This application claims the priority of Korean Patent Application No. 10-2004-0073920, filed on Sep. 15, 2004, in the Korean Intellectual Property Office, the disclosure of which is incorporated herein in its entirety by reference.
1. Field of the Invention
The present invention relates to a polymerase chain reaction (PCR) apparatus using Marangoni convection, and more particularly, to a novel PCR apparatus having an open reaction chamber including a high-temperature sidewall and a low-temperature sidewall erected on a substrate and facing each other, in which the control of heating, cooling, and cycling is not necessary.
2. Description of Related Art
A polymerase chain reaction (PCR) is a reaction used to clone a fragment of a DNA molecule through cyclic heating/cooling to abundantly increase the amount of the fragment. In order to complete a cycle of cloning in a PCR, the temperature of a DNA sample must be changed from T1 to T3, i.e., T1 (denaturing temperature)→T2 (annealing temperature)→T3 (extension temperature).
In a conventional PCR apparatus shown in
In another conventional PCR apparatus disclosed in U.S. Pat. No. 5,270,183 and shown in
In a conventional PCR apparatus disclosed in Proc. Miniaturized Total Analysis Systems (uTAS 2001), Luisiana State University, Steven A. Soper et al., pp. 459-461, shown in
In a conventional PCR apparatus disclosed in Krishnan et al., SCIENCE, vol. 298, Oct. 25, 2002, shown in
In a conventional PCR apparatus disclosed in U.S. Pat. No. 6,586,233, shown in
As described above, in conventional PCR apparatuses, since the chamber containing a DNA buffer solution is heated and cooled in a cyclic manner to amplify a fragment of a DNA molecule, it is difficult to control temperatures, there is high power consumption, and it takes a long time to accomplish the amplification.
In this regard, the present inventors have made many efforts to solve the aforementioned problems, and have found that a PCR amplifier using Marangoni convection can provide many advantages such as reductions in power consumption and amplification time, and simplification of a temperature control circuit because the PCR amplification can be automatically obtained by a surface tension flow generated by a temperature difference in the interface between the fluid and air when both the sidewalls of the chamber are kept in constant temperatures.
The present invention provides a novel PCR apparatus using Marangoni convection.
The present invention also provides a PCR method using the PCR apparatus.
The present invention also provides a method of manufacturing the PCR apparatus.
The present invention also provides a lab-on-a-chip and an inkjet spotter including the PCR apparatus.
According to an aspect of the present invention, there is provided a polymerase chain reaction apparatus comprising: a substrate; a high-temperature sidewall erected on the substrate; a low-temperature sidewall erected on the substrate and facing the high-temperature sidewall; and a reaction chamber consisting of the substrate, the high-temperature sidewall, and the low-temperature sidewall, wherein a sample contained in the reaction chamber is repetitively thermal-circulated between the high-temperature sidewall and the low-temperature sidewall using Marangoni convection generated by a surface tension gradient resulting from a temperature difference in an interface between the sample and air.
A polymer chain reaction (PCR) is a method of amplifying a particular DNA region in several tens thousands of or hundreds thousands of times by repeating a DNA synthesis reaction between two kinds of primers interposing the particular DNA region by using a DNA synthesis enzyme in a test tube. Generally, a cycle of the PCR includes denaturing double strands into a single strand, annealing two kinds of primers interposing a target region of the denatured single DNA strand, and extending the primers to produce complementary sequences on the target region.
In the PCR, the denaturing of the double strands is performed at a high temperature of 90° C., and the primer combination and the DNA synthesis are performed at relatively low temperatures of 50˜60° C. and 70˜75° C., respectively. Therefore, a thermal cycler is necessary to perform the PCR.
In the apparatus according to an embodiment of the present invention, Marangoni convection is generated by a surface tension gradient resulting from a temperature gradient in an interface between a reactive fluid and air. As a result, the fluid flows from a high-temperature region to a low-temperature region. Therefore, the apparatus according to the present invention is discriminated from a conventional apparatus using Rayleigh-Benard convection, in which a buoyancy flow from the high-temperature region to the low-temperature region is generated by a density gradient resulting from a temperature difference in the fluid.
The present invention provides the first method and apparatus adopting a principle of Marangoni convection into PCR amplification. The PCR amplification apparatus uses a surface tension flow in a container having an interface (free surface) between the fluid and the air. Therefore, the reaction chamber used in the PCR apparatus according to the present invention is preferably not closed, but is open such that an interface exists between the fluid and air.
The reaction chamber may further include a cover as far as it comprises an interface between the fluid and air. The cover may be combined with the substrate or a sidewall in a single body.
The high-temperature sidewall may be heated to a temperature appropriate to denature the reactive fluid near the high-temperature sidewall. The high-temperature sidewall may be heated by a heater to a constant temperature of 92˜97° C., preferably, 95° C.
The heater may be embodied in various ways such that the high-temperature sidewall can be heated, such as a thin film resistive heater, a heater using a heat exchanger, a radiation heater, and a hot air blasting heater. More preferably, the heater is a thin film heater made of a material selected from a group consisting of platinum, polysilicon, and tantal aluminum. Also, the heater may be installed in the inside or outside of the sidewall, and a sensor for adjusting the temperature may be provided with the heater.
The low-temperature sidewall may be cooled to a temperature appropriate to anneal the reactive fluid near the low-temperature sidewall. The low-temperature sidewall may be cooled by a cooler to a constant temperature of 44˜56° C., preferably, 50° C.
The cooler may be embodied in various ways such that the sidewall can be cooled, such as a cooling fan or a thermal cycler. Preferably, the cooler may be a Peltier device. The cooler may be installed in the inside or outside of the low-temperature sidewall, and a sensor for adjusting the temperature may be provided together with the cooler.
