as software, hardware or firmware, and may be described as a non-transitory computer-readable storage medium storing a set of instructions capable of being executed by a processor (e.g., computer, tablet, smartphone, etc.), that when executed by the processor causes the processor to control perform any of the steps, including but not limited to: displaying, communicating with the user, analyzing, modifying parameters (including timing, frequency, intensity, etc.), determining, alerting, or the like.

[0038] In general, an air-matrix DMF apparatus as disclosed herein may have any appropriate shape or size. The air-matrix DMF apparatuses described herein generally include at least one hydrophobic surface and a plurality of activation electrodes adjacent to the surface; either the hydrophobic surface may also be a dielectric material or an additional dielectric material/layer may be positioned between the actuation electrodes and the hydrophobic surface. For example, in some variations, the air-matrix DMF includes a series of layers on a printed circuit board (PCB) forming a first or bottom plate. The outer (top) surface of this plate is the hydrophobic layer. Above this layer is the air gap (air gap region) along which a reaction droplet may be manipulated. In some variations a second plate may be positioned opposite from the first plate, forming the air gap region between the two. The second plate may also include a hydrophobic coating and in some variations may also include a ground electrode or multiple ground electrodes opposite the actuation electrodes. The actuation electrodes may be configured for moving droplets from one region to another within the DMF device, and may be electrically coupled to a controller (e.g., control circuitry) for applying energy to drive movement of the droplets in the air gap. As mentioned, this plate may also include a dielectric layer for increasing the capacitance between the reaction droplet and the actuation electrodes. The reaction starting materials and reagents, as well as additional additive reagents may be in reservoirs that may be dispensed into the air gap, where the reaction mixture is typically held during the reaction. In some instances the starting materials, reagents, and components needed in subsequent steps may be stored in separate areas of the air gap layer such that their proximity from each other prevents them from prematurely mixing with each other. In other instances, the air gap layer may include features that are able to compartmentalize different reaction mixtures such that they may be close in proximity to each other but separated by a physical barrier. In general, the floor of the air gap is in the first plate, and is in electrical contact with a series of actuation electrodes.

[0039] In some embodiments, one of the plates can be integrated into a reader device, and the other plate can be integrated into a removable, disposable cartridge, that when attached to the reader, form a two plate digital microfluidics system similar to that described herein. The reader device can be a permanent, reusable device that contains all or a bulk of the electronics for controlling the DMF system, and may optionally also containing sensors (i.e. sensors for measuring color and/or light, temperature or pH) for analyzing the droplets in the device. In addition, the actuation electrodes can be disposed on a film, which can also be made of a dielectric material. The film can be removably attached to one of the plates, such as the plate on the reader or the plate on the cartridge, while the other plate can have the ground electrode(s). For example, U.S. Patent Nos. 8,187,864; 8,470,153; 8,821,705; 8,993,348; and 9,377,439, which are hereby incorporated by reference in their entireties, describe cartridge based DMF systems.

[0040] FIG. 10 is a schematic depicting a removable film or sheet with electrodes and/or pre-loaded with reagents that can be removably attached to one of the plates. The film 10 may optionally have an at least one pre-loaded reagent depot 12 mounted (i.e. spotted and dried/frozen) on a hydrophobic front surface of the film 10. This disposable substrate 10 may be any thin dielectric sheet or film so long as it is chemically stable toward the reagents pre-loaded thereon. For example, any polymer based plastic may be used, such as for example saran wrap. In addition to plastic food-wrap, other substrates, including generic/clerical adhesive tapes and stretched sheets of paraffin, were also evaluated for use as replaceable DMF substrates.

[0041] As shown, the disposable sheet 10 can be affixed to the electrode array 16 of the DMF device 14 with a back surface of the sheet 10 adhered or suctioned to the electrode array 16 in which the reagent depot 12 deposited on the surface of the sheet 10 (across which the reagent droplets are translated) is aligned with pre-selected individual electrode 18 of the electrode array 16 as shown in steps (1) and (2) of FIG. 10. One or more reagents droplets 20 and 22 can deposited onto the device prior to or during an assay. As can be seen from step 3 of FIG. 10, during the assay reagent droplets 20 and 22 can be actuated over the top of film 10 to facilitate mixing and merging of the assay reagent

droplets 20 and 22 with the desired reagent depot 12 over electrode 18.

[0042] After the reaction has been completed, the disposable film 10 may then be peeled off as shown in step (4) and the resultant reaction products 26 analyzed if desired as shown in step (5). A fresh disposable film 10 may then be attached to the DMF device 14 for the next round of analysis. The product 26 can be also analyzed while the removable substrate is still attached to the device DMF device 14. This process can be recycled by using additional pre-loaded substrates. In addition, the droplets containing reaction product(s) may be split, mixed with additional droplets, incubated for cell culture if they contain cells.

[0043] In some embodiments as shown in FIG. 11, the film 10 may also have a plurality of electrodes 23 that are attached and/or embedded within the film 10. The film 10 may have electrical contacts and/or junctions that electrically couple the film 10 and electrodes 23 to complementary electrical contacts and junctions on the top or bottom plate of the DMF device. In this embodiment, the plate to which the film 10 is attached may not have any electrodes and instead may only have electrical contacts and/or junctions for electrically coupling with the film 10.

[0044] The air gap DMF apparatuses described herein may also include other elements for providing the needed reaction conditions. For instance, the air gap DMF apparatuses may include one or more thermal regulators (e.g., heating or cooling element such as thermoelectric modules) for heating and cooling all or a region (thermal zone) of the air gap. In other instances, heating or cooling may be provided by controlling endothermic or exothermic reactions to regulate temperature. The air gap DMF apparatuses may also include temperature detectors (e.g., resistive temperature detector) for monitoring the temperature during a reaction run. In addition, the DMF apparatuses may also include one or more magnets that can be used to manipulate magnetic beads in an on demand fashion. For example, the magnet(s) can be an electromagnet that is controlled by a controller to generate a magnetic field that can agitate or immobilize magnetic beads.

[0045] Thus, the air gap DMF apparatuses described herein may include one or more thermal zones. Thermal zones are regions on the air gap DMF apparatuses (e.g., the air gap) that may be heated or cooled, where the thermal zones may transfer the heating or cooling to a droplet within the thermal zone through one or more surfaces in contact with the air gap region in the zone (e.g., the first plate). Heating and cooling may be through a thermal regulator such as a thermoelectric module or other type of temperature-modulating component. The temperature of one or many thermal zones may be monitored through a temperature detector or sensor, where the temperature information may be communicated to a computer or other telecommunication device. The temperature is typically regulated between 4°C and 100°C, as when these apparatuses are configured to perform one or more reactions such as, but not limited to: nucleic acid amplifications, like LAMP, PCR, molecular assays, cDNA synthesis, organic synthesis, etc.

