Magnetic particle separation device operating system and negative pressure filling

Abstract

Aspects of the present disclosure include a system for transporting liquid from a chamber into one or more collection vessels. The system may be semi-automatic or fully automatic. The system may be embodied in a sample preparation device such as a cylindrical cartridge. The system includes a plunger chamber that creates a negative pressure to fill one or more collection vessels. The plunger chamber is actuated using a pivotable lock arm and a trigger coupled to the arm. A method of using the system for transporting liquid from the chamber into one or more collection vessels is also provided.

Description

Technical Field

[0001] Cross - reference to Related Applications This application claims the benefit of U.S. Provisional Patent Application No. 63 / 143,587, filed on January 29, 2021, which is hereby incorporated by reference in its entirety.

[0002] Introduction The analysis of biological samples often involves determining the presence of a target analyte in the sample. If present, the target analyte is isolated from the sample and analyzed using downstream applications such as amplification, immunoassay, etc. Target analytes such as nucleic acids are isolated using techniques including column - based isolation and purification, reagent - based isolation and purification, magnetic bead - based isolation and purification, and other techniques. Reagents, kits, and instruments for the isolation and purification of nucleic acids are available. Sub - optimal sample preparation can lead to sub - optimal results in downstream applications, and thus optimized versions of kits have emerged to address variations in sample sources such as blood, plant tissue, fungi, bacteria, or viruses.

[0003] The sample preparation process includes releasing nucleic acids from their native biological sources using chaotropic nucleic acid extraction techniques (e.g., lysis of cells such as patient cells, or lysis of microorganisms such as viruses, bacteria, fungi, etc.), binding the nucleic acids to a solid phase (e.g., paramagnetic particles) using silica or iron oxide nucleic acid chemistry, separating the solid phase from the residual lysate solution using magnetic separation techniques, washing to remove unwanted materials, and eluting or separating the nucleic acids from the solid phase using fluid handling techniques. At the completion of the sample preparation protocol, the liquid containing the nucleic acids is transferred to a collection container such as a PCR tube or strip. There is interest in automating all or individual aspects of sample preparation to increase throughput, reduce user error, and / or limit the user's exposure to harmful substances.

Summary of the Invention

[0004] Aspects of this disclosure include a system for transporting a liquid from a chamber into one or more collection containers. The system may be semi-automatic or fully automatic. The system may reside in a sample preparation device such as a cylindrical cartridge. The system includes a plunger chamber that generates negative pressure to fill one or more collection containers. The plunger chamber is controlled using a pivotable lock arm and a trigger coupled to the arm.

[0005] A method is also provided for using a system to transport liquid from a chamber into one or more collection containers. [Brief explanation of the drawing]

[0006] [Figure 1] An exploded view of a sample preparation cartridge 100 according to one embodiment is shown. [Figure 2A] Figure 1 shows the inside of the cylindrical structure 110 of the sample preparation cartridge. [Figure 2B] A plunger assembly according to one embodiment is shown. [Figure 2C] The sealing plate assembly is shown from below. The pivotable locking arm is shown in a separated view. The trigger is shown in a further separated view. [Figure 2D] The pivotable lock arm 151 and cap 160 are shown. [Figure 3] A cutaway view of a sample preparation cartridge according to one embodiment of the present disclosure is shown. Some components of the cartridge are not shown. [Figure 4] A cutaway view of a sample preparation cartridge according to one embodiment of the present disclosure is shown. Some components of the cartridge are not shown. [Figure 5A] This shows a sample preparation cartridge 100 in a pre-operational stage, where the cap is in the pre-operational stage and the spring has not yet been activated. [Figure 5B] This shows a sample preparation cartridge 100 in a pre-operational stage, where the cap is in the pre-operational stage and the spring has not yet been activated. [Figure 5C] This shows a sample preparation cartridge 100 in a pre-operational stage, where the cap is in the pre-operational stage and the spring has not yet been activated. [Figure 5D] This shows a sample preparation cartridge 100 in a pre-operational stage, where the cap is in the pre-operational stage and the spring has not yet been activated. [Figure 6A] The sample preparation cartridge 100 is shown in the operational stage, with the cap in the post-operation stage and the spring activated. [Figure 6B] The sample preparation cartridge 100 is shown in the operational stage, with the cap in the post-operation stage and the spring activated. [Figure 6C] The sample preparation cartridge 100 is shown in the operational stage, with the cap in the post-operation stage and the spring activated. [Figure 6D] The sample preparation cartridge 100 is shown in the operational stage, with the cap in the post-operation stage and the spring activated. [Figure 7A] The sample preparation cartridge 100 is shown in the negative pressure trigger stage. The lock arm 151 is pivoted relative to the shaft 152 of the sealing plate assembly. [Figure 7B] The sample preparation cartridge 100 is shown in the negative pressure trigger stage. The lock arm 151 is pivoted relative to the shaft 152 of the sealing plate assembly. [Figure 7C] The sample preparation cartridge 100 is shown in the negative pressure trigger stage. The lock arm 151 is pivoted relative to the shaft 152 of the sealing plate assembly. [Figure 7D] The sample preparation cartridge 100 is shown in the negative pressure trigger stage. The lock arm 151 is pivoted relative to the shaft 152 of the sealing plate assembly. [Figure 8A] Further details of the fluid channel located at the bottom of the cartridge are shown. [Figure 8B] Further details of the fluid channel located at the bottom of the cartridge are shown. [Figure 9A]The configuration of channel 145 connecting chamber 140 to collection container 130 and channel 146 connecting chamber 120 to collection container 130 is shown. [Figure 9B] The configuration of channel 145 connecting chamber 140 to collection container 130 and channel 146 connecting chamber 120 to collection container 130 is shown. [Figure 9C] The configuration of channel 145 connecting chamber 140 to collection container 130 and channel 146 connecting chamber 120 to collection container 130 is shown. [Figure 10A] An additional view of the sealing plate assembly is shown. [Figure 10B] An additional view of the sealing plate assembly is shown. [Figure 10C] An additional view of the sealing plate assembly is shown. [Figure 11A] The cap 160 shown alone at different angles is shown. [Figure 11B] The cap 160 shown alone at different angles is shown. [Figure 11C] The cap 160 shown alone at different angles is shown. [Figure 12A] A device with a rotatable platform and a magnet is shown. [Figure 12B] A device with a rotatable platform and a magnet is shown. [Figure 13] An exploded view of a sample preparation cartridge 300 according to an embodiment is shown. [Figure 14] The plunger assembly and the trigger assembly are shown. [Figure 15] A cutaway view of the plunger assembly is shown. [Figure 16] The plunger assembly is shown. [Figure 17A] The sample preparation cartridge with the cap open before the plunger assembly is operable is shown. [Figure 17B] The sample preparation cartridge with the cap open before the plunger assembly is operable is shown. [Figure 17C]This shows the sample preparation cartridge with the cap open, before the plunger assembly is operational. [Figure 17D] This shows the sample preparation cartridge with the cap open, before the plunger assembly is operational. [Figure 18A] This shows the sample preparation cartridge with the cap closed after the plunger assembly has been activated. [Figure 18B] This shows the sample preparation cartridge with the cap closed after the plunger assembly has been activated. [Figure 18C] This shows the sample preparation cartridge with the cap closed after the plunger assembly has been activated. [Figure 18D] This shows the sample preparation cartridge with the cap closed after the plunger assembly has been activated. [Figure 19A] This shows the sample preparation cartridge during the negative pressure trigger phase. [Figure 19B] This shows the sample preparation cartridge during the negative pressure trigger phase. [Figure 19C] This shows the sample preparation cartridge during the negative pressure trigger phase. [Figure 19D] This shows the sample preparation cartridge during the negative pressure trigger phase. [Figure 20A] This shows a top view of the sealing plate assembly of the sample preparation cartridge 300. [Figure 20B] This shows a diagram of the bottom of the cap 360 of the sample preparation cartridge 300. [Figure 21A] This shows a sample preparation cartridge with the cap open. [Figure 21B] This shows the sample preparation cartridge with the cap closed. [Figure 21C] This shows a magnetic accessory configured to hold a sample preparation cartridge. [Modes for carrying out the invention]

[0007] Aspects of the present disclosure include a system for transporting a liquid from a chamber into one or more collection containers. The system may be semi-automatic or fully automatic. The system may be embodied in a sample preparation device such as a cylindrical cartridge. The system includes a plunger chamber that generates negative pressure to fill one or more collection containers. The plunger chamber is controlled using a pivotable lock arm and a trigger coupled to the arm.

[0008] A method is also provided for using a system to transport liquid from a chamber into one or more collection containers.

[0009] Before the system, sample preparation device, and method are described in more detail, it should be understood that this disclosure is not limited to the specific embodiments described and is therefore, of course, subject to change. It should also be understood that the terms used herein are for the purpose of describing specific embodiments only and are not intended to be limiting.

[0010] Where a range of values ​​is provided, unless the context explicitly indicates otherwise, it is understood that each intermediate value between the upper and lower limits of that range, up to one-tenth of the lower limit unit, and any other listed values ​​or intermediate values ​​within this range are included in the System, Sample Preparation Devices and Methods. The upper and lower limits of these smaller ranges may independently be included in smaller ranges and are likewise included in the System, Sample Preparation Devices and Methods, according to any specifically excluded limits in the range described. Where a range described includes one or both limits, ranges excluding one or both of those limits are also likewise included in the System, Sample Preparation Devices and Methods.

[0011] Certain ranges having a number preceded by the term “approximately” are presented herein. In this specification, the term “approximately” is used to provide literal support for the exact number preceded by it, and for numbers that are close to or approximate the number preceded by the term. When determining whether a number is close to or approximates a specifically enumerated number, that close or approximate unenumerated number may be a number that, in the context in which it is presented, provides a substantial equivalent of the specifically enumerated number.

[0012] Unless otherwise defined, all technical and scientific terms used herein have the same meanings as those generally understood by those skilled in the art to which this disclosure belongs. Any methods and materials similar to or equivalent to those described herein may also be used in the practice or testing of the systems, sample preparation devices and methods, but representative and exemplary systems, sample preparation devices and methods are described below.

[0013] All publications and patents cited herein are incorporated herein by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference, and are incorporated herein by reference to disclose and illustrate methods and / or materials relating to the cited publications. Any citation of a publication is of its disclosure prior to the filing date, and the present invention should not be construed as acknowledging that the present invention does not have prior rights to such publication by features of the prior invention. Furthermore, the dates of the publications provided may differ from the actual publication dates, and these may need to be verified independently.

[0014] It should be noted that, as used herein and in the appended claims, the singular forms “a,” “an,” and “the” refer to multiple subjects unless the context clearly indicates otherwise. It should also be noted that the claims may be designed to exclude any optional elements. Thus, this statement is intended to function as an antecedent for the use of exclusive terms such as “solely” and “only,” or for the use of “negative” limitation, relating to the enumeration of claim elements.

[0015] As will be apparent to those skilled in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has individual components and features that can be readily separated from or combined with any of the features of several other embodiments without departing from the scope or spirit of the sample preparation cartridge, method and sample preparation unit. Any enumerated method may be performed in the order of the enumerated events or in any other logically possible order.