The sample experiences DNA denaturing near the high-temperature sidewall, and the fluid at the surface of the reactive fluid rapidly flows to the low-temperature sidewall due to Marangoni convection, where the fluid is annealed. Then, a lower region of the reactive fluid slowly flows from the low-temperature sidewall to the high-temperature sidewall, thereby generating extension, i.e., the synthesis of new DNA strands.
A gap between the high-temperature sidewall and the low-temperature sidewall may be 2 mm to 3 cm. In the conventional PCR apparatus using a buoyancy flow, since the buoyancy is proportional to the volume of a container, a driving force decreases as the size of the container decreases. However, in the PCR apparatus according to the present invention, since the surface tension is proportional to the area of the fluid surface, a sufficient driving force can be obtained even when the container is small. Therefore, the PCR apparatus according to an embodiment of the present invention can be embodied in a DNA chip, a subminiature DNA detector, or a lap-on-a-chip.
The reaction chamber may be made of a material selected from a group consisting of glass, quartz, silicon, plastic, polymer, ceramic, and metal. Preferably, the reaction chamber is made by etching a silicon wafer using photolithography, i.e., a typical semiconductor manufacturing process.
The reaction chamber may have an optical detection window. Through the optical detection window, the PCR reaction in the chamber can be optically detected using a conventional PCR detection method in a real-time manner.
According to another aspect of the present invention, there is provided a polymerase chain reaction method comprising: putting a sample into the reaction chamber of any one of the above-described polymerase chain reaction apparatuses, maintaining temperatures of the high-temperature sidewall and the low-temperature sidewall constant; and repetitively thermal-circulating the sample contained in the reaction chamber between the high-temperature sidewall and the low-temperature sidewall using Marangoni convection.
The sample may include a typical template DNA, oligonucleotide primers, four dNTP's (i.e., dATP, dCTP, dGTP, and dTTP), a thermostable DNA polymerase, and a reactive buffer.
The high-temperature sidewall may be maintained at a constant temperature of 92˜97° C., appropriate for denaturing the DNA sample, and the low-temperature sidewall may be maintained at a constant temperature of 48˜54° C., appropriate for annealing the sample.
The sample may contain a fluorescent material to detect amplification of a nucleic acid in a real-time manner. The amplification sample may be a plasmid DNA. A driving fluid may be produced by adding primers, dNDP, a base, and a buffer solution containing a DNA polymerization enzyme into an initial sample. Distinct amplification DNA bands are visible when the fluorescent material in the DNA sample that has been amplified using the PCR reaction is detected.
According to still another aspect of the present invention, there is provided a method of manufacturing a PCR apparatus including a photolithographic process. In the method, photolithography is applied to a first substrate to form the pattern of a flow path and a PCR chamber on its upper surface. The first substrate may be made of a material selected from a group consisting of silicon, glass, polycarbonate, polydimethylsiloxane, and polymethylmetaacrylate. The first substrate may be etched to have a desired thickness by wet etching or dry etching such as a reactive ion etching. If necessary, the photolithographic process and the etching process may be repeated several times to allow the flow path and the chamber to have varying depths. A hydrophobic treatment is applied to the upper portion of a second substrate, which is a cover for preventing evaporation of the DNA reaction fluid in the PCR chamber to resist wetting. After patterns of an inlet and an outlet for the sample are formed on the first substrate through photolithography, the inlet and the outlet are finished by sound-blasting. If it is necessary to form an electrode structure on the second substrate, electrode patterns are formed through photolithography and are obtained using a lift-off procedure. Subsequently, the first and second substrates are bonded using a method such as anodic bonding, fluorine bonding, thermal bonding, or polymer film bonding.
According to still another aspect of the present invention, there is provided a lab-on-a-chip comprising any one of the above-described polymerase chain reaction apparatuses and an electrophoresis performing unit connected to the polymerase chain reaction apparatus in a fluidic manner.
When the sample in the chip passes through the PCR apparatus, the DNA is amplified. When the sample passes through the electrophoresis performing unit, the DNA is separated depending on its molecular amount or charge to detect target DNA.
The substrates may be made of a material selected from a group consisting of glass, quartz, silicon, plastic, polymer, ceramic, or metal. The electrophoresis unit may have multiple channels performing capillary electrophoresis. The PCR amplification apparatus and the electrophoresis performing unit may be formed on a substrate through photolithography.
According to still another aspect of the present invention, there is provided an inkjet spotter comprising: any one of the above-described polymerase chain reaction apparatuses formed on a substrate; a restrictor connected to the polymerase chain reaction apparatus in a fluidic manner; an ejecting chamber storing a DNA solution from the polymerase chain reaction apparatus via the restrictor; an ejecting driving element providing a driving force of the DNA solution ejection; and a nozzle ejecting the DNA solution from the ejecting chamber.
The inkjet spotter according to the present invention may be similar to a typical inkjet spotter used to manufacture a conventional DNA micro-array except for a PCT apparatus. The ejecting driving element may be a thermal type (similar to that disclosed in U.S Pat. No. 4,438,191), a Piezo type (similar to that disclosed in U.S. Pat. No. 5,748,214), or an electric field type (similar to that disclosed in U.S. Pat. No. 4,752,783).
The above and other features and advantages of the present invention will become more apparent by describing in detail exemplary embodiments thereof with reference to the attached drawings in which:
According to an aspect of the present invention, there is provided a polymerase chain reaction apparatus comprising: a substrate; a high-temperature sidewall erected on the substrate; a low-temperature sidewall erected on the substrate and facing the high-temperature sidewall; and a reaction chamber consisting of the substrate, the high-temperature sidewall, and the low-temperature sidewall, wherein a sample