WO2009025881A1

WO2009025881A1 - Thermal cycler for pcr including temperature control bladder

Info

Publication number: WO2009025881A1
Application number: PCT/US2008/056473
Authority: WO
Inventors: Phil Belgrader
Original assignee: Akonni Biosystems
Priority date: 2007-08-23
Filing date: 2008-03-11
Publication date: 2009-02-26
Also published as: JP2010536374A; US8906652B2; EP2190571A4; JP5318102B2; US7955840B2; CN104498354A; US20110269191A1; CN101808725A; CA2697264A1; EP2190571A1; US8329433B2; US20090053772A1; US20130177945A1

Abstract

Methods and devices for performing chemical reactions under controlled temperature are described. In one embodiment, the devices provided by the invention comprise a housing diminished hold a reaction chamber disposed within an interior volume of the housing. The reaction chamber has thermally conductive interior and exterior surfaces defining an internal volume therein at a first temperature. The device also includes at least one temperature-control substance at a second temperature into said bladder and expel said temperature-control substance, the bladder expands to about substantially at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance the said internal volume of reaction chamber.

Description

THERMAL CYCLER FOR PCR INCLUDING TEMPERATURE CONTROL BLADDER

1 Background of the Invention

1.1 Field of the Invention

[0001] The invention relates to devices for performing chemical reactions, and in particular automated devices for performing polymerase chain reaction (PCR). Still more particularly, the present invention provides methods and apparatus for controlling reaction temperatures in an automated PCR device. The present invention has applications in the areas of analytical chemistry, molecular biology, and process chemistry.

1.2 The Related Art

[0002] Polymerase Chain Reaction (PCR) has become a mainstay of biochemical laboratories, and with good reason: this elegant method of replicating oligonucleotides using polymerase enzymes, such as Tag polymerase, has been a major factor in the explosion of biotechnological research and products. The process and its applications are well known those persons having ordinary skill in the art (Ausubel, Brent et al. 1992). In brief, PCR enables the rapid replication of oligonucleotides, in particular DNA, so that single copies of an oligonucleotide can be transformed into a significant concentration to enable further manipulation or analysis. The PCR procedure involves: transferring target oligonucleotide from a sample into a crude extract; adding an aqueous solution containing various enzymes, buffers, triphosphates (dNTPS), and complimentary oligonucleotide primers to the extract to form a reaction mixture; cycling the temperature of the reaction mixture between two or three temperatures (e.g., 90°C-96°C, 37°C-65°C, and 72°C) repeatedly to enable replication of the target oligonucleotides; and then delecting the amplified oligonucleotides. Intermediate steps, e.g., purification of reaction products and incorporation of surface-bending primers, also may be included. Each cycle doubles the number of target oligomer sequences. PCR techniques can amplify a single molecule of an oligonucleotide or oligoribonucleotide about 10⁶- to about 10⁹-fold.

[0003] Because genetic information can be used to establish the identities of individuals and the types of organisms, and because PCR is capable of creating analyzable quantities of genetic material from very small samples, many technologies exist to facilitate the application of PCR to analytical and forensic tasks. In particular, the use of PCR to identify unidentified bodies and criminals is widely used in law enforcement and the military. The application of PCR to national defense and homeland security is also an area of active biodefense development. Also, doctors and hospitals increasingly want access to portable PCR technology for use in care giving. Examples of such uses include:

• Screening blood, saliva, or urine samples for multiple infectious diseases associated with upper respiratory, intestinal, or STD infections.

• Determining if an infectious disease is resistant to antibiotics.

• Determining if an infection is viral or bacterial.

• Identifying an individual's susceptibility to an adverse drug reaction.

• Diagnosing a cancer type (e.g., breast, prostate, ovarian, pancreatic).

• Identifying an individual's predisposition to Alzheimer's disease.

[0004] These applications have created a heavy demand for automated PCR apparatuses that can process small sample concentrations on-site at remote locations to provide analytical data to investigators and medical workers.