[0016] System for negative pressure filling As summarized above, aspects of the present disclosure include systems and sample preparation devices, such as sample preparation cartridges, configured to transport liquid from a chamber into one or more collection containers. These systems and sample preparation devices comprising such systems are useful for transporting solutions containing or suspected to contain a target analyte (e.g., elution buffer) into one or more collection containers for analysis of the target analyte. Semi-automatic or fully automated filling of the collection containers reduces reliance on the user while minimizing user error. Using negative pressure to fill the collection containers can have several advantages compared to directly forcing the liquid out using a plunger in the chamber. For example, the use of negative pressure can increase the amount of liquid transferred from the chamber, minimizing the loss of the target analyte. In addition, the shapes of the chamber and plunger do not need to be perfectly matched to generate a leak-proof seal sufficient to force the liquid out of the chamber.

[0017] According to a particular embodiment, a system for transporting liquid from a chamber into one or more collection containers may include a plunger chamber, a pivotable locking arm, and a trigger attached to the arm. The plunger chamber may include a plunger assembly and a spring. In a particular embodiment, the spring portion of the plunger assembly may be positioned outside the plunger chamber. When activated, the plunger assembly compresses the spring. When the pivotable locking arm is in a first position, it engages with the plunger assembly to activate the plunger assembly. When the pivotable locking arm is in a second position, it disengages from the plunger assembly, allowing the plunger assembly to retract away from the spring and create a vacuum in the plunger chamber. A trigger is coupled to the pivotable locking arm. When the trigger is engaged by force or physical interference, it disengages the locking arm and the plunger assembly. The plunger chamber is fluidly connected to a channel that connects the chamber to one or more collection containers. The vacuum created in the plunger chamber draws liquid from the chamber through the channel into one or more collection containers.

[0018] In certain embodiments, the system includes two collection containers. In certain embodiments, the system includes three collection containers. In certain embodiments, the system includes four or more collection containers. In certain embodiments, each of the two or more collection containers contains substantially equal volumes of liquid in the chamber. For example, the volumes of liquid transferred to two or more containers may differ by no more than ±20%. In certain examples, the chamber containing the liquid has a volume of about 1 ml to 100 ul, for example, 750 to 100 ul, 500 to 100 ul, or 250 to 100 ul. The system may transfer the entire volume or a portion thereof to the collection chamber. When there are two or more collection chambers, the system may transfer substantially equal volumes of liquid to two or more containers. In certain cases, the chamber may contain about 250 ul of liquid, and the system may transfer the liquid to two collection containers, each receiving about 125 ul of liquid.

[0019] In a particular embodiment, the system includes two collection containers, and a channel connecting the chamber to the two collection containers branches into two subchannels that are fluidly connected to the two collection containers.

[0020] The collection container may be any suitable container. In certain embodiments, the collection container may be a PCR tube, or a similar thin-walled container or strip that facilitates a thermal circulation or isothermal reaction.

[0021] According to a particular embodiment, the plunger chamber is substantially cylindrical in shape, and the plunger assembly includes a rigid structure and a cylindrical compressible structure. The rigid structure includes a narrow elongated region having a substantially curved end and a substantially flat end opposite to the curved end. The curved end engages with the lock arm, and the flat end is attached to the compressible structure. The flat end may be wider to improve attachment with the compressible structure. The compressible structure forms a seal with the inner surface of the plunger chamber. The curved end reduces friction between the plunger assembly and the lock arm, thereby reducing the amount of force required to cause relative movement between the plunger assembly and the lock arm. The seal formed between the compressible structure and the inner surface of the plunger chamber facilitates the purging of air from the chamber and associated channels when the lock arm pushes the plunger assembly down. The seal also facilitates the generation of negative pressure by forming a vacuum when the lock arm releases downward pressure on the plunger assembly, thereby allowing the plunger assembly to retract. The spring facilitates the formation of a vacuum by increasing the force that causes the plunger assembly to retract after the downward pressure by the lock arm is released. Although the plunger chamber is exemplified herein as having a cylindrical structure, other shapes of the plunger chamber are also possible. For example, the compressible structure of the plunger chamber and plunger assembly may be cubic or cubic in shape.

[0022] The height and diameter of the plunger chamber can be varied based on the volume of liquid in the chamber, the viscosity of the liquid, the amount of liquid being transferred, the material of the spring, etc. In certain examples, the plunger chamber may have a height of 10 cm to 1 cm, for example, 5 cm to 1 cm, 4 cm to 1 cm, or 3 cm to 1 cm. The plunger chamber may have an inner diameter of 1 cm to 0.1 cm, for example, 1 cm to 0.3 cm or 1 cm to 0.5 cm. The plunger chamber may have an inner volume of about 1 ml to 200 ul, for example, 900 ul to 300 ul, 800 ul to 300 ul, or 700 ul to 400 ul. The rigid structure of the plunger chamber and plunger assembly may be formed from plastic. The compressible structure of the plunger assembly may be formed from rubber or a similar material. The flat end of the plunger assembly may be substantially cylindrical and may have a diameter that matches the diameter of the compressible structure. The compressible structure may be substantially cylindrical in shape and may have a diameter such that it forms a seal with the inner surface of the plunger chamber. The seal may be tight enough to prevent a considerable amount of air from passing through the seal while allowing relative movement of the plunger assembly and the plunger chamber. A spring may be disposed within the plunger chamber below the plunger assembly and in contact with the compressible structure. The spring may have a diameter substantially equal to or smaller than the diameter of the plunger chamber. The height of the spring may be such that it is not compressed in the absence of downward pressure from the lock arm. In certain examples, the height of the spring may be such that it is slightly compressed in the absence of downward pressure from the lock arm. The plunger chamber includes an opening at its upper end, which is large enough to allow the plunger assembly and spring to be placed inside the plunger chamber. The bottom end of the plunger chamber includes a smaller opening configured to accommodate the plunger assembly and spring, and is wide enough to allow air movement. In certain embodiments, the bottom end of the plunger chamber is substantially flat. In other embodiments, the bottom end of the plunger chamber may be curved.

[0023] In certain embodiments, a pivotable lock arm may be a substantially flat, elongated structure comprising a first region and a second region. Optionally, the second region may include an extension extending below the plane of the flat, elongated structure. The first region may be pivotably mounted on a shaft, and the second region engages with a plunger assembly. The second region may have a reduced surface area compared to the first region. The reduced surface area represents a narrower surface available for contact with the plunger assembly. The narrower surface facilitates the relief of pressure from the plunger assembly when the lock arm is moved by requiring relatively small movements. The surface area of ​​the second region may be reduced by the presence of a notch in the second region to provide a narrower surface. In certain embodiments, the notch may be located on the side edge of the second region of the lock arm. In certain embodiments, the notch may be located in the central area of ​​the second region of the lock arm, for example, the notch may be a through-hole sized so that the curved end of the plunger assembly passes through the hole. In certain embodiments, the second region includes two notches, with the first and second notches located on opposite side edges of the second region, or the first notch is located on a side edge and the second notch is located in the center of the second region. The second region of the lock arm may include a first area that contacts the curved end of the plunger assembly and a second area adjacent to the first area, the second area including a bevel leading to the notch. The bevel can accelerate the movement of the curved end of the plunger assembly toward the notch, thereby increasing the momentum with which the plunger assembly slides into the notch. Thus, the bevel can reduce the amount of force required to move the lock arm relative to the plunger assembly. The notch may be curved, and the diameter of the curve may be large enough to allow the curved end of the plunger assembly to slide through. In embodiments where the notch is located on only one side edge of the second region of the lock arm, it is understood that the notch is located on the side edge that moves toward the plunger assembly to release downward pressure on the plunger assembly.

[0024] In certain embodiments, the trigger may be detachably coupled to the lock arm. The trigger may be made of a magnetically responsive material and may be configured to snap into or onto the lock arm. The magnetically responsive material may be iron, nickel, cobalt, its oxides, its derivatives, or combinations thereof. In other embodiments, the trigger may be fixedly coupled to the lock arm. For example, the lock arm and trigger may be a single structure formed by injection molding. In certain embodiments, the lock arm may be substantially planar, and the trigger may extend downward from the lock arm. In other embodiments, the lock arm and trigger may be located in the same plane.

[0025] To make the plunger assembly operable, the system may include an actuation assembly for positioning a pivotable lock arm in a first position. The actuation assembly may include a cap. The cap may include a first surface opposite to a second surface, and a plurality of push rods extending from the second surface. The first region of the pivotable lock arm may include an opening through which the lock arm is pivotably mounted on the shaft, and the first region includes a lip region surrounding the opening, the lip region configured to provide a surface area that can be engaged by the push rods at two contact points located substantially opposite each other in the diametrically opposed direction. The system may include a sealing plate assembly having a substantially planar region with an upper surface opposite to a lower surface, the shaft being located within the sealing plate assembly and extending at least below the plane of the sealing plate assembly, and optionally above the plane of the sealing plate assembly. The lock arm is positioned pivotably and slidably on the shaft. The lock arm is positioned adjacent to the lower surface of the sealing plate assembly before being engaged by the push rods at two contact points. The locking arm is configured to slide downwards on the shaft, away from the lower surface, when it engages with the push rod.

[0026] The shaft may have a larger effective diameter in the region adjacent to the lower surface compared to the region further away from the lower surface, so that the pivotable arm can pivot more freely around the shaft when the lock arm is pushed away from the lower position adjacent to the lower surface.

[0027] The sealing plate assembly may include two through apertures positioned on opposite sides in the diametrical direction of the shaft, the apertures being aligned with contact points on the lock arm and the push rod so that the push rod passes through the apertures and contacts the lock arm.

[0028] The shaft may be hollow and may include a recess located on its inner surface. The cap may include a centrally located engaging structure extending from a second surface of the cap, the engaging structure including a projection that reversibly engages with the recess. When the projection is positioned in the recess, the push rod is not in contact with the locking arm.

[0029] The engaging structure may be a rod-shaped structure comprising a plurality of fingers extending from the distal end of the rod-shaped structure, the projection being located at the distal end of the plurality of fingers, the shaft in the sealing plate assembly having a diameter greater than the diameter of the engaging structure, and the shaft including a lip at its distal end. When downward pressure is applied to the cap, the projection disengages from the recess, the projection is positioned below the lip, and the engaging structure is allowed to slide downward on the shaft so that the cap cannot retract.

[0030] In certain embodiments, a sample preparation device, such as a cylindrical cartridge described herein, may include a disclosed system for transporting liquid from a chamber into one or more collection containers. Thus, the sample preparation device may include a chamber and one or more collection containers. The sample preparation device may further include a plunger chamber, a pivotable locking arm, a trigger, a sealing plate assembly, and a cap. In the sample preparation device, the sealing plate assembly is fixedly positioned across the upper end of the device, and the cap is fixedly positioned across the sealing plate assembly. In the pre-operation stage, the cap is fixedly positioned spaced apart from the upper surface of the sealing plate assembly. In the post-operation stage, the cap is fixedly positioned adjacent to the upper surface of the sealing plate assembly. The sample preparation device may also include an additional chamber for sample preparation. For example, the device may include a chamber in which a biological sample is combined with a lysis buffer and a target analyte, such as magnetic particles that bind to nucleic acids present in the sample. The magnetic particles may be referred to as capture beads. These magnetic particles may be functionalized to capture the target analyte. For example, the magnetic particles may include a surface that binds to nucleic acids. The magnetic particles may also include immobilized oligonucleotides, peptides, and / or proteins that bind to the target analyte. The device may also include a chamber for removing molecules, cellular debris, etc., that are nonspecifically attached to the magnetic particles. Such a chamber may contain a non-aqueous phase that is immiscible with the lysis buffer, or it may contain a washing solution.