[0046] An air gap DMF apparatus may also include one or more thermal voids. Thermal voids may be disposed adjacent to the different thermal zones. The thermal voids are typically regions in which heat conduction is limited, e.g., by removing part of the plate (e.g., first plate) (forming the "void")- These voids may be strategically placed to isolate one thermal zone from another which allows the correct temperatures to be maintained within each thermal zone.

[0047] In general, any of the air-matrix DMF apparatuses described herein may include a separate reaction chamber that is separate or separable from the air gap of the apparatus, but may be accessed through the air gap region. The reaction chamber typically includes a reaction chamber opening that is continuous with the lower surface of the air gap (e.g., the first plate), and a reaction chamber well that forms a cup-like region in which a droplet may be controllably placed (and in some variations, removed) by the apparatus to perform a reaction when covered. The cover may be a mechanical cover (e.g., a cover the seals or partially seals the reaction chamber opening, or a cover that encapsulates, encloses or otherwise surrounds the reaction droplet, such as an oil or wax material that mixes with (then separates from and surrounds) the reaction droplet when the two are combined in the reaction chamber.

[0048] In general, the reaction chamber opening may be any shape or size (e.g., round, square, rectangular, hexagonal, octagonal, etc.) and may pass through the first (e.g., lower) plate, and into the reaction chamber well. In some variations, the reaction chamber opening passes through one or more actuation electrodes; in particular, the reaction chamber opening may be completely or partially surrounded by an actuation electrode.

[0049] FIG. 1 shows a top view of an exemplary air- matrix DMF apparatus 101. As shown, the DMF device may include a series of paths defined by actuation electrodes. The actuation electrodes 103 are shown in FIG. 1 as a series of squares, each defining a unit cell. These actuation electrodes may have any appropriate shape and size, and are not limited to squares. For example, the unit cells formed by the actuation electrodes in the first layer may be round, hexagonal, triangular, rectangular, octagonal, parallelogram-shaped, etc. In the example of FIG. 1 , the squares representing the unit cells may indicate the physical location of the actuation electrodes in the DMF device or may indicate the area where the actuation electrode has an effect (e.g., an effective area such that when a droplet is situated over the denoted area, the corresponding actuation electrode may affect the droplet' s movement or other physical property). The actuation electrodes 103 may be placed in any pattern. In some examples, actuation electrodes may span the entire corresponding bottom or top surface the air gap of the DMF apparatus. The actuation electrodes may be in electrical contact with starting sample chambers (not shown) as well as reagent chambers (not shown) for moving different droplets to different regions within the air gap to be mixed with reagent droplets or heated.

[0050] In the air-matrix apparatuses described herein, the first (lower) plate may also include one or more reaction chamber openings (access holes) 105, 105'. Access to the reaction chamber wells may allow reaction droplets to be initially introduced or for allowing reagent droplets to be added later. In particular, one or more reaction droplets may be manipulate in the air gap (moved, mixed, heated, etc.) and temporarily or permanently moved out of the air gap and into a reaction chamber well though a reaction chamber opening. As shown, some of the reaction chamber openings 105' pass through an actuation electrode. As will be shown in greater detail herein, the reaction chamber may itself include additional actuation electrodes that may be used to move a reaction chamber droplet into/out of the reaction chamber well. In some variations one or more actuation electrodes may be continued (out of the plane of the air gap) into the reaction chamber well.

[0051] In general, one or more additional reagents may be subsequently introduced either manually or by automated means in the air gap. In some instances, the access holes may be actual access ports that may couple to outside reservoirs of reagents or reaction components through tubing for introducing additional reaction components or reagents at a later time. As mentioned, the access holes (including reaction chamber openings) may be located in close proximity to a DMF actuation electrode(s). Access holes may also be disposed on the side or the bottom of the DMF apparatus. In general, the apparatus may include a controller 110 for controlling operation of the actuation electrodes, including moving droplets into and/or out of reaction chambers. The controller may be in electrical communication with the electrodes and it may apply power in a controlled manner to coordinate movement of droplets within the air gap and into/out of the reaction chambers. The controller may also be electrically connected to the one or more temperature regulators (thermal regulators 120) to regulate temperature in the thermal zones 115. One or more sensors (e.g., video sensors, electrical sensors, temperature sensors, etc.) may also be included (not shown) and may provide input to the controller which may use the input from these one or more sensors to control motion and temperature.

[0052] As indicated above, surface fouling is an issue that has plagued microfluidics, including DMF devices. Surface fouling occurs when certain constituents of a reaction mixture irreversibly adsorbs onto a surface that the reaction mixture is in contact with. Surface fouling also appears more prevalent in samples containing proteins and other biological molecules. Increases in temperature may also contribute to surface fouling. The DMF apparatuses and methods described herein aim to minimize the effects of surface fouling. One such way is to perform the bulk of the reaction steps in a reaction chamber that is in fluid communication with the air gap layer. The reaction chamber may be an insert that fits into an aperture of the DMF device as shown in FIGS. 2B and 2C. FIG. 2B shows the floor (e.g., first plate) of an air gap region coupled to a centrifuge (e.g., Eppendorf) tube 205 while FIG. 2C incorporates a well- plate 207 (e.g., of a single or multi-well plate) into the floor of the air gap region. A built-in well 209 may also be specifically fabricated to be included in the air-matrix DMF apparatus as shown in FIG. 2D. When a separate or separable tube or plate is used, the tubes may be coupled to the DMF device using any suitable coupling or bonding means (e.g., snap-fit, friction fit, threading, adhesive such as glue, resin, etc., or the like).

[0053] In general, having a dedicated reaction chamber within the DMF device minimizes surface fouling especially when the reaction is heated. Thus, while surface fouling may still occur within the reaction chamber, it may be mainly constrained to within the reaction chamber. This allows the majority of the air gap region floor to remain minimally contaminated by surface fouling and clear for use in subsequent transfer of reagents or additional reaction materials if needed, thus allowing for multi-step or more complex reactions to be performed. When the reaction step or in some instances, the entire reaction is completed, the droplet containing the product may be moved out of the reaction chamber to be analyzed. In some examples, the product droplet may be analyzed directly within the reaction chamber.