[0005] As note above, a fundamental operation during the PCR process is thermal cycling, i.e., the raising and lowering of reaction temperatures to enable the amplication process, in which the temperature of the reaction mixture is driven between about 60⁰C and about 95°C as often as fifty or more times. A thermal cycle typically has four segments: heating the sample to a first temperature; maintaining the sample at the first temperature; cooling the sample to a lower temperature; and maintaining the temperature at the lower temperature. Conventional PCR instrumentation typically uses an aluminum block holding as many as ninety-six conical reaction tubes in which the sample and necessary reagents for amplication are contained. The block is heated and cooled during the PCR amplication process, often using either a Peltier heating/cooling apparatus, or a closed-loop liquid heating/cooling system in which flowing through channels machined into the aluminum block. However, the large mass of the aluminum block, and the conductivity of aluminum, limit the rates of heating and cooling to about 1 ⁰C per second; so a fifty-cycle PCR amplification process takes at least about two hours.

[0006] Moreover, the cooling rate of the aluminum block is significantly lower than the heating rate. The asymmetry between the heating and cooling rates reduces the efficiency of the PCR process. For example, unwanted side reactions can occur at temperatures between the extremes creating unwanted DNA products, such as so- called "primer-dimers" and anomalous amplicons that consume reagents necessary for the desired PCR reaction. Other processes, e.g., ligand binding (organic or enzymatic) also suffer from unwanted side reactions under nonuniform temperatures that often degrade the analysis. For these reasons, optimization of the PCR process and similar biochemical reaction processes requires that the desired optimal reaction temperatures be reached as quickly as possible, spending minimal time at intermediate temperatures. Therefore the reaction vessels containing the reactants must be designed to optimize heating and cooling rates, to permit real time optical interrogation, and to accept various sample volumes.

[0007] One automated PCR system is the MATCI device disclosed in U.S. Patent No.

5,589,136 (Northrup, Raymond P. Mariella et al. 1996), which describes a device that uses a modular approach to thermal cycling and 30 analysis: Each reaction is performed in its own thermal cycling sleeve, and each sleeve has its own associated optical excitation source and fluorescence detector. The low thermal mass of the thermal cycling sleeve allows the MATCl device to realize extremely fast thermal cycling: samples can be heated at a rate of up to 30°C/sec. and cooled at rate as great as 5°C/sec. Two other commercially available systems, sold under the trade names GeneXpert (Cepheid, Sunnyvale, CA) and Razor (Idaho Technology, Inc.), use disposable fluidic cartridges, each containing an flexible reaction chamber that expands under pressure to make tight contact with a solid heater located in the instrument (Petersen, McMillan et al. 1999). The Razor uses a flexible fluidic pouch and actuators that move a reaction slug within the pouch; the reaction zone walls of the pouch make tight contact with two solid heaters. In both cases, the heater is a solid and the disposable cartridge or pouch contains one or more reaction zones, each with a thin, flexible wall that makes thermal contact with the heater. Still another technology, sold commercially under the trade names TruDiagnosis™ and TruArray by Akonni Biosystems (Fredericksburg, MD), rapidly screen a sample for hundreds of disease markers at one time by using hundreds of molecular biosensors arrayed in a microarray the size of a fingernail. The samples are conveyed through the array using microfluidic channels. The Akonni technology can provide accurate diagnostic results in less than 30 minutes to support an informed and timely treatment decision.

[0008] Nevertheless current approaches to handling thermal cycling are limited, depending on flexibility in the disposable component to create satisfactory thermal contact with the instrument hardware, arc needed. In particular, methods and apparatus that provide the desired cycling performance without reliance on special reaction chamber materials offer the promise of reduced cost and greater efficiency. The present invention meets these and other needs.

2 Summary of the Invention

[0009] The present invention provides methods and apparatus for controlling the temperature of a container, such as a reaction vessel in which chemical reagents are combined to produce reaction products under controlled temperatures.

[0010] In a first aspect, the present invention provides a device for performing a chemical reaction. In one embodiment, the devices provided by the invention comprise a housing dimensioned to hold a reaction chamber disposed within an interior volume of the housing. The reaction chamber has thermally conductive interior and exterior surfaces defining an internal volume therein at a first temperature. The device also includes at least one thermally conductive temperature-control bladder disposed therein, which bladder is configured to receive a temperature- control substance at a second temperature into the bladder and expel the temperature-control substance from the bladder. The bladder is further configured such that upon receiving the temperature-control substance, the bladder expands to abut substantially at least a portion of the exterior surfaces of the reaction chamber to enable thermal exchange between the temperature-control substance and the internal volume of reaction chamber.