[0031] As used herein, the term “distal end” refers to the end located further away from the reference point, compared to the proximal end, which is located closer to the reference point. In this context, the distal end of a rod-shaped structure is the end located toward the bottom end of the rod-shaped structure, while the upper end of the rod-shaped structure is attached to the cap. The terms “horizontal” and “vertical” are used to indicate an absolute reference point, i.e., direction relative to the Earth's surface. However, these terms should not be interpreted as requiring structures to be absolutely parallel or absolutely perpendicular to each other. For example, a first vertical structure and a second vertical structure are not necessarily parallel to each other. The terms “up” and “bottom” or “upper” or “lower” are used, with “up” referring to the surface that is always higher than the bottom relative to the absolute reference point, i.e., the Earth's surface. The terms “upward” and “downward” are also relative to the absolute reference point, with “upward” always being against Earth's gravity, and “downward” always being toward Earth's gravity.

[0032] In certain embodiments, the sample preparation device may be a cylindrical cartridge comprising the system for transporting liquid from a chamber into one or more collection containers. Thus, a cylindrical cartridge is provided comprising a system of components for transferring liquid from a chamber into one or more collection containers. The cylindrical cartridge may include a cylindrical structure having an upper end, a lower end, and an annular wall extending between the upper and lower ends. A chamber containing liquid, such as elution buffer, may be located within the annular wall. The cylindrical structure may include a plurality of chambers located within the annular wall, the chambers extending between the outer surface of the annular wall and the inside of the cylindrical structure. The cylindrical cartridge includes the plunger chamber described herein, a pivotable locking arm, a trigger, a sealing plate assembly, and a cap. While the sample preparation device is exemplified as a cylindrical cartridge, the cylindrical shape is not essential. For example, instead of a cylindrical structure, a sample preparation cartridge comprising a system for transporting liquid from a chamber into one or more collection containers may have a cubic or cubic shape.

[0033] Further details of the systems and sample preparation devices of this disclosure are provided with reference to drawings illustrating specific embodiments. It is understood that the systems and sample preparation devices, such as cartridges, described herein are not limited to specific figures and may be modified.

[0034] Figure 1 shows an exploded view of a sample preparation device provided herein. The sample preparation device is a cylindrical cartridge including a cylindrical structure 110 with a chamber 120. The chamber 120 is fluidly connected to a collection container 130 and a plunger chamber 140. A plunger assembly 141 and a spring 142 are disposed within the plunger chamber 140. The upper end of the cylindrical structure 110 is closed by a sealing plate assembly 150. The sealing plate assembly 150 is connected to a cap 160. A trigger 170 is also depicted. A cover 180 is attached to the outer surface of the annular wall. Sealing films 190a and 190b are attached to the upper and bottom surfaces of the bottom surface of the cylindrical structure, respectively, forming a channel that fluidly connects the chamber 120 to the collection container 130 and the plunger chamber 140. A clip 195 for attaching the collection chamber to the bottom surface of the cylindrical structure is shown. An engagement structure 162 extending from the lower surface of the cap is depicted. The engagement structure 162 includes three projections that engage with recesses present in the shaft 152 of the sealing plate assembly when the cap is in the pre-actual position. These projections are pushed under the lip of the shaft and are not retractable when the cap is in the lower position.

[0035] Figure 2A shows the inside of the cylindrical structure 110 of the sample preparation cartridge depicted in Figure 1. The channel 145 that fluidly connects the chamber 120 to the collection container is partially visible. The plunger chamber 140 is also depicted. Figure 2B shows the plunger assembly 141 having a rigid structure 141a with a curved end and a compressible structure 141b. The figures are not drawn to a constant scale.

[0036] Figure 2C shows the sealing plate assembly viewed from below. A shaft 152 is visible, positioned in the center. A lock arm 151 is depicted, slidably and pivotably mounted on the shaft. Enlarged views of the lock arm 151 and the trigger 170 attached to the lock arm 151 are shown.

[0037] Figure 2D shows the pivotable lock arm 151 and cap 160. The top two images show the pivotable lock arm 151 in an inverted orientation. The lock arm 151 includes a first region having an opening 156 and a second region that is narrower than the first region and includes a notch 152. The second surface of the lock arm is shown in the topmost image. The second surface forms a bevel 153 leading to the notch, to facilitate movement of the curved end of the plunger assembly from the region 154 of the second surface to the notch 152. The third image depicts the lock arm in a front-up orientation. The area of ​​the lock arm surrounding the opening 156 provides a lip including two contact points 155a and 155b on the upper surface that contact the push rods 161a and 161b, respectively. The cap 160 is depicted in an inverted orientation. The push rod is designed to reduce friction between the upper surface of the lock arm and the push rod by applying pressure to the lock arm 151 using a relatively small contact point when the lock arm is moved around the central opening 156 or when the shaft rotates while the lock arm is held in place.

[0038] Figure 3 shows a cutaway view of the sample preparation device. Chamber 120, from which the liquid is transferred to a collection container (not shown) and a plunger chamber 140, is depicted in different orientations. Channels 145 and 146, which fluidically connect the chamber, the plunger chamber, and the collection container, are partially depicted. Specifically, channel 145 connects chamber 120 to the collection container, while channel 146 connects plunger chamber 140 to the collection container.

[0039] Figure 4 shows a cutaway view of the sample preparation cartridge. The sample preparation device includes a chamber 120 and a plunger chamber 140. A plunger assembly 141 and a spring 142 are disposed within the plunger chamber 140.

[0040] Figures 5A–5D show the sample preparation cartridge 100 in the pre-operation stage, where the cap is in the “pre-operation” stage and the spring has not yet been activated. In Figure 5A, the cap 160 is in the pre-operation stage. In the pre-operation stage, the projection of the engagement structure 162 (see Figure 1) is locked in a recess located on the inner surface of the shaft 152. Figure 5B is a cutaway view of the cartridge 100 from the top. Parts of the cap 160 and the sealing plate assembly are not shown to allow for a clearer image. The engagement structure 162 is partially visible in Figure 5B within the shaft in the sealing plate assembly. The lock arm 151, with a notch 152 located on the side edge of the lock arm, is also visible. Figure 5C is a magnified view of the area of ​​the lock arm 151, which extends downward from the rest of the plane of the lock arm. The trigger 170 is attached to the lock arm 151. In the pre-operation stage, the lock arm and trigger are positioned at a higher level within the cartridge. Figure 5D shows an internal view of the cartridge. The rigid structure 141a of the plunger assembly 141 is in contact with the lock arm, and the compressible structure 141b is in contact with the spring 142. When the cap is in the pre-actual stage, the spring 142 is not compressed.

[0041] Figures 6A–6D show the sample preparation cartridge 100 in the actuated stage, with the cap in the post-actuated stage and the spring actuated. The cap 160 is pressed down. Push rods 161a and 161b drive the lock arm 151 and trigger 170 downward. The lock arm 151 pushes down the plunger assembly 141, which then compresses the spring 142. The downward movement of the plunger assembly 141 expels air from the plunger chamber 140. The system is now actuated. In Figure 6A, the chamber 120 is shown filled with liquid to be transferred to the collection container 130. The cover 180 is also visible. In Figure 6B, the lock arm 151 is moving down the shaft 152. A cutaway shows the cap engagement structure 162 inserted into the shaft 152 and the push rods 161a and 161b pushed down on the lock arm 151. Figure 6C shows a magnified view of a portion of the downward-extending lock arm 151 and the trigger 170 attached to the lock arm 151. Compared to Figure 5C, the lock arm and trigger move downward within the cartridge. Figure 6D shows the inside of the cartridge. The engagement structure 162 of the cap 160 is located within the shaft 152 of the sealing plate assembly, and a projection of the engagement structure is located below the end of the shaft 152, where it prevents the cap from being removed.

[0042] Figures 7A–7D show the sample preparation cartridge 100 in the negative pressure trigger phase, where the rigid structure of the plunger assembly moves through the notch in the lock arm 151, and the downward pressure from the plunger assembly is removed. Removing the downward pressure causes the spring to launch upward. Due to the compressible structure on the plunger assembly forming a seal with the inner wall of the plunger chamber, the upward movement results in a decrease in air pressure in the newly created volume below. This pressure drop draws the liquid out of the chamber 120, dividing it almost equally between the two PCR tubes 130 at the bottom of the cartridge. Figure 7A depicts the chamber 120 after the liquid has been transferred out. Figure 7B shows that the position of the lock arm 151 relative to the shaft 152 remains constant. Due to the rotation of the shaft relative to the lock arm 151, the rigid structure 141a moves through the notch present on the side edge of the lock arm 151. Figure 7C shows that, relative to the positions of the lock arm and trigger in Figure 6C, the lock arm 151 and trigger 170 have moved laterally as the lock arm 151 rotates around the shaft 152. Figure 7D shows that the engagement structure 162 of the cap 160 is locked on the shaft 152, the push rods 161a and 161b are still pressing down on the lock arm 151, the rigid structure 141a with a curved end has passed through the notch of the lock arm, the spring 170 has been released from its compressed state, the compressible structure 141b of the plunger assembly is being pushed upward, and a vacuum has been created in the plunger chamber.

[0043] Next, an exemplary configuration of channels connecting chamber 120 to collection container 130 is described. This configuration is particularly useful when the aim is to equally divide the liquid in chamber 120 among multiple collection containers, for example, two collection containers 130, as depicted in Figure 8A. Figure 8A shows a sample preparation cartridge 100 having a cylindrical structure 110 with three chambers positioned in an annular wall. Chamber 118 is fluidically connected to channel 118a. Channel 118a may be used to fill chamber 118 with a fluid, for example, a lysis buffer. Chamber 120 is fluidically connected to channel 120a. Channel 120a may be used to fill chamber 120 with a fluid, for example, an elution buffer. Channel 120a is connected to the bottom region of chamber 120 via an inlet 123. In this example, chamber 119 contains ambient air and is not connected to a channel. Channel 146 connects chamber 120 to collection container 130. Channel 146 is connected to the drain hole 125 in the bottom region of the chamber 120. Channel 145 connects the plunger chamber 140 to the collection container 130. In Figure 8B, the plunger chamber 140 is visible together with channels 145 and 146. Both channels include a T-joint. When negative pressure is generated, air is displaced from the system, thereby drawing the liquid out of the chamber 120 and distributing it into the collection container 130. The liquid path in channel 146 and the path in channel 145 through which the air is displaced are positioned well above the final liquid filling height in the collection container to prevent immersion in the liquid as it is distributed into the collection container. This prevents the air displacement path on channel 145 from becoming wet and prematurely stopping the filling of the collection container. Additional features depicted in Figure 8B include buffer pack support features 507 and 508 that can hold the bottom end of a buffer pack placed in the cartridge. Channel 118a extends from the bottom of the buffer pack support feature section 507 to the chamber 118. Channel 120a extends from the bottom of the buffer pack support feature section 508 to the chamber 120.