[0054] In order to bring the droplet(s) containing the starting materials and the reagent droplets into the reaction chamber, additional actuation electrodes, which may also be covered/coated with a dielectric and a hydrophobic layer (or a combined hydrophobic/dielectric layer), may be used. FIGS. 3A-3E shows a series of drawings depicting droplet 301 movement into and out of an integrated well 305. As this series of drawings show, in addition to lining the floor of the air gap layer, additional actuation electrodes 307 line the sides and the bottom of the well. In some variations, the same actuation electrode in the air gap may be extended into the reaction chamber opening. The actuation electrodes 307 (e.g., the reaction chamber actuation electrodes) may be embedded into or present on the sides and bottom of the well for driving the movement of the droplets into/out of the reaction chamber well. Actuation electrodes may also cover the opening of the reaction chamber. In FIG. 3 A, a droplet 301 (e.g., reaction droplet) in the air gap layer may be moved (using DMF) to the reaction chamber opening. The actuation electrodes 307 along the edge of the well and the sides of the well maintain contact with the droplet as it moved down the well walls to the bottom of the well (shown in FIGS. 3B and 3C). Once in the reaction chamber well, the droplet may be covered (as described in more detail below, either by placing a cover (e.g., lid, cap, etc.) over the reaction chamber opening and/or by mixing the droplet with a covering (e.g., encapsulating) material such as an oil or wax (e.g., when the droplet is aqueous). In general, the droplet may be allowed to react further within the well, and may be temperature-regulated (e.g., heated, cooled, etc.), additional material may be added (not shown) and/or it may be observed (to detect reaction product). Alternatively or additionally, the droplet may be moved out of the well using the actuation electrodes; if a mechanical cover (e.g., lid) has been used, it may be removed first. If an encapsulating material has been used it may be left on.

[0055] In some variations contacts may penetrate the surfaces of the reaction chamber. For example, there may be at least ten electrical insertion points in order to provide sufficient electrical contact between the actuation electrodes and the interior of the reaction chamber. In other examples there may need to be at least 20, 30, or even 40 electrical insertion points to provide sufficient contact for all the interior surfaces of the reaction chamber. The interior of the reaction chamber may be hydrophobic or hydrophilic (e.g., to assist in accepting the droplet). As mentioned, an electrode (actuation electrode) may apply a potential to move the droplets into and/or out of the well.

[0056] In general, the actuation electrodes may bring the droplet into the well in a controlled manner that minimizes dispersion of the droplet as it is moved into the well and thus maintaining as cohesive a sample droplet as possible. FIGS. 3D and 3E show the droplet being moved up the wall of the well and then out of the reaction chamber. This may be useful for performing additional subsequent steps or for detecting or analyzing the product of interest within the droplet, although these steps may also or alternatively be performed within the well. Actuation electrodes may be on the bottom surface, the sides and the lip of the well in contact with the air gap layer; some actuation electrodes may also or alternatively be present on the upper (top) layer.

[0057] In instances where the reaction compartment is an independent structure integrated with the DMF devices as those shown in FIGS. 2A and 2B, the thickness of the substrate (e.g., PCB) may be similar to what is commonly used in DMF fabrication. When the reaction compartment is an integrated well structure fabricated in the bottom plate of the DMF device as shown in FIG. 2D, the thickness of the substrate may be equivalent to the depth of the well.

[0058] In another embodiment, the electrodes embedded in the reaction compartments can include electrodes for the electrical detection of the reaction outputs. Electrical detection methods include but are not limited to electrochemistry. In some instances, using the changes in electrical properties of the electrodes when the electrodes contact the reaction droplet, reagent droplet, or additional reaction component to obtain information about the reaction (e.g., changes in resistance correlated with position of a droplet).

[0059] The apparatuses described herein may also prevent evaporation. Evaporation may result in concentrating the reaction mixture, which may be detrimental as a loss of reagents in the reaction mixture may alter the concentration of the reaction mixture and result in mismatched concentration between the intermediate reaction droplet with subsequent addition of other reaction materials of a given

concentration. In some variations, such as with enzymatic reactions, enzymes are highly sensitive to changes in reaction environment and loss of reagent may alter the effectiveness of certain enzymes. Evaporation is especially problematic when the reaction mixture has to be heated to above ambient temperature for an extended period of time. In many instances, microfluidics and DMF devices utilize an oil-matrix for performing biochemical type reactions in microfluidic and DMF devices to address unwanted evaporation. One major drawback of using an oil matrix in the DMF reaction is the added complexity of incorporating additional structures to contain the oil.

[0060] The methods and apparatuses described herein may prevent or limit evaporation by the use of wax (e.g., paraffin) in minimizing evaporation during a reaction. A wax substance may include substances that are composed of long alkyl chains. Waxes are typically solids at ambient temperatures and have a melting point of approximately 46°C to approximately 68°C depending upon the amount of substitution within the hydrocarbon chain. However, low melting point paraffins can have a melting point as low as about 37°C, and some high melting point waxes can have melting points about 70-80°C. In some instances higher melting point waxes may be purifying crude wax mixtures.

[0061] As mentioned, wax is one type of sealing material that may be used as a cover (e.g., within a reaction chamber that is separate from the plane of the air gap). In some variations, wax may be used within the air gap. In particular, the wax may be beneficially kept solid until it is desired to mix it with the reaction droplet so that it may coat and protect the reaction droplet. Typically the wax material (or other coating material) may be mixed with the reaction droplet and enclose (e.g., encapsulate, surround, etc.) the aqueous reaction droplet.

[0062] When a reaction droplet is maintained within a paraffin coating, not only is evaporation minimized, but the paraffin may also insulate the reaction droplet from other potentially reaction interfering factors. In some instances, a solid piece of paraffin or other wax substance may be placed within a thermal zone of the air gap layer of the DMF device. For example, during a reaction, actuation electrodes may move a reaction droplet to a wax (e.g., paraffin) body. Upon heating to a melting temperature, the wax body may melt and cover the reaction droplet. The reaction then may continue for an extended period of time (including at elevated temperatures) without need to replenish the reaction solvents, while preventing loss by evaporation. For example wax-encapsulated droplet may be held and/or moved to a thermal zone to control the temperature. The temperature may be decreased or increased (allowing control of the phase of the wax as well, as the wax is typically inert in the reactions being performed in the reaction droplet). The temperature at that particular thermal zone may be further increased to melt the paraffin and release the reaction droplet. The reaction droplet may be analyzed for the desired product when encapsulated by the liquid or solid wax, or it may be moved to another region of the DMF device for further reaction steps after removing it from the wax covering. Paraffins or other wax materials having the desired qualities (e.g. melting point above the reaction temperature) may be used. For example, paraffins typically have melting points between 50 and 70 degrees Celsius, but their melting points may be increased with increasing longer and heavier alkanes.

