WO2019035998A1 - Systems with fluid path control and regulation - Google Patents

Systems with fluid path control and regulation Download PDF

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Publication number
WO2019035998A1
WO2019035998A1 PCT/US2018/000281 US2018000281W WO2019035998A1 WO 2019035998 A1 WO2019035998 A1 WO 2019035998A1 US 2018000281 W US2018000281 W US 2018000281W WO 2019035998 A1 WO2019035998 A1 WO 2019035998A1
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WIPO (PCT)
Prior art keywords
chamber
device
chambers
configured
fluid
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PCT/US2018/000281
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French (fr)
Inventor
Benjamin Frank GELDHOF
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Modernatx, Inc.
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Priority to US201762546815P priority Critical
Priority to US62/546,815 priority
Application filed by Modernatx, Inc. filed Critical Modernatx, Inc.
Publication of WO2019035998A1 publication Critical patent/WO2019035998A1/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J19/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00279Features relating to reactor vessels
    • B01J2219/00281Individual reactor vessels
    • B01J2219/00286Reactor vessels with top and bottom openings
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00351Means for dispensing and evacuation of reagents
    • B01J2219/00389Feeding through valves
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00351Means for dispensing and evacuation of reagents
    • B01J2219/00418Means for dispensing and evacuation of reagents using pressure
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718Type of compounds synthesised
    • B01J2219/0072Organic compounds
    • B01J2219/00722Nucleotides
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502738Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by integrated valves

Abstract

The invention provides devices, systems, and methods for carrying out reactions, e.g., producing nucleic acids, e.g., RNA having a poly(A) sequence, e.g., mRNA, for therapeutic or other use.

Description

SYSTEMS WITH FLUID PATH CONTROL AND REGULATION

BACKGROUND OF THE INVENTION

Fluidic systems for performing chemical and biological reactions have been used for the small- and large-scale production of a wide variety of pharmaceutically and industrially relevant molecules. Fluidic control systems often require complex networks of flexible tubing and corresponding engineering controls to ensure proper flow of fluid through the system. The complexity of such systems can require extensive time to setup and can result in mistakes in setup or operation as a result of user error.

One exemplary use for fluidic systems is as controllable biochemical reactors for the production of nucleic acids, e.g., ribonucleic acids (RNA). RNA plays an important role in the regulation, coding, and expression of genes. Cellular organisms include many different kinds of RNA, each of which may perform a unique role within a biological system. Certain RNA molecules include a sequence of nucleotides including only adenine nucleobases. So-called poly(A) sequences (also known as poly(A) tails or regions) are thought to stabilize the RNA and to facilitate the termination of transcription, the export of the RNA from cellular regions such as the nucleus, and translation. An RNA having a poly(A) sequence may be a messenger RNA (mRNA). mRNA molecules encode polypeptides and are responsible for gene expression. In recent years, RNA molecules having poly(A) sequences (e.g., mRNA) have been identified as potentially useful therapeutic and/or prophylactic agents for a variety of pharmaceutical applications, in particular as individualized cancer vaccines where the template for producing the mRNA was obtained, sequenced, and synthesized directly from an afflicted patient to produce an mRNA encoding a cancer antigen.

Current fluidic assemblies for the large scale production of molecules, e.g., therapeutically sufficient amounts of a pure nucleic acid, such as mRNA, are expensive, relatively slow, expose sensitive reagents and products to the local environment around the apparatus, and can be difficult to operate. Thus, there is need in the field for an inexpensive, flexible platform which minimizes user error and the risk of contamination.

SUMMARY OF THE INVENTION

The invention provides devices, systems, and methods for carrying out reactions, e.g., producing nucleic acids, e.g., RNA having a poly(A) sequence, e.g., mRNA, for therapeutic or other use.

In one aspect, the invention provides a device having a rigid housing; a first chamber for a volume of fluid; a fluid inlet and a fluid outlet in fluid communication with the first chamber; one or more fluidic channels at least in part defined in the rigid housing and in fluid communication with the fluid inlet or fluid outlet; and at least one valve, where the flow of fluid into or out of the first chamber is controlled by the at least one valve.

In some embodiments, the at least one valve is closed at atmospheric pressure. In some embodiments, the at least one valve is controlled by an external actuator. In some embodiments, the at least one valve is actuated electrically, magnetically, hydraulically, pneumatically, or by a combination thereof. In some embodiments, the at least one valve is a diaphragm valve, solenoid valve, pinch valve, or a combination thereof. In further embodiments, the device contains one or more sensors configured to measure a property of a fluid in the device, e.g., flow rate, temperature, pressure, pH, light, air bubbles, or conductivity. In further embodiments, the device contains more chambers, e.g., a second chamber for a volume of fluid that is fluidically connected to the first chamber by one of the one or more fluidic channels; a third chamber for a volume of fluid that is fluidically connected to the first and/or second chamber by one of the one or more fluidic channels; a fourth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third chamber by one of the one or more fluidic channels; a fifth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth chamber by one of the one or more fluidic channels; a sixth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth chamber by one of the one or more fluidic channels; a seventh chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth chamber by one of the one or more fluidic channels; an eighth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh chamber by one of the one or more fluidic channels; or a ninth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh and/or eighth chamber by one of the one or more fluidic channels. In a further embodiment, the device contains additional valves, e.g., one for each chamber, such as a second valve that controls flow into or out of the second chamber, a third valve that controls flow into or out of the third chamber, a fourth valve that controls flow into or out of the fourth chamber, a fifth valve that controls flow into or out of the fifth chamber, a sixth valve that controls flow into or out of the sixth chamber, a seventh valve that controls flow into or out of the seventh chamber, an eighth valve that controls flow into or out of the eighth chamber, or a ninth valve that controls flow into or out of the ninth chamber.

In certain embodiments, the device is configured for performing an enzymatic reaction and has first through fourth and an optional fifth chamber. The first, second, third, and fourth chambers are configured to house reagents for the enzymatic reaction and are fluidically connected to one of the first through fourth chambers or the optional fifth chamber that is configured for carrying out the enzymatic reaction. In one embodiment, the device contains a heat source operably connected to the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction. In further embodiments, the device includes one or more pumps for moving fluid into or out of the first through fourth chambers or the optional fifth chamber. In some embodiments, the first through third chambers are fluidically connected to the fifth chamber either in series or parallel.

In certain embodiments, the device is configured for purifying reaction products and includes first through sixth chamber and a purification matrix to which the reaction products bind. The first, second, and third chambers are configured to house reagents for sanitation, the fourth and fifth chambers are configured to house reagents for washing the reaction products, the sixth chamber is configured to house an eluent, an optional seventh chamber is configured to house sample to be purified, an optional eighth chamber is configured to house a purified sample, and an optional ninth chamber is configured to house fluid waste. The purification matrix is disposed downstream of the first through sixth chambers and the optional seventh chamber and upstream of the optional eighth and ninth chambers. The first through sixth chambers and the optional seventh, eighth and ninth chambers are fluidically connected to the purification matrix by the one or more fluidic channels. In one embodiment, the purification matrix is a resin. In further embodiments, the device contains one or more sensors, e.g., to measure temperature, light, solution conductivity, pressure, or presence of air bubbles. In one embodiment, the device contains one or more sensors for pressure and air bubbles upstream of the purification matrix and one or more sensors for light, conductivity, and/or temperature downstream of the purification matrix. In further embodiments, the device contains one or more pumps for moving fluid into and out of the first through sixth chambers and the optional seventh, eighth and ninth chambers.