[0044] Figures 9A–9C provide additional details of the configuration of the air displacement channel 145 and the liquid path channel 146. In Figures 9A–9B, the upper panel shows a diagram of the chamber and channels viewed from the top of the cartridge. The lower panel shows a side view of the chamber and channels. In the pre-operation stage (see 1-Pre-operation stage), when the cap is positioned away from the upper surface of the sealing plate assembly and the spring is not yet activatable, the system is filled with air at ambient pressure. The plunger chamber 140, channels 145 and 146, and the collection container 130 are occupied by the atmosphere. In the 2-Post-Activation stage, when the cap is pressed, a fluid (e.g., elution buffer) fills the chamber 120. Pressing down the cap also compresses the plunger assembly, activating the spring. The downward movement of the compressible structure 141b displaces air out of the plunger chamber. The displaced air is vented to the atmosphere. As illustrated in Figures 5-7, when the cap is in the post-activation stage and the spring is activated, the trigger 170 moves downward. This process, which is filling the collection containers 3a and 3b, occurs quickly and is divided into two sections for illustrative purposes. As the trigger 170 moves laterally, the spring fires, pushing the compressible structure 141b upward and generating negative pressure within the system. The negative pressure creates an suction force within the channel 145 and collection chamber 130, which then draws fluid from chamber 120 into channel 146. As the negative pressure draws the fluid, it enters the two collection containers. Because the remaining air pressure in the collection containers is equal, the fluid is evenly divided between the collection containers. In Figures 9A-9C, when chamber 120 is empty, i.e., when it does not contain liquid, chamber 120 is not depicted. Empty chambers and channels indicate that the internal space is occupied by air or vacuum. Pointed chambers and channels indicate the presence of liquid.

[0045] Figure 13 shows an exploded view of the sample preparation device 300 provided herein. The sample preparation device is a cylindrical cartridge including a cylindrical structure 310 having a chamber 320. The chamber 320 is fluidly connected to a collection container 330 and a plunger chamber 340 (not shown in this figure). A plunger assembly 341 is positioned within the plunger chamber 340. A sealing plate assembly 350 is attached to the upper end of the cylindrical structure 310. The sealing plate assembly 350 is covered by a cap 360. A trigger assembly 355 is also depicted. A flexible cover 380 is attached to the outer surface of the annular wall of the cylindrical structure 310. Sealing films 390a and 390b are attached to the upper and bottom surfaces of the bottom region of the cylindrical structure, respectively, forming channels that fluidly connect the chamber 320 to the collection container 330 and the plunger chamber 340. A clip 395 for attaching the collection chamber to the bottom surface of the cylindrical structure is shown.

[0046] Figure 14 shows a zoomed-in view of the plunger assembly 341, the spring 342, and the trigger assembly 355. The rigid structure 341a of the plunger assembly 341 includes an external region that is larger than the outer diameter of the plunger chamber and substantially equal in diameter to the spring 342, such that when the plunger assembly moves downward, the external region of the rigid structure engages with the spring. The internal region of the rigid structure 341a is sized to fit inside the plunger chamber. The internal region of the rigid structure is fixedly attached to a compressible structure 341b. The compressible structure 341b is positioned inside the plunger chamber (not shown in this figure). The external region of the rigid structure 341a of the plunger assembly 340 includes an engagement structure 341c that is sized to fit into a notch 351a in the pivotable engagement arm 351. The pivotable engagement arm 351 is attached to the movable trigger 370. The trigger 370 is movable toward the plunger chamber by applying a magnetic force to the metal ball 370a. The movement of the trigger 370 forces the engaging arm 351 to pivot clockwise. The clockwise movement of the engaging arm 351 allows the engaging structure 341c to be released from the notch 351a.

[0047] Figure 15 shows a cutaway view of the plunger chamber 340, spring 342, rigid structure 341a, and compressible structure 341b.

[0048] Figure 16 shows the plunger assembly 341 and the spring 342. The rigid structure 341 includes the engaging structure 341c.

[0049] Figures 17A–17D show the sample preparation cartridge 300 in the pre-operation stage, where the cap is in the “pre-operation” or open stage and the plunger assembly has not yet been made operational. The cap 360 is positioned across the cylindrical structure. A centrally positioned shaft extends from the bottom region of the cap and aligns with a centrally positioned through-opening within the sealing plate. Three push rods 361 extending from the bottom region of the cap are positioned above the plunger assembly and configured to align perpendicularly with the plunger assembly. A cutaway view of the plunger assembly shows an inwardly positioned inclined surface 341d, and when downward pressure is applied to the rigid structure 341a by the push rods 361, the rigid structure slides downward across the inclined surface 341d. In the cap-open stage, the compressible structure 341b is positioned in the bottom region of the plunger chamber 340. The rigid structure 341a of the plunger assembly 341 includes an internal region positioned inside the plunger chamber and an external region positioned around the outside of the plunger chamber. The engaging structure 341c is positioned outside the plunger chamber. The internal region of the rigid structure 341a includes an inclined surface 341d, and with respect to the inclined surface 341d, the rigid structure can move downward when a downward pressure is applied to the rigid structure and upward when the downward pressure is released. The trigger 370 is omitted in this figure.

[0050] Figures 18A–18D show the sample preparation cartridge 300 in the operational stage, with the cap 360 in the post-operation stage and the plunger assembly operational. In this stage, the push rod 361 engages with the rigid structure 341, forcing the engaging structure 341c down into the notch 351a of the pivotable lock arm 351, and the spring 342 is compressed. The trigger 370 is omitted in this figure.

[0051] Figures 19A–19D show the sample preparation cartridge 300 in the negative pressure trigger phase, where the rigid structure of the plunger assembly has moved back up. The upward movement of the rigid structure is facilitated by the inclined surface 341d, leading to the upward movement of the compressible structure 341b, thereby generating negative pressure within the plunger chamber 340. The upward movement is caused by the release of the structure 341c from the notch in the pivotable lock arm 351. The trigger 370 is omitted in this figure.

[0052] Figure 20A shows the upper surface of a sealing plate 350 that is fixedly attached to the cylindrical structure of the cartridge. The sealing plate includes an alignment structure 390 having three through holes, configured to allow the passage of a push rod 361 extending from the lower surface of the cap 360 (Figure 20B).

[0053] Figures 21A and 21B show the sample preparation cartridge in the open and closed cap states, respectively. Figure 21C shows a magnetic accessory configured to hold the sample preparation cartridge 300 in close contact with one or more magnets (not shown). The magnetic accessory can be sized to fit into an instrument equipped with a motor for rotating the sample preparation cartridge.

[0054] A sample preparation cartridge may have multiple chambers for sample preparation, for example, for isolating nucleic acids from a sample, but the sample preparation cartridge depicted in the figure includes at least three chambers. The chambers may be located inside the cartridge or several may be located on the same outer surface. In the cartridge depicted in the figure, the annular wall comprises cavities forming the opening sides of each of the multiple chambers, and one or more channels providing fluid communication between the multiple chambers. The channels are formed by recesses within the annular wall and have opening sides. One or more covers are attached across the outer surface of the annular wall, covering and fluidly sealing the opening sides of the chambers and the opening sides of the recesses. A plunger chamber may be located inside the cartridge. The plunger chamber may be positioned adjacent to the chamber through which the liquid is transferred. Additional components of the sample preparation cartridge are described in more detail below.

[0055] Cylindrical structure Cylindrical means that a cylindrical structure can be substantially a right cylinder. A cylindrical structure can be rotatable around an axis formed by a line connecting the center of the bottom end of the cylindrical structure and the center of the top end of the cylindrical structure. For example, a cylindrical structure may rotate clockwise or counterclockwise when viewed from above, looking down at the top of the cylindrical structure. Alternatively, a cylindrical structure may rotate both clockwise and counterclockwise. In some cases, the range of motion of a cylindrical structure may encompass less than or equal to the total rotation around the axis of the cylinder, such as three-quarters of a rotation, or half a rotation, or one-third of a rotation. In certain embodiments, a cylindrical structure may rotate a full rotation clockwise and a full rotation counterclockwise. In certain embodiments, a cylindrical structure may rotate a full rotation clockwise and less than a full rotation counterclockwise, or vice versa. The rotation of the cylindrical structure may be used to mix the contents of one or more chambers, or to position a magnet located in a cylinder housing adjacent to a chamber to cause aggregation of magnetic particles present in the chamber and / or to transfer the aggregated magnetic beads from one chamber to another, or to generate negative pressure in the plunger chamber by triggering the rotation of a lock arm.

[0056] As summarized above, the cylindrical structure comprises multiple cavities within the annular wall that form a chamber with multiple sides open on the annular wall. For example, the multiple cavities may be recesses within the annular wall that deform the continuous surface of the annular wall. "Sides open" means that the annular wall does not cover such sides of the chamber. In certain cases, the deformed annular wall may form closed sides of the chamber, and areas corresponding to the sides of the annular wall deformed to form cavities may form open sides of the chamber.

[0057] According to a particular embodiment, the opening sides of multiple chambers are located outside the annular wall. For example, the annular wall may be deformed inward from the outside to form an inwardly deformed cavity within the annular wall. In such a case, the opening sides of the chambers may be areas corresponding to the sides of the annular wall that have been inwardly deformed to form the cavity. In such cases, the inwardly deformed annular wall may form the closed sides of the chambers. The volume of the chamber may represent a measurement corresponding to the volume of the recess within the annular wall. The chamber may be any convenient volume, and in some cases, 1 cm 3 ~3cm 3 or 2cm 3 ~5cm 3 etc., 1cm 3 ~about 5cm 3 It may vary up to a certain point. In other cases, the chamber may contain a fluid of any convenient volume, which in some cases may vary from 1 μL to approximately 5,000 μL, such as 1 μL to 100 μL, or 1,000 μL to 3,000 μL, or 2,000 μL to 5,000 μL. Each chamber in a plurality of chambers may have the same volume or different volumes. The depth of the chamber, measured as the distance from the outer surface of the annular wall to the inner side of the chamber, may be of any convenient size, which in some cases may be 0.1 cm or more, such as 1 cm or 5 cm. Each chamber in a plurality of chambers may have the same depth or different depths.

[0058] According to a particular embodiment, multiple chambers are positioned close to each other on the annular wall. For example, the distance between the lateral boundary of the first chamber and the nearest lateral boundary of the second chamber may be about 0.1 cm or more, such as 0.5 cm to 1 cm, for example, 0.5 cm, 0.75 cm, or 5 cm. The distance between pairs of sides of adjacent chambers may be the same or different for multiple chambers. A plunger chamber may be positioned adjacent to a third chamber, which may be a chamber containing an analyte isolated from the sample. This chamber is also referred to as an elution chamber. The plunger chamber may be positioned adjacent to the annular wall, on the annular wall, or more centrally within the cylindrical structure. In a particular example, the distance between the wall of the third chamber closest to the plunger chamber and the wall of the plunger chamber closest to the third chamber may be less than 5 cm, for example, about 0.1 cm to 4 cm, 0.5 cm to 2 cm, etc.