[001 1 ]In some embodiments, the aforementioned thermal exchange between the temperature-control substance and the internal volume of the reaction chamber is effective to change the temperature of the internal volume of the reaction chamber from the first temperature to a third temperature at least intermediate the first and second temperature. In more specific embodiments, thermal exchange between the temperature-control substance and the internal volume of the reaction chamber is effective to change the temperature of a substance contained within the reaction chamber from the first temperature to a third temperature at least intermediate the first and second temperatures.

[0012] In a second aspect, the present invention provides a method for changing the temperature of the internal volume of a container. The method of the invention comprises providing a housing dimensioned to hold a reaction chamber disposed within an interior volume of the housing, the reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume at a first temperature. The housing further includes at least one thermally conductive temperature-control bladder disposed within the housing which is configured to receive a temperature-control substance at a second temperature into the bladder and expel the temperature-control substance from the bladder. The bladder is further configured such that upon receiving the temperature-control substance the bladder expands to abut substantially at least a portion of the exterior surfaces of the reaction chamber to enable thermal exchange between the temperature-control substance and the internal volume of reaction chamber. The method further includes introducing the temperature-control substance under conditions effective to cause an expansion of the bladder to bring the bladder into substantially abutting the at least a portion of the exterior surfaces of the reaction chamber to enable thermal exchange between the temperature-control substance and the internal volume of reaction chamber.

[0013] In some embodiments, the aforementioned thermal exchange between the temperature-control substance and the internal volume of the reaction chamber is effective to change the temperature of the internal volume of the reaction chamber from the first temperature to a third temperature at least intermediate the first and second temperature. In more specific embodiments, thermal exchange between the temperature-control substance and the internal volume of the reaction chamber is effective to change the temperature of a substance contained within the reaction chamber from the first temperature to a third temperature at least intermediate the first and second temperatures.

[0014] In other embodiments, the method includes introducing a substance into the internal volume of the reaction chamber. Sill other embodiments, include maintaining the expansion of the bladder for a period sufficient to change the temperature of the substance to a third temperature intermediate the first temperature and the second temperature. In yet other embodiments, third temperature is substantially equal to the second temperature. In still more embodiments, the substance comprises a mixture of PCR reactants, and the third temperature is effective to induce a PCR reaction.

[0015] In another aspect, the present invention provides a device for performing a chemical reaction, comprising a reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume within the reaction chamber at a first temperature. The device also includes at least one thermally conductive temperature-control bladder disposed proximal to the reaction chamber, the bladder being configured to receive a temperature-control substance at a second temperature into the bladder and expel the temperature-control substance from the bladder; and the bladder being further configured such that upon receiving the temperature-control substance the bladder expands to abut substantially at least a portion of the exterior surfaces of the reaction chamber to enable thermal exchange between the temperature-control substance and the internal volume of reaction chamber.

[0016] In yet another aspect, the invention provides a method for changing the temperature of the internal volume of a container, comprising providing a reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume within the reaction chamber at a first temperature. Providing also at least one thermally conductive temperature-control bladder proximal to the reaction chamber, which is configured to receive a temperature- control substance at a second temperature into the bladder and expel the temperature-control substance from the bladder. The bladder is further configured such that upon receiving the temperature-control substance the bladder expands to abut substantially at least a portion of the exterior surfaces of the reaction chamber to enable thermal exchange between the temperature-control substance and the internal volume of reaction chamber. The method further includes introducing the temperature-control substance under conditions effective to cause an expansion of the bladder to bring the bladder into substantially abutting the at least a portion of the exterior surfaces of the reaction chamber to enable thermal exchange between the temperature-control substance and the internal volume of reaction chamber.

[0017] These and other aspects and advantages will become apparent when the

Description below is read in conjunction with the accompanying Drawings.

3 Brief Description of the Drawings

[0018] Figures IA, IB, and 1C illustrate one embodiment of a device in accordance with the present invention. Figure IA is a partial cut-away view of such a device. Figure IB is a cut-away top view of the interior of such a device, with the bladder in a substantially deflated state. Figure 1C is a cut-away top view of the interior of such a device, with the bladder in a substantially inflated state to provide thermal contact with a reaction vessel.

[0019] Figure 2 is a partial cut-away view of another embodiment of a device in accordance with the present invention that comprises multiple sets of bladders.

[0020] Figure 3 is a schematic illustrating one exemplary embodiment of the invention.

[0021] Figure 4 is a graph showing heating and cooling as a function of time for the embodiment illustrated in Figure 3.