In certain embodiments, the device is configured for performing tangential flow filtration and includes three chambers and a filter between first and second chambers. The first chamber is configured to recirculate sample to be filtered, the second chamber is configured to house waste filtrate, and the third chamber is configured to house diafiltration solution, wherein the first and third chambers are fluidically connected by the one or more fluidic channels. In a further embodiment, the device contains a backpressure valve disposed on the outlet of the first chamber. In further embodiments, the device contains two pressure sensors located in the first chamber. In further embodiments, the device has a first pump for moving fluid past the filter. In a further embodiment, the device has a second pump configured to move fluid from the third chamber to the first chamber.

In certain embodiments, the device is configured for performing clarification filtration and includes two chambers and a filter disposed between the first and second chambers. The first chamber is configured to house the sample to be clarified and is fluidically connected to the second chamber, which is configured to store the clarified sample. In a further embodiment, the device contains a pressure sensor located upstream of the filter. In further embodiments, the device contains a pump for moving fluid into and out of the first and second chambers.

In any of the preceding embodiments, the device is ergonomically connectable to a control system for actuation.

In another aspect, the invention provides kits containing a device for performing a process, the device having a rigid housing; a first chamber for a volume of fluid; a fluid inlet and a fluid outlet in fluid communication with the first chamber; one or more fluidic channels at least in part defined in the rigid housing and in fluid communication with the fluid inlet or fluid outlet; at least one valve, where the flow of fluid into or out of the first chamber is controlled by the at least one valve; and one or more reagents for use in the first chamber. In one embodiment, the one or more reagents are stored in the first chamber. In some embodiments, the at least one valve is closed at atmospheric pressure. In some embodiments, the at least one valve is controlled by an external actuator. In some embodiments, the at least one valve is actuated electrically, magnetically, hydraulically, pneumatically, or by a combination thereof. In some embodiments, the at least one valve is a diaphragm valve, solenoid valve, pinch valve, or a combination thereof. In further embodiments, the device of the kit contains one or more sensors configured to measure a property of a fluid in the device, e.g., flow rate, temperature, pressure, pH, light, air bubbles, or conductivity.

In further embodiments, the device of the kit contains more chambers, e.g., a second chamber for a volume of fluid that is fluidically connected to the first chamber by one of the one or more fluidic channels; a third chamber for a volume of fluid that is fluidically connected to the first and/or second chamber by one of the one or more fluidic channels; a fourth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third chamber by one of the one or more fluidic channels; a fifth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth chamber by one of the one or more fluidic channels; a sixth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth chamber by one of the one or more fluidic channels; a seventh chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth chamber by one of the one or more fluidic channels; an eighth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh chamber by one of the one or more fluidic channels; or a ninth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh and/or eighth chamber by one of the one or more fluidic channels. In a further embodiment, the device of the kit contains additional valves, e.g., one for each chamber, such as a second valve that controls flow into or out of the second chamber, a third valve that controls flow into or out of the third chamber, a fourth valve that controls flow into or out of the fourth chamber, a fifth valve that controls flow into or out of the fifth chamber, a sixth valve that controls flow into or out of the sixth chamber, a seventh valve that controls flow into or out of the seventh chamber, an eighth valve that controls flow into or out of the eighth chamber, or a ninth valve that controls flow into or out of the ninth chamber.

In certain embodiments, the device ot the kit is configured tor performing an enzymatic reaction and has first through fourth and an optional fifth chamber. The first, second, third, and fourth chambers are configured to house reagents for the enzymatic reaction and are fluidically connected to one of the first through fourth chambers or the optional fifth chamber that is configured for carrying out the enzymatic reaction. In one embodiment, the device contains a heat source operably connected to the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction. In further embodiments, the device includes one or more pumps for moving fluid into or out of the first through fourth chambers or the optional fifth chamber. In some embodiments, the first through third chambers are fluidically connected to the fifth chamber either in series or parallel. . In some embodiments, the kits includes nucleotide reagents, a reaction buffer, and a quenching buffer. For example, the first chamber contains a nucleic acid, the second chamber contains nucleotide reagents, the third chamber contains a reaction buffer, and/or the fourth chamber contains a quench buffer.

In certain embodiments, the device of the kit is configured for purifying reaction products and includes first through sixth chamber and a purification matrix to which the reaction products bind. The first, second, and third chambers are configured to house reagents for sanitation, the fourth and fifth chambers are configured to house reagents for washing the reaction products, the sixth chamber is configured to house an eluent, an optional seventh chamber is configured to house sample to be purified, an optional eighth chamber is configured to house a purified sample, and an optional ninth chamber is configured to house fluid waste. The purification matrix is disposed downstream of the first through sixth chambers and the optional seventh chamber and upstream of the optional eighth and ninth chambers. The first through sixth chambers and the optional seventh, eighth and ninth chambers are fluidically connected to the purification matrix by the one or more fluidic channels. In one embodiment, the purification matrix is a resin. In further embodiments, the device contains one or more sensors, e.g., to measure temperature, light, solution conductivity, pressure, or presence of air bubbles. In one embodiment, the device contains one or more sensors for pressure and air bubbles upstream of the purification matrix and one or more sensors for light, conductivity, and/or temperature downstream of the purification matrix. In further embodiments, the device contains one or more pumps for moving fluid into and out of the first through sixth chambers and the optional seventh, eighth and ninth chambers. In some embodiments, the kit include sodium hydroxide, neutralization buffer, equilibration buffer, high salt washing solution, low salt washing solution, and/or eluent. For example, the first chamber contains sodium hydroxide, the second chamber contains a neutralization buffer, the third chamber contains an equilibration buffer, the fourth chamber contains a high salt washing solution, the fifth chamber contains a low salt washing solution, and/or the sixth chamber contains an eluent.

In certain embodiments, the device of the kit is configured for performing tangential flow filtration and includes three chambers and a filter between first and second chambers. The first chamber is configured to recirculate sample to be filtered, the second chamber is configured to house waste filtrate, and the third chamber is configured to house diafiltration solution, wherein the first and third chambers are fluidically connected by the one or more fluidic channels. In a further embodiment, the device contains a backpressure valve disposed on the outlet of the first chamber. In further embodiments, the device contains two pressure sensors located in the first chamber. In further embodiments, the device has a first pump for moving fluid past the filter. In a further embodiment, the device has a second pump configured to move fluid from the third chamber to the first chamber. In certain embodiments, the kit includes diafiltration solution, e.g., stored in the third chamber.

In certain embodiments, the device of the kit is configured for performing clarification filtration and includes two chambers and a filter disposed between the first and second chambers. The first chamber is configured to house the sample to be clarified and is fluidically connected to the second chamber, which is configured to store the clarified sample. In a further embodiment, the device contains a pressure sensor located upstream of the filter. In further embodiments, the device contains a pump for moving fluid into and out of the first and second chambers.

