Thermal cycling device and assembly

Abstract

Among other things, the present application provides thermal cycler apparatuses and thermal cycling methods that provides heating and cooling of reactions within a reaction cartridge. In certain embodiments, a thermal cycler assembly comprises: (a) a heat source; and (b) at least one heat-exchanging module, each of which include: a thermal well for receiving a reaction cartridge, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; means for transferring heat from the heat source to the thermal well; and means for cooling the thermal well. Also provided is a reaction cartridge suitable for use with the thermal cycler assembly and methods of using a thermal cycler assembly for performing reactions (e.g., non-isothermal reactions), such as nucleic acid amplification reactions (e.g., non-isothermal nucleic acid reactions).

Description

THERMAL CYCLING DEVICE AND ASSEMBLYCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to and the benefit of U.S. Provisional Application number 63 / 693,940 filed on September 12, 2024, the disclosure of which is incorporated by reference herein in its entirety.FIELD OF THE INVENTION

[0002] The present application pertains to the field of thermal cycling devices and systems. More particularly, the present application pertains to devices and systems for performing non-isothermal reactions, such as nucleic acid amplification reactions, and methods of use thereof.BACKGROUND

[0003] Since the discovery of DNA, many nucleic acid amplification technologies have been developed to detect the presence, absence, or amount of specific DNA or RNA sequences. The Polymerase Chain Reaction (PCR) is a technique used to amplify and, thereby, detect or quantify a specific nucleic acid sequence of interest. This technique has formed the basis of numerous assays for detecting particular, target, nucleic acid sequences. Multiplex PCR employs PCR to amplify and detect multiple target sequences simultaneously. While other nucleic acid amplification technologies have been developed, PCR remains the most commonly used in molecular diagnostic assays.

[0004] Thermal cyclers are used to perform PCR, ligase chain reaction (LCR), or other methods for nucleic acid amplification. Typically, there are three temperature-dependent stages that constitute a single cycle of PCR: template denaturation (~95°C.); primer annealing (55°C to 65°C); and primer extension (~72°C) using a thermostable polymerase. These temperatures stages are cycled (e.g., for about 40 times) to amplify the target nucleic acid.

[0005] Some thermal cycler designs vary the temperature of a heat source to achieve denaturation, annealing, and extension temperatures. For example, U.S. Patent No.7,537,377 assigned to Applied Biosystems relates to a device that includes a sample block, a number of Peltier thermal electric devices and heat sink, clamped together. The sample block temperature is adjusted by the thermoelectric devices controlled by a computer. A reaction vessel is inserted into the sample block, and heat is transferred to the reaction vessel by contact with the sample block. The Applied Biosystems' GeneAmp® PCR System 9700 and Veriti™ Thermal Cycler have maximum block temperature ramp rates of 2.0°C / sec and 3.7°C / sec, respectively (Applied Biosystems. (2010). Specification Sheet: Veriti™ Thermal Cyclers and GeneAmp® PCR System 9700. Publication No. 04SP08-01.).

[0006] Typically, a sample block in a thermal cycler contains wells for holding multiple conically-shaped tubes that taper at the end. For example, U.S. Patent No. 5,475,610 relates to a sample tube having thin walls for decreasing the delay between changes in the temperature of the sample block and corresponding changes in temperature of the reaction mixture. Two different sample tube sizes are disclosed, but each has a thin-walled conical section that fits or nests into a matching conical recess in the sample block. This patent teaches that cones with 17 angles relative to the longitudinal axis are used to prevent jamming of the tubes into the sample block but to allow snug fit.

[0007] A disadvantage of using conically-shaped tubes is that design and / or manufacturing differences between sample blocks and / or tubes can lead to inconsistent or incomplete surface contact between the block and the tube, which, in turn, can cause inconsistent or inefficient heat transfer to the reaction mixture in the tube. For example, eENZYME LLC is a manufacturer of PCR tubes and their website states: "Measurements of the dimensions of different brands of cycler blocks show substantial differences in the internal contact angles of the wells. This means that a PCR tube, strip or plate, when placed in a block, will have a different fit. The development of PCR tubes during the last decade was no more than a miniaturisation of existing larger volume tubes (1.5 ml), and never took into account the internal shape of the thermal block holes. Furthermore, this internal shape is heavily influenced by differences in manufacturing techniques and the application of block coatings. BlOplastics has slightly modified the regular angle of PCR tubes to improve the surface contact in the blocks of all main brands of thermal cyclers. It goes without saying that a good block-tube contact is of vital importance for a good thermal cycling reaction." (https: / / www.eenzyme.com / eu8-tubestrips.aspx, accessed on February 9, 2024)

[0008] Various technologies have been developed to try to improve surface contact between samples blocks and tubes. For example, U.S. Patent No. 6,556,940 describes a thermocycler having a heated lid that tightly seals the individual wells by pressing the sealing film to the top surface of the multiwell plate. Air pressure arising inside the tightly sealed wells at elevated temperatures then deforms the elastic walls of the wells of the ultrathin-walled plate and thereby brings them into close thermal contact with the sample block. A disadvantage of this technology is it requires ultrathin-walled plates and a heated lid that presses down on the sealing film to create air pressure.

[0009] In another example, Bartsch et al. (2015) disclosed a rotary zone thermal cycler that uses plastic tubing and fixed-temperature blocks whereby "The tube rests in a groove on the outer surface of the heater block (right) and is tensioned against the block to maximize thermal coupling and sample ramp rate." Both the heating and cooling ramp rates are approximately 10°C / sec. Disadvantages of this invention include the requirement for multiple heat blocks; requirement for a rotary mechanism; and potential puncture or leakage of the plastic tubing.

[0010] Instead of a conically-shaped tube, U.S. Patent No. 10,562,030 discloses the use of a reaction vessel that includes two opposing major planar walls spaced apart from each other by minor planar walls, wherein the minor planar walls are offset from each other by about 90°. Taking advantage of the planar walls of the reaction vessel, "the TOS [Thermal Optical Subassembly] includes one or more mechanisms that move the thermal control device so as to pressingly engage at least one surface of the reaction vessel when positioned within the diagnostic device so as to improve efficiency of thermal cycling." In some embodiments, the "pressingly engage" mechanism comprises a thermal contact mechanism that includes a slidable component that translates movement between an open configuration (see FIG. 24B of U.S. Patent No. 10,562,030) and a clamped configuration (see FIG. 24A of U.S. Patent No. 10,562,030) in which a thermoelectric cooler face of the thermal control device is engaged against the side of a reaction vessel. The thermal contact mechanism can include a movable and / or adjustable bracket that slides up and down along a vertically extending mount to provide alignment of an optical component with the reaction vessel, and is also movable laterally toward the thermal control device to provide thermal contact with the reaction vessel for thermal cycling. Compared to standard conical tubes, this planar reaction vesselhas the advantage of increased surface area contact when pressed against the heating mechanism. A commercial instrument incorporating this technology has a maximum heating ramp rate of 10°C / sec from 50°C to 95°C (Cepheid. (2005). SmartCycler II: Operator Manual. D1819 Rev D). However, a drawback associated with this technology is requirement and complexity of the thermal control device, which requires a movable bracket and an additional mechanism to press the thermal control device against the reaction vessel.

[0011] U.S. Patent 6,660,228 also describes an alternative to a standard conically shaped tube. In this patent, the reaction vessel also includes planar sides. However, this reaction vessel has the additional disadvantage of requiring a locating tab that is used to properly position the vessel in a heat-exchanging module. This "locating tab" is an additional feature that is molded along with the rest of the reaction vessel and adds cost and complexity to the manufacturing of the reaction vessel.

[0012] Thus, there remains a need for a thermal cycler system that provides improved heat transfer to and from a reaction vessel during heating and cooling, without the need for extraneous elements, or complicated or expensive moveable components.

[0013] The above information is provided for the purpose of making known information believed by the applicant to be of possible relevance to the present disclosure. No admission is necessarily intended, nor should be construed, that any of the preceding information constitutes prior art against the present disclosure.SUMMARY

[0014] An object of the present application is to provide a thermal cycler assembly and thermal cycling system that provides heating and cooling of reactions within a reaction cartridge. The thermal cycler assembly, system and method of the present application can provide improved heating and cooling of reactions within a reaction vessel in comparison to heating and cooling of reactions within a standard conical tube used in a heating block. A further object is to provide a simple and efficient thermal cycler apparatus and thermal cycling system that avoids or minimizes the need for additional components for moving and positioning the reaction vessel.

[0015] In accordance with one aspect of the present application, there is provided a thermal cycler assembly comprising: (a) a heat source; and (b) at least one heat-exchanging module, each of said at least one heat-exchanging module comprising: a thermal well for receiving a reaction cartridge, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; means for transferring heat from the heat source to the thermal well; and means for cooling the thermal well.

[0016] In some embodiments, the first pair of opposing planar side panels are major planar panels and the second pair of opposing planar panels are minor planar panels, and wherein at least one of the major panels is angled by at least 1 degree and not more than 45 degrees from the bottom panel.

[0017] In some embodiments, the thermal cycler assembly further comprises a lid for the thermal well that is moveable between an open position and a closed position, such that when in the closed position the lid pressingly engages a closure cap or a top of the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

[0018] In some embodiments, the thermal cycler assembly further comprises a lid for the thermal well that is moveable between an open position and a closed position, such that when in the closed position the lid pressingly engages a top of a reaction cartridge assembly, said reaction cartridge assembly comprising the reaction cartridge and a closure cap, in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

[0019] In some embodiments, the lid further comprises means to expel fluids and / or reagents in the closure cap and / or the reaction cartridge. For example, the lid optionally comprises means to expel the fluids and / or the reagents in the closure cap and / or the reaction cartridge into a reaction reservoir of the reaction cartridge.