[0022] Figure 5 is a graph showing heating and cooling as a function of time for the embodiment illustrated in Figure 3.

4 Description of Some Embodiments of the Invention

[0023] In a first aspect, the present invention provides a device for controlling the temperature of a defined volume. In one embodiment, the defined volume is a reaction chamber configured for holding chemical reactants and performing a chemical reaction therein at controlled temperatures. In a more particular one embodiment, shown in Figure IA (1000), the device provided by the invention includes a housing (1004). The housing can be constructed from materials and designs well known to persons having ordinary skill in the art. Examples of such materials include, without limitation, plastics, metals, ceramics, composites, and the like. Examples of housing embodiments include those in which the housing is of lightweight construction (e.g., thin plastic), hermetically sealed (e.g., for containing harmful substances, such as hazardous chemical and biological substances), or capable of holding a vacuum in the interior space. Thus, in some embodiments, the housing includes means for reducing the pressure (i.e., inducing a vacuum) within the housing (i.e., within interior space 1012 ; and in other embodiments, the housing includes one or more inlets or ports for adding reagents. The housing may also include sensors, reactant supplies, and other components as will be familiar to those persons having ordinary skill in the art. Still more designs and specifications will be familiar to persons having ordinary skill in the art. The particular choices of materials and design will depend on the anticipated function and operating conditions of the device as will be understood by persons having ordinary skill in the art. The device (1000) further comprises a reaction chamber (1008) arranged within the interior space of the housing (1012). The reaction chamber includes a thermally conductive outer wall (1016) and a thermally conductive inner wall (1020) defining an internal volume within the reaction chamber (1024) as shown in Figures IB and 1 C The reaction chamber can be constructed from materials and designs well known to persons having ordinary skill in the art. Examples of such materials include, without limitation, plastics, metals, ceramics, composites, and the like. Exemplary embodiments include those in which the reaction chamber is of lightweight construction (e.g., thin plastic), hermetically sealed (e.g., for containing harmful substances, such as 20 hazardous chemical and biological substances), or capable of holding a vacuum. In some embodiments, the reaction chamber is designed to hold a single mixture of materials; and, in more particular embodiments, includes a cap or other seal to create a closed system. In other embodiments, the reaction chamber has a substantially tubular design through which mixtures of materials travel in defined and disjoint volumes, commonly referred to as "slugs" (see Figure 2). Still more designs and specifications will be familiar to persons having ordinary skill in the art. For example, the reaction chamber may include one or more inlets or ports for adding reagents or removing reaction products, internal sensors, and windows for external sensors. The particular choices of materials and design will depend on the anticipated function and operating conditions of the device as will be understood by persons having ordinary skill in the art.

[0025] Returning to Figure IA, also disposed within the interior of the housing are one or more temperature-control pouches or temperature-control bladders (1028) that are disposed proximal to the reaction chamber and configured to control, mediate, or otherwise modify the temperature of the internal volume of the reaction chamber (1024). The pouch or bladder is composed of a material having suitable mechanical and thermal properties, as will be understood by persons having ordinary skill in the art. Examples of suitable materials include, but are not limited to: silicone, latex, mylar, polyurcthanc, polypropylene, and polycthlcnc. In other embodiments the above-described bladders comprise a gel material healed by a heat source such as a resistive or peltier heater. Each bladder is configured to accept a temperature control material (show at 1036 in Figure 1C), such as a liquid or gas at a controlled temperature, that is introduced into the hollow space {1040, see Figure IB) of bladder 1028, e.g., through inlets and outlets such as shown at 1028 and 1032, respectively, in Figure 1. The temperature-control substance can be stored in a reservoir or other repository from which the temperature of the temperature-control substance can be modified by an operator. In another embodiment, withdrawal of the temperature-control substance from the bladder after introduction is effective to return the bladder to the above-described disengaged state by reducing, and optionally preventing, the above-described thermal exchange. Thus, by introducing and withdrawing the temperature-control substance, the temperature of the internal volume can be modulated in a controlled fashion. In one embodiment, the temperature control material is water, and the bladder is connected to a water circuit that can provide water at a desired temperature to the bladder. Suitable temperature-control materials, means for regulating the temperature of such materials, and means for introducing such materials to, and withdrawing them from, the pouch or bladder is also familiar to those having ordinary skill in the art.