In another aspect, the invention provides a system for producing a nucleic acid containing one or more rigid housings and one or more fluidic channels at least in part defined in the rigid housing and first and second modules. The first module is implemented in the one or more housings and configured for performing an enzymatic reaction, wherein the first module contains first, second, third, and fourth chambers configured to house fluid reagents for the enzymatic reaction and are fluidically connected to an optional fifth chamber by the one or more fluidic channels, and one of the first through fourth chambers or the optional fifth chamber is configured for carrying out the enzymatic reaction. The first module contains at least one valve to control the flow of fluid into or out of any of the first through fourth chambers or the optional fifth chamber. The second module is implemented in the one or more housings and configured for purifying reaction products, wherein the second module contains first, second, and third chambers configured to house fluid reagents for sanitation, fourth and fifth chambers configured to house fluid reagents for washing the reaction products, a sixth chamber configured to house an eluent, an optional seventh chamber configured to house sample to be purified, an optional eighth chamber configured to house a purified sample, and an optional ninth chamber configured to house fluid waste, wherein a purification matrix is disposed downstream of the first through sixth chambers and the optional seventh chamber and upstream of the optional eighth and ninth chambers, and the first through sixth chambers and the optional seventh, eighth and ninth chambers are fluidically connected to the purification matrix by the one or more fluidic channels. The second module contains at least one valve to control the flow of fluid into or out of any of the first through sixth chambers and optional seventh, eighth and ninth chambers; and one or more pumps for moving fluid within and between the first and second modules. In a further embodiment, the system contains a third module implemented in the one or more housings and configured for performing tangential flow filtration. The third module contains a first chamber configured to recirculate a sample to be filtered, a second chamber configured to house waste filtrate, a third chamber configured to house diafiltration buffer, and a filter between the first and second chambers, wherein the first and third chambers are fluidically connected by the one or more fluidic channels wherein the first module contains at least one valve to control the flow of fluid into or out of any of the first through third chambers. In a further embodiment, the system contains a fourth module implemented in the one or more housings and configured for performing clarification filtration. The fourth module contains a first chamber configured to house the sample to be clarified, a second chamber configured to store the clarified sample, and a filter between the first and second chambers, wherein the first module contains at least one valve to control the flow of fluid into or out of the first and/or second chamber.

In some embodiments, the at least one valve of any module is a diaphragm valve, solenoid valve, pinch valve, or a combination thereof. In some embodiments, the at least one valve of any module is actuated electrically, magnetically, hydraulically, pneumatically, or a combination thereof. In some embodiments, the at least one valve of any module is closed at atmospheric pressure. In further embodiments, the first module contains a heat source operably connected to the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction. In further embodiments, the system contains one or more pumps for moving fluid into or out of the first through fourth chambers or the optional fifth chamber of the first module. In some embodiments, in the first module, the first chamber contains a nucleic acid, the second chamber contains nucleotide reagents, the third chamber contains a reaction buffer, and the fourth chamber contains a quench buffer. In some embodiments, in the second module, the purification matrix is a resin. In some embodiments, in the second module, the first chamber contains sodium hydroxide, the second chamber contains a neutralization buffer, the third chamber contains an equilibration buffer, the fourth chamber contains a high salt washing solution, and the fifth chamber contains a low salt washing solution. In further embodiments, the second module contains one or more sensors, e.g., to measure temperature, light, solution conductivity, pressure, or presence of air bubbles. In some embodiments, the second module contains one or more sensors for pressure and air bubbles upstream of the purification matrix and one or more sensors for light, conductivity, and/or temperature downstream of the purification matrix. In further embodiments, the system contains one or more pumps for moving fluid into and out of the first through sixth chambers or the optional seventh, eighth, and ninth chambers of the second module. In a further embodiment, the third module contains a backpressure valve disposed on the outlet of the first chamber. In further embodiments, the third module contains two pressure sensors located in the first chamber. In further embodiments, the system contains a first pump for moving fluid from the first chamber to the filter in the third module. In further embodiments, the system contains a second pump configured to move fluid from the third chamber to the first chamber in the third module. In a further embodiment, the fourth module contains a pressure sensor located upstream of the filter. In further embodiments, the system contains a pump for moving fluid into and out of the first and second chambers of the fourth module. In a related aspect, the invention provides a method for producing a purified nucleic acid by providing a system as described herein. In the first module, the first chamber contains a nucleic acid, the second chamber contains nucleotide reagents, the third chamber contains a reaction buffer, and the fourth chamber contains a quench buffer. In the second module, the first chamber contains sodium hydroxide, the second chamber contains a neutralization buffer, the third chamber contains an equilibration buffer, the fourth chamber contains a high salt washing solution, and the fifth chamber contains a low salt washing solution. In the third module, the third chamber contains diafiltration buffer. The method includes, in the first module, introducing the nucleic acid, nucleotide reagents, and reaction buffer into one of the first through fourth chambers or the optional fifth chamber under conditions so that the nucleic acid is amplified in a template dependent manner; contacting the quench buffer with the contents of one of the first through fourth chambers or the optional fifth chamber to stop amplification and produced a quenched amplified sample; and transferring the quenched amplified sample to the purification matrix in the second module. The method further includes, in the second module, contacting the purification matrix with the sodium hydroxide, neutralization buffer, and equilibration buffer; loading the quenched amplified sample onto the purification matrix; washing the sample with the high salt and the low salt washing solutions; eluting the sample from the purification matrix to produce an eluted sample; and transferring the eluted sample to the first chamber of the third module. The method further includes, in the third module, passing the sample in the first chamber through the filter disposed between the first chamber and second chamber under tangential flow filtration conditions; collecting the retentate in the second chamber; and transferring the retentate to the first chamber of the fourth module. The method further includes, in the fourth module, passing the through the filter to produce a purified sample.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 is a scheme of a device configured to carry out an enzymatic reaction. The device includes a rigid housing 101 , multiple channels 102, and multiple valves 103. The device includes five chambers. Three chambers 104, 105, and 106 include reagents for an enzymatic reaction, and one chamber 107 includes a quenching buffer. The reaction takes place in a fifth chamber 108, to which the remaining four chambers are fluidically connected. Valves 103 are used to control the addition of fluids to chamber 108. Chambers 104-107 include inlets 109 that allow for introduction of reagents.

Figure 2 is a scheme of a device configured to carry out a purification. The device includes a rigid housing 101 , multiple channels 102, and multiple valves 103. The device includes nine chambers and a purification matrix 204. Chambers 201 include sanitation solutions; chambers 202 include washing solutions, chamber 203 includes an eluent, and chamber 205 includes nucleic acid to be purified. Each of chambers 201 , 202, 203, and 205 is fluidically connected upstream of the purification matrix. Waste from the purification matrix is directed to chamber 206, and eluted nucleic acid is directed to chamber 207. Valves 103 are used to control the addition of fluids to purification matrix 204 and to chambers 206 and 207. Fluid inlets for chambers 201 , 202, and 203 are not shown.

Figure 3 is a scheme of a device configured to carry out tangential flow filtration. The device includes a rigid housing 101 , multiple channels 102, and a valve 103. Chamber 301 includes the solution being filtered, which is separated from chamber 302 by filter 303. Chamber 304 includes feed solution to maintain constant volume in chamber 301 . Figure 4 is a scheme of a device configured to carry out a clarification filtration. The device includes a rigid housing 101 , multiple channels 102, and a valve 103. Chamber 401 includes the solution being filtered, which is separated from chamber 402 by filter 403.

DETAILED DESCRIPTION

The invention relates to devices, systems, and methods for producing and purifying a nucleic acid, e.g., RNA having a poly(A) sequence, e.g., mRNA. The devices and systems feature a rigid housing in which one or more fluidic channels are at least partly defined. The invention is advantageous in simplifying fluidic connections relative to the use of flexible tubing. In particular, the rigid housing can define the fluid connections and thus flow paths within an individual device or system and allow for ease of connection to components, e.g., other devices, systems, or fluid containers. This feature reduces or eliminates user error in making fluidic connections. The devices and systems are also preferably disposable, which is advantageous in preventing contamination between samples. In particular, the invention is useful in the production of small amounts of nucleic acids, such as those tailored to a specific individual or rare indication.