[0063] FIG. 4A shows a time-sequence images (numbered 1-4) taken from an example using a wax body within the air matrix as discussed above, showing profound reduction in evaporation as compared to a control without wax (shown in FIG. 4B, images 1-2). In FIG. 4A, the first image, in the top right, shows an 8 L reaction droplet 603 that has been moved by DMF in the air matrix apparatus to a thermal zone ("heating zone") containing a solid wax body (e.g., paraffin wall 601). Once in position, the reaction droplet may be merged with a solid paraffin wall (e.g., thermally printed onto DMF), as shown in image 2 of FIG. 4A, or the wax material may be melted first (not shown). In FIG. 4A image 3, the thermal zone is heated (63 °C) to or above the melting point of the wax material thereby melting the paraffin around the reaction droplet, and the reaction droplet is surrounded/encapsulated by the wax material, thus preventing the droplet from evaporation as shown in FIG. 4A images 3 and 4. Using this approach, in the example shown in FIG. 4A image 4, the volume of reaction droplets was maintained roughly constant at 63 °C for an incubation time approximately two hours long (120 min). An equivalent experiment without the paraffin wall was performed, and shown in FIG. 4B. The left picture (image 1) in FIG. 4B shows the reaction droplet 603 'at time zero at 63 °C and the right picture of FIG. 4B shows the reaction droplet after 60 minutes at 63 °C. As shown, the reaction droplet almost completely evaporated within approximately an hour' s time at 63 °C.

[0064] Through this approach of enclosing a droplet in a shell of liquid wax, the reaction volume and temperature are maintained constant without the use of oil, a humidified chamber, off-chip heating, or droplet replenishment methods. Waxes other than paraffin can be used to prevent droplet evaporation as long as their melting temperature is higher than the ambient temperature, but lower or equal to the reaction temperature. Examples of such waxes include paraffin, bees and palm waxes. The wax-like solids can be thermally printed on the DMF device surface by screen-, 2D- or 3D-printing. This wax- mediated evaporation prevention solution is an important advancement in developing air-matrix DMF devices for a wide variety of new high-impact applications.

[0065] As mentioned, the wax-based evaporation methods described may be used in conjunction with the DMF devices having a reaction chamber feature, or they may be used without separate reaction chambers. When used within a reaction chamber, the wax may be present in the reaction chamber and the reaction droplet may be moved to the reaction chamber containing wax for performing the reaction steps requiring heating. Once the heating step has completed, the reaction droplet may be removed from the reaction chamber for detection or to perform subsequent reaction steps within the air gap layer of the DMF device. [0066] In other embodiments, the wax may be liquid at room temperature or an oil can be used instead of a wax or a solid wax can be heated until it is liquid. Instead of a heated reaction zone with wax, the liquid wax or oil can be mixed with a reagent before introducing the mixture into the DMF device in order to prevent the reagent from evaporating. The reagent droplet will then have a liquid wax or oil shell surrounding the reagent, which can be manipulated as described above. In some

embodiments, the liquid wax/oil can be added manually to the reagent by the user. In other embodiments, the liquid wax/oil and the reagent can be dispensed from reservoirs, mixed together, and introduced into the DMF device using a pump by the DMF device.

[0067] The methods and apparatuses described herein may be used for preventing evaporation in air- matrix DMF devices and may enable facile and reliable execution of any chemistry protocols on DMF with the requirement for a temperature higher than the ambient temperature. Such protocols include, but are not limited to, DNA/RNA digestion/fragmentation, cDNA synthesis, PCR, RT-PCR, isothermal reactions (LAMP, rolling circle amplification-RCA, Strand Displacement Amplification-SDA, Helicase Dependent Amplification-HDA, Nicking Enzyme Amplification reaction-NEAR, Nucleic acid sequence- based amplification-NASBA, Single primer isothermal amplification-SPIA, cross-priming amplification- CPA, Polymerase Spiral Reaction-PSR, Rolling circle replication-RCR), as well as ligation-based detection and amplification techniques (ligase chain reaction-LCR, ligation combined with reverse transcription polymerase chain reaction-RT PCR, ligation-mediated polymerase chain reaction-LMPCR, polymerase chain reaction ligation detection reaction-PCR/LDR, ligation-dependent polymerase chain reaction-LD-PCR, oligonucleotide ligation assay-OLA, ligation-during-amplification-LDA, ligation of padlock probes, open circle probes, and other circularizable probes, and iterative gap ligation-IGL, ligase chain reaction-LCR, over a range of temperatures (37-100 °C) and incubation times (> 2 hr). Additional protocols that can be executed using the systems and methods described herein include hybridization procedures such as for hybrid capture and target enrichment applications in library preparation for new generation sequencing. For these types of applications, hybridization can last up to about 3 days (72h). Other protocols include end-repair, which can be done, for example, with some or a combination of the following enzymes: DNA Polymerase I, Large (Klenow) Fragment (active at 25°C for 15 minutes), T4 DNA Polymerase (active at 15°C for 12 minutes), and T4 Polynucleotide Kinase (active at 37°C for 30 minutes). Another protocol includes A-Tailing, which can be done with some or a combination of the following enzymes: Taq Polymerase (active at 72°C for 20 minutes), and Klenow Fragment (3'→5' exo-) (active at 37°C for 30 minutes). Yet another protocol is ligation by DNA or RNA ligases.

Manipulation and Processing of Encapsulated Droplets

[0068] Although the encapsulation of droplets in wax may prevent or reduce evaporation while executing chemistry protocols at elevated temperatures, after protocol completion, it has been discovered that when the droplet is removed and separated from the wax, e.g., by driving the droplet using the electrodes of the DMF apparatus, a small amount of liquid wax remains with the droplet as a coating even when the aqueous droplet is moved away from the wax, and that this wax coating may prevent or interfere with subsequent processing and analysis of the reaction droplet, particularly as the droplet cools and the wax solidifies around the droplet after the droplet is moved out of the heating zone. Therefore, in some embodiments, the wax encapsulated reaction droplet can be accessed through the wax coating using the systems and methods described herein, which enables facile and reliable execution of downstream biochemical processes.

[0069] To access the reaction droplet through the wax coating after the reaction droplet has been separated from the bulk liquid wax in the heating zone, an additional hydrophobic (e.g., oil) material may be added to the reaction droplet to help dissolve the solidified wax encapsulated the reaction droplet. For example, a carrier droplet (i.e., an aqueous droplet enclosed in a thin layer of oil) can be merged with the encapsulated reaction droplet. The carrier droplet gains access to the reaction droplet by having the oil from the carrier droplet dissolve and/or merge with the thin wax layer encapsulating the reaction droplet. Other materials other than oil may be used by the carrier droplet to break through the wax layer encapsulating the reaction droplet. For example, materials that are immiscible with aqueous reaction droplet and are capable of dissolving wax may be used, such as carbon tetrachloride, chloroform, cyclohexane, 1,2-dichloroethane, dichlorome thane, diethyl ether, dimethyl formamide, ethyl acetate, heptane, hexane, methyl-tert-butyl ether, pentane, toluene, 2,2,4-trimethylpentane, and other organic solvents. Other materials that may be used to break through the wax layer include ionic detergents such as cetyltrimethylammonium bromide, Sodium deoxycholate, n-lauroylsarcosine sodium salt, sodium n- dodecyl Sulfate, sodium taurochenodeoxycholic; and non-ionic detergents such as

dimethyldecylphosphine oxide (APO-10), dimethyldodecylphosphine oxide (APO-12), n-Dodecyl-β-Ο- maltoside (ULTROL®), n-dodecanoylsucrose, ELUGENT™ Detergent, GENAPOL® C-100,