[0026] In one embodiment, the introduction of the temperature-control material into the bladder is effective to induce expansion of the bladder from a substantially non- abutting disengaged position (see Figure IB) to an engaged position in which the bladder abuts substantially at least a portion of the outer wall (1016) of the reaction chamber (see Figure 1 C), providing thereby thermal exchange between the temperature control material and the internal volume of the reaction chamber (J 024) through the walls of the bladder and reaction chamber. Thus, in one embodiment, the internal volume of the reaction chamber is at a first temperature, the temperature-control material is at a second temperature, and the thermal contact between the two is effective to change the temperature of the internal volume of the reaction chamber from the first temperature to a third temperature that is at least intermediate the first and second temperature. In a more specific embodiment, the third temperature is substantially equal to the second temperature. In more specific embodiments, the internal volume of the reaction chamber contains a substance, such as a mixture of reactants or an analyte, is at a temperature substantially equal to the first temperature prior to the above- described thermal exchange and brought to a temperature substantially equal to the third temperature following such thermal exchange. In a still more particular embodiment in which the internal volume contains a substance, the third temperature is substantially equal to the second temperature. One, two, or more pouches or bladders can be arranged proximal to the reaction chamber by analogy to the descriptions provided herein, as illustrated in Figure 2 at (2000). There, a housing (2004), such as described above, includes a reaction chamber (2008) that holds a series of slugs of reactants (2009, 2010, 2011), which are transported through the reaction chamber and in contact with the interior surface of the reaction chamber (2014). Proximally adjacent the reaction chamber are two sets of temperature-control pouches or bladders arrayed in pairs on opposing sides of the reaction chamber (2016, 2020), connected with inlets (2017) and outlets (2018), which operate as described above. In one embodiment, the slugs are transported through the internal volume of the reaction chamber and paused at defined locations whereupon one or more the bladders engages the outer wall of the reaction chamber (2038) to modulate the temperature of the slug by thermal exchange as described above. The bladders may be filled with a temperature-control substance at single temperature, to provide substantially equal heat exchange by all bladders, or different bladders can hold temperature-control substances at different temperatures. In some embodiments, different bladders can even hold different temperature-control substances to provide different thermal exchange properties.

[0028] In another embodiment, the substance (which may be in the form of one or more slugs) contained in the internal volume of the reaction chamber is a mixture of reagents for performing a PCR reaction. In a more specific embodiment, the reaction chamber is a disposable analytical cartridge, such as available commercially, that holds the PCR reagents. In a more specific embodiment, the reaction cartridge is inserted into the housing and the temperature-control substance is introduced into bladders, which thereby expand and told the cartridge and heat the rcactants for a prc-dctcrmincd time. At a chosen moment, the temperature-control substance is withdrawn, and the bladders deflate to reduce or check further thermal exchange. This disengaged configuration can be maintained for a determined period, after which the bladders are again engorged to bring the reactants back to the earlier temperature or, optionally, a different temperature. Successive phases of engagement and disengagement, using temperature-control substances at a constant or varying temperature, can be performed to perform reactions at defined time-temperature cycles Such thermal cycling will be familiar to persons having ordinary skill in the art. f0029] One particular embodiment includes a single, static reaction chamber containing reactants for a PCR amplification of an oligomer. One or more bladder(s) is (are) brought into contact with the reaction chamber, each of which bladders contain the same circulating temperature-control substance. A valve diverts the temperature-control substance from two or more reservoirs of temperature-control substance that are at different temperatures, so that the PCR mixture can be brought to different temperatures by exchanging the temperature-control fluids in the bladders. During the thermal cycling, a temperature-control substance at 95°C is circulated into the bladders to heat, and thereby denature the oligomers, and then withdrawn. Next, a temperature-control substance at 60⁰C is circulated into the bladders to enable the primers to hybridize and extend to generate PCR amplication product. This sequence is performed for between about 30 and about 50 cycles.

[0030] In another embodiment, two bladders are brough into contact with a single reaction chamber, wherein each bladder contains a circulating temperature-control substance at a different temperature (e.g., one at 95°C and the other at 60⁰C). Expansion and contraction of the bladders as described above determines which bladder makes contact with the reaction chamber or channel. In still another embodiment, a single reaction chamber has two or more reaction zones in a single channel. Each zone interfaces with a different bladder; and each bladder is at a different temperature, e.g., 95⁰C and 60⁰C respectively. The reaction slug is moved hack and forth between temperature zones to produce the desired thermal cycling. (See Figure 2, described above.)