Devices

A device of the invention includes a rigid housing, one or more fluidic channels, and one or more chambers for a volume of fluid. The channels may be at least partly defined in the rigid housing. For example, a channel may be partially formed in the rigid housing and sealed by another layer, e.g., of flexible or rigid material. Alternatively, channels are fully defined by the rigid housing. Channels may be of any cross-section, e.g., round, square, rectangular, or triangular. Chambers may also be partly or wholly defined in the rigid housing in a similar manner. Alternatively, a chamber may be formed by sealing a flexible or rigid material on the housing to define an enclosed volume. Chambers may be any suitable shape, e.g., spherical, hemispherical, conical, cylindrical, rectangular solid, or pyramidal. When more than one chamber is present, the chambers may be linked to one another via a channel or linked directly, e.g., separated by a filter. Multiple chambers may be linked in series such that fluid can flow from one chamber to the next, e.g., where it contacts another fluid or dried reagents or where it is acted upon, e.g., by a change in temperature, agitation, e.g., mixing or shaking, or sensing. Chambers may also be linked in parallel, e.g., where multiple fluids are introduced separately into one chamber or where multiple fluids are passed sequentially through one chamber.

Channels may be of any appropriate size, e.g., having a cross-sectional dimension of 50 μπι to 5 mm, such as 100 μπι to 500 Mm, 500 \im to 1 mm, or 1 mm to 5 mm. Chambers may also be of any appropriate size, e.g., to hold 100 μί. to 500 mL, e.g., 250 μΙ to 1 mL, 1 mL to 10 ml_, 10 mL to 100 mL, or 100 mL to 500 mL. When multiple channels and chambers are present, each may have a different size. In some cases, a chamber holds 100 mL and has a port to connect it to an external reservoir holding more fluid.

Devices will have one or more fluid inputs/outputs, with certain pathways potentially operating as both. Inputs/outputs may be to a channel or chamber in the housing. For example, individual chambers may have inlets that allow for loading of reagents. Inlets and outlets may mate with another fluid channel, e.g., having a connector that mates with a complementary connector, may be valved, or may be a septum or similar pierceable structure, e.g., a foil disk. For example, an inlet or outlet of a device may connect to tubing or other fluid source or storage container or may connect to another device of the invention, e.g., one configured to carry out a different process.

The devices also include one or more valves to control fluid flow into and/or out of a chamber in the device. Valves may be used to start, stop, or throttle, e.g., pulse, fluid flow in the device. Valves useful for a device of the present invention include diaphragm valves, solenoid valves, pinch valves, or a combination thereof. Other types of valves are known in the art. Valves may be configured to be operated by an external actuator that interfaces with the device during use. Alternatively, the device can include an integrated actuator. Valves can be controlled manually, electrically, magnetically, hydraulically, pneumatically, or by a combination thereof. In certain embodiments, the valve is closed at rest, e.g., under atmospheric pressure for a diaphragm valve, and opened by an actuator during use. Valves may be simply on/off or may allow for controlling the direction of flow between three or more channels.

Devices may also include or interface with a pump. Any suitable pump may be employed. A pump may be a source of low pressure, e.g., capable of providing vacuum and/or suction, or high pressure, e.g., capable of providing pressurized gas or liquid. Other examples of pumps are peristaltic pumps, syringe pumps, rotary pumps, momentum transfer pumps, diffusion pumps, scroll pumps, and/or diaphragm pumps. A pump may also act by pressing on or rolling over a chamber to force fluid into a particular channel. Alternatively, fluid movement may be controlled by gravity or capillarity. Multiple pumps and mechanisms for fluid movement may be employed in a single device. Valves may be used with pumps to control the direct and timing of fluid flow.

A device may also include sensors or be configured to mate with sensors, e.g., for flow rate, temperature, pressure, pH, light, presence of air bubbles, solution conductivity, etc. Flow rate sensors useful for the present invention include propellers, orifice plates, Coriolis meters, ultrasonic, and Venturi sensors. Temperature sensors useful in the present invention include thermistors, thermocouples (e.g., Type T), resistive temperature detectors (RTDs), and thermometers. Pressure transducers useful for a device of the present invention include, but are not limited to, inductive, resistive, piezoelectric, and capacitive pressure sensors. pH and conductivity sensors are typically electrode-based and are in contact with fluid housed within the device. Sensors for light include, but are not limited to, photodiodes, photoresistors, array detectors (e.g., CCD or CMOS), and junction-based semiconductor devices. Light sensors, e.g., for absorbance or fluorescence, may be employed for monitoring the present of reactants, intermediates, products, or impurities. Sensors for measuring the presence of bubbles include optical, e.g., light diffraction, electrical, ultrasonic, and capacitive sensors.

A device may also include or be configured to mate with a component to change temperature, e.g., to heat and/or cool one or more chambers in the device. Such components include heat pipes,

Peltier devices, resistive heaters, and channels or chambers for circulation of fluid, e.g., heated or cooled water or other liquid or gas. Temperatures control may also be effected chemically, by reactions that produce heat or cooling, especially in single-use devices.

A device may also include or be configured to mate with a component for mixing, agitation, or shaking. Mixing may occur by moving fluid inside a chamber, e.g., by pumping in and out or by compressing and expanding a chamber. Mixing may also occur by mechanical action, where the chamber includes a moving component, such as a magnetic stir bar or paddle, which is actuated to mix the contents of the chamber. Other mixers include ultrasonic and vibrational mixers, where the actuator is operably connected to the chamber, either as part of the device or as a separate component. Shaking may occur by shaking the entire device, as with commercial shakers.

A device may also include a component for purification, e.g., a purification matrix or a filter. The purification matrix may separate on any appropriate basis, e.g., cation exchange, anion exchange, affinity (e.g., for a specific nucleic acid sequence or poly(A) tail), size, or polarity, e.g., reverse phase. Typically, the purification matrix is a resin that may be formulated in beads. Useful resins include oligo(dT), hydroxyapatite, agarose, e.g., Sepharose™, silica gel, and polyacrylamide.

Filtration may be employed to purify based on size and/or polarity, e.g., product nucleic acid from starting material or particulates. The device may also be configured to employ tangential flow filtration. Filters may be made from any suitable material including polyethersulfone, polysulfone, polyimide, polyvinylidenedifluoride (PVDF), cellulose acetate, regenerated cellulose (e.g., low-binding regenerated cellulose), and ceramics. The porosity of a filter is, for example, between 0.2 and 1 im. Additionally or alternatively, a filter may be configured to pass compounds of a certain molecular weight. For example, a filter useful for tangential flow filtration may have a molecular weight cutoff (MWCO) of between 3,000 to 100,000 Daltons (Da).

A device may be configured to carry out a particular process, e.g., an enzymatic reaction to amplify a nucleic acid or one or more purification processes, e.g., tangential flow filtration. Such devices will include chambers and channels to house the reagents and carry out the intended processes. A single device may include all of the chambers and channels necessary to carry out one or more processes. Alternatively, portions of a single process may be distributed across two or more devices that are linked together. Devices may be linked together to perform several processes in series, e.g., with the output of one device connected to the input of the next device.