[0020] In some embodiments, the lid does not comprise means for heating or cooing the thermal well.

[0021] In some embodiments, the thermal cycler assembly further comprises a controller for controlling the heat-exchanging module to cycle between heating and cooling by alternating and controlling operation of the heat source, the means for transferring heat to the thermal well(s) and the means for cooling the thermal well(s).

[0022] In some embodiments, the means for transferring heat from the heat source to the thermal well comprises a finned heat sink and / or a microheater.

[0023] In some embodiments, the means for cooling the thermal well comprises a thermoelectric cooler.

[0024] In some embodiments, the thermal cycler assembly further comprises an optical detection system, wherein the optical detection system comprises an excitation light source and a photodetector and, optionally, a filter wheel. When the thermal cycler assembly further comprises an optical detection system, optionally, the housing of the thermal well includes two or more openings to permit light to enter and exit the thermal well, for example, wherein the thermal well comprises a first opening for excitation light from a light source to enter into the housing to excite a reaction mixture in the reaction cartridge, and a second opening for light emitted from the reaction mixture to exit the housing for detection by the photodetector.

[0025] In some embodiments, the reaction cartridge for use in the thermal cycler assembly comprises a reaction reservoir formed from a bottom wall and a first pair of opposing major planar side walls spaced apart from a second pair of opposing minor planar side walls, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees from the bottom wall.

[0026] In some embodiments, the reaction cartridge for use in the thermal cycler assembly comprises a reaction reservoir having a flat, optically transmissive (e.g., optically transparent) side wall and a flat, optically-transmissive (e.g., optically transparent) bottom wall, or a molded lens in the bottom wall and a flat, optically transmissive side wall angularly offset from the closed, molded lens by an angle of from approximately 90° to approximately 120°, preferably 90°.

[0027] In some embodiments, the thermal cycler assembly further comprises a device base, wherein the device base comprises the thermal well of the at least one heat-exchanging module. Optionally, the device base is configured to receive a lid.

[0028] In some embodiments, the device base comprises means for guiding a lid from an open position to a closed position, such that when in the closed position the lid pressingly engages a closure cap, a top of the reaction cartridge, and / or a top of a reaction cartridge assembly comprising the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well. Optionally, the means for guiding the lid comprises one or more tracks and / or the lid comprises one or more guiding features configured to engage with the guiding means of the device base.

[0029] In accordance with another aspect of the present application, there is provided a thermal cycler assembly comprising: (a) a heat source; and (b) at least one heat-exchanging module comprising: (i) a thermal well for receiving a reaction cartridge assembly, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; (ii) means for transferring heat from the heat source to the thermal well; and (iii) means for cooling the thermal well.

[0030] In accordance with another aspect of the present application, there is provided a thermal cycler assembly comprising: (a) a heat source; and (b) a device base comprising at least one heat-exchanging module, wherein the at least one heat-exchanging module comprises: (i) a thermal well for receiving a reaction cartridge, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; (ii) means for transferring heat from the heat source to the thermal well; and (iii) means for cooling the thermal well.

[0031] In some embodiments, the thermal cycler assembly further comprises a lid for the thermal well. Optionally, the lid is moveable between an open position and a closed position, such that when in the closed position the lid pressingly engages a top of a reaction cartridge assembly comprising the reaction cartridge and a closure cap in the thermal wellwith sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

[0032] In some embodiments, the device base comprises means for guiding the lid from an open position to a closed position, such that when in the closed position the lid pressingly engages a closure cap, a top of the reaction cartridge, and / or a top of a reaction cartridge assembly comprising the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well. Optionally, the means for guiding the lid comprises one or more tracks and / or the lid comprises one or more guiding features configured to engage with the guiding means of the device base.

[0033] In some embodiments, the lid comprises one or more guiding features configured to engage with the guiding means of the device base.

[0034] In some embodiments, the lid comprises means for expelling fluids and / or reagents into a reaction reservoir of a reaction cartridge.

[0035] In accordance with another aspect of the present application, there is provided a reaction cartridge comprising a reaction reservoir for accommodating a reaction mixture, said reaction reservoir being formed from a bottom wall and a first pair of opposing major planar side walls spaced apart from a second pair of opposing minor planar side walls, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees from the bottom wall.

[0036] In some embodiments, one of the minor planar side walls of the reaction cartridge comprises or consists of a flat, optically transmissive (e.g., optically transparent) wall, and the bottom wall comprises a molded lens.

[0037] In some embodiments, the four side walls of the reaction cartridge terminate at a top edge that defines an opening and the opening is sized to receive a closure cap.

[0038] In some embodiments, the reaction cartridge further comprises an upper portion comprising a receiving reservoir, wherein the four side walls of the reaction reservoir terminate at a top edge that defines an opening, the upper portion is connected to the topedge such that there is fluid communication between the reaction reservoir and the receiving reservoir.

[0039] In some embodiments, the reaction cartridge is formed, in whole or in part, of a thermally stable plastic.

[0040] In some embodiments, the reaction cartridge is configured to receive a closure cap comprising a top wall, a cap body depending therefrom that is sized and configured to fit in the upper receiving reservoir, and a cap component for sealing the reaction reservoir at the upper open region and / or for transferring materials into the reaction reservoir when the cap body is positioned in the upper receiving reservoir.

[0041] In accordance with another aspect of the present application, there is provided a method for performing a non-isothermal reaction comprising: (a) providing a thermal cycler assembly as described herein; (b) inserting a reaction cartridge, such as the reaction cartridge described herein, into the at least one thermal well of the thermal cycling assembly, wherein the reaction cartridge comprises a reaction reservoir containing a sample mixed with one or more chemicals or reagents; and (c) performing at least one thermal cycle by sequentially heating the reaction reservoir to a first temperature using the means for transferring heat from the heat source to the thermal well, maintaining the first temperature for a first preset time, cooling the reaction reservoir to a second temperature using the means for cooling the thermal well and maintaining the second temperature for a second preset time.

[0042] In some embodiments, the at least one thermal cycle further comprises warming the reaction reservoir to a third temperature that is between the first and the second temperature, and maintaining the third temperature for a third preset time.

[0043] In some embodiments, the at least one thermal cycle includes at least 20 cycles, at least 30 cycles or about 40 cycles.

[0044] In some embodiments, the method is for performing nucleic acid amplification, for example, by PCR.

[0045] In some embodiments, the method comprises pressingly engaging a closure cap or a top of the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well. Optionally, the comprises exerting a constant force on the closure cap and / or the top of the reaction cartridge to maintain the side walls of the reaction cartridge flush with the side panels of the thermal well, method

[0046] In some embodiments, the method comprises expelling fluids and / or reagents into the reaction reservoir. In accordance with another aspect of the present application, there is provided a method for performing a reaction comprising: (a) providing a thermal cycler assembly as described herein; (b) inserting a reaction cartridge, such as a reaction cartridge as described herein, or a reaction cartridge assembly comprising a reaction cartridge into the at least one thermal well of the thermal cycling assembly, wherein the reaction cartridge comprises a reaction reservoir containing a sample mixed with one or more chemicals or reagents; and (c) heating the reaction reservoir to a first temperature using the means for transferring heat from the heat source to the thermal well.BRIEF DESCRIPTION OF THE FIGURES

[0047] For a better understanding of the application as described herein, as well as other aspects and further features thereof, reference is made to the following description which is to be used in conjunction with the accompanying drawings, where:

[0048] Figure 1 is a top perspective view of a thermal cycling apparatus according to one embodiment of the present application;

[0049] Figure 2 is a cross-section of the thermal cycling apparatus depicted in Figure 1; and

[0050] Figure 3 is a side view of a reaction cartridge including a reagent reservoir, according to one embodiment of the present application that is suitable for use in the thermal cycling apparatus depicted in claims 1 and 2; and

[0051] Figure 4 is a cross-section the reaction cartridge depicted in Figure 3;

[0052] Figure 5 is a top perspective view of a closure cap according to one embodiment of the present application;

[0053] Figure 6 is a cross-section of the closure cap depicted in Figure 5;

[0054] Figure 7 is a top plan view of a reaction cartridge assembly according to one embodiment, comprising a reaction cartridge as shown in Figures 3 and 4 and a closure cap as shown in Figures 5 and 6;

[0055] Figure 8 is a cross-section of the reaction cartridge assembly depicted in Figure 7;

[0056] Figure 9 is a top plan view of a reaction cartridge assembly, according to one embodiment;

[0057] Figure 10 is a cross-section of the reaction cartridge assembly, as shown in Figure 9;

[0058] Figure 11 is a schematic showing a top plan view of a closure cap;

[0059] Figure 12 is a cross-section of the closure cap, as shown in Figure 11;

[0060] Figure 13 is a bottom plan view of an exemplary lid;

[0061] Figure 14 is a top plan view of a device base;

[0062] Figure 15 is a top-down view of an exemplary device base, as shown in Figure 15;

[0063] Figure 16 is a cross-sectional view of an exemplary lid, reaction cartridge assembly, and device base in an open position;

[0064] Figure 17 is a top plan view of an exemplary lid and device base in a closed position; and

[0065] Figure 18 is a cross-sectional view of an exemplary lid, reaction cartridge assembly, and device base in a closed position.DETAILED DESCRIPTION

[0066] Definitions

[0067] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which technologies disclosed herein belong.