HECAMEG®, n-Heptyl β-D-glucopyranoside, n-Hexyl-b-D-glucopyranoside, n-Nonyl-b-D- glucopyranoside, NP-40 Alternative, n-Octanoylsucrose, n-Octyl-b-D-glucopyranoside, n-Octyl-b-D- thioglucopyranoside, PLURONIC® F-127, Saponin, TRITON® X-100, TRITON® X-114, TWEEN® 20, TWEEN® 80, Tetronic 90R4. At temperatures where a wax remains liquid, a carrier droplet encapsulated with wax may also be used to break through the wax encapsulating the reaction droplet. However, for lower temperatures where the wax solidifies, a carrier droplet coated with wax generally cannot be used since solid wax will prevent droplet movement.

[0070] For example, FIG. 7A illustrates a setup similar or the same as that shown in FIG. 4A. The setup includes a DMF device interfaced to a heating element placed below or within the bottom DMF substrate, hence generating discrete heating zones 900 on the bottom DMF substrate. Alternatively, the heating element can be placed above or within the top substrate to form a heating zone on the top substrate. However, forming the heating zone on the bottom substrate allows visual access. On the bottom substrate, a hydrophilic region 902 is printed or otherwise formed or disposed around the actuating electrodes in the electrode array 904 that are in the heating zone 900. One or more wax walls 906 or wax structures, which can be solid at room temperature, can be assembled on the top substrate by, for example, thermal printing to overlay a portion of the hydrophilic region 902 adjacent to the electrodes in the heating zone 900 on the bottom plate when the DMF device is assembled. Alternatively, the wax walls 906 or wax structures can be formed directly on the bottom plate around the electrodes in the heating zone 900. In yet another embodiment, the wax walls 906 can be placed on a removable sheet that can be removably attached to either the top plate or the bottom plate. The removable sheet can have a hydrophobic surface on one side for interacting with the droplet and an adhesive on the other side for adhering to the top or bottom plate. Reagents and other materials can also be placed on the removable sheet to interact with the droplets. In some embodiments, the top plate or the bottom plate can be part of a removable cartridge that is combined with the other plate and electronics to form the working DMF device. As described herein, a reaction droplet 908 can be transported to the heating zone 900 along a path of actuating electrodes, which may be a relatively narrow path formed by a single line of actuating electrodes to the heating zone 900. Then the heating zone 900 is heated, and the wax wall 906 surrounding the heating zone 900 and reaction droplet 908 melts to encapsulate the reaction droplet 908 in liquid wax 910 as shown in FIG. 7B (frame i), thereby preventing or reducing evaporation from the reaction droplet 908 during the reaction protocol. The hydrophilic region 902 surrounding the heating zone 900 functions to pin or localize the liquid wax 910 in place in the heating zone 900 and allows the reaction droplet 908 to break away as described below.

[0071] As shown in FIG. 7B (frames ii-iv), the process of breaking away or separating the encapsulated reaction droplet 908 from liquid wax 910 can be accomplished by driving the aqueous reaction droplet 908 away from the heating zone 900 and the liquid wax 910 by actuating the actuating electrodes in the heating zone and path. As the aqueous reaction droplet 908 is actuated away from the heating zone 900, the hydrophilic region 902 surrounding the liquid wax 910 helps hold the liquid wax 910 in place as the reaction droplet 908 moves away from the heating zone 900, which causes the liquid wax 910 encasing the droplet 908 to begin to neck and eventually break off from the droplet 908, thereby leaving trace or small quantities of liquid wax 910 surrounding the separated reaction droplet 908. In general, the heating zone 900 is single use only to avoid cross-contamination. However, in situations where cross-contamination is not an issue, the heating zone 900 may be reused by heating and melting the wax within the heating zone and then moving the next droplet into the reheated liquid wax 910.

[0072] Because the reaction droplet may be surrounded by a thin layer of liquid wax 910 after separation from the heating zone 900, it may be difficult to merge the reaction droplet 908 with another aqueous droplet since the liquid wax 910 coating may act as a barrier. In addition, the liquid wax 910 may solidify as the droplet cools to form a physical barrier that impedes merger with another droplet. Therefore, to facilitate merging of a liquid wax 910 coated reaction droplet 908 or a cooled reaction droplet 908 with a solid wax coating with another droplet, a carrier droplet 912 can be used to merge with the reaction droplet 908 as shown in FIG. 7B (frame v). The carrier droplet 912 can be an aqueous droplet that is coated with a thin layer of oil or another organic solvent as described above. The aqueous portion of the carrier droplet 912 can include additional reagents, beads coated (or not) with DNA/RNA probes or antibodies or antigens for performing separations, uncoated beads, magnetic beads, beads coated with a binding moiety, solid phase reversible immobilization (SPRI) beads, water for dilution of the reaction droplet, enzymes or other proteins, nanopores, wash buffers, ethanol or other alcohols, formamide, detergents, and/or other moieties for facilitating further processing of the reaction droplet 908. As shown in FIG. 8A (frames i-iv), when the carrier droplet 912 and the reaction droplet 908 are moved by the actuating electrodes to the same location, the thin layer of oil surrounding the carrier droplet 912 can merge with the thin layer of liquid wax surrounding the reaction droplet 908, thereby facilitating the merger of the aqueous portions of the two droplets 908, 912 to form a combined droplet 914.

[0073] After the carrier droplet 912 has been merged with the reaction droplet 908, further processing of the combined droplet 914 can proceed, such as extracting an analyte from the combined droplet 914 and/or perform other steps such as hybridizing capture probes, digesting the reaction product using an enzyme, amplifying the reaction product with a set of primers, and the like. For example, the carrier droplet 912 can be carrying beads for extracting the analyte, e.g., DNA or RNA or proteins. When the droplets are merged, the beads, which can be magnetic, can be used to mix the combined droplet 914 by application of a magnetic field. The target analyte binds to the beads, which can be immobilized against the substrate by the magnetic field to form a bead pellet 916, as shown in FIG. 8B (frame i). Next, the combined droplet 914 can be moved away from the immobilized bead pellet 916, leaving the bead pellet 916 with bound analyte on the substrate, as shown in FIG. 8B (frames ii-iii). The combined droplet 914 can be moved away from the immobilized bead pellet 916 by actuating the electrodes.