The housing of a device may be made of any suitable rigid material. Such materials include, e.g., polymers (such as polystyrene, polypropylene, polyvinyl chloride, polytetrafluoroethylene,

polyoxymethylene, polyether ether ketone, and polycarbonate), ceramics, metals (e.g., stainless steel), glass, or combinations thereof. Flexible components may be made of any suitable material, such as polyethylene and polyvinylidene chloride.

Systems and kits

The invention also features systems for carrying out various processes, e.g., amplification and purification of a nucleic acid. Systems may include a single device or multiple devices connected together to carry out the desired processes. Systems may also include valve actuators, sensors, pumps, mixers, shakers, agitators, and associated controllers, e.g., a computer, to carry out the processes.

Systems may also include reservoirs for fluids to be added to or removed from one or more devices, and systems may be configured to aliquot the output of the process into a bulk container or individual doses of nucleic acid. Systems may also include a structure to hold the device or devices and other components. Such a structure may be configured to allow the device or devices to hang, e.g., on hooks similar to a peg board, to allow ease of installation of a device and ease of connection to other devices, sensors, pumps, controllers, etc. The invention also features kits including a device or system of the invention and one or more reagents for carrying out a process as described herein.

Methods

The devices and systems of the invention may be employed for any process involving fluid reagents. In particular, the invention features methods of producing a nucleic acid, e.g., DNA or RNA, such as mRNA. Typically, the process is an enzymatic amplification, based on a template nucleic acid. The enzymatic reaction may employ any suitable enzyme for nucleic acid amplification, such as a DNA polymerase, RNA polymerase, or ligase. For each reaction, the device or system will include the necessary reagents, such as nucleotide triphosphates (either NTPs, dNTPs, or a combination thereof), oligonucleotides for ligation, reaction and quenching buffers, and ions. In addition to amplification, the methods may also modify the nucleic acid, e.g., by 5' capping, by adding a 3' tail, or by chemically modifying the nucleic acid, e.g., by conjugation. Such reactions may employ chemical or enzymatic reagents. Nucleic acids produced may further be purified through one or more processes and aliquoted into a suitable medium, e.g., a fluid suitable for pharmaceutical use. Devices and systems for purification may include a purification matrix and/or a filter for use in the methods. Reagents for filtration, e.g., feed buffer, or purification, e.g., eluents, washing solutions (such as high or low salt solutions), and sanitation solutions, may also be stored on the device or system for use in the methods.

Examples

The invention will now be described in the following non-limiting examples.

Enzymatic reactions

Enzymatic reactions, such as in vitro transcription, are used to produce nucleic acids, e.g., for therapeutic use. In this example, a device or system, configured for performing an enzymatic reaction, such as in vitro transcription, has five chambers (Figure 1 ). Four of the chambers are source chambers containing a reagent for use in the reaction (104, 105, 106, 107), e.g., enzyme, template nucleic acid, nucleotide triphosphates or oligonucleotides, a reaction buffer, e.g., a IVT or capping reaction buffer, and a quench buffer, e.g., including EDTA. The reaction takes place in the fifth chamber (108), which is fluidically connected to the other four chambers by channels (102). In an alternative embodiment, one of the reagent chambers is large enough to accommodate the other reagents, and the fifth chamber is eliminated. All reagents except for the quenching buffer can be combined in the fifth chamber in any order, and these chambers may be connected serially to the fifth chamber or in parallel. The chamber with the quenching buffer is separately connected to the fifth chamber. The reaction reagents are pumped into the fifth chamber, e.g., by opening a valve (103) controlling flow from each chamber. The reagents can be mixed or agitated in the fifth chamber and allowed to react to produce nucleic acid. The chamber may be connected to a heater to control the reaction, e.g., via thermal cycling. Once the reaction is complete, the quenching buffer is combined with the reaction products (either in the fifth chamber or in the quenching buffer chamber). The reaction products can then be transferred to another device or another portion of a device or system for modification or purification.

Purification

A device or system may be configured to purify a nucleic acid, e.g., mRNA produced by an enzymatic reaction. In this example, the device contains nine chambers and a purification matrix (Figure 2). The first three chambers (201 ) house reagents for sanitation, e.g., sodium hydroxide solution, a neutralization buffer, e.g., including NaCI, and an equilibration buffer, e.g., including NaCI. The fourth and fifth chambers (202) house reagents for washing the nucleic acid, e.g., low and high salt solutions, e.g., 0.1 and 0.5 M NaCI. The sixth chamber (203) houses eluent, e.g., water or a buffer solution, for the nucleic acid. The seventh chamber (205) houses the nucleic acid sample prior to being loaded on the purification matrix. In certain embodiments, this chamber may be eliminated and replaced with a sample feed from another device or system or portion thereof. The eighth chamber (207) houses eluted nucleic acid, and the ninth chamber stores waste (206). The eighth chamber may be omitted if the eluted nucleic acid is passed directly to another device or part of a system, and the ninth chamber may be omitted if the waste is directed to a reservoir external to the device or system. The purification matrix (204) is located between the first through seventh chambers and the eighth and ninth chambers. In some embodiments, the purification matrix is an oligo(dT) resin. Before the resin is contacted by the sample, the resin is first sanitized by passing the sodium hydroxide, neutralization buffer, and equilibration buffers through it in sequence. After sanitizing, the nucleic acid is loaded onto the purification matrix and washed with high and then low salt solutions. The nucleic acid is then eluted from the purification matrix, e.g., with water, and stored. Sensors upstream of the purification matrix measure the pressure and presence of air bubbles. Air bubbles can be used to detect when a reagent chamber, such as the RNA sample chamber, is depleted, and air bubbles are directed towards the waste chamber prior to the purification matrix. A pressure sensor can be used to detect the presence of an overpressure event. Sensors for conductivity, light, e.g., UV light, and temperature may be downstream of the purification matrix. A sensor for pH may be configured to indicate whether the sodium hydroxide used to sanitize the purification matrix was neutralized by the neutralization buffer prior to loading sample onto the purification matrix. The light sensor may be configured to indicate the presence or absence of nucleic acid, e.g., RNA, in the eluate. The conductivity sensor may be configured to indicate which of the salt buffers is in use at any point in the purification process. Fluids can be pumped through the purification matrix by opening appropriate valve 103.

In some embodiments, each of the first seven chambers of the device, corresponding to the three sanitation chambers, the two wash chambers, the eluent chamber, and the sample chamber, are fluidically connected to the fluid inlet of the purification matrix in parallel by channels 102. However, other configurations are possible, for example, chambers may be connected in series such that the fluids pass through the purification matrix in the correct order. The eighth and ninth chambers of the device, corresponding to the eluted nucleic acid and waste chambers, are connected in parallel, e.g., by a switchable valve, to the outlet of the purification matrix.

Tangential Flow Filtration

A device or system of the invention may be configured for performing tangential flow filtration and include three chambers and a filter (Figure 3). In this example, the first chamber (301 ) is configured as a recirculating chamber, holding the sample to be filtered. The second chamber (302) is configured to house the filtrate and is separated from the first chamber by the filter (303). The third chamber (304) is configured as a feed chamber to hold a diafiltration buffer, e.g., 0.1 mM citrate or water, to maintain volume lost from the first chamber because of filtration via a channel 102. The feed solution is circulated through the first chamber via a channel 102 to allow materials to pass through the filter. The retentate and/or the filtrate may be collected for further use.