[0068] As used in the specification and claims, the singular forms "a," "an," and "the" include plural references unless the context clearly dictates otherwise.

[0069] The term "comprising," as used herein, will be understood to mean that the list following is non-exhaustive and may or may not include any other additional suitable items, for example one or more further feature(s), component(s) and / or ingredient(s) as appropriate.

[0070] The term "consisting of," as used herein, refers to compositions, methods, devices, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment. As used herein, the term "consisting essentially of" refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the present disclosure. Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term "about."

[0071] Reference throughout this specification to "one embodiment," "an embodiment," "another embodiment," "a particular embodiment," "a related embodiment," "a certain embodiment," "an additional embodiment," or "a further embodiment" or combinations thereof means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment. Thus, the appearances of the foregoing phrases in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics may be combined in any suitable manner in one or more embodiments.

[0072] The term "and / or" as used in a phrase such as "A and / or B" herein is intended to include "A and B," "A or B," "A," and "B".

[0073] The terms "about" and "approximately" are used herein as equivalents. Any numerals used in this application with or without about / approximately are meant to cover any normal fluctuations appreciated by one of ordinary skill in the relevant art. In certain embodiments, the term "approximately" or "about" refers to a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).

[0074] The term "amplification reaction" is used herein to refer to a reaction in which multiple copies of an original nucleic acid sequence are generated, typically by repeating an enzymatic duplication process for a number of cycles. When additional copies can be made from each of the duplicate copies made in an earlier cycle, the amplification process is said to be exponential with respect to the number of cycles. In certain embodiments, an amplification reaction is an isothermal amplification reaction. In certain embodiments, an amplification reaction is a non-isothermal amplification reaction.

[0075] Some amplification reactions, for example PCR and LCR, involve cycles of alternately high and low set temperatures, a process known as "thermal cycling." Amplification reactions which use thermal cycling are referred to as non-isothermal amplification reactions. PCR is an amplification reaction in which a polymerase enzyme, usually thermostable, generates multiple copies of the original sequence by extension of a primer using the original nucleic add as a template. PCR is described in more detail in U.S. Patent Nos 4,683,202 and 4,683,195 and elsewhere. LCR or "Ligase Chain Reaction" is a nucleic add amplification reaction in which a ligase enzyme, usually thermostable, generates multiple copies of the original sequence by ligating two or more oligonucleotide probes while they are hybridized to the target. LCR, and its variation, Gap LCR, are described in more detail in EP-A-320-308, EP-A-439-182 and WO 93 / 100447 and elsewhere.

[0076] Some amplification reactions, for example Loop-Mediated Isothermal Amplification (LAMP), Whole Genome Amplification (WGA), Strand Displacement Amplification (SDA), Helicase-Dependent Amplification (HDA), Recombinase Polymerase Amplification (RPA), Nucleic Acid Sequences Based Amplification (NASBA), and Transcription Mediated Amplification (TMA), do not involve cycling temperatures. In certain embodiments, an isothermal amplification reaction maintains a substantially constant or fixed temperature during amplification.

[0077] The term "amplicon" or "amplicon molecule," as used herein, refers to a target piece of nucleic acid (DNA or RNA), that is the source and / or product of nucleic acid amplification. In certain embodiments, an amplicon molecule is a nucleic acid molecule generated by transcription from a template nucleic acid molecule, or a nucleic acid molecule having a sequence complementary thereto, or a double-stranded nucleic acid including any such nucleic acid molecule. Transcription can be initiated from a primer.

[0078] The term "lens", as used herein, refers to a transparent substance with curved sides for concentrating or dispersing light rays. In some embodiments, a lens is transparent (e.g., transmissive) to light, for example, light having a visible, near infrared, infrared, and / or ultraviolet (UV) spectrum.

[0079] As used herein, in its broadest sense, the term "nucleic acid" refers to any compound and / or substance that is or can be incorporated into an oligonucleotide chain. In some embodiments e.g., as set forth herein, a nucleic acid is a compound and / or substance that is or can be incorporated into an oligonucleotide chain via a phosphodiester linkage. As will be clear from context, in some embodiments e.g., as set forth herein, the term nucleic acid refers to an individual nucleic acid residue (e.g., a nucleotide and / or nucleoside), and in some embodiments e.g., as set forth herein refers to a polynucleotide chain comprising a plurality of individual nucleic acid residues. A nucleic acid can be or include DNA, RNA, or a combination thereof. A nucleic acid can include natural nucleic acid residues, nucleic acid analogs, and / or synthetic residues. In some embodiments e.g., as set forth herein, a nucleic acid includes natural nucleotides (e.g., adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxy guanosine, and deoxycytidine). In some embodiments e.g., as set forth herein, a nucleic acid is or includes of one or more nucleotideanalogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3 -methyl adenosine, 5-methylcytidine, C-5 propynyl-cytidine, C-5 propynyl-uridine, 2- aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5 -propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7- deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 0(6)-methylguanine, 2-thiocytidine, methylated bases, intercalated bases, and combinations thereof).

[0080] In some embodiments e.g., as set forth herein, a nucleic acid has a nucleotide sequence that encodes a functional gene product such as an RNA or protein. In some embodiments e.g., as set forth herein, a nucleic acid includes one or more introns. In some embodiments e.g., as set forth herein, a nucleic acid includes one or more genes. In some embodiments e.g., as set forth herein, nucleic acids are prepared by one or more of isolation from a natural source, enzymatic synthesis by polymerization based on a complementary template (in vivo or in vitro), reproduction in a recombinant cell or system, and chemical synthesis.

[0081] In some embodiments e.g., as set forth herein, a nucleic acid analog differs from a nucleic acid in that it does not utilize a phosphodiester backbone. For example, in some embodiments e.g., as set forth herein, a nucleic acid can include one or more peptide nucleic acids, which are known in the art and have peptide bonds instead of phosphodiester bonds in the backbone. Alternatively or additionally, in some embodiments e.g., as set forth herein, a nucleic acid has one or more phosphorothioate and / or 5'-N-phosphoramidite linkages rather than phosphodiester bonds. In some embodiments e.g., as set forth herein, a nucleic acid comprises one or more modified sugars (e.g., 2'-fluororibose, ribose, 2'- deoxyribose, arabinose, and hexose) as compared with those in natural nucleic acids.

[0082] In some embodiments, e.g., as set forth herein, a nucleic acid is or includes at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 20, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000 or more residues. In some embodiments, e.g., as set forth herein, a nucleic acid is partly or wholly single stranded, or partly or wholly double stranded.

[0083] As used herein the terms "sample" and "biological sample" means any sample, including, but not limited to cells, organisms, lysed cells, cellular extracts, nuclear extracts, components of cells or organisms, extracellular fluid, media in which cells are cultured, blood, plasma, serum, gastrointestinal secretions, tissues, homogenates of tissues or tumors, synovial fluid, feces, saliva, sputum, cyst fluid, amniotic fluid, cerebrospinal fluid, peritoneal fluid, lung lavage fluid, semen, lymphatic fluid, tears, vaginal fluids and / or secretions, and prostatic fluid. In addition, a sample can be a viral or bacterial sample, a sample obtained from an environmental source or a body of water (e.g., a lake, a reservoir, a well, ground water, wastewater), a forensic sample, a food sample (e.g., a food source believed to be contaminated), soil extracts, pesticide residues, or airborne spores.

[0084] As used herein, the term "substantially" refers to the qualitative condition of exhibiting total or near-total extent or degree of a characteristic or property of interest.

[0085] The term "thermal cycler" or "thermocycler" is used herein to refer to a device used to heat, cool and / or hold a nucleic acid amplification reaction mixture between or at a set temperature for a set time duration over a set number of cycles. Thermocyclers used for real-time and / or quantitative PCR or LCR additionally comprise detection systems, typically optical detection systems, for monitoring reaction product generation. Real-time PCR (RT- PCR) detection systems are typically optical detection systems for measuring fluorescence signal generated during each amplification cycle as the fluorophore binds to the target sequence in amplicons.

[0086] Among other things, the present application provides an apparatus and system for performing heat-exchanging chemical reactions, such as nucleic acid amplification reactions. An apparatus includes a means for receiving a reaction vessel for accommodating a sample or reaction mixture for chemical reaction and, optionally, optical detection.

[0087] Thermal Cycler Assembly

[0088] The present disclosure provides an apparatus for thermally controlling a sample mixed with one or more chemicals or reagents. A sample can also be mixed with diluents or buffers. A sample can be an aqueous solution containing particles, cells, microorganisms, ions, or small and large molecules, such as proteins and nucleic acids, etc. In a particularuse, a sample may be a bodily fluid (e.g., blood, urine, saliva, sputum, seminal fluid, spinal fluid, mucus, or other bodily fluids). Alternatively, a sample can be a solid made soluble in a liquid or the sample may be an environmental sample such as ground or wastewater, soil extracts, pesticide residues, or airborne spores placed in a liquid.

[0089] A thermal cycler assembly comprises a heat-exchanging module that comprises at least one thermal well that is sized and shaped for receiving and holding a reaction cartridge for thermal processing. Exemplary reaction cartridges and reaction cartridge assemblies are described in, for example, PCT App. No. PCT / CA2025 / 051192, filed on September 9, 2025, which is incorporated by reference in its entirety. A thermal cycler assembly is useful for performing heat-exchanging chemical reactions, such as nucleic acid amplification, and, optionally, for optically detecting target analytes (e.g., target sequences or amplicons).