Alternatively, the combined droplet 914 can be held in place while the bead pellet 916 is moved away from the combined droplet 914. The bead pellet 916 can be moved away and separated from the combined droplet 914 by, for example, moving the magnetic field (e.g., by moving the magnet generating the magnetic field) that is engaging the bead pellet 916 away from the combined droplet 914. In some embodiments, the combined droplet 914 can be actively immobilized through actuation of the electrodes in contact with the droplet and/or surrounding the droplet. Alternatively or in addition, the droplet 914 can be passively immobilized through natural adhesive forces between the droplet and substrate on which the droplet is contacting, as well as physical structures, such as retaining walls that partially surround the combined droplet 914 while having an opening for passing the bead pellet 916. As shown in FIG. 8C (frames i and ii), an aqueous droplet 918 can be moved over the bead pellet 916 to resuspend the beads with the bound analyte. See Example 3 described below for an embodiment of this procedure used for miRNA purification.

Plasma Extraction

[0074] FIGS. 9A-9E illustrate a DMF device 1000 with a sample inlet 1002 for receiving a sample, such as whole blood, and a sample outlet 1004 that deposits a droplet of the sample into the air gap between the top plate 1006 and bottom plate 1008 for manipulation by the actuation electrodes 1010. A separation membrane 1012, such as plasma separation membrane for separating plasma from whole blood, can be positioned between the sample inlet 1002 and sample outlet 1004 for filtering the sample.

[0075] To form the sample inlet 1002, a cover plate 1014, with a hole or port that can serve as the sample inlet 1002, can be placed over a hole or port in the top plate 1006 that can serve as the sample outlet 1004. The cover plate 1014 can be made of a hydrophobic or super -hydrophobic material or can be coated with a hydrophobic or super -hydrophobic layer 1016, as shown in FIG. 9B. A water droplet on a super-hydrophobic surface has a contact angle of greater than 150 degrees, while a water droplet on a hydrophobic surface has a contact angle greater than 90 degrees but less than 150 degrees. In addition, the top surface of the top plate 1006 can also be coated with a hydrophobic or super-hydrophobic material. The separation membrane 1012 can sandwiched between the hydrophobic surfaces of the cover plate 1014 and top surface of the top plate 1006. Making these surfaces hydrophobic prevents or greatly reduces the spread of blood out of the sample inlet 1002 and over the cover plate 1014. In addition, as the blood sample saturates and passes through the separation membrane 1012, the hydrophobic surfaces prevent or greatly reduce the spread of blood out of the membrane and into the gap between the cover plate 1014 and top plate 1006. The separation membrane 1012 can be made of a porous, hydrophilic material, with the pore size decreasing through the membrane thickness such that larger pores are located on the sample inlet 1002 side and smaller pores are located on the sample outlet 1004 side. In some embodiments, a gasket can be placed between the cover plate 1014 and top plate 1006 and around the separation membrane 1012 in order to prevent the spread of blood between the cover plate 1014 and top plate 1006. The sample outlet 1004, which can be formed as a hole in the top plate 1006, can optionally have a hydrophilic surface, such as from a hydrophilic coating or layer or from constructing the top plate 1006 from a hydrophilic material. A hydrophilic coating or layer may help draw the plasma through the separation membrane 1012 and into the sample outlet 1004.

[0076] For example, in one embodiment, a cover plate 1014 having about a 1 mm to 10 mm ID hole (e.g. a 4 mm ID hole) can be spray-coated on both sides with a super-hydrophobic layer (e.g., -500 nm layer of NeverWet®) followed by post-baking in an oven (100 °C, 10 min). The top plate 1006 of the DMF device 1000 can have about a 1 to 20 mm ID hole (e.g. a 10 mm ID hole) that is aligned with the hole in the cover plate 1014. The hole in the top plate 1006 may be larger than the hole in the cover plate 1014. For example, the hole in the top plate 1006 may be about 3 to 10 mm larger than the hole in the cover plate 1014. The top surface of the top plate 1006 that faces the cover plate 1014 can also be coated with a super-hydrophobic layer (as above) and the other side of the top plate 1006 with the ground electrode can be spin-coated with a hydrophobic layer (e.g., a 50 nm layer of Teflon- AF 1600) followed by post-baking as above. The bottom plate 1008 of the DMF device 1000 can be fabricated from a six- layer PCB substrate bearing copper electrodes (e.g., a 43 μπι thick layer) plated with nickel (e.g., a 185 μηι thick layer) and gold (e.g. a 3.6 μιη thick layer) that can be formed by conventional photolithography and etching techniques, and covered with dielectric tape (e.g. a 25 μπι thick layer) or coating. The PCB substrate can have an array of electrodes, such as one-hundred and twenty actuation electrodes (e.g. each 3.5 mm x 3.5 mm) with inter-electrode gaps of about 10 to 100 μπι (e.g. 40 μπι). The cover plate 1014 and top plate 100 can be assembled using screws, bolts, snaps, adhesives and/or other fasteners, with the separation membrane (e.g. PALL plasma separation membrane, Ann Arbor, MI) sandwiched in between. The bottom plate 1008 and top plate 1006 can be assembled with one or more spacers disposed between the two plates that separates the two plates by about 100 to 1000 μηι (e.g. about 300 μπι). For example, the spacer can be formed from one or more layers of double-sided tape (e.g. three pieces of double-sided tape having a total thickness of -300 μπι). The double-sided tape can provide dual functions of spacing and fastening the top plate to the bottom plate.

[0077] As described above, in some embodiments, one of the plates can be integrated into a reader device, and the other plate can be integrated into a removable cartridge, that when attached to the reader, form a two plate digital microfluidics system similar to that described herein. In addition, the actuation electrodes can be disposed on a film, which can also be made of a dielectric material. The film can be removably attached to one of the plates, such as the plate on the reader or the plate on the cartridge, while the other plate can have the ground electrode(s). For example, the film can be attached to the PCB substrate of the bottom plate.

[0078] The process for extracting plasma from whole blood samples into the DMF device and onto the electrodes is depicted in FIGS. 9A-9E. As shown, a sample of whole blood (e.g. 300 μΚ) can be spotted directly onto a prewetted (e.g. with tris buffer) separation membrane 1012— faster flow is achieved through the separation membrane 1012 as a result of enhanced capillary forces due to prewetting. The sample can have a volume less than 100 to 5000 μL·, or between 100 to 500 μί. The sample can be incubated for less than about 1 to 10 minutes (e.g. 1, 2, 3, 4, or 5 min) or between 1 to 10 minutes, and during that time plasma transfers from the bottom of separation membrane 1012 to the receiving DMF device surface with the actuation electrodes (e.g. the surface of the bottom plate) by gravity and capillary forces of the receiving DMF surface. In some embodiments, negative and/or positive pressure can be used to drive the fluid through the membrane. For example, a negative pressure can be generated between the plates at the fluid outlet using a pump, such as a displacement pump, and/or a positive pressure can be generated at the fluid inlet using a pump. The pressure and enhanced flow rate can be maintained below a desired threshold to reduce or prevent hemolysis, which can interfere with some types of nucleic acid assays. In some embodiments, the base flow rate using a 2 cm diameter membrane without pressure enhancement is between about 50 to 200 microliters per minute (i.e., 50, 60, 70, 80, 90, 100, 110, or 120 microliters per minute). The flow rate can depend on the size and characteristics of the membrane (i.e., pore size and pore distribution) as well as the magnitude of the applied positive and/or negative pressure. In some embodiments, the enhanced flow rate through the membrane with pressure enhancement can be less than 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100% more than the base flow rate through the membrane without pressure enhancement. The positive and/or negative pressure used to enhance the flow rate can be set or modulated to achieve the above flow rates.