In certain embodiments, the device or system further includes pressure sensors. These sensors may be configured to measure the pressure of both sides of the filter. In some embodiments, the first chamber contains two pressure sensors. One sensor is disposed in the inlet of the first chamber, and the other sensor is disposed on the outlet of the first chamber. The average pressure measurement of the two sensors is used to maintain a controlled overpressure in the first chamber to aid in filtration. In some embodiments, the device or system includes a backpressure valve 1 03 to maintain constant pressure against the filter. The backpressure is installed on the return line of the first chamber, thereby restricting flow of fluid leaving the chamber. This results in an overpressure caused by the feed pump against the filter.

Pumps in the device or system or coupled to the device or system control the recirculation of the sample and addition of feed solution from the third chamber.

Clarification filtration

A device or system of the invention may be configured for performing clarification filtration to remove particulates. In this example, the device or system includes two chambers separated by a filter (Figure 4). The filter (403) allows the nucleic acid to pass through but prevents particulates from passing. The first chamber (401 ) is configured to house the sample to be clarified, and the second chamber (402) is configured to house the clarified sample. Channels 102 allow for introduction and removal of fluid. A pump in the device or system or coupled to the device or system controls the filtration in conjunction with valve 103.

In some embodiments, the device or system includes a pressure sensor located upstream of the filter to facilitate the detection of a pressure spike due to a clogged filter.

System

In this example, a system includes a single device or multiple devices for carrying out the enzymatic reaction and purification described in preceding examples. The system may also be further configured to carry out the tangential flow filtration and/or clarification filtration as described above. Each of the processes to be carried out may be implemented in a separate device, where the devices are coupled together. Alternatively, the individual processes may be distributed across multiple, physically separable devices or in a single device. The system may also include the various pumps, sensors, and controllers necessary to carry of the process. As discussed above, certain chambers for storing a starting material or product for a particular step may be eliminated when the starting material is provided from the preceding step or where the product is provided to the next step directed. The system may also include a structure for holding the device or devices and the accompanying components.

Other embodiments are in the claims.