[0090] Each of the at least one thermal wells includes a housing comprising a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels. In some embodiments, the planar side panels within each of the first and second pairs of opposing planar side panels have the same dimensions as each other, while the dimensions of the planar side panels in the first pair are the same as or different from the dimensions of the planar side panels of the second pair. The planar side panels each include bottom edges that connect with the bottom panel of the well, thereby forming a housing having a closed bottom end and an upper opening.

[0091] In some embodiments, a first pair of opposing planar side panels are major planar panels spaced apart from each other by a second pair of opposing minor planar panels, wherein at least one of the major panels is angled by at least 1 degree and not more than 45 degrees from the bottom panel. As used herein, the term "major" refers to a panel that is larger in dimensions than a "minor" panel. This configuration allows a thermal well as described herein to accept a reaction cartridge comprising a reaction reservoir formed from a bottom wall and a first pair of opposing major planar side walls spaced apart from a second pair of opposing minor planar side walls, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees from the bottom wall.

[0092] In some embodiments, a thermal cycler assembly additionally includes means for pressing down a reaction cartridge inserted into a thermal well so as to wedge it into the thermal well and thereby maintain contact of the side walls of the reaction cartridge flush with the corresponding side panels of the thermal well. Optionally, a means for pressing down a reaction cartridge is a lid that when closed pressingly engages a closure cap or a top of the reaction cartridge in the thermal well with sufficient force to urge the reaction cartridge into the thermal well such that the side walls of the reaction cartridge become flush with the corresponding side panels of the thermal well. Maintaining flush contact between side panels of a thermal well and side walls of a reaction cartridge aids in efficiently transferring heat from the thermal well to a solution (e.g., a reaction mixture) in a reaction reservoir.

[0093] In certain embodiments, a means for pressing down a reaction cartridge is a lid that when closed pressingly engages a closure cap or a top of the reaction cartridge in a thermal well with sufficient force to expel fluids and / or reagents in the closure cap and / or reaction cartridge. Fluids and / or reagents in a closure cap and / or reaction cartridge can be expelled into a reaction reservoir of a reaction cartridge as described herein. In certain embodiments, a plug-type element depends from or extends from a bottom surface of a lid. A plug-type element can be configured to be received by, for example, a closure cap of a reaction cartridge assembly. For example, a plug-type element can be or include a protrusion (e.g., a pin) used to depress a plunger in a closure cap positioned in an upper portion of a receiving reservoir of a reaction cartridge. A plug-type element can be used to expel fluids and / or reagents (e.g., contained in the closure cap) into a reaction reservoir of the reaction cartridge. In certain embodiments, a plug-type element is substantially cyclindrical or conical in shape. In certain embodiments, a plug-type element is removable from the lid.

[0094] In certain embodiments, a lid is configured to be received by an opening in a device base. In certain embodiments, a lid when moved from an open position to a closed position pressingly engages a closure cap or a top of a reaction cartridge in a thermal well disposed in a device base with sufficient force to urge the reaction cartridge into the thermal well such that the side walls of the reaction cartridge become flush with the corresponding side panels of the thermal well.

[0095] In certain embodiments, a lid and device base comprise an engagement mechanism to allow for the lid to move from an open position to a closed position to pressingly engage with a closure cap or a reaction cartridge in a thermal well. In certain embodiments, the configuration of the engagement mechanism allows for substantially even pressure to be applied across the top surfaces of the closure cap and / or reaction cartridge positioned in the thermal well.

[0096] In certain embodiments, a device base comprises an opening with means for guiding a lid from an open position to a closed position. In certain embodiments, a means for guiding engages with guide features of the lid in an open position and allows for the lid to move into a closed position. In certain embodiments, a guiding means comprises a track or slot which engages with guide features of a lid. In certain embodiments, a guiding means comprises two or more tracks. In certain embodiments, guiding features of a lid comprise one or more protrusions which depend from a side wall of a lid. In certain embodiments, at least one of the one or more protrusions extend substantially perpendicular to the side wall of the lid.

[0097] In some embodiments, a lid does not comprise a heater / cooler or heating / cooling element.

[0098] In some embodiments, the planar side panels and the bottom panel of a thermal well are made entirely or in part from a heat conducting material, such as a metal with good heat conducting properties, e.g. aluminium, copper.

[0099] A thermal cycler assembly further includes one or more heat source or heating elements, means for transferring heat from the heat source(s) or elements to the thermal well(s), and a means for cooling a thermal well(s). In some embodiments, a thermal well comprises a heat source such that a reaction cartridge can be directly contacted with the heat source, thus obviating the requirement for a further cartridge holder. In some embodiments, a heat source for heating a thermal well(s) is a thermoelectric heater (e.g., a Peltier device).

[0100] In some embodiments, a means for transferring heat from the heat source to a thermal well is a heat sink, such as a finned heat sink. Optionally, a means for transferring heat additionally includes a fan.

[0101] In some embodiments, a means for cooling a thermal well(s) is a thermoelectric cooler (e.g., a Peltier device).

[0102] In some embodiments, a means for cooling a thermal well(s) is the same as a heat source or heating element. For example, a thermoelectric heater / cooler such as a Peltier device can be used to heat and cool a reaction cartridge.

[0103] A thermal cycler assembly optionally includes a controller, such as a personal computer or network computer, that provides a user interface to the assembly and controls the operation of the assembly, for example to cycle between heating and cooling by alternating and controlling operation of the heat source, the means for transferring heat to the thermal well(s), and the means for cooling the thermal well(s).

[0104] In some embodiments, the housing of a thermal well includes two or more small openings to permit light to pass. For example, a thermal well can include a small opening for excitation light from a light source to enter into the housing to excite a reaction mixture in a reaction cartridge housed therein, and a second small opening for light emitted from the reaction mixture to exit the housing for detection by a photodetector.

[0105] In some embodiments, a thermal cycler assembly comprises or is for use with an optical detection system, wherein the optical detection system comprises an excitation light source and a photodetector. In some embodiments, an optical detection system further comprises a filter wheel.

[0106] In some embodiments, components of the optical detection system are arranged to provide an angle of about 90° between excitation and detection paths. The approximately 90° angle between excitation and detection paths assures that a minimum amount of excitation radiation (e.g., excitation light) entering through a first opening of the thermal well exits through the second opening. Also, an approximately 90° angle permits a maximum amount of emitted radiation to be collected via a second opening.

[0107] Figures 1 and 2 depict heat exchanger module 10 of a thermal cycler assembly according to one embodiment of the present application. As illustrated in Figures 1 and 2, heat exchanger module 10 includes thermal well 20 having an upper open end 22 for receiving a reaction cartridge (not shown). Thermal well 20 is positioned between two finned heat sinks 32 and 34, each having a corresponding fan 36 and 38. Heat exchanger module 10 additionally includes microheaters 40 and 42, that are positioned adjacent to at least a portion of side panels 50 and 52, respectively, of thermal well 20, and thermoelectric coolers 60 and 62, which are also positioned adjacent to at least a portion of side panels 50 and 52, respectively, of thermal well 20.

[0108] The thermal cycle assembly can additionally include a controller (not shown), that controls the operation of the heating and cooling elements of heat exchanger module 10, namely finned heat sinks 32 and 34, microheaters 40 and 42, and thermoelectric coolers 60 and 62. Thus, a controller can be used to cycle between heating and cooling of thermal well 20 to provide thermal cycling for a reaction in a reaction cartridge, for example a nucleic acid amplification reaction.

[0109] As shown in Figure 1, heat exchanger module 10 is included in a thermal cycler assembly that further comprises an optical detection system. The optical detection system that comprises or is for use with a light source (not shown), and further comprises filter wheel 70 and filter 72. Side panel 54 of thermal well 20 comprises opening 80 such that light from a light source (not shown) passing through filter wheel 70 enters thermal well 20 through opening 80, for example, to excite a reaction mixture in a reaction cartridge seated in thermal well 20.

[0110] As depicted in Figure 2, in one embodiment, side panel 56 of thermal well 20 comprises exit opening 82, that allows light emitted from a reaction mixture in a reaction cartridge seated in thermal well 20 to exit and be detected and / or quantified by a photodetector (not shown) that optionally forms part of the optical detection system.

[0111] In some embodiments, thermal well 20 includes an exit opening (not shown) on bottom panel 58 that allows light emitted from a reaction mixture in a reaction vessel seated in thermal well 20 to exit and be detected and / or quantified by a photodetector.Thermal well 20 can include exit openings on one or both of a side panel and the bottom panel. The reaction cartridge for use with the thermal cycler assembly will include portions having an optically transmissive (e.g., optically transparent) material that align with the position of openings in thermal well 20. Including exit openings on one or more side panels as well as the bottom panel permits variation in the reaction cartridges that can be employed in the thermal cycler assembly.

[0112] The thermal cycling assembly optionally includes a base unit with processing electronics for receiving a plurality of heat exchanging modules, for example, as depicted in Figures 1 and 2, and for independently controlling each module.

[0113] Reaction Cartridge Assembly

[0114] Among other things, the present application provides for a reaction cartridge assembly for use in a thermal cycler apparatus as described herein. In certain embodiments, a reaction cartridge assembly comprises a reaction cartridge, useful for performing reactions, such as nucleic acid amplification reactions, in embodiments described herein. In certain embodiments, a reaction cartridge as described and exemplified in PCT App. No. PCT / CA2025 / 051192, filed on September 9, 2025, and incorporated by reference in its entirety, is used in embodiments as described herein.