[0079] Once the plasma contacts the DMF surface with the actuation electrodes 1010, the actuation electrodes contacting the plasma and around the contact point are activated, thereby pulling the plasma towards the DMF surface using electrowetting forces, and then a volume between 10-250 μL· (e.g., -70 μί) of the extracted plasma is actuated by actuation electrodes of the DMF device 1000 for further processing. In some embodiments, a sensor can be used for feedback control by detecting when the plasma contacts the bottom plate, and the actuation electrodes can be activated when the sensors detect the plasma on the plate. For example, the actuation electrodes and/or separate sensor electrodes can be used to measure capacitance, which changes when liquid covers the electrode. In some embodiments, the actuation electrodes 1012 below the sample outlet 1004 can be activated before the extracted plasma contacts the actuation electrodes and can be kept on until a sufficient amount of plasma has been extracted or can be kept on for a set or predetermined amount of time, such as about 1, 2, 3, 4, or 5 minutes. As mentioned above, one of the key features of the assembled architecture is the super hydrophobic environment surrounding the separation membrane 1012 which prevents or reduces the likelihood that blood sample overflows from the edge of the separation membrane and into the gap between the cover plate and top plate, which allows the DMF device to achieve a maximum or increased volume of plasma flow through the separation membrane. The systems and methods described herein result in extraction yields up to 2X the volume of plasma extraction from a given sample volume in comparison to benchtop lateral flow methods. Moreover, the quality of plasma collected using this DMF device is surprisingly comparable to plasma prepared by centrifugation and lateral-flow methods with respect to the degree of RBC hemolysis. The system is designed for facile reconfiguration and reprogramming, for accommodation of a wide range of blood volumes and plasma output.

EXAMPLE 1 : Device Fabrication and Assembly

[0080] DMF apparatuses that include embedded centrifuge tubes and/or well-plate wells (e.g., FIGS. 2B, 2C) were constructed by drilling 5.5 mm diameter holes into 3 mm thick PCB substrates, bearing copper (43 μπι thick) plated with nickel (185 μιη) and gold (3.6 μιη) for electrodes and conductive traces. Tubes and wells were then inserted into holes. DMF devices with embedded wells (e.g., FIG. 2D) were fabricated with holes (5 mm diameter, 10 mm depth) drilled in 15 mm thick PCB substrates. Actuation electrodes (each 10 mm x 10 mm) were formed by conventional photolithography and etching, and were coated with soldermask (-15 pm) as the dielectric. As shown in FIGS. 3A-3E, some of the electrodes were formed around and adjacent to the hole which served as the access point to reaction compartments. The electrical contact pads were masked with polyimide tape (DuPont; Hayward, CA), and the substrate was spin-coated with a 50 nm layer of Teflon- AF (1 % wt/wt in Fluorinert FC-40, 1500 rpm for 30 sec) and then baked at 100 °C for 3 h. The top plate of the DMF device, consisting of a glass substrate coated uniformly with unpatterned indium tin oxide (ITO) (Delta Technologies Ltd; Stillwater, MN) with 5.5 mm diameter PDMS plugs was spin-coated with 50 nm of Teflon-AF, as described above.

[0081] Prototype devices fabricated as described above performed better or as well as air-gap DMF apparatuses without reaction chambers. EXAMPLE 2: Quantifying evaporation prevention using waxes

[0082] To qualitatively evaluate the effect of wax bodies to prevent evaporation in our assays, loop mediated amplification (LAMP) reactions were executed while covered in liquid paraffin wax in tubes on the benchtop using a real-time PCR Machine. As shown in FIG. 5, the LAMP assay amplified miR-451, and the Ct values with and without paraffin were comparable (-13 cycles), indicating no significant effect on the assay. For LAMP on DMF, the reaction droplet (8 μυ> was driven to heating zone (as shown in FIG. 4A). There, the droplet wets the solid paraffin wax wall which under conditional heating at 63 °C will melt into liquid wax to encircle the reaction volume and maintain it intact throughout the incubation time at 63 °C. FIG. 6A shows a LAMP assay using paraffin-mediated methods, while FIG. 6B shows a LAMP assay using conventional methods. In FIG. 6A, the two upper traces are for a hemolyzed sampled while the two lower traces are for a non-hemolyzed sample. The two traces of each are to show repeatability of the runs using wax-mediated air matrix DMF. In FIG. 6B, the conventional LAMP assay for a hemolyzed sample are shown in upper two traces while the non-hemolyzed LAMP runs are shown in lower two traces. Again, the two upper and two lower traces each are to show result repeatability. The wax-mediated approach on DMF generated results comparable in Ct values to those generated by conventional LAMP in tubes as shown in FIGS. 6 A and 6B.

EXAMPLE 3: miRNA purification

[0083] Human Panel A beads from the TaqMan® miRNA ABC Purification Kit (Thermo Fisher Scientific). Aliquots of miRNA (4ul), or "reaction droplets", were loaded onto the DMF platform and brought to an array of electrodes overlaying the heating zone such that the droplet came into contact with the paraffin wall. The heating zone was then heated (65 °C, 2 min) to melt the paraffin around the droplet. Once the paraffin melted, the reaction droplets were driven away from the heating zone and merged with miRNA Binding Beads (4 x 106 beads; Fig 3A) in 2ul of mineral oil (i.e., carrier droplet). After mixing, the droplets were incubated (30°C, 30 min) to allow miRNA to bind to the miRNA Binding Beads.