[0031 ] In other embodiments, one or more of the above-described bladders is replaced by a resistive heater, a pclticr, or temperature-controlled air, cither singly or in combination.

[0032] In still other embodiments, the above-described reaction chamber is replaced with a microarray having immobilized primers at each microarray spot.

5 Examples

[0033] Figure 3 provides a schematic illustration of one embodiment of the invention (3000). A pump (3002) of standard construction as will be understood by those having ordinary skill in the art, was connected to and outlet line (3004) that carried water through a heat exchanger (3006) made using materials known to persons having ordinary skill in the art. The outlet line from the heat exchanger (3008) carried the water to a first heater (3010) configured to heat the water to about 95°C. The water was then passed through a branch (3012) that splits the path into the bladder unit (3014), which includes a first bladder support (3016) coupled to a first bladder (3018) in a substantially opposing arrangement to a second bladder support (3020) coupled to a second bladder (3022). Water exiting the bladder unit (3014) is combined back into a single path by a second branch (3024) and then passes into a second heater (3026) configured to heat the water to about 65°C. A return path (3028) brings the water back to the pump. Each of the bladders has a capacity of five milliliters (ml), each of the heaters can hold 22 ml, and the heat exchanger can hold between five ml and 22 ml. By cycling the water reversibly between each of the heaters and heat exchanger, the bladders can cycle the temperature of a sample held in the bladder unit between a nominal starting temperature, 65°C, and 95°C. [0034] The performance of the device described with reference to Figure 3 is shown in Figure 4. There, water at an initial temperature of about 65°C in about three to four seconds (i.e., heated at a rate of about 9.8°C/s), held at that temperature for about one minute, cooled back to the starting temperature in about five seconds (i.e., at a rate of about 77°C/s), then heated to about 95°C in about 10 seconds, held at that temperature for about 75 seconds-80 seconds, and then cooled to about 40⁰C.

[0035] A second example of the performance of the device described with reference to Figure 3 is shown in Figure 5. There, water in a reaction chamber was held between a pair of bladders is heated to 95⁰C and held at the temperature for at least ten seconds, then cooled back to about 65°C in about two seconds (i.e., at a rate of about 15°C/s), held at the temperature for about 25 seconds, heated to about 95°C in about three seconds (i.e., at a rate of about 10°C/s), held at that temperature for about one second, and then cooled again to about 65°C in about three seconds, held at that temperature for about 25 seconds. The heating and cooling cycle was repeated as described and shown:

[0036] In an exemplary embodiment of a method for operation of the above-described invention, an operator places a sample for PCR amplification in a disposable cartridge reaction chamber. The cartridge is loaded into the instrument and aligned with the relaxed, i.e., disengaged, bladders. Instrument operation is initiated, and the bladders are charged with circulating temperature-control fluid. The fluid reservoirs begin heating to reach operating temperature while the sample is being processed. The processed sample is nixed with PCR reagents on the cartridge, and the mixture is moved to the PCR reaction chamber. Thermal cycling is performed in the cartridge reaction chamber by valve control of two reservoirs of fluids at different temperatures (e.g., at 95°C and 60⁰C). The thermal cycling continues for between about 30 and about 45 cycles. The reaction mixture containing the desired PCR product is then moved to a microarray component. When the instrument's operation is completed, the bladder is drained, thereby relieving the pressure to no longer make contact with the cartridge. The cartridge is then removed from the instrument. 6 Conclusion

[0037] Thus it will be seen that the present invention provides important apparatuses and methods for controlling the temperature in a reaction chamber, and especially, a reaction chamber used to perform PCR reactions. Exemplary advantages provided by the apparatuses and methods described herein include, but are not limited to the following:

• Bladders allow simplified fluidic-based heat transfer to a disposable cartridge for efficient and reproducible thermal cycling in the cartridge.

• Deflated bladders allow easy insertion of disposable cartridges containing a reaction chamber.

• Use of bladder avoids liquid interconnects to the disposable cartridge for fluid circulation.

[0038] Although various specific embodiments and examples have been described herein, those having ordinary skill in the art will understand that many different implementations of the invention can be achieved without departing from the spirit or scope of this disclosure. For example, encryption and decryption can be performed using a single software module or more than two software modules. The modules described herein can be implemented using a variety of techniques and can be part of the operating system as well as plug-ins. Still other variations will be clear to those having ordinary skill in the art.