[0115] In certain embodiments, a reaction cartridge comprises an upper portion having a receiving reservoir formed of a housing having an upper open end and a lower open end; a bottom portion comprising a bottom wall and side walls that form a reaction reservoir for accommodating a reaction mixture, wherein the lower open end of the housing of the upper portion is fixedly or removably attached to an upper opening of the reaction reservoir to thus provide fluid communication between the receiving reservoir and the reaction reservoir.

[0116] The present application further details a reaction cartridge assembly comprising a reaction cartridge and a closure cap for use in a thermal cycler apparatus as described herein.

[0117] Closure Cap

[0118] A closure cap comprises a cap body adapted to fit within the upper open end of the receiving reservoir of the reaction cartridge. The closure cap further comprises a top wall with the cap body depending therefrom and being configured to be received within the housing of the receiving reservoir. In certain embodiments, closure cap as described and exemplified in PCT App. No. PCT / CA2025 / 051192, filed on September 9, 2025, and incorporated by reference in its entirety, is used in embodiments as described herein.

[0119] In some embodiments the cap body has a similar volume to that of the receiving reservoir and is configured to be matingly received in the receiving reservoir. In one example of this embodiment, if the housing forming the receiving reservoir is generally cylindrical, then the cap body can be similarly cylindrical and comprise a cylindrical wall that is sized to be flush against the internal surface of the cylindrical housing of the receiving reservoir when the cap body is positioned within the upper open end of the receiving reservoir of the reaction cartridge. Alternatively, if the housing is generally cuboid in shape, then the cap body can be similarly cuboid and also sized such that the walls of the cap body are flush against the internal surface of the cuboid housing of the receiving reservoir when the cap body is positioned within the upper open end of the receiving reservoir of the reaction cartridge.

[0120] In some embodiments, a cap body has a smaller volume than the volume of a receiving reservoir and is configured to be received in the receiving reservoir without contacting the internal surfaces of the reservoir housing. In this embodiment, the top wall of a closure cap is sized and configured to sealingly engage the housing of the receiving reservoir at the upper open end thereof.

[0121] A closure cap further includes a component for sealing a reaction reservoir at the upper opening thereof and / or for transferring materials, such as a fluid or reaction reagents, into the reaction reservoir. In one embodiment, this component comprises a hollow shaft extending from the top wall, through the cap body and terminating at the upper opening of the reaction reservoir. In some examples, the hollow shaft is cylindrical or tubular. In other examples, the hollow shaft tapers down from the top wall.

[0122] In some embodiments, the shaft terminates at a tip that is configured to seal the upper opening of the reaction reservoir so that the reaction reservoir is longer in fluid communication with the receiving reservoir. This allows a pre-determined volume of fluid to be sealed in the reaction reservoir, thus obviating the requirement for a metering mechanism, pipette, or other liquid measuring device. Optionally, the tip of the shaft extends into the reaction reservoir.

[0123] In some embodiments, the shaft is not hollow and contains reaction reagents held within or affixed to the tip or an interior surface thereof, such that the reaction reagents can be contacted with fluid in the reaction reservoir when the tip of the shaft seals the reaction reservoir.

[0124] In some embodiments, a closure cap further comprises a plunger that is movable (or displaceable) within the shaft, whereby depressing the plunger causes reaction reagents to be expelled from the shaft into the reaction reservoir.

[0125] In certain embodiments, a lid that when moved from an open position to a closed position, pressingly engages a closure cap or a top of the reaction cartridge in the thermal well with sufficient force to urge the reaction cartridge into the thermal well such that the side walls of the reaction cartridge become flush with the corresponding side panels of the thermal well.

[0126] In certain embodiments, a means for pressing down a reaction cartridge depresses a plunger in a closure cap, causing reaction reagents to be expelled from the shaft into the reaction reservoir.

[0127] In some embodiments, a reaction cartridge comprises a temporary and removable barrier between a receiving reservoir and a reaction reservoir. Disruption or puncture of the barrier will allow passage of one or more reagent into the reaction reservoir. In one example, a temporary and removable barrier is punctured when a plunger is depressed to expel reagents from within the shaft through the punctured barrier.

[0128] In some embodiments, a barrier is a plastic film.

[0129] In another embodiment, a reaction reservoir contains a lyophilized bead and a shaft terminates in a tip that punctures the barrier and allows the passage of one or more reagent into the reaction reservoir before it is sealed by the mating of the tip of the shaft with the reaction reservoir.

[0130] In some embodiments, reaction reagents within a shaft are in lyophilized form, for example, a lyophilized bead containing a mixture of reagents. The lyophilized reagents are then reconstituted when they contact fluid in the reaction reservoir. In certain embodiments, excipients are added to a lyophilized bead to increase the structural integrity and / or stability of the bead so that the bead does not immediately dissolve when contacted with fluid. Instead, a lyophilized bead can dissolve gradually during a reaction, for example, during an initial denaturation phase of a PCR. This is particularly useful if lyophilized reagents are affixed to the tip of the shaft and not within it.

[0131] In some embodiments, depressing a plunger pushes (either directly or indirectly) against a displaceable retaining member disposed within the shaft of a closure cap. A displaceable retaining member disposed within the shaft of a closure cap can serve to retain or hold reaction reagents within the shaft. In some embodiments, a depressing a plunger pushes a lyophilized bead through the shaft of a closure cap, causing the retaining member to be pushed out of the shaft and into an interior surface of the hollow shaft of a closure cap. In some embodiments, a retaining member is configured be hingedly connected to an interior surface of the shaft of a closure cap. In some embodiments, a retaining member is configured to hingedly connect to a shaft insert. In some embodiments, a retaining member is configured to hingedly connect to a shaft insert.

[0132] In some embodiments, depressing a plunger pushes a lyophilized bead against a rigid element at the tip of the shaft thereby fracturing the bead and causing it to be expelled and come into contact with fluid in the reaction reservoir.

[0133] In some embodiments, a plunger can be removed from the shaft after reagents have been expelled therefrom. Optionally, the plunger is replaced by a lid to close the shaft.

[0134] In some embodiments, a plunger is disposed completely within a closure cap. Disposing a plunger within a closure cap (for example during manufacturing and prior toshipment to a user) prevents the plunger from being depressed prior to use and releasing reaction reagents within the closure cap during, for example, shipment and user handling.

[0135] In certain embodiments, a plunger can be depressed using a closure cap insert as a lid. A closure cap insert is configured to depress the plunger. In certain embodiments, a closure cap insert comprises a top wall and an insert body depending therefrom, wherein the insert body is sized and configured to fit in a hollow shaft of a closure cap for depressing a plunger through the hollow shaft of the closure cap towards a reaction reservoir.

[0136] In certain embodiments, an interconnection mechanism securedly holds a closure cap in place in an upper receiving reservoir. In some embodiments, a closure cap securedly mates to an upper receiving reservoir of a reaction cartridge assembly when inserted into the supper receiving reservoir. In certain embodiments, an interconnection mechanism (e.g., a detent mechanism, a protrusion) from a housing wall of a receiving reservoir (e.g., an upper receiving reservoir) is configured to securedly mate with a closure cap. For example, a groove around a portion of or the whole closure cap can be configured to mate with a protrusion from a housing wall of a receiving reservoir. The groove of the closure cap and the protrusion from the housing wall of the receiving reservoir form an interconnection mechanism to securedly mate the components together.

[0137] In certain embodiments, an identification tag (e.g., as described herein) is disposed on a closure cap.

[0138] In certain embodiments, a shaft of a closure cap is configured to allow gas to escape as a plunger is depressed through the shaft. In some embodiments, a shaft comprises a channel extending along a wall of the shaft from a top wall of the closure cap and terminating at or before the aperture in the bottom surface of the cap body. In certain embodiments, the channel is a grooved channel.

[0139] Reaction Cartridge

[0140] The present application also provides a reaction cartridge for use in a thermal cycler apparatus described above. The reaction cartridge is useful for performing reactions, such as nucleic acid amplification reactions. In certain embodiments, a reaction cartridge asdescribed and exemplified in PCT App. No. PCT / CA2025 / 051192, filed on September 9, 2025, and incorporated by reference in its entirety, is used in embodiments as described herein.

[0141] In certain embodiments, a reaction cartridge comprises an upper portion having a receiving reservoir and a bottom portion comprising a reaction reservoir.

[0142] In some embodiments of the present application, a reaction cartridge comprises: an upper opening and a reaction reservoir for accommodating a reaction mixture and formed from a bottom wall and four side walls, wherein the four side walls comprise two opposing major planar walls spaced apart from each other by minor planar walls, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees. As used herein, the term "major" refers to a wall that is larger in dimensions than a "minor" wall. This configuration allows the reaction cartridge to be accepted into a thermal well of the present thermal cycler assembly such that the walls of the reaction cartridge remain in close contact with the panels of the corresponding thermal well, thereby facilitating efficient heat transfer.

[0143] In some embodiments of the present application the reaction cartridge additionally comprises: an upper portion comprising a receiving reservoir formed of a generally cylindrical or rectangular housing having an upper open end and a lower open end, wherein the lower open end is fixedly or removably attached to the reaction reservoir at the upper opening of the reaction reservoir to thereby provide fluid communication between the receiving reservoir and the reaction reservoir.

[0144] In some embodiments the reaction cartridge is for use with a closure cap adapted to sealingly fit within the upper opening of the reaction reservoir. Alternatively, if the cartridge includes the receiving reservoir, then the reaction cartridge is for use with a closure cap adapted to matingly fit within the receiving reservoir. In some embodiments, for example when the reaction cartridge is to be employed in a method that includes optical interrogation, for improved detection, the closure cap is opaque such that light does not enter or exit the reaction reservoir through the closure cap.