Claims

What is claimed is: CLAIMS
1 . A device for performing a process comprising:
a) a rigid housing;
b) a first chamber for a volume of fluid;
c) a fluid inlet and a fluid outlet in fluid communication with the first chamber; d) one or more fluidic channels at least in part defined in the rigid housing and in fluid communication with the fluid inlet or fluid outlet; and
e) at least one valve,
wherein the flow of fluid into or out of the first chamber is controlled by the at least one valve.
2. The device claim 1 , wherein the at least one valve is closed at atmospheric pressure.
3. The device of claims 1 or 2, wherein the at least one valve is controlled by an external actuator.
4. The device of any one of claims 1 -3, wherein the at least one valve is actuated electrically, magnetically, hydraulically, pneumatically, or by a combination thereof.
5. The device of any one of claims 1 -4, wherein the at least one valve is a diaphragm valve,
solenoid valve, pinch valve, or a combination thereof.
6. The device of any one of claims 1 -5, further comprising one or more sensors configured to
measure a property of a fluid in the device.
7. The device of claim 6, wherein the one or more sensors measures flow rate, temperature, pressure, pH, light, air bubbles, or conductivity.
8. The device of any one of claims 1 -7, further comprising a second chamber for a volume of fluid that is fluidically connected to the first chamber by one of the one or more fluidic channels.
9. The device of claim 8, further comprising a second valve that controls flow into or out of the second chamber.
10. The device of any one of claims 8-9, further comprising a third chamber for a volume of fluid that is fluidically connected to the first and/or second chamber by one of the one or more fluidic channels.
1 1 . The device of claim 10, further comprising a third valve that controls flow into or out of the third chamber.
12. The device of any one of claims 10-1 1 , further comprising a fourth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third chamber by one of the one or more fluidic channels.
13. The device of claim 12, further comprising a fourth valve that controls flow into or out of the fourth chamber.
14. The device of any one of claims 12-13, further comprising a fifth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth chamber by one of the one or more fluidic channels.
15. The device of claim 14, further comprising a fifth valve that controls flow into or out of the fifth chamber.
16. The device of any one of claims 14-15, further comprising a sixth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth chamber by one of the one or more fluidic channels.
17. The device of claim 16, further comprising a sixth valve that controls flow into or out of the sixth chamber.
18. The device of any one of claims 16-17, further comprising a seventh chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth chamber by one of the one or more fluidic channels.
19. The device of claim 18, further comprising a seventh valve that controls flow into or out of the seventh chamber.
20. The device of any one of claims 18-19, further comprising an eighth chamber for a volume of fluid that is fluidically connect to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh chamber by one of the one or more fluidic channels.
21. The device of claim 20, further comprising an eighth valve that controls flow into or out of the eighth chamber.
22. The device of any one of claims 20-21 , further comprising a ninth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh and/or eighth chamber by one of the one or more fluidic channels.
23. The device of claim 22, further comprising a ninth valve that controls flow into or out of the ninth chamber.
24. The device of claim 12 or 13, wherein the device is configured for performing an enzymatic
reaction, the first, second, third, and fourth chambers are configured to house reagents for the enzymatic reaction and are fluidically connected to an optional fifth chamber by the one or more fluidic channels, and one of the first through fourth chambers or the optional fifth chamber is configured for carrying out the enzymatic reaction.
25. The device of claim 24, further comprising a heat source operably connected to the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction.
26. The device of claims 24 or 25, further comprising one or more pumps for moving fluid into or out of the first through fourth chambers or the optional fifth chamber.
27. The device of any one of claims 24-26, wherein the first through third chambers are fluidically connected to the fifth chamber either in series or parallel.
28. The device of claim 16 or 17, wherein the device is configured for purifying reaction products and further comprises a purification matrix to which the reaction products bind, the first, second, and third chambers are configured to house reagents for sanitation, the fourth and fifth chambers are configured to house reagents for washing the reaction products, the sixth chamber is configured to house an eluent, an optional seventh chamber is configured to house sample to be purified, an optional eighth chamber is configured to house a purified sample, and an optional ninth chamber is configured to house fluid waste, wherein the purification matrix is disposed downstream of the first through sixth chambers and the optional seventh chamber and upstream of the optional eighth and ninth chambers, and the first through sixth chambers and the optional seventh, eighth and ninth chambers are fluidically connected to the purification matrix by the one or more fluidic channels.
29. The device of claim 28, wherein the purification matrix comprises a resin.
30. The device of claim 28 or 29, further comprising one or more sensors.
31 . The device of claim 30, wherein the one or more sensors measure temperature, light, solution conductivity, pressure, or presence of air bubbles.
32. The device of claim 31 , comprising one or more sensors for pressure and air bubbles upstream of the purification matrix and one or more sensors for light, conductivity, and/or temperature downstream of the purification matrix.
33. The device of any one of claims 28-32, further comprising one or more pumps for moving fluid into and out of the first through sixth chambers and the optional seventh, eighth, and ninth chambers.
34. The device of claims 10 or 1 1 , wherein the device is configured for performing tangential flow filtration and further comprises a filter between the first and second chambers, the first chamber is configured to recirculate sample to be filtered, the second chamber is configured to house waste filtrate, and the third chamber is configured to house diafiltration solution, wherein the first and third chambers are fluidically connected by the one or more fluidic channels.
35. The device of claim 34, further comprising a backpressure valve disposed on an outlet of the first chamber.
36. The device of any one of claims 34-35, further comprising two pressure sensors located in the first chamber.
37. The device of any one of claims 34-36, further comprising a first pump for moving fluid past the filter.
38. The device of claim 37, further comprising a second pump configured to move fluid from the third chamber to the first chamber.
39. The device of claim 8 or 9, wherein the device is configured for performing clarification filtration and further comprising a filter disposed between the first and second chambers, the first chamber is configured to house the sample to be clarified and is fluidically connected to the second chamber, which is configured to store the clarified sample.
40. The device of claim 39, further comprising a pressure sensor located upstream of the filter.
41 . The device of any one of claims 39-40, further comprising a pump for moving fluid into and out of the first and second chambers.
42. The device of any one of claims 1 -41 , wherein the device is economically connectable to a control system for actuation.
43. A kit, comprising:
a) a device for performing a process comprising
i) a rigid housing;
ii) a first chamber for a volume of fluid;
iii) a fluid inlet and a fluid outlet in fluid communication with the first chamber;
iv) one or more fluidic channels at least in part defined in the rigid housing and in fluid communication with the fluid inlet or fluid outlet; and
v) at least one valve, wherein the flow of fluid into or out of the first chamber is controlled by the at least one valve; and
b) one or more reagents for use in the first chamber.
44. The kit of claim 43, wherein the one or more reagents are stored in the first chamber.
45. The kit of claim 43 or 44, wherein the at least one valve is closed at atmospheric pressure.
46. The kit of any one of claims 43-45, wherein the at least one valve is controlled by an external actuator.
47. The kit of any one of claims 43-46, wherein the at least one valve is actuated electrically,
magnetically, hydraulically, pneumatically, or by a combination thereof.
48. The kit of any one of claims 43-47, wherein the at least one valve is a diaphragm valve, solenoid valve, pinch valve, or a combination thereof.
49. The kit of any one of claims 43-48, wherein the device further comprises one or more sensors configured to measure a property of a fluid in the device.
50. The kit of claim 49, wherein the one or more sensors measure flow rate, temperature, pressure, pH, light, air bubbles, or solution conductivity.
51. The kit of any one of claims 43-50, wherein the device further comprises a second chamber for a volume of fluid that is fluidically connected to the first chamber by one of the one or more fluidic channels.
52. The kit of claim 51 , wherein the device further comprises a second valve that controls flow into or out of the second chamber.
53. The kit of claims 51 or 52, wherein the device further comprises a third chamber for a volume of fluid that is fluidically connected to the first and/or second chamber by one of the one or more fluidic channels.
54. The kit of claim 53, wherein the device further comprises a third valve that controls flow into or out of the third chamber.
55. The kit of claims 53 or 54, wherein the device further comprises a fourth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third chamber by one of the one or more fluidic channels.
56. The kit of claim 55, wherein the device further comprises a fourth valve that controls flow into or out of the fourth chamber.
57. The kit of claims 55 or 56, wherein the device further comprises a fifth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth chamber by one of the one or more fluidic channels.
58. The kit of claim 57, wherein the device further comprises a fifth valve that controls flow into or out of the fifth chamber.
59. The kit of claims 57 or 58, wherein the device further comprises a sixth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth chamber by one of the one or more fluidic channels.
60. The kit of claim 59, wherein the device further comprises a sixth valve that controls flow into or out of the sixth chamber.
61 . The kit of claims 59 or 60, wherein the device further comprises a seventh chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth chamber by one of the one or more fluidic channels.
62. The kit of claim 61 , wherein the device further comprises a seventh valve that controls flow into or out of the seventh chamber.
63. The kit of claims 61 or 62, wherein the device further comprises an eighth chamber for a volume of fluid that is fluidically connect to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh chamber by one of the one or more fluidic channels.
64. The kit of claim 63, wherein the device further comprises an eighth valve that controls flow into or out of the eighth chamber.
65. The kit of claims 63 or 64, wherein the device further comprises a ninth chamber for a volume of fluid that is fluidically connected to the first and/or second and/or third and/or fourth and/or fifth and/or sixth and/or seventh and/or eighth chamber by one of the one or more fluidic channels.
66. The kit of claim 65, wherein the device further comprises a ninth valve that controls flow into or out of the ninth chamber.
67. The kit of claims 55 or 56, wherein the device is configured for performing an enzymatic reaction, the first, second, third, and fourth chambers are configured to house reagents for the enzymatic reaction and are fluidically connected to an optional fifth chamber by the one or more fluidic channels, and one of the first through fourth chambers or the optional fifth chamber is configured for carrying out the enzymatic reaction.
68. The kit of claim 67, wherein the device further comprises a heat source operably connected to the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction.
69. The kit of claims 67 or 68, wherein the device further comprises one or more pumps for moving fluid into or out of the first through fourth chambers or the optional fifth chamber.