7 Bibliography

[0039] The following reference are each incorporated in their entireties and for all purposes.

[0040] Ausubel, F. M., Brent, R., et ai, Eds. (1992). Short Protocols in Molecular

Biology. Current Protocols in Molecular Biology. New York, John Wiley & Sons.

[0041] Northrup, M. A., Raymond P. Mariella, J., etal. (1996). Silicon-Based Sleeve Devices for Chemical Reactions. US 5,589,136.

[0042] Petersen, K. E., McMillan, W. A., et al. (1999). Reaction Vessel for Heat Exchanging Chemical Processes. US 5,958,349.

Claims

WHAT IS CLAIMED:

1. A device for performing a chemical reaction, comprising: a housing, said housing dimensioned to hold a reaction chamber disposed within an interior volume of said housing, said reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume within said reaction chamber, said interior volume being at a first temperature; and at least one thermally conductive temperature-control bladder disposed within said housing, said bladder being configured to receive a temperature-control substance at a second temperature into said bladder and expel said temperature-control substance from said bladder; and said bladder being further configured such that upon receiving said temperature-control substance said bladder expands to abut substantially at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and said internal volume of reaction chamber.

2. The device of claim 1, wherein said thermal exchange between said temperature- control substance and said internal volume of said reaction chamber is effective to change the temperature of said internal volume of said reaction chamber from said first temperature to a third temperature at least intermediate said first and second temperature.

3. The device of claim 2, wherein said third temperature is substantially equal to said second temperature.

4. The device of claim 2, wherein said thermal exchange between said temperature- control substance and said internal volume of said reaction chamber is effective to change the temperature of a substance contained within said reaction chamber from said first temperature to a third temperature at least intermediate said first and second temperature.

5. The device of claim 4, wherein said third temperature is substantially equal to said second temperature.

6. The device of claim 1 , further comprising said reaction chamber disposed within said interior volume of said housing.

7. The device of claim 1, wherein said bladder comprises an inlet for accepting said temperature-control substance and an outlet for expelling said temperature-control substance.

8. The device of claim 1, wherein said bladder is configured to contract from said abutting said at least a portion of said exterior surfaces of said reaction chamber upon expelling said temperature-control substance from said bladder to enable thereby at least a reduction of said thermal exchange between said between said temperature-control substance and said internal volume of said reaction chamber.

9. The device of claim 8, wherein said reduction of said thermal exchange between said between said temperature-control substance and said internal volume of said reaction chamber is effective to substantially prevent said thermal exchange between said between said temperature-control substance and said internal volume of said reaction chamber.

10. The device of claim 1 , further comprising means for reducing the pressure within the internal volume of said housing.

1 1. The device of claim 1 , further comprising means for supplying and removing said temperature-control substance from said bladder.

12. The device of clam 1 , wherein said temperature-control substance is a fluid.

13. A method for changing the temperature of the internal volume of a container, comprising: providing a housing, said housing dimensioned to hold a reaction chamber disposed within an interior volume of said housing, said reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume within said reaction chamber, said interior volume being at a first temperature; and said housing further including at least one thermally conductive temperature-control bladder disposed within said housing, said bladder being configured to receive a temperature-control substance at a second temperature into said bladder and expel said temperature-control substance from said bladder; and said bladder being further configured such that upon receiving said temperature-control substance said bladder expands to abut substantially at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and said internal volume of reaction chamber; introducing said temperature-control substance under conditions effective to cause an expansion of said bladder to bring said bladder into substantially abutting said at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and said internal volume of reaction chamber.

14. The method of claim 13, further comprising maintaining said expansion of said bladder to maintain said thermal exchange for a period sufficient to change the temperature of said internal volume of said reaction chamber from said first temperature to at least a third temperature intermediate said first temperature and said second temperature.

15. The method of claim 14, wherein said third temperature is substantially equal to said second temperature.

16. The method of claim 13, further comprising introducing a substance into said internal volume of said reaction chamber.

17. The method of claim 16, further comprising maintaining said expansion of said bladder for a period sufficient to change the temperature of said substance to a third temperature intermediate said first temperature and said second temperature.

18. The method of claim 17, wherein said third temperature is substantially equal to said second temperature.

19. The method of claim 18, wherein said substance comprises a mixture of PCR reactants, and said third temperature is effective to induce a PCR reaction.