[0145] The present reaction cartridge is amenable to production using injection molding, while also, optionally, providing optical performance sufficient to permit optical (e.g., fluorescent) detection of reaction products within the reaction reservoir of the cartridge.

[0146] In some embodiments, the reaction cartridge comprises a first flat, optically transmissive (e.g., optically transparent) surface on one side of the reaction reservoir and a second flat, optically transmissive (e.g., optically transparent) surface or, preferably, a molded lens in the bottom wall of the reaction reservoir.

[0147] In accordance with some embodiments, the first flat, optically transmissive surface on one side of the reaction cartridge is angularly offset at an angle of from about 90° to about 120° to the second flat, optically transmissive surface or molded lens, preferably about 90°.

[0148] In some embodiments, a reaction cartridge comprises a reaction reservoir for accommodating a reaction mixture, for example a nucleic acid amplification reaction mixture, that is sized to accommodate a reaction mixture having a volume in a range of: from about less than 1 nanoliter to about 1 milliliter; from about 1 nL to about 10 nL; from about 1 nL to about 1 pL; from about 1 pL to about 1 mL; from about 1 pL to about 10 pL; from about 1 nL to about 1.5 nL; from about 2 nL to about 2.5 nL; from about 3 nL to about 3.5 nL; from about 4 nL to about 4.5 nL; from about 5 nL to about 5.5 nL; from about 6 nL to about 6.5 nL; from about 7 nL to about 7.5 nL; from about 8 nL to about 8.5 nL; from about9 nL to about 9.5 nL; from about 10 nL to about 20 nL; from about 30 nL to about 40 nL; from about 50 nL to about 60 nL; from about 70 nL to about 80 nL; from about 90 nL to about 100 nL; from about 200 nL to about 300 nL; from about 400 nL to about 500 nL; from about 600 nL to about 700 nL; from about 800 nL to about 900 nL; from about 1 pL to about10 pL; from about 20 pL to about 30 pL; from about 40 pL to about 50 pL; from about 60 pL to about 70 pL; from about 80 pL to about 90 pL; from about 100 pL to about 200 pL; from about 300 pL to about 400 pL; from about 500 pL to about 600 pL; from about 700 pL to about 800 pL; or from about 900 pL to about 1 mL or more. In some embodiments, the reservoir for the reaction mixture is sized to contain a volume in the range of: from less than about 1 nanoliter to about 1 nL; from about 1.5 nL to about 2 nL; from about 2.5 nL to about 3 nL; from about 3.5 nL to about 4 nL; from about 4.5 nL to about 5 nL; from about 5.5 nL toabout 6 nL; from about 6.5 nL to about 7 nL; from about 7.5 nL to about 8 nL; from about 8.5 nL to about 9 nL; from about 9.5 nL to about 10 nL; from about 20 nL to about 30 nL; from about 40 nL to about 50 nL; from about 60 nL to about 70 nL; from about 80 nL to about 90 nL; from about 100 nL to about 200 nL; from about 300 nL to about 400 nL; from about 500 nL to about 600 nL; from about 700 nL to about 800 nL; from about 900 nL to about 1 pL; from about 10 pL to about 20 pL; from about 30 pL to about 40 pL; from about 50 pL to about 60 pL; from about 70 pL to about 80 pL; from about 90 pL it to about 100 pL; from about 200 pL to about 300 pL; from about 400 pL to about 500 pL; from about 600 pL to about 700 pL; from about 800 pL to about 900 pL; or from about 1 mL to more than about 1 mL.

[0149] In some embodiments, walls of the reaction cartridge comprise an inner surface.

[0150] In some embodiments, walls of the reaction reservoir terminate at a top edge that defines an opening to the reaction reservoir of the reaction cartridge. In some embodiments, the reaction cartridge further comprises an upper element including a receiving reservoir for receiving a sample and / or one or more reagents. The upper element can be generally in the form of an open-ended funnel or cylinder that is fixedly or removably attached at an opening to the reaction reservoir to provide fluid communication between the receiving reservoir and the reaction reservoir. In some embodiments there is a temporary and removable barrier between the receiving reservoir and the reaction reservoir. Such a barrier can be disrupted to allow passage of a sample and / or one or more reagent from the receiving reservoir into the reaction reservoir

[0151] In some embodiments, a reaction cartridge is in whole or in part made from plastic, glass, natural polymers, synthetic polymers, metal, or combinations thereof. In some embodiments, a reaction cartridge is made of any material suitable for conditions for nucleic acid amplification reactions, such as nucleic acid amplification reaction mixtures, chemical reagents and / or thermal cycling, such as, a thermally stable plastic. In some embodiments, the reaction cartridge is made, at least in part, of polypropylene.

[0152] Figures 3 to 13 depict an illustrative, non-limiting examples of reaction cartridges, reaction cartridge assemblies, and closure caps of the present disclosure which can be used with thermocyclers and thermocycler assemblies described herein.

[0153] Figure 3 is a schematic structural diagram of a reaction cartridge 100 according to another embodiment of the present application. Figure 4 is a cross-section of reaction cartridge 100. As shown in Figures 3 and 4, reaction cartridge 100 includes a reaction reservoir 120 formed by four connecting side walls 122 (not shown), 124, 126, and 128 and bottom wall 130. Reaction cartridge 100 further includes receiving reservoir 150 for receiving a sample and / or reagent(s). Receiving reservoir 150 is removably or fixedly attached to upper open end 140 of reaction reservoir 120.

[0154] In the embodiments in which receiving reservoir 150 is removably attached to upper open end 140 of reaction reservoir 120, receiving reservoir 150 can be removed following addition of a sample and / or reagent(s) to allow a reaction mixture to be sealed within reaction reservoir 120 with a cap or lid (not shown).

[0155] In the embodiments in which receiving reservoir 150 is fixedly attached to upper open end 140 of reaction reservoir 120, a cap or a lid can be used to seal top, open end 155 of receiving reservoir 150. Alternatively, a plug-type element or cap can be matingly received in receiving reservoir 150 and thereby allow a reaction mixture to be sealed within reaction reservoir 120.

[0156] To facilitate fit within a thermal well of the present thermal cycler assembly, reaction reservoir 120 includes two opposing major planar walls 122 (not shown) and 126 spaced apart from each other by minor planar walls 124 and 128, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees

[0157] In some embodiments, reaction reservoir 120 has a rectangular pyramidal or square pyramidal shape truncated by bottom wall 130.

[0158] In the embodiment shown in Figures 3 and 4, all or a portion of bottom wall 130 forms lens 132. In some embodiments, at least one of side walls 122, 124, 126, and 128 is formed of or comprises an optically transmissive material.

[0159] In one embodiment, light from a light source (not shown) that passes through the at least one optically transmissive side wall can be used to excite a reaction mixture within reaction reservoir 120 and the resulting emission light can then be collimated by lens 132 and detected by a photodetector (not shown), for example, in performing real-time PCR.

[0160] In another embodiment, light from a light source (not shown) is collimated by lens 132 and can be used to excite a reaction mixture within reaction reservoir 120. The resulting emission light then exits through the at least one optically transmissive side wall and is detected by a photodetector (not shown), for example, in performing real-time PCR.

[0161] Incorporating a lens in a reaction cartridge minimizes light reflections and refractions and improves the signal-to-noise ratio in comparison to a standard conical reaction tube. This is true if the excitation light source has a lens in front of it, because light passing through the lens will be reflected and refracted by the bottom curvature (or side curvature) of the standard conical reaction tube.

[0162] Figure 5 is a schematic showing a top perspective view of a closure cap 200 according to one embodiment. Figure 6 is a cross-section of closure cap 200. As shown in Figures 5 and 6, closure cap 200 comprises a cap body 220, having an internal shaft 230, depending from top wall 240 having a cap body adapted to fit within the upper open end of the receiving reservoir of the reaction cartridge. The closure cap further comprises a top wall with the cap body depending therefrom and being configured to be received within the housing of the receiving reservoir. Cap body 220 comprises air vents 222 and 224 into shaft 230.

[0163] Closure cap 200 further includes plunger 250, which is movable within shaft 230. Figures 5 and 6 illustrate plunger 250 fully depressed into shaft 230 toward dispensing hole 232 through which fluid or reagents found within shaft 230 can be expelled, for example, into the reaction reservoir of a reaction cartridge as described herein. In certain embodiments, pressingly engaging a lid with closure cap 200 facilitates the depression of plunger 250 into shaft 230 towards dispensing hole 232.

[0164] Figure 6 further illustrates the presence of lyophilized bead 234 adjacent dispensing hole 232. Lyophilized bead 234 can contain lyophilized reagents that can be reconstitutedwhen they contact fluid in a reaction reservoir when, for example, a lid is pressingly engaged with closure cap 200 in a thermal well.

[0165] Figure 7 is a top plan view of a reaction cartridge assembly 300 comprising reaction cartridge 100 and closure cap 200, according to an embodiment. Figure 8 is a cross-section of reaction cartridge assembly 300.

[0166] Figures 7 and 8 depict reaction cartridge assembly 300 with cap body 220 of closure cap 200 seated in receiving reservoir 150 of reaction cartridge 100. As shown Figures 7 and 8, when closure cap 200 is fully seated in receiving reservoir 150, the circumferential edges of top wall 240 engage with the upper edge of closure cap 200 and further includes plunger 250, which is movable within shaft 230. Figures 5 and 6 illustrate plunger 250, which can be depressed by, for example, pressingly engaging a plug-type element of a lid (not depicted) configured to push the plunger into shaft 230 toward dispensing hole 232 through which fluid or reagents found within shaft 230 can be expelled into reaction reservoir 120.