[0059] As summarized above, the sample preparation cartridge includes one or more channels that provide fluid communication between a plurality of chambers. In certain embodiments, the channels are wide enough through which one or more paramagnetic particles (PMPs) used to isolate the target analyte can be transported. In certain embodiments, one or more of the channels between chambers are formed by recesses in the annular wall. Recesses in the annular wall mean recesses or cavities within the annular wall that are capable of providing fluid communication between chambers. In some cases, the recesses are formed within the outer surface of the annular wall such that a first chamber and a second chamber, formed with opening sides on the outer surface of the annular wall, are interconnected by recesses within the outer surface of the annular wall between such a first chamber and a second chamber. The recesses in the annular wall may have any convenient length, width, and depth.

[0060] In certain embodiments, the recess is located on the side of multiple chambers. The side of multiple chambers means the left or right side of the chamber, rather than the upper or bottom side, when the axis of the cylindrical structure is oriented vertically, formed between the center of the bottom and center of the top of the cylindrical structure. Positioning the recess on the side of multiple chambers means that the recess can interconnect the right side of a first chamber with the left side of a second chamber, thereby enabling fluid communication between such first and second chambers through the recess. The recess between chambers may be substantially a straight line between a point on the first chamber and a point on the second chamber. The recess between the first and second chambers may have substantially the same width and depth in the annular wall along the entire length of the recess, or it may vary. Recesses between different pairs of chambers may have different or the same dimensions. The recess may be conveniently shaped so that PMP can be translated through it.

[0061] In certain embodiments, the recess is positioned on the side of one or more chambers at a substantially constant height above the bottom end of the cylindrical structure. In these embodiments, the recess between pairs of chambers may be substantially linear. In these embodiments, the recess and chambers may be molded such that a linear path exists, starting from the left end of the leftmost chamber and passing through each of the multiple chambers to the rightmost chamber. The recess on the side of one or more chambers may be positioned at any convenient height above the bottom end of the cylindrical structure. In certain embodiments of these embodiments, the height above the bottom end of the cylindrical structure where the recess is positioned corresponds to the vertical midpoint of one or more chambers. In certain embodiments, when the lock arm is pushed downward by closing the cap, the trigger attached to the lock arm may be at approximately the same level as the recess. In such embodiments, the same magnet used to transfer the PMP from one chamber to another through the recess can also be used to engage the trigger and prevent the trigger from moving while the cylindrical cartridge is rotating. In other embodiments, a separate magnet is used to engage the trigger.

[0062] In certain embodiments, the shape of one or more of the chambers is generally rectangular. A generally rectangular chamber means that the two-dimensional shape of the recess into the annular wall is longer in length than in width. The height and width of each chamber may be any convenient height and width. The height and width of each rectangular chamber may be the same or different.

[0063] In certain embodiments, the shape of a chamber connected to another chamber by one or more channels is such that, with respect to the lateral portion of the chamber adjacent to the channels, the height of the chamber at each lateral position of the chamber decreases as such position approaches the channels. In some cases, the height of such a chamber at each lateral position decreases linearly to form a tapered region. Such a tapered inlet into a recess can facilitate the transport of aggregated PMP from the chamber to the channels.

[0064] In certain embodiments, one or more of the chambers are provided with drainage holes. Drainage holes are holes through which fluid can pass and exit the chamber. In certain embodiments, the drainage holes are sized such that a significant amount of liquid cannot be discharged through the holes under the influence of gravity.

[0065] One or more of the chambers may include openings configured for ventilation of the chamber, filling the chamber with fluid, and / or discharge of fluid from the chamber.

[0066] In certain embodiments, the inside of a cylindrical structure comprises one or more wells. A well means one or more enclosures within the interior of the cylindrical structure. The enclosures may be of any convenient size or shape. For example, an enclosure may be substantially cylindrical, having a closed bottom end, annular walls, and an open top end. In these embodiments, the cylindrical structure may further comprise channels within the cylindrical structure that provide fluid communication between such wells and one or more of the chambers. In some cases, each well is interconnected with a different chamber via one or more channels.

[0067] In certain embodiments, the multiple chambers form a first chamber, a second chamber, and a third chamber. In certain embodiments, the first chamber is adjacent to the second chamber, the second chamber is adjacent to the first and third chambers, and the third chamber is adjacent to the second chamber. In certain embodiments, the cylindrical structure further includes a first recess in the annular wall that provides fluid communication between the first chamber and the second chamber, and a second recess in the annular wall that provides fluid communication between the second chamber and the third chamber. In certain embodiments, the first chamber is a dissolution chamber, the second chamber is an immiscible phase chamber or a washing chamber, and the third chamber is an elution chamber. A dissolution chamber means a chamber that contains a buffer fluid, such as a dissolution buffer fluid, during use of the sample preparation cartridge. An immiscible phase chamber means a chamber that contains an immiscible phase, such as a fluid that is immiscible with the aqueous phase, during use of the sample preparation cartridge. In some cases, the immiscible phase is an oil. In other cases, the immiscible phase is air. A washing chamber refers to a chamber that contains a washing solution during the use of a cartridge. An elution chamber refers to a chamber that contains an elution buffer fluid, such as an elution buffer fluid, during the use of a sample preparation device. A plunger chamber may be located adjacent to the elution chamber and may be in fluid communication with the elution chamber.

[0068] The first chamber may include an opening at the top of the chamber. This opening may be configured as an inlet. The inlet may be configured to introduce a lysis buffer, sample, and / or mixtures thereof. Therefore, the inlet may have a diameter suitable for pipetting, injecting, or pumping the lysis buffer, sample, and / or mixtures thereof. In some cases, the second chamber may also include an opening at the top of the chamber. This opening may be configured as an inlet for introducing an immiscible phase, such as oil, into the second chamber. In some cases, the third chamber may also include an opening at the top of the chamber. This opening may be configured as an inlet for introducing an elution buffer into the third chamber.

[0069] In certain examples, the first chamber may include a compartment positioned on or below the bottom region of the first chamber. The compartment may include an opening that fluidly connects the compartment to the inside of the first chamber. The compartment may contain paramagnetic particles (PMPs). The PMPs can be freeze-dried. In certain embodiments, the first chamber includes an opening at the bottom of the chamber, which is configured as an inlet for a lysis buffer, and the first chamber includes an opening at the top of the first chamber, which is configured as a sample inlet. In certain embodiments, the compartment includes an inlet that fluidly connects the compartment to a channel, and an outlet that fluidly connects the compartment to the inside of the first chamber.

[0070] In certain examples, the second chamber may not include any openings other than those connecting it to the first and third chambers. The second chamber may contain air. When the first and third chambers are filled with liquid, the air in the second chamber is compressed due to the absence of vents in the second chamber. The compressed air acts as a "cleaning" environment for the PMP, which is transferred from the first chamber through the second chamber containing the compressed air to the third chamber.

[0071] In certain examples, the third chamber includes an opening in the bottom region of the chamber. The opening is configured to drain from the third chamber. The third chamber may also include an opening in the bottom region of the chamber, which is configured to fill the third chamber, unlike the opening for draining from the third chamber. In certain cases, the drain hole may have a smaller diameter than the filling hole such that the drain hole does not allow liquid to pass through at atmospheric pressure and requires a higher pressure to allow liquid to pass through. The bottom opening of the third chamber is fluidically connected to one or more collection containers. The collection containers may be two separate tubes, for example, thin-walled polypropylene tubes suitable for PCR, as described above. The bottom opening of the third chamber may be fluidically connected to two channels separated from the opening to fill the two collection containers with substantially equal volumes of liquid drained from the third chamber under the influence of the vacuum generated in the plunger chamber.

[0072] Figure 1 shows a cylindrical cartridge 100 according to one embodiment. In this example, the cylindrical structure 110 includes three cavities within the annular wall that form chambers 118, 119, and 120 with three sides open on the annular wall, and two recesses that form interconnects with sides open. In Figure 1, only two of the chambers are visible. The third chamber 120 is fluidly connected to the collection container 130 and the plunger chamber 140. As can be seen, the open sides of chambers 118, 119, and 120 are located outside the annular wall, and chambers 118, 119, and 120 are positioned adjacent to each other. An interconnect 220a provides fluid communication between chambers 118 and 119, and another interconnect 220b provides fluid communication between chambers 119 and 120. In this example, interconnects 220a and 220b are channels which are recesses within the annular wall, with interconnect 220a positioned on the sides of chambers 118 and 119 and interconnect 220b positioned on the sides of chambers 119 and 120. As shown in the figure, the recesses that form interconnects 220a and 220b between the chambers are at a substantially constant height above the bottom end of the cylindrical structure 110.

[0073] cover As summarized above, the sample preparation cartridge includes one or more covers that cover the opening sides of multiple chambers and the interconnections for forming channels. In certain embodiments, the covers are curved to fit with the outer surface of a cylindrical structure. Curving means that the cover is not substantially flat when attached to the cylindrical structure. When the covers cover the chambers, the fluids disposed within the chambers are contained within them. The use of covers to form the walls of chambers within a cylindrical device allows for walls that are significantly thinner than the annular walls of the cylindrical structure. The use of covers to form the walls of chambers within a cylindrical device allows for walls made from materials different from those of the cylindrical structure. In certain embodiments, a single cover may cover all of the multiple chambers, or it may cover a subset of the multiple chambers and all or a subset of the interconnections between the chambers. The covers may be of any convenient size and shape, and the size and shape of the covers may be modified.

[0074] The cover may be made of any suitable material that is curved and can be attached to the outer surface of the annular wall. For example, the cover may be made of plastic, metal, paper, glass, etc. If a metallic material is used for the cover, the metal may be nonmagnetic, i.e., it may not contain a significant amount of iron. Paper covers may include a non-wetting coating, such as a wax coating. The cover may be substantially opaque or substantially transparent. The cover may be attached to the annular wall by any suitable means, such as by adhesive, by locally heating the outside of the annular wall or the cover or both, or by screwing the cover into the annular wall by snapping the cover into a groove created in the annular wall. The cover may be thin enough not to significantly reduce the magnetic force of the outer magnet in the chamber. For example, the cover may be thin enough to allow paramagnetic particles (PMPs) present in the chamber to aggregate in response to an outer magnet positioned adjacent to the chamber, and to allow the aggregated PMPs to traverse channels connecting adjacent chambers in response to the relative movement of the cylindrical structure and the outer magnet. The cover may have a thickness of less than 1 cm, less than 0.5 cm, less than 0.1 cm, for example, 1 mm to 5 mm. In certain embodiments, the cover may be a film, for example, an adhesive film.