20. The method of claim 13, further comprising withdrawing said temperature-control substance from said bladder to cause thereby said bladder to contract from said exterior wall of said reaction chamber.

21. The method of claim 20, wherein said contraction is effect to reduce said thermal exchange between said temperature control fluid and said exterior wall of said reaction chamber.

22. The method of claim 21 , further comprising allowing said interior volume of said reaction chamber to return to a fourth temperature substantially equal to said first temperature.

23. A device for performing a chemical reaction, comprising: a reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume within said reaction chamber, said interior volume being at a first temperature; and at least one thermally conductive temperature-control bladder disposed proximal to said reaction chamber, said bladder being configured to receive a temperature-control substance at a second temperature into said bladder and expel said temperature-control substance from said bladder; and said bladder being further configured such that upon receiving said temperature-control substance said bladder expands to abut substantially at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and said internal volume of reaction chamber.

24. The device of claim 24, wherein said thermal exchange between said temperature- control substance and said internal volume of said reaction chamber is effective to change the temperature of said internal volume of said reaction chamber from said first temperature to a third temperature at least intermediate said first and second temperature.

25. The device of claim 25, wherein said third temperature is substantially equal to said second temperature.

26. The device of claim 25, wherein said thermal exchange between said temperature- control substance and said internal volume of said reaction chamber is effective to change the temperature of a substance contained within said reaction chamber from said first temperature to a third temperature at least intermediate said first and second temperature.

27. The device of claim 27, wherein said third temperature is substantially equal to said second temperature.

28. The device of claim 24, further comprising said reaction chamber disposed within said interior volume of said housing.

29. The device of claim 24, wherein said bladder comprises an inlet for accepting said temperature-control substance and an outlet for expelling said temperature-control substance.

30. The device of claim 24, wherein said bladder is configured to contract from said abutting said at least a portion of said exterior surfaces of said reaction chamber upon expelling said temperature-control substance from said bladder to enable thereby at least a reduction of said thermal exchange between said between said temperature-control substance and said internal volume of said reaction chamber.

31. The device of claim 30, wherein said reduction of said thermal exchange between said between said temperature-control substance and said internal volume of said reaction chamber is effective to substantially prevent said thermal exchange between said between said temperature-control substance and said internal volume of said reaction chamber.

32. The device of claim 24, further comprising means for reducing the pressure within the internal volume of said housing.

33. The device of claim 24, further comprising means for supplying and removing said temperature-control substance from said bladder.

34. The device of clam 24, wherein said temperature-control substance is a fluid.

35. A method for changing the temperature of the internal volume of a container, comprising: providing a reaction chamber having thermally conductive interior and exterior surfaces defining an internal volume within said reaction chamber, said interior volume being at a first temperature; and at least one thermally conductive temperature-control bladder proximal to said reaction chamber, said bladder being configured to receive a temperature-control substance at a second temperature into said bladder and expel said temperature-control substance from said bladder; and said bladder being further configured such that upon receiving said temperature-control substance said bladder expands to abut substantially at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and said internal volume of reaction chamber; introducing said temperature-control substance under conditions effective to cause an expansion of said bladder to bring said bladder into substantially abutting said at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and said internal volume of reaction chamber.

36. The method of claim 35, father comprising maintaining said expansion of said bladder to maintain said thermal exchange for a period sufficient to change the temperature of said internal volume of said reaction chamber from said first temperature to at least a third temperature intermediate said first temperature and said second temperature.

37. The method of claim 36, wherein said third temperature is substantially equal to said second temperature.

38. The method of claim 35, further comprising introducing a substance into said internal volume of said reaction chamber.

39. The method of claim 38, father comprising maintaining said expansion of said bladder for a period sufficient to change the temperature of said substance to a third temperature intermediate said first temperature and said second temperature.

40. The method of claim 39, wherein said third temperature is substantially equal to said second temperature.

41. The method of claim 40, wherein said substance comprises a mixture of PCR reactants, and said third temperature is effective to induce a PCR reaction.

42. The method of claim 35, further comprising withdrawing said temperature-control substance from said bladder to cause thereby said bladder to contract from said exterior wall of said reaction chamber.

43. The method of claim 42, wherein said contraction is effect to reduce said thermal exchange between said temperature control fluid and said exterior wall of said reaction chamber.

4. The method of claim 43, further comprising allowing said interior volume of said reaction chamber to return to a fourth temperature substantially equal to said first temperature.