[0167] Figure 8 further illustrates the presence of lyophilized bead 234 adjacent dispensing hole 232. Lyophilized bead 234 can contain lyophilized reagents that can be reconstituted when they contact fluid in reaction reservoir 120.

[0168] Figures 9 and 10 illustrate an embodiment in which a reaction cartridge assembly (as depicted in Figures 7 and 8) is configured for the bottom portion comprising reaction reservoir 120 to fit within thermal well 20 of thermal cycler assembly 10. As illustrated Figures 7 and 8, reaction reservoir 120 includes two opposing major planar walls 122 and 124 spaced apart from each other by minor planar walls 126 and 128 (not shown).

[0169] In some embodiments, reaction reservoir 120 has a rectangular pyramidal or square pyramidal shape truncated by bottom wall 130.

[0170] With this configuration of reaction reservoir 120, the reaction cartridge can be positioned with reaction reservoir 20 in thermal well 20 such that side walls 122 and 124 are flush with side panels side 50 and 52 of thermal well 20. In certain embodiments, configuring side walls flush with side panels of a thermal well allows for more effective (e.g., efficient) heat transfer from the thermal well to a solution in a reaction reservoir. In certainembodiments, a lid can be used to pressingly engage reaction cartridge 100 and / or reaction cartridge assembly 300 into thermal well 20 such that gaps between side walls 122 and 124 and side panels side 50 and 52 of thermal well 20 are substantially removed and contact between side walls 122 and 124 and side panels side 50 and 52 is enhanced.

[0171] Figure 11 is a schematic showing a top plan view of a closure cap 400 according to an embodiment of the present application. Figure 12 depicts a cross-section of closure cap 400 depicted in Figure 11. As shown in Figures 11 and 12, closure cap 400 comprises cap body 402 depending from top wall 404. In certain embodiments, cap body 402 is adapted to fit within an upper open end of a receiving reservoir of a reaction cartridge. Closure cap 400 further comprises a top wall with cap body 402 depending therefrom and being configured to be received within the housing of the receiving reservoir. Cap body 402 comprises air vent 410. Air vent 410 is a grooved channel, which allows gases (e.g., air) to pass through the channel along a wall of shaft 412 and escape from a reaction cartridge assembly.

[0172] Closure cap 400 further includes plunger 414, which is movable within shaft 412. In certain embodiments, a plug-type element depending from a bottom surface of a lid and configured to depress plunger 414 can be used to depress plunger 414 into shaft 412 toward dispensing hole 416, causing fluid or reagents found within shaft 412 to be expelled, for example, into a reaction reservoir of a reaction cartridge as described herein.

[0173] Closure cap 400 further illustrates lyophilized bead 418 being held in place by trap door 420. Trap door 420 is a displaceable retaining member disposed within shaft 412. Trap door 420 is hingedly connected to shaft insert 422. Trap door 420 forms an approximately 135° angle with shaft insert 422 when in a closed position, as shown. Shaft insert 422 can be inserted into shaft 412 such that trap door 420 contacts shelf 924. Shelf 424 forms a protrusion from a wall of shaft 412. The portion of shelf 424 in contact with trap door 420 is configured to allow to trap door 420 to slide past shelf 424 without catching as plunger 914 is depressed. A wall of shaft 412 is configured to receivingly mate with trap door 420 as plunger 414 is depressed when a plug-type element engages with plunger 414. Depressing plunger 414 causes lyophilized bead 418 to move towards dispensing hole 416.

[0174] Figure 13 depicts a bottom plan view of an exemplary lid 500, according to an embodiment of the present application. Lid 500 comprises round base 510 configured to matingly engage with an opening of a device base. Lid 500 can be used as a means for pressing a reaction cartridge into a thermal well to wedge it into the thermal well. Pad 530 depends from bottom 515 of base 510. In certain embodiments, pad 530 is configured to pressingly engage with a reaction cartridge or reaction cartridge assembly. Pin 535 extends from bottom 515 of base 510. Pin 535 is configured to engage with a plunger of a closure cap. In certain embodiments, pin 535 may act as a plunger of a closure cap.

[0175] Figure 13 also depicts protrusions 520, 525 which extend substantially perpendicular from side wall 540 of base 510 of the lid 500. Protrusions 520, 525 act as guiding features and are configured to engage slidingly with a track in an opening of a device base.

[0176] Figures 14 and 15 depict a top-plan view and a top-down view, respectively, of device base 600. Device base 600 has circular opening 605 which is configured to receive a reaction cartridge and / or a reaction cartridge assembly. Additionally, opening 605 is configured to matingly receive lid 500. Slots 610, 615 are configured to receive protrusions 520, 525 from lid 500 into tracks 620, 625 (not shown). Tracks 620, 625 (not shown) guide lid 500 from an open position to a closed position to pressingly engage with a reaction cartridge or reaction cartridge assembly positioned in a thermal well within device base 600.

[0177] Figure 16 depicts a cross-sectional view of device base 600 and lid 500 in an open position. In the open position, pin 535 is positioned above plunger 414. Depressions 550, 555 are shown extending from to surface 560 of lid 500. Protrusions 520, 525 are shown positioned above slots 610, 615 in a wall of opening 605. Additionally, lid 500 is depicted as having depressions 550, 555 on top surface 560 of lid 500. Depressions 550, 555 are configured to allow a user to grip and twist lid 500 such that protrusions 520, 525 travel along tracks 620, 625 to terminal position 630 where pad 530 of lid 500 pressingly engages with the top of closure cap 400. In certain embodiments, pad 530 of lid 500 also or, alternatively, pressingly engages with the top of reaction cartridge 100. Engaging with closure cap 400 and / or reaction cartridge 100 pushes walls of reaction reservoir 210 into contact with walls of thermal well 20.

[0178] In Figure 16, pin 535 is position above plunger 414. Lyophilized bead 414 is held in position within shaft 412 by trap door 420, which is hinged ly attached to shaft insert 422.

[0179] Figures 17 and 18 depict a top-plan view and cross-sectional view, respectively, of device base 600 and lid 500 in a closed position. Lid 500 has been inserted into opening 605 of device base 600. Additionally or alternatively, in certain embodiments, pad 530 of lid 500 engages with the top of reaction cartridge 100. In Figure 17, pin 535 has completely depressed plunger 414 through shaft 412 of the causing lyophilized bead 414 to be ejected from shaft 412 and into reaction reservoir 210. As plunger 414 is depressed into shaft 412, trap door 420, which is hinged ly attached to shaft insert 422, is displaced out of the hollow portion of shaft 412 and into a wall of shaft 412 such that it allows for plunger 414 to slide down towards dispensing hole 416 and expel lyophilized bead 418 into reaction reservoir 120.

[0180] Method of Use

[0181] Among other things, the present application further provides methods for performing a reaction (e.g., an isothermal reaction, a non-isothermal reaction). In certain embodiments, a reaction is a thermal cycling reaction (e.g., a non-isothermal nucleic acid amplification reaction) and, optionally, monitoring the reaction and its products using optical detection. In some embodiments, a method is for nucleic acid amplification of a target sequence (e.g., a target nucleic acid sequence) or combination of target sequences.

[0182] In some embodiments, a reaction is a non-isothermal nucleic acid amplification reaction, and the method comprises inserting a reaction cartridge into a thermal well of the present thermal cycling assembly and thermally controlling a reaction mixture within the reaction reservoir of the reaction cartridge. A reaction mixture can be, for example, a sample mixed with one or more chemicals or reagents, within the reaction reservoir of a reaction cartridge. A sample may also be mixed with diluents and / or buffers. A sample may be an aqueous solution containing particles, cells, microorganisms, ions, or small and large molecules, such as proteins and nucleic acids, etc. In a particular use, a sample may be a bodily fluid (e.g., blood, urine, saliva, sputum, seminal fluid, spinal fluid, mucus, or other bodily fluids) or an extraction or component thereof. Alternatively, a sample may be a solidmade soluble in a liquid or a sample may be an environmental sample such as ground or wastewater, soil extracts, pesticide residues, or airborne spores placed in a liquid.

[0183] Thermally controlling a reaction mixture is performed using a heat-exchanging module by cycling through heating or cooling of panels of a thermal well, which are in contact with the walls of a reaction cartridge.

[0184] Methods can additionally include optically interrogating a reaction mixture using an optical detection system in a thermal cycling assembly, as described herein. Optics of an assembly can include a light source for providing excitation light to the reaction mixture in the reaction cartridge (e.g., through one of the lens or the flat, optically transmissive side wall) and a photodetector for detection of light emitted (e.g., through the other of the lens or the flat, optically transmissive side wall) from the reaction mixture following excitation. Light emission is used to detect and / or quantify target reaction products (e.g., amplicons). A thermal cycling assembly may also include a controller, such as a personal computer or a network computer, that provides a user interface to the thermal cycling assembly and controls the operation of the assembly to perform a method.

[0185] All publications, patents and patent applications mentioned in this Specification are indicative of the level of skill of those skilled in the art to which this invention pertains and are herein incorporated by reference to the same extent as if each individual publication, patent, or patent applications was specifically and individually indicated to be incorporated by reference.

[0186] The invention being thus described, it will be obvious that the same may be varied in many ways. Such variations are not to be regarded as a departure from the spirit and scope of the invention, and all such modifications as would be obvious to one skilled in the art are intended to be included within the scope of the following claims.