[0075] According to a particular embodiment, the inner surface of the cover facilitates the movement of a PMP in contact with it. Facilitating the movement of the PMP means that the inner surface of the cover can be configured such that the PMP can be more reliably translated from a first position on the cover to a second position on the cover while remaining in contact with the inner surface of the cover. For example, the inner surface of the cover may be polished to reduce friction between the PMP and the inner surface of the cover as the PMP moves along the cover. Transitioning from a first position on the cover to a second position on the cover means, in a particular case, that the PMP moves along the inside of the cover, or, in a particular case, that the PMP is held in a fixed position while the cartridge is moved from a first position to a second position, or, in a particular case, that both the PMP and the cartridge are moved.

[0076] Paramagnetic particles are magnetic particles that can deposit the target analyte on them, for example, nucleic acids. PMPs are magnetically responsive. Magnetically responsive particles contain or are composed of magnetically responsive materials. Examples of magnetically responsive materials include paramagnetic materials, ferromagnetic materials, ferrimagnetic materials, and metamagnetic materials. Suitable examples of paramagnetic materials include iron, nickel, and cobalt, as well as Fe3O4, BaFe 12 O 19 Examples include metal oxides such as CoO, NiO, Mn2O3, Cr2O3, and CoMnP. PMPs may consist of paramagnetic materials surrounded by non-magnetic polymers, for example, magnetic materials covered with polymer materials, or magnetic materials embedded in a polymer matrix. Such particles may be referred to as magnetic beads or paramagnetic beads.

[0077] Figure 1 also shows a recess 245 that can function as a housing to provide additional functionality to the cartridge. For example, the recess may house a barcode or a QR code. The code may be printed directly on the cartridge or on a substrate attached to the cartridge. The code can be used to assign a unique identifier to the cartridge. The depth and position of the recess may be coordinated with the location of a code reader to ensure proper focus and alignment with the code reader.

[0078] Figure 1 shows additional sealing films 190a and 190b cooperating to provide upper and bottom walls of channels connecting the chamber to individual wells in an embodiment in which the wells are contained in a cartridge and / or the chamber 120 is connected to a collection container 130. For example, the channel may be an opening in the bottom wall, which extends from the bottom of the chamber 120 to the inlet of the collection container. The side walls of the opening are formed by the bottom wall, and the upper and bottom walls are provided by sealing films 190a and 190b, respectively.

[0079] In some embodiments, the cartridge may include a plurality of chambers, each having an opening in its upper region. The opening in the upper region of the first chamber can be used to introduce the lysis buffer, PMP, and sample into the first chamber. The second chamber may contain air as the immiscible phase and may not contain any openings (other than the interconnections to the first and third chambers). The second chamber may contain oil as the immiscible phase and may include an opening in its upper region for introducing oil into the second chamber. The third chamber may include an opening for introducing the elution buffer into the third chamber, which can be closed by a sealing plate assembly.

[0080] Buffer pack In certain embodiments, the sample preparation cartridge may include a buffer pack. The buffer pack may include one or more fluid packs. Each fluid pack may contain a fluid. The fluid pack may contain any convenient amount of any convenient fluid. In some embodiments, the fluid pack may include a lysis buffer pack, an immiscibility phase pack, and an elution buffer pack. In some embodiments, the fluid pack may include a lysis buffer pack and an elution buffer pack. In certain embodiments, the immiscibility phase may contain oil. In certain embodiments, the immiscibility phase may contain air. In some cases, one or more of the fluid packs may further include PMP or capture beads. The capture beads may be magnetic or non-magnetic. The capture beads may be functionalized to bind to the target analyte. The capture beads may have a portion immobilized on their surface for binding to the target analyte. This portion may be an oligonucleotide, a peptide, or a protein (e.g., an antibody). The fluid pack may contain any convenient amount of PMP, measured, for example, based on the volume or weight of the PMP. For example, if PMP is included in a fluid pack, it may be mixed with the fluid. In some cases, PMP may be included in a fluid pack containing a lysis buffer.

[0081] In certain embodiments, the buffer pack is configured to fit into a well of a cylindrical structure. For example, if the well is molded as a substantially hollow cylinder, the buffer pack may be molded as a cylinder that fits into the well of the cylindrical structure.

[0082] In some embodiments, the lysis buffer can be formulated to release nucleic acids from a wide range of samples, such as tissue samples, cells, viruses, or bodily fluid samples. The lysis buffer can also be designed to lyse all types of pathogens, such as viruses, bacteria, fungi, and protozoan pathogens. Such a lysis buffer may contain chaotropic agents, particularly guanidine hydrochloride.

[0083] Sealing plate assembly The sealing plate assembly includes a sealing plate positioned at the upper end of a cylindrical structure. The sealing plate may be substantially circular in shape and can snap into or onto the upper region of the cylindrical structure to close the upper end. The sealing plate may include a centrally positioned shaft of any preferred length. The shaft may be a hollow shaft. In certain embodiments, the shaft may extend above the sealing plate. In certain embodiments, the shaft may extend below the sealing plate. The length of the shaft below the sealing plate may be less than or equal to the height of the cylindrical structure.

[0084] An example of a sealing plate assembly 150 is shown in Figure 2C. The top figure shows the lower side of the sealing plate assembly. Guide features 157a-157c, uniformly arranged around the periphery of the sealing plate, are depicted. The shaft 152 of the sealing plate assembly has a higher effective outer diameter in the region of the shaft directly adjacent to the lower surface of the sealing plate. The pivotable lock arm 151 is initially positioned relatively tightly around this region of the shaft. A higher effective outer diameter can be achieved by adding extra shaft material to the region.

[0085] In certain embodiments, the sealing plate may include an opening within the region of the sealing plate on a pivotable locking arm. The opening may be large enough to expose two opposite regions in the diametrical direction of the locking arm. In other embodiments, the sealing plate may include two openings within two regions of the sealing plate on a pivotable locking arm. Also depicted in Figure 2C, but not required in some embodiments, are buffer packs 158 which may be used to supply lysis buffer and elution buffer to the cartridge chambers 118 and 119, respectively.

[0086] Figures 10A–10C show additional drawings of the sealing plate assembly. Figure 10A is an exploded view of the sealing plate assembly 150, showing the sealing plate 159, the pivotable locking arm 151, and the buffer packs 290a and 290b. Snap-in features 157a–157c for securing the sealing plate assembly on the cylindrical structure are depicted. The hollow shaft 152 is positioned approximately at the center of the plate and extends downward toward the bottom of the cylindrical structure and upward toward the cap. Finger-like structures 291a and 291b for holding the buffer packs are also visible. A top view of the sealing plate assembly is shown in Figure 10B. The hollow shaft extends over the plane of the sealing plate. The sealing plate includes two openings 292a and 292b on the upper surface of the locking arm 151, which are aligned with substantially diametrically opposite regions, with which the push rod of the cap contacts the locking arm. An inverted view of the sealing plate assembly is shown in Figure 10C.

[0087] cap As summarized above, in certain embodiments, the sample preparation cartridge further includes a cap slidably positioned on top of a cylindrical structure. Slidably positioned means that the cap can be positioned on top of the cylindrical structure so that it can slide toward the cylindrical structure.

[0088] Figures 11A–11C show the cap 160 individually from different angles. Figure 11A shows the orientation in which the cap 160 is attached to the cylindrical structure by engaging a projection 164 with a recess located on the inner wall of the shaft present within the sealing plate assembly, to which the sealing plate assembly is attached. The projection 164 is located at the distal end of an engaging structure 162 on a finger-like extension 166, which can expand outward in the absence of pressure, be compressed together when sliding within the shaft of the sealing plate assembly, and expand outward again as it slides through the shaft, so that the projection is positioned below the distal end of the shaft (see Figures 6D and 7D). The cap is depicted having a central dome, but other configurations are also within the scope of the present invention. For example, in certain embodiments, the cap may be substantially flat, and the length of the engaging structure is reduced accordingly to fit properly within the shaft of the sealing plate and within the cylindrical structure. Push rods 161a and 161b extending from the lower surface of the cap are visible in Figures 11B and 11C. Additional features that may be included in the cap but are not essential to the system for transferring liquid from the chamber into the collection container include a plunger 169. In embodiments in which the sealing plate assembly includes buffer packs, e.g., a dissolution buffer pack and an elution buffer pack, the plunger can be used to release buffer from the buffer pack wells. For example, pressing down the cap to bring it into close contact with the sealing plate assembly can release the buffer and simultaneously activate a system for triggering negative pressure in the plunger chamber.

[0089] An exemplary sample preparation device that includes a system for transporting an elution buffer containing a target analyte into one or more collection containers for analysis of the target analyte is described in more detail in PCT application PCT / US2020 / 066926, filed on 23 December 2020, which is incorporated herein by reference in its entirety. Specific examples of buffer packs and caps, and related systems for the operation of the buffer packs for the delivery of the buffer to one or more chambers of the sample preparation device, are provided in a U.S. provisional patent application co-filed with this application, attorney reference number ADDV-082PRV, entitled "Magnetic Particle Separation Device Buffer Pack and Cap Design," which is incorporated herein by reference in its entirety.

[0090] System and Method Furthermore, this specification provides a system capable of semi-automatically or automatically transferring liquid from one chamber to one or more collection chambers. For example, the chamber may be an elution chamber containing an elution buffer and a target analyte, such as nucleic acids isolated from a biological sample.

[0091] In certain embodiments, the system may include a sample preparation cartridge, such as a cartridge having components for transferring liquid from the cartridge chamber into one or more collection chambers of the cartridge. The system may further include an apparatus on which the cartridge is placed. For example, the apparatus may be the apparatus shown in Figure 10A. The apparatus may further include a removable or permanently attached magnet. The magnet may be positioned sufficiently adjacent to the trigger of the assembly so that the trigger can be effectively prevented from moving. The apparatus may include a motor that rotates a platform on which the cylindrical cartridge is placed. While the magnetic trigger is held in place by the magnet, the rotation of the platform rotates the cartridge. As described herein, the rotation of the cartridge causes a rigid structure of the plunger mechanism to slide against the lock arm. When the rigid structure slides away from the lock arm, it moves upward due to the force stored in the compressed spring, thereby generating negative pressure in the plunger chamber.

[0092] Herein, an exemplary method for using a system for transferring liquid from the chamber of a cartridge into one or more collection chambers of the cartridge is described. A cartridge with a pre-operation cap positioned is placed on a rotatable platform of the instrument. An exemplary cartridge is depicted in Figure 5A. An exemplary instrument having a rotatable platform that engages with a cartridge is depicted in Figures 10A and 10B. After the cartridge is placed in the instrument, the user loads a biological sample into the chamber of the cartridge. For example, the user may pipette the sample into chamber 300. In certain embodiments, the user may also introduce a lysis buffer into chamber 300, or a mixture of the lysis buffer and the sample into chamber 300. In other embodiments, the cartridge may be configured to automatically fill chamber 300 with the lysis buffer. For example, after loading the sample into chamber 300, the user may push the cap downward. As described herein, pushing the cap downward may cause a plunger in the cap to perforate the lysis buffer pack present in the sealing plate assembly. Next, a lysis buffer may flow into the lysis chamber 118. The lysis chamber, lysis buffer, or sample may also contain PMPs. The instrument platform 3000 may reciprocate and rotate the cartridge to facilitate cell / virus lysis and release of the target analyte, e.g., nucleic acid. The PMPs are functionalized to bind to and immobilize the target analyte. The instrument may stop the reciprocating rotation of the cartridge and rotate the cartridge so that the chamber 118 is adjacent to a magnet 2000 located within the instrument 1000. The magnet 2000 is depicted as a removable magnet. The magnet is housed within a support structure which includes means for removably securing the magnet within the instrument. Such means may include snap-in features sized to fit inside or outside corresponding features within the instrument. The magnet aggregates the PMPs. The magnet is positioned such that the aggregates substantially form at the opening of channel 220a, which fluidly connects the lysis chamber 118 to the intermediate chamber 119.The intermediate chamber 119 may contain a wash buffer or an immiscible phase such as oil or air. The instrument then rotates the cartridge to transport the aggregates into the intermediate chamber 119 through channel 220a. Although not shown in Figure 5A, the cartridge may include an immiscible phase chamber followed by an additional chamber, such as a wash chamber. The instrument then rotates the cartridge to transport the aggregates into chamber 120 through channel 220b. Chamber 120 may be pre-filled with elution buffer during the manufacture of the cartridge, or it may be pre-filled by the user before or after the cartridge is placed in the instrument. In certain embodiments, chamber 120 may be filled with elution buffer when the cap is pressed down by the user. In these embodiments, the cap may include a plunger that forces the elution buffer out of the elution buffer pack in the sealing plate assembly. The elution buffer then fills chamber 120 through an inlet connected to an inlet and a channel extending between the inlet and the well in which the elution buffer pack is placed.

[0093] As described herein, when the user places a cartridge with the cap in the pre-actuated stage into the sample processing instrument, the push rods 161a and 161b do not apply downward pressure to the pivotable lock arm 151. The trigger 170 is positioned relatively high relative to the bottom of the cylindrical cartridge. At this height, the trigger is not engageable by the magnet 2000 in the instrument 1000. When the user pushes down the cap, the push rods 161a and 161b force the shaft 152 downward by pushing down the pivotable lock arm 151, thereby pushing down the rigid structure 141a of the plunger assembly and compressing the spring 142. The compressible structure 141b also moves downward, allowing air to be expelled from the plunger chamber 140. See Figures 6A–6D. The trigger is pushed further down to a height near the bottom of the cartridge, matching the height of the magnet relative to the bottom of the cartridge. At this height, the magnetic force generated by the magnet can engage the trigger. At this point, the spring is in an operable position and is accumulating potential energy.

[0094] Once the PMP is transported to chamber 120, nucleic acids or other target analytes are released from the PMP into the elution buffer. The PMP can then be agglomerated by a magnet and transported backward to an intermediate chamber, for example, either the washing chamber 119 or the dissolution chamber 118. In the final step, a rotatable platform rotates the cartridge so that the trigger aligns with the magnet, and then continues to rotate the cartridge. The magnetic force acting on the trigger fixes the end of the pivotable lock arm, causing the arm to pivot around the shaft. The relative movement of the cartridge and the lock arm causes the rigid structure 141a to slide away from under the lock arm, and the plunger mechanism is launched again under the momentum provided by the potential energy stored in the compressed spring, creating a vacuum in the plunger chamber (see Figures 7A-7D).

[0095] The vacuum generates negative pressure in a channel extending from the drain hole 125 at the bottom of the chamber 120 to the inlet of the collection container 130. The negative pressure forces the liquid out of the chamber 120 and into the collection container 130. When the trigger is moved, a spring is released, pushing a compressible structure upward and generating negative pressure within the system. The negative pressure creates an attractive force in the channel 145 and the collection container 130, which then draws the fluid from the chamber 120 into the channel 146. As the negative pressure draws the fluid in, the fluid enters the two collection containers 130. Because the remaining air pressure in the collection containers 130 is equal, the fluid is evenly divided between the collection containers.

[0096] The system and method of using the system utilize a magnet and a magnetically responsive trigger to generate negative pressure within the plunger chamber, resulting in the transfer of liquid (e.g., elution buffer) from the chamber 120 into the collection container 130, although the trigger may be fixed so that the cartridge rotates by utilizing a physical barrier instead of a magnet. As described herein, the trigger may protrude from the cartridge and its movement may be prevented by a physical barrier.

[0097] Magnets, if present, may be mounted on a housing that is permanently or removablely arranged within the device. A magnet means any object capable of generating a magnetic field outside itself. For example, a magnet can generate a magnetic field capable of attracting paramagnetic particles. In some cases, the magnet may be a permanent magnet or an electromagnet. In certain embodiments, the magnet is positioned close to the outside of the annular wall of the cartridge.

[0098] The rotatable platform of the equipment can be operated using a motor. By automating the motor, the method of transporting liquid from the chamber into one or more collection containers can be automated. The motor can also be controlled by a computer program, which, when executed by a processor, causes the motor to perform the use of the system as disclosed herein.

[0099] In one particular embodiment, the motor rotates the cylindrical cartridge in increments of 1.8°.

[0100] In some embodiments, the motor rotates the cylindrical structure to return it to a predetermined position where, for example, the magnet is positioned close to the dissolution chamber, immiscibility chamber, elution chamber, or trigger.

[0101] A motor can be configured to provide only a fraction of a full 360° rotation. For example, a motor can be configured to provide only a rotation of 60° to 120°, preferably 80° to 110°, more preferably 90° to 100°, and most preferably about 90°.

[0102] Additional features added to the sample preparation device In certain embodiments, the system, sample preparation device, and instrument may include additional functions that can monitor a particular aspect of sample preparation and / or the method of using the device.

[0103] For example, a sample preparation device / instrument may include a temperature sensor capable of monitoring and reporting the temperature of reagents within various chambers of the sample preparation device. The sample preparation instrument may also be provided with means for controlling temperature, such as a heater or cooler, capable of providing a desired temperature within one or more chambers of the sample preparation device.

[0104] The sample preparation instrument may be equipped with a fluorometer for reading fluorescence in one or more chambers of the sample preparation cartridge. The fluorometer, if present, may preferably be configured to provide on-demand readings with specific parameters without any movement caused by a motor.

[0105] In further embodiments, the sample preparation apparatus may be equipped with a camera for capturing images during the sample preparation process. One or more cameras may be positioned or configured to capture images from one or more chambers of the device.

[0106] The devices disclosed herein are suitable for nucleic acid detection methods in short periods of time, for example, less than 20 minutes, less than 15 minutes, less than 10 minutes, or less than 5 minutes, for example, 1 to 5 minutes.

[0107] In some cases, the cartridge and associated instruments are configured such that a sample can be loaded, the cover is pressed down, and the remaining processing steps are automated. Therefore, results can be obtained with minimal user intervention. In particular, the user may only need to load the sample into the cartridge, load the cartridge into the instrument (though not necessarily in that order), press down the cap, and operate the analytical instrument to analyze the sample. The instrument is configured to process the sample, isolate nucleic acids from the sample, deliver the nucleic acids into collection containers, such as PCR tubes, perform analyses such as PCR, present the results, for example, display them on a screen, provide printouts, store them in a computer system, or transmit the results to a remote computer system. Therefore, the cartridges disclosed herein can be used with appropriate sample analysis instruments, such as Abbott's ID NOW® instruments, where the only user intervention steps are loading the sample into the cartridge, loading the cartridge into the analytical instrument (though not necessarily in that order), and pressing down the cap. Existing computer programs that control sample analysis instruments can be modified to handle and process samples from the cartridges disclosed herein.

[0108] In certain embodiments, the sample is a sample of whole blood, serum, plasma, sputum, nasal fluid, saliva, mucus, semen, urine, vaginal fluid, tissue, organs, and / or similar material from a mammal (e.g., human, rodent (e.g., mouse), or any other mammal of interest). In other embodiments, the sample is an aggregate of cells from a non-mammalian source, e.g., bacteria, yeast, insects (e.g., fruit flies), amphibians (e.g., frogs (e.g., xenopus)), viruses, plants, or any other non-mammalian nucleic acid sample source.

[0109] In certain embodiments, rotating the cylindrical cartridge from a first position to a second position includes rotating the cylindrical cartridge so that the entire span of the dissolution chamber rotates across the magnet. That is, the cylindrical cartridge may be rotated so that the entire lateral span of the dissolution chamber is exposed to the magnet.

[0110] Similarly, in certain embodiments, rotating the cylindrical cartridge from a second position to a third position involves rotating the cylindrical cartridge so that the entire span of the unmixed phase chamber rotates across the magnet. That is, the cylindrical cartridge can be rotated so that the entire lateral span of the unmixed phase chamber is exposed to the magnet.

[0111] The method of the present disclosure may include the additional steps of filling a dissolution chamber with dissolution buffer and paramagnetic particles from a fluid pack contained in a buffer pack, and filling an elution chamber with elution buffer from a fluid pack contained in a buffer pack. In embodiments utilizing a non-air immiscible phase, the step may additionally include filling an immiscible phase chamber with an immiscible phase from a fluid pack contained in a buffer pack.

[0112] In certain embodiments, the fluid is transferred from a fluid pack contained within a buffer pack to a chamber by applying pressure to the fluid in the fluid pack, forcing the fluid through channels in the cylindrical structure of the sample preparation device. For example, the fluid may include a dissolution buffer, an immiscible phase, and an elution buffer, some of which contain paramagnetic particles. In some cases, the immiscible phase contains oil.

[0113] In certain embodiments, when the fluid is transferred from the fluid pack, pressure is applied to the fluid in the fluid pack by applying a mechanical force to the cap of a sample preparation device equipped with a plunger for engaging with the fluid pack.

[0114] The cap may be configured to provide the user with tactile, visual, and / or auditory feedback to indicate that the cap is properly positioned. For example, when the user applies downward pressure, the cap may slide downward along the shaft of the sealing plate assembly, producing a clicking sound to indicate that the cap is properly positioned. In other embodiments, the cap may initially slide rapidly downward and then, in response to further downward pressure from the user, stop moving further, indicating that the cap is properly positioned.

[0115] Therefore, the above description merely illustrates the principles of this disclosure. Those skilled in the art will understand that various configurations embodying the principles of the present invention and falling within its spirit and scope can be devised, although these are not expressly described or illustrated herein. Furthermore, all examples and conditional statements listed herein are intended primarily to assist the reader in understanding the principles of the present invention and the concepts to which the inventors have contributed to the advancement of the art, and should be interpreted not as limitations to such specifically listed examples and conditions. Moreover, all descriptions herein listing the principles, aspects, and embodiments of the present invention, as well as specific examples thereof, are intended to encompass both their structural and functional equivalents. In addition, such equivalents are intended to include both currently known equivalents and those to be developed in the future, regardless of structure, i.e., any elements to be developed that perform the same function. Therefore, the scope of the present invention is not intended to be limited to the exemplary embodiments illustrated and described herein. Rather, the scope and spirit of the present invention are embodied by the appended claims.