Beads were captured by engaging an external magnet positioned below the bottom plate. Once a pellet was formed, the beads were recovered from solution by moving the magnet laterally along the bottom plate while simultaneously actuating the electrodes positioned below the reaction droplet (Fig 3B). The miRNA Binding Beads were then resuspended in water (4ul) using the DMF platform and transferred to a centrifuge tube for elution of miRNA (70°C, 3 min; Fig 3C). The efficiency of miRNA recovery from paraffin-encased miRNA droplets was evaluated against recovery from miRNA droplets without paraffin, but only in oil. RT-qPCR analysis of miRNA prepared by the system from samples with and without paraffin encasement generated comparable Ct values. EXAMPLE 4: Plasma separation device

[0084] Cover plates bearing 4 mm ID hole were spray-coated on both sides with a super - hydrophobic layer (-500 nm, NeverWet®) followed by post-baking in an oven (100 °C, 10 min). Device top plates with 10 mm ID holes were coated with a super -hydrophobic layer (as above) on one side and the side comprising of ground electrode was spin-coated with a hydrophobic layer (50 nm, Teflon- AF1600) followed by post-baking as above. The bottom plate of the DMF device was designed in CAD systems, and Gerber files were outsourced to a third-party company for fabrication. Briefly, a six-layer PCB substrate bearing copper electrodes (43 μπι thick) plated with nickel (185 μηι) and gold (3.6 μπι) were formed by conventional photolithography and etchingl5, and covered with dielectric tape (25 μπι). The substrate featured an array of one -hundred and twenty actuation electrodes (each 3.5 x 3.5 mm) with inter-electrode gaps of 40 μηι. The cover and top plates were assembled by means of screws with the plasma separation membrane (PALL, Ann Arbor, MI) sandwiched in between. The bottom and top plates were assembled with a spacer consisting of three pieces of double-sided tape (total thickness of -300 μπι).

[0085] A sample of whole blood (300 μί.) was spotted directly onto a prewetted (with tris buffer) separation membrane. The sample was incubated for 3 minutes and during that time plasma transferred from the bottom of the separation membrane to the receiving DMF device surface by capillary forces of the receiving DMF surface. Once the plasma contacted the DMF surface, the actuation electrodes were activated, thereby pulling the plasma towards the DMF surface using electrowetting forces. Once a sufficient volume of plasma was collected (-70 μί), the actuation electrodes were actuated by the DMF device for further processing of the collected plasma droplet.

[0086] When a feature or element is herein referred to as being "on" another feature or element, it can be directly on the other feature or element or intervening features and/or elements may also be present. In contrast, when a feature or element is referred to as being "directly on" another feature or element, there are no intervening features or elements present. It will also be understood that, when a feature or element is referred to as being "connected", "attached" or "coupled" to another feature or element, it can be directly connected, attached or coupled to the other feature or element or intervening features or elements may be present. In contrast, when a feature or element is referred to as being "directly connected", "directly attached" or "directly coupled" to another feature or element, there are no intervening features or elements present. Although described or shown with respect to one embodiment, the features and elements so described or shown can apply to other embodiments. It will also be appreciated by those of skill in the art that references to a structure or feature that is disposed "adjacent" another feature may have portions that overlap or underlie the adjacent feature.

[0087] Terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. For example, as used herein, the singular forms "a", "an" and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms "comprises" and/or "comprising," when used in this specification, specify the presence of stated features, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, and/or groups thereof. As used herein, the term "and/or" includes any and all combinations of one or more of the associated listed items and may be abbreviated as "/".

[0088] Spatially relative terms, such as "under", "below", "lower", "over", "upper" and the like, may be used herein for ease of description to describe one element or feature's relationship to another element(s) or feature(s) as illustrated in the figures. It will be understood that the spatially relative terms are intended to encompass different orientations of the device in use or operation in addition to the orientation depicted in the figures. For example, if a device in the figures is inverted, elements described as "under" or "beneath" other elements or features would then be oriented "over" the other elements or features. Thus, the exemplary term "under" can encompass both an orientation of over and under. The device may be otherwise oriented (rotated 90 degrees or at other orientations) and the spatially relative descriptors used herein interpreted accordingly. Similarly, the terms "upwardly", "downwardly", "vertical", "horizontal" and the like are used herein for the purpose of explanation only unless specifically indicated otherwise.

[0089] Although the terms "first" and "second" may be used herein to describe various

features/elements (including steps), these features/elements should not be limited by these terms, unless the context indicates otherwise. These terms may be used to distinguish one feature/element from another feature/element. Thus, a first feature/element discussed below could be termed a second feature/element, and similarly, a second feature/element discussed below could be termed a first feature/element without departing from the teachings of the present invention.

[0090] Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising" means various components can be co-jointly employed in the methods and articles (e.g., compositions and apparatuses including device and methods). For example, the term "comprising" will be understood to imply the inclusion of any stated elements or steps but not the exclusion of any other elements or steps.

[0091] As used herein in the specification and claims, including as used in the examples and unless otherwise expressly specified, all numbers may be read as if prefaced by the word "about" or

"approximately," even if the term does not expressly appear. The phrase "about" or "approximately" may be used when describing magnitude and/or position to indicate that the value and/or position described is within a reasonable expected range of values and/or positions. For example, a numeric value may have a value that is +/- 0.1% of the stated value (or range of values), +/- 1% of the stated value (or range of values), +/- 2% of the stated value (or range of values), +/- 5% of the stated value (or range of values), +/- 10% of the stated value (or range of values), etc. Any numerical values given herein should also be understood to include about or approximately that value, unless the context indicates otherwise. For example, if the value "10" is disclosed, then "about 10" is also disclosed. Any numerical range recited herein is intended to include all sub-ranges subsumed therein. It is also understood that when a value is disclosed that "less than or equal to" the value, "greater than or equal to the value" and possible ranges between values are also disclosed, as appropriately understood by the skilled artisan. For example, if the value "X" is disclosed the "less than or equal to X" as well as "greater than or equal to X" (e.g., where X is a numerical value) is also disclosed. It is also understood that the throughout the application, data is provided in a number of different formats, and that this data, represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular data point "10" and a particular data point "15" are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.

[0092] Although various illustrative embodiments are described above, any of a number of changes may be made to various embodiments without departing from the scope of the invention as described by the claims. For example, the order in which various described method steps are performed may often be changed in alternative embodiments, and in other alternative embodiments one or more method steps may be skipped altogether. Optional features of various device and system embodiments may be included in some embodiments and not in others. Therefore, the foregoing description is provided primarily for exemplary purposes and should not be interpreted to limit the scope of the invention as it is set forth in the claims.

[0093] The examples and illustrations included herein show, by way of illustration and not of limitation, specific embodiments in which the subject matter may be practiced. As mentioned, other embodiments may be utilized and derived there from, such that structural and logical substitutions and changes may be made without departing from the scope of this disclosure. Such embodiments of the inventive subject matter may be referred to herein individually or collectively by the term "invention" merely for convenience and without intending to voluntarily limit the scope of this application to any single invention or inventive concept, if more than one is, in fact, disclosed. Thus, although specific embodiments have been illustrated and described herein, any arrangement calculated to achieve the same purpose may be substituted for the specific embodiments shown. This disclosure is intended to cover any and all adaptations or variations of various embodiments. Combinations of the above embodiments, and other embodiments not specifically described herein, will be apparent to those of skill in the art upon reviewing the above description.