Claims

WE CLAIM:

1. A thermal cycler assembly comprising: a. a heat source; and b. at least one heat-exchanging module comprising: i. a thermal well for receiving a reaction cartridge, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; ii. means for transferring heat from the heat source to the thermal well; and iii. means for cooling the thermal well.

2. The thermal cycler assembly according to claim 1, wherein the first pair of opposing planar side panels are major planar panels and the second pair of opposing planar panels are minor planar panels, and wherein at least one of the major panels is angled by at least 1 degree and not more than 45 degrees from the bottom panel.

3. The thermal cycler assembly according to claim 1 or 2, further comprising a lid for the thermal well that is moveable between an open position and a closed position, such that when in the closed position the lid pressingly engages a closure cap or a top of the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

4. The thermal cycler assembly according to claim 1 or 2, comprising a lid for the thermal well that is moveable between an open position and a closed position, such that when in the closed position the lid pressingly engages a top of a reaction cartridge assembly, said reaction cartridge assembly comprising the reaction cartridge and a closure cap, in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

5. The thermal cycler assembly according to claim 3 or 4, wherein the lid further comprises means to expel fluids and / or reagents in the closure cap and / or the reaction cartridge.

6. The thermal cycler assembly according to claim 5, wherein the lid comprises means to expel the fluids and / or the reagents in the closure cap and / or the reaction cartridge into a reaction reservoir of the reaction cartridge.

7. The thermal cycler assembly according to claims 3 to 6, wherein the lid does not comprise means for heating or cooing the thermal well.

8. The thermal cycler assembly according to any one of claims 1 to 7, further comprising a controller for controlling the heat-exchanging module to cycle between heating and cooling by alternating and controlling operation of the heat source, the means for transferring heat to the thermal well(s) and the means for cooling the thermal well(s).

9. The thermal cycler assembly according to any one of claims 1 to 8, wherein the means for transferring heat from the heat source to the thermal well comprises a finned heat sink and / or a microheater.

10. The thermal cycler assembly according to any one of claims 1 to 9, wherein the means for cooling the thermal well comprises a thermoelectric cooler.

11. The thermal cycler assembly according to any one of claims 1 to 10, further comprising an optical detection system, wherein the optical detection system comprises an excitation light source and a photodetector and, optionally, a filter wheel.

12. The thermal cycler assembly according to claim 11, wherein the housing of the thermal well includes two or more openings to permit light to enter and exit the thermal well.

13. The thermal cycler assembly according to claim 12, wherein the thermal well comprises a first opening for excitation light from a light source to enter into the housing to excite a reaction mixture in the reaction cartridge, and a second opening for light emitted from the reaction mixture to exit the housing for detection by the photodetector.

14. The thermal cycler assembly according to any one of claims 1 to 13, wherein the reaction cartridge comprises a reaction reservoir formed from a bottom wall and a first pair of opposing major planar side walls spaced apart from a second pair of opposing minor planar side walls, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees from the bottom wall.

15. The thermal cycler assembly according to any one of claims 1 to 14, wherein the reaction cartridge comprises a flat, optically transmissive side wall and a flat, optica lly- transmissive bottom wall, or the reaction cartridge comprises a molded lens in the bottom wall and a flat, optically transmissive side wall angularly offset from the molded lens by an angle of from approximately 90° to approximately 120°, preferably 90°.

16. The thermal cycler assembly according to any one of claims 1 to 15, wherein the thermal cycler assembly further comprises a device base, wherein the device base comprises the thermal well of the at least one heat-exchanging module.

17. The thermal cycler assembly according to any one of claim 16, wherein the device base is configured to receive a lid.

18. The thermal cycler assembly according to claim 16 or 17, wherein the device base comprises means for guiding a lid from an open position to a closed position, such that when in the closed position the lid pressingly engages a closure cap, a top of the reaction cartridge, and / or a top of a reaction cartridge assembly comprising the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

19. The thermal cycler assembly according to claim 18, wherein the means for guiding the lid comprises one or more tracks.

20. The thermal cycler assembly according to claim 18 or 19, wherein the lid comprises one or more guiding features configured to engage with the guiding means of the device base.

21. A thermal cycler assembly comprising: a. a heat source; and b. at least one heat-exchanging module comprising: i. a thermal well for receiving a reaction cartridge assembly, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; ii. means for transferring heat from the heat source to the thermal well; and iii. means for cooling the thermal well.

22. A thermal cycler assembly comprising: a. a heat source; and b. a device base comprising at least one heat-exchanging module, wherein the at least one heat-exchanging module comprises: i. a thermal well for receiving a reaction cartridge, said thermal well comprising a housing formed of a bottom panel and a first pair of opposing planar side panels spaced apart from a second pair of opposing planar side panels; ii. means for transferring heat from the heat source to the thermal well; and iii. means for cooling the thermal well.

23. The thermal cycler assembly according to claim 22, further comprising a lid for the thermal well.

24. The thermal cycler assembly according to claim 23, wherein the lid is moveable between an open position and a closed position, such that when in the closed position the lid pressingly engages a top of a reaction cartridge assembly comprising the reaction cartridge and a closure cap in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

25. The thermal cycler assembly according to claim 23 or 24, wherein the device base comprises means for guiding the lid from an open position to a closed position, such that when in the closed position the lid pressingly engages a closure cap, a top of the reaction cartridge, and / or a top of a reaction cartridge assembly comprising the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

26. The thermal cycler assembly according to claim 25, wherein the means for guiding the lid comprises one or more tracks.

27. The thermal cycler assembly according to claims 25 or 26, wherein the lid comprises one or more guiding features configured to engage with the guiding means of the device base.

28. The thermal cycler assembly according to any one of claims 25 to 27, wherein the lid comprises means for expelling fluids and / or reagents into a reaction reservoir of a reaction cartridge.

29. A reaction cartridge comprising a reaction reservoir for accommodating a reaction mixture, said reaction reservoir being formed from a bottom wall and a first pair of opposing major planar side walls spaced apart from a second pair of opposing minor planar side walls, wherein at least one of the major walls is angled by at least 1 degree and not more than 45 degrees from the bottom wall.

30. The reaction cartridge of claim 29, wherein one of the minor planar side walls comprises or consists of a flat, optically transmissive wall, and the bottom wall comprises a molded lens.

31. The reaction cartridge according to claim 29 or 30, wherein the four side walls terminate at a top edge that defines an opening and the opening is sized to receive a closure cap.

32. The reaction cartridge according to claim 29 or 30, further comprising an upper portion comprising a receiving reservoir, wherein the four side walls of the reaction reservoir terminate at a top edge that defines an opening, the upper portion is connected to the top edge such that there is fluid communication between the reaction reservoir and the receiving reservoir.

33. The reaction cartridge according to any one of claims 29 to 32, wherein the reaction cartridge is formed, in whole or in part, of a thermally stable plastic.

34. The reaction cartridge according to claim 32 or 33, wherein the reaction cartridge is configured to receive a closure cap comprising a top wall, a cap body depending therefrom that is sized and configured to fit in the upper receiving reservoir, and a cap component for sealing the reaction reservoir at the upper open region and / or for transferring materials into the reaction reservoir when the cap body is positioned in the upper receiving reservoir.

35. A method for performing a non-isothermal reaction comprising: a. providing the thermal cycler assembly according to any one of claims 1 to 28; b. inserting a reaction cartridge into the at least one thermal well of the thermal cycling assembly, wherein the reaction cartridge comprises a reaction reservoir containing a sample mixed with one or more chemicals or reagents; and c. performing at least one thermal cycle by sequentially heating the reaction reservoir to a first temperature using the means for transferring heat from the heat source to the thermal well, maintaining the first temperature for a first preset time,cooling the reaction reservoir to a second temperature using the means for cooling the thermal well and maintaining the second temperature for a second preset time.

36. The method according to claim 35, wherein the reaction cartridge is the reaction cartridge according to any one of claims 29 to 34.

37. The method according to claim 35 or 36, wherein the at least one thermal cycle further comprises warming the reaction reservoir to a third temperature that is between the first and the second temperature, and maintaining the third temperature for a third preset time.

38. The method according to any one of claims 35 to 37, wherein the at least one thermal cycle includes at least 20 cycles, at least 30 cycles or about 40 cycles.

39. The method according to any one of claims 35 to 38, wherein the method is for performing nucleic acid amplification.

40. The method according to any one of claims 35 to 39, wherein the method comprises pressingly engaging a closure cap or a top of the reaction cartridge in the thermal well with sufficient force to bring the side walls of the reaction cartridge flush with the side panels of the thermal well.

41. The method according to claim 40, wherein the method comprises exerting a constant force on the closure cap and / or the top of the reaction cartridge to maintain the side walls of the reaction cartridge flush with the side panels of the thermal well.

42. The method according to any one of claims 35 to 41, wherein the method comprises expelling fluids and / or reagents into the reaction reservoir.

43. A method for performing a reaction comprising: a. providing a thermal cycler assembly according to any one of claims 1 to 28;b. inserting a reaction cartridge or a reaction cartridge assembly comprising a reaction cartridge into the at least one thermal well of the thermal cycling assembly, wherein the reaction cartridge comprises a reaction reservoir containing a sample mixed with one or more chemicals or reagents; and c. heating the reaction reservoir to a first temperature using the means for transferring heat from the heat source to the thermal well.

44. The method according to claim 43, wherein the reaction cartridge is the reaction cartridge according to any one of claims 29 to 34.

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