Claims

1. A system for transporting liquid from a chamber into one or more collection containers, A plunger chamber comprising a plunger assembly and a spring, wherein the plunger chamber compresses the spring when the plunger assembly is operable, A pivotable locking arm, In the first position, the lock arm and the plunger assembly are engaged such that the lock arm presses down on the plunger assembly, thereby enabling the spring to actuate. In the second position, the lock arm and the plunger assembly are disengaged, allowing the plunger assembly to retract away from the spring and create a vacuum in the plunger chamber, the pivotable lock arm, A trigger coupled to the pivotable lock arm, which, when engaged by force or physical interference, disengages the lock arm and the plunger assembly, is provided. The plunger chamber is fluidly connected to a channel that connects the chamber containing the liquid to one or more collection containers. A system wherein the vacuum draws the liquid from the chamber containing the liquid through the channel into one or more collection containers.

2. The system according to claim 1, wherein the system comprises two collection containers, and the channel branches into two subchannels that are fluidly connected to the two collection containers.

3. The plunger chamber is substantially cylindrical in shape, and the plunger assembly comprises a rigid structure and a compressible structure. The rigid structure comprises a narrow region having a substantially curved end and a substantially flat end opposite to the substantially curved end, wherein the substantially curved end engages with the lock arm and the flat end is attached to the compressible structure. The system according to claim 1 or 2, wherein the compressible structure forms a seal with the inner surface of the plunger chamber.

4. The system according to claim 3, comprising a sealing plate assembly having a substantially planar region having an upper surface opposite to a lower surface, the shaft of the sealing plate assembly being located in the center of the sealing plate assembly, and extending above and below the plane of the sealing plate assembly, the pivotable lock arm having a substantially flat, elongated structure comprising a first region and a second region, the first region being pivotably attached to the shaft, the second region engaging with the plunger assembly, and the second region having a surface with a reduced area compared to the first region.

5. The system according to claim 4, wherein the surface area is reduced by the presence of a notch in the second region.

6. The system according to claim 5, wherein the second region of the lock arm comprises a first area that contacts the substantially curved end of the plunger assembly and a second area adjacent to the first area, the second area including a slope leading to the notch.

7. The system according to claim 5 or 6, wherein the notch is located on the side edge of the second region.

8. The system according to claim 5 or 6, wherein the notch is located in the center of the second region.

9. The system according to any one of claims 5 to 8, wherein the notch has a substantially circular edge.

10. The system according to any one of claims 5 to 9, wherein the second region comprises two notches, the first notch and the second notch located on the opposite side edge of the second region, or the first notch is located on the side edge and the second notch is located in the center of the second region.

11. The system according to any one of claims 4 to 10, wherein the trigger is detachably or permanently coupled to the lock arm.

12. The system according to any one of claims 4 to 11, wherein the trigger is coupled to a portion of an arm extending downward from the lock arm.

13. The system according to any one of claims 4 to 12, wherein the trigger includes a magnetically responsive material.

14. The system according to claim 13, wherein the magnetically responsive material includes iron, nickel, cobalt, oxides thereof, derivatives thereof, and combinations thereof.

15. The pivotable lock arm is positioned in a first position, and the actuation assembly further comprises an actuation assembly for making the plunger assembly operable, wherein the actuation assembly is A cap comprising a first surface opposite to the second surface, and a plurality of push rods extending from the second surface, The system according to any one of claims 4 to 14, wherein the first region of the substantially flat, elongated structure of the pivotable lock arm comprises an opening through which the arm is pivotably mounted on the shaft, and the first region comprises a lip region surrounding the opening, the lip region is configured to provide a surface area that can be engaged by the push rod at two contact points located substantially opposite each other in the diametrical direction.

16. The system according to claim 15, wherein the lock arm is positioned pivotably and slidably on the shaft, and is disposed adjacent to the lower surface of the sealing plate assembly before it is engaged by the push rod at the two contact points, and is configured to slide downward on the shaft away from the lower surface once it is engaged with the push rod.

17. The system according to claim 16, wherein the shaft has a larger effective diameter in the region adjacent to the lower surface compared to a region further away from the lower surface, so that the pivotable arm can pivot more freely around the shaft when the lock arm is pushed away from the lower position adjacent to the lower surface.

18. The system according to claim 16 or 17, wherein the sealing plate assembly comprises two through apertures positioned on opposite sides in the diametrical direction of the shaft, the apertures being aligned with the two contact points on the lock arm and the push rod such that the push rod passes through the apertures and contacts the lock arm.

19. The system according to any one of claims 16 to 18, wherein the shaft is hollow and has a recess located on the inner surface of the shaft, the cap has a centrally located engaging structure extending from the second surface of the cap, the engaging structure has a projection that reversibly fits into the recess, and when the projection is positioned in the recess, the push rod does not apply downward pressure to the lock arm.

20. The system according to claim 19, wherein the engaging structure is a rod-shaped structure comprising a plurality of fingers extending from the distal end of the rod-shaped structure, the projection is located at the distal end of the plurality of fingers, the shaft in the sealing plate assembly has a diameter greater than the diameter of the engaging structure, the shaft has a lip at its distal end, and when downward pressure is applied to the cap, the projection is disengaged from the recess, the projection is positioned below the lip, and the engaging structure is allowed to slide downward on the shaft so that the cap cannot be retracted.

21. The system according to claim 19 or 20, comprising a cylindrical cartridge having an upper end, a lower end, and an annular wall extending between the upper end and the lower end, wherein the cylindrical cartridge comprises a chamber, a plunger chamber, a pivotable lock arm, a trigger, a sealing plate assembly, and a cap, the sealing plate assembly being fixedly positioned across the upper end of the cylindrical cartridge, and the cap being fixedly positioned across the sealing plate assembly when a downward force is applied to the cap.

22. The system according to claim 21, wherein the trigger comprises a magnetic material, the system further comprises a magnet positioned adjacent to the outer surface of the annular wall, the cylindrical cartridge is rotatable to a position in which the trigger is positioned adjacent to the magnet, and the magnetic force from the magnet holds the lock arm in place and disengages the lock arm from the plunger assembly while the cylindrical cartridge rotates.

23. The system according to claim 21 or 22, wherein the trigger comprises a non-magnetic material, the system further comprises a columnar structure positioned adjacent to the outer surface of the annular wall, the cylindrical cartridge is rotatable to a position where the trigger is positioned adjacent to the columnar structure, the trigger comprises a protruding region extending from within the cylindrical cartridge to the outside of the annular wall, the columnar structure provides the physical interference to engage with the trigger, and when the cylindrical cartridge rotates, the lock arm disengages from the plunger assembly.

24. The system according to any one of claims 1 to 23, wherein the spring is positioned in the inner region of the plunger chamber.

25. The system according to any one of claims 1 to 23, wherein the spring is positioned around the outside of the plunger chamber.

26. The plunger assembly comprises a rigid structure and a compressible structure, The rigid structure comprises an external region positioned around the external region of the plunger chamber and surrounding the upper end of the plunger chamber, and the external region comprises an engaging structure extending away from the external region. The engagement structure is sized to slidably fit into the notch within the pivotable lock arm. The rigid structure is positioned inside the plunger chamber and has an internal region that is fixedly attached to the compressible structure, The system according to claim 25, wherein the compressible structure is positioned in the bottom region of the plunger chamber when the pivotable lock arm and the engagement structure engage, and retracts away from the bottom region of the plunger chamber when the engagement structure is released from the pivotable lock arm.

27. The system according to claim 26, wherein the trigger comprises a shaft region rotatably engaged with a metal ball, the metal ball being movable toward the plunger chamber when a magnetic force is applied, and when the metal ball moves toward the plunger chamber, the pivotable lock arm rotates, leading to the release of an engagement structure extending away from the external region of the rigid structure of the plunger assembly.

28. The system according to claim 27, wherein the trigger and the pivotable lock arm are configured as a single structure, and the pivotable lock arm is held in a groove that structurally supports the arm while allowing the arm to rotate.

29. The pivotable lock arm is positioned in a first position, and the actuation assembly further comprises an actuation assembly for making the plunger assembly operable, wherein the actuation assembly is A cap comprising a first surface opposite to the second surface, and a plurality of push rods extending from the second surface, When downward pressure is applied to the cap, the plurality of push rods engage with the plunger assembly, forcing the rigid structure to move downward. The system according to any one of claims 26 to 28, wherein the downward movement of the rigid structure causes the engaging structure of the rigid structure to lock into the notch of the pivotable lock arm, thereby enabling the plunger assembly to operate.

30. The system according to any one of claims 1 to 29, wherein the system is semi-automatic.

31. The system according to any one of claims 1 to 29, wherein the system is automatic.

32. A method for transporting a liquid from a chamber into one or more collection containers, To provide a system according to any one of claims 1 to 31, Moving the pivotable lock arm to the first position, wherein the lock arm engages with the plunger assembly, thereby making the plunger assembly operable and compressing the spring; To enable the chamber to be automatically filled with the liquid, This includes engaging the trigger, thereby disengaging the pivotable lock arm from the plunger assembly, allowing the plunger assembly to retract away from the spring and generate a vacuum within the plunger chamber, A method wherein the vacuum draws the liquid from the chamber through the channel into one or more collection containers.

33. The method according to claim 32, wherein the system comprises a cylindrical cartridge as described in claim 21, and providing the system comprises providing the cylindrical cartridge, wherein the sealing plate assembly is fixedly positioned over the upper end of the cylindrical cartridge, the cap is positioned such that the projection is positioned within the recess, and the push rod is not in contact with the lock arm.

34. The method of claim 33, wherein the system comprises a cylindrical cartridge as described in claim 20, and moving the pivotable lock arm to the first position includes applying downward pressure to the cap so that the projection is disengaged from the recess, thereby allowing the engagement structure to slide downward on the shaft, so that the projection is positioned below the lip and the cap cannot retract, and the push rod pushes the lock arm away from the lower position adjacent to the lower surface of the sealing plate assembly.

35. The method according to claim 32, wherein the system comprises a cylindrical cartridge as described in claim 21, and providing the system comprises providing the cylindrical cartridge, wherein the sealing plate assembly is fixedly positioned across the upper end of the cylindrical cartridge, the cap is positioned across the sealing plate and perpendicularly aligned with the sealing plate, and the push rod is not in contact with the plunger assembly.

36. The method according to any one of claims 32 to 35, wherein applying downward pressure to the cap includes manually pushing down the cap.

37. The method according to any one of claims 31 to 36, wherein the system is arranged in association with an instrument for processing biological samples, and, if present, isolates a target analyte and provides the target analyte into the liquid in the chamber.

38. The method according to any one of claims 31 to 37, wherein engaging the trigger includes physically contacting the trigger, thereby disengaging the pivotable lock arm from the plunger assembly.

39. The method according to any one of claims 33 to 35, wherein the system comprises a cylindrical cartridge as described in claim 22, and engaging the trigger involves positioning the trigger adjacent to the magnet, the magnetic force from the magnet holds the lock arm in a predetermined position and disengages the lock arm and the plunger assembly while the cylindrical cartridge rotates.

40. The method according to any one of claims 33 to 35, wherein the system comprises a cylindrical cartridge as described in claim 21, and engaging the trigger involves positioning the trigger adjacent to the magnet, and the magnetic force from the magnet moves the lock arm, moving the lock arm to the second position while the cylindrical cartridge remains stationary.

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