70. The kit of any one of claims 67-69, wherein the first chamber comprises a nucleic acid.
71 . The kit of any one of claims 67-69, wherein the second chamber comprises nucleotide reagents.
72. The kit of any one of claims 67-69, wherein the third chamber comprises a reaction buffer.
73. The kit of any one of claims 67-69, wherein the fourth chamber comprises a quench buffer.
74. The kit of claims 59 or 60, wherein the device is configured for purifying reaction products and further comprises a purification matrix to which the reaction products bind, the first, second, and third chambers are configured to house reagents for sanitation, the fourth and fifth chambers are configured to house reagents for washing the reaction products, the sixth chamber is configured to house an eluent, an optional seventh chamber is configured to house sample to be purified, an optional eighth chamber is configured to house a purified sample, and an optional ninth chamber is configured to house fluid waste, wherein the purification matrix is disposed downstream of the first through sixth chambers and the optional seventh chamber and upstream of the optional eighth and ninth chambers, and the first through sixth chambers and the optional seventh, eighth and ninth chambers are fluidically connected to the purification matrix by the one or more fluidic channels.
75. The kit of claim 74 wherein the purification matrix comprises a resin.
76. The kit of any one of claims 74-75, wherein the first chamber comprises sodium hydroxide.
77. The kit of any one of claims 74-75, wherein the second chamber comprises a neutralization buffer.
78. The kit of any one of claims 74-75, wherein the third chamber comprises an equilibration buffer.
79. The kit of any one of claims 74-75, wherein the fourth chamber comprises a high salt washing solution.
80. The kit of any one of claims 74-75, wherein the fifth chamber comprises a low salt washing
solution.
81 . The kit of any one of claims 74-75, wherein the device further comprises one or more sensors.
82. The kit of claim 81 , wherein the one or more sensors measure temperature, light, solution
conductivity, pressure, or presence of air bubbles.
83. The kit of claim 82, wherein the device comprises one or more sensors for pressure and air bubbles upstream of the purification matrix and one or more sensors for light, conductivity, and/or temperature downstream of the purification matrix.
84. The kit of any one of claims 74-83, further comprising one or more pumps for moving fluid into and out of the first through sixth chambers and the optional seventh, eighth, and ninth chambers.
85. The kit of claims 53 or 54, wherein the device is configured for performing tangential flow filtration and further comprises a filter between the first and second chambers, the first chamber is configured to recirculate sample to be filtered, the second chamber is configured to house waste filtrate, and the third chamber is configured to house diafiltration solution, wherein the first and third chambers are fluidically connected by the one or more fluidic channels.
86. The kit of claim 85, wherein the device further comprises a backpressure valve disposed on an outlet of the first chamber.
87. The kit of any one of claims 85-86, wherein the device further comprises two pressure sensors located in the first chamber.
88. The kit of any one of claims 85-87, further comprising a first pump for moving fluid from the first chamber to the filter.
89. The kit of claim 88, further comprising a second pump configured to move fluid from the third chamber lo the first chamber.
90. The kit of claims 51 or 53, wherein the device is configured for performing clarification filtration and further comprising a filter disposed between the first and second chambers, the first chamber is configured to house the sample to be clarified and is fluidically connected to the second chamber, which is configured to store the clarified sample.
91 . The kit of claim 90, wherein the device further comprises a pressure sensor located upstream of the filter.
92. The kit of any one of claims 90-91 , further comprising a pump for moving fluid into and out of the first and second chambers.
93. A system for producing a nucleic acid comprising:
a) one or more rigid housings and one or more fluidic channels at least in part defined in the rigid housing;
b) a first module implemented in the one or more housings and configured for performing an enzymatic reaction, wherein the first module comprises first, second, third, and fourth chambers configured to house fluid reagents for the enzymatic reaction and fluidically connected to an optional fifth chamber by the one or more fluidic channels, and one of the first through fourth chambers or the optional fifth chamber is configured for carrying out the enzymatic reaction, and wherein the first module comprises at least one valve to control the flow of fluid into or out of any of the first through fourth chambers or the optional fifth chamber;
c) a second module implemented in the one or more housings and configured for purifying reaction products, wherein the second module comprises first, second, and third chambers configured to house fluid reagents for sanitation, fourth and fifth chambers configured to house fluid reagents for washing the reaction products, a sixth chamber configured to house an eluent, an optional seventh chamber configured to house sample to be purified, an optional eighth chamber configured to house a purified sample, and an optional ninth chamber configured to house fluid waste, wherein a purification matrix is disposed downstream of the first through sixth chambers and the optional seventh chamber and upstream of the optional eighth and ninth chambers, and the first through sixth chambers and the optional seventh, eighth and ninth chambers are fluidically connected to the purification matrix by the one or more fluidic channels, and wherein the second module comprises at least one valve to control the flow of fluid into or out of any of the first through sixth chambers and optional seventh, eighth and ninth chambers; d) a first controller for actuating the at least one valve of the first and second modules; and e) one or more pumps for moving fluid within and between the first and second modules.
94. The system of claim 93, further comprising a third module implemented in the one or more
housings and configured for performing tangential flow filtration, wherein the third module comprises a first chamber configured to recirculate a sample to be filtered, a second chamber configured to house waste filtrate, a third chamber configured to house diafiltration buffer, and a filter between the first and second chambers, wherein the first and third chambers are fluidically connected by the one or more fluidic channels wherein the first module comprises at least one valve to control the flow of fluid into or out of any of the first through third chambers.
95. The system of claim 93 or 94, further comprising a fourth module implemented in the one or more housings and configured for performing clarification filtration, wherein the fourth module comprises a first chamber configured to house the sample to be clarified, a second chamber configured to store the clarified sample, and a filter between the first and second chambers, wherein the first module comprises at least one valve to control the flow of fluid into or out of the first and/or second chamber.
96. The system of any one of claims 93-95, wherein the at least one valve of any module is a
diaphragm valve, solenoid valve, pinch valve, or a combination thereof.
97. The system of any one of claims 93-96, wherein the at least one valve of any module is actuated electrically, magnetically, hydraulically, pneumatically, or a combination thereof.
98. The system of any one of claims 93-97, wherein the at least one valve of any module is closed at atmospheric pressure.
99. The system of any one of claims 93-98, wherein the first module further comprises a heat source operably connected to the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction.
100. The system of any one of claims 93-99, further comprising one or more pumps for moving fluid into or out of the first through fourth chambers or the optional fifth chamber of the first module.
101. The system of any one of claims 93-100, wherein, in the first module, the first chamber comprises a nucleic acid, the second chamber comprises nucleotide reagents, the third chamber comprises a reaction buffer, and the fourth chamber comprises a quench buffer.
102. The system of any one of claims 93-101 , wherein, in the second module, the purification matrix comprises a resin.
103. The system of any one of claims 93-102, wherein, in the second module, the first
chamber comprises sodium hydroxide, the second chamber comprises a neutralization buffer, the third chamber comprises an equilibration buffer, the fourth chamber comprises a high salt washing solution, and the fifth chamber comprises a low salt washing solution.
104. The system of any one of claims 93-103, wherein the second module further comprises one or more sensors.
105. The system of claim 104, wherein the one or more sensors measure temperature, light, solution conductivity, pressure, or presence of air bubbles.
106. The system of claim 1 4 or 105, wherein the second module comprises one or more sensors for pressure and air bubbles upstream of the purification matrix and one or more sensors for light, conductivity, and/or temperature downstream of the purification matrix.
107. The system of any one of claims 93-106, further comprising one or more pumps for moving fluid into and out of the first through sixth chambers or the optional seventh, eighth, and ninth chambers of the second module.
108. The system of claim 94, wherein the third module further comprises a backpressure valve disposed on an outlet of the first chamber.
109. The system of claim 94 or 108, wherein the third module further comprises two pressure sensors located in the first chamber.
1 10. The system of any one of claims 94, 108, and 109, further comprising a first pump for moving fluid from the first chamber to the filter in the third module.
1 1 1 . The system of any one of claims 94 and 108-1 10, further comprising a second pump configured to move fluid from the third chamber to the first chamber in the third module.
1 12. The system of claim 95, wherein the fourth module further comprises a pressure sensor located upstream of the filter.
13. The system of claim 95 or 1 12, further comprising a pump for moving fluid into and out of the first and second chambers of the fourth module. 14. A method of producing purified nucleic acid, comprising:
a) providing a system of any one of claims 95-1 13, wherein, in the first module, the first chamber comprises a nucleic acid, the second chamber comprises nucleotide reagents, the third chamber comprises a reaction buffer, and the fourth chamber comprises a quench buffer; in the second module, the first chamber comprises sodium hydroxide, the second chamber comprises a neutralization buffer, the third chamber comprises an equilibration buffer, the fourth chamber comprises a high salt washing solution, and the fifth chamber comprises a low salt washing solution; and in the third module, the third chamber comprises diafiltration buffer;
b) in the first module, introducing the nucleic acid, nucleotide reagents, and reaction buffer into the one of the first through fourth chambers or the optional fifth chamber configured for carrying out the enzymatic reaction under conditions so that the nucleic acid is amplified in a template dependent manner; contacting the quench buffer with the contents of the one of the first through fourth chambers or the optional fifth chamber to stop amplification and produced a quenched amplified sample; and transferring the quenched amplified sample to the purification matrix in the second module, directly or via the optional seventh chamber;
c) in the second module, contacting the purification matrix with the sodium hydroxide, neutralization buffer, and equilibration buffer; loading the quenched amplified sample onto the purification matrix; washing the sample with the high salt and the low salt washing solutions; eluting the sample from the purification matrix to produce an eluted sample; and transferring the eluted sample to the first chamber of the third module, directly or via the optional eighth chamber;
d) in the third module, passing the sample in the first chamber through the filter disposed between the first chamber and second chamber under tangential flow filtration conditions; collecting the retentate in the second chamber; and transferring the retentate to the first chamber of the fourth module; and
e) in the fourth module, passing the through the filter to produce a purified sample.
PCT/US2018/000281 2017-08-17 2018-08-17 Systems with fluid path control and regulation WO2019035998A1 (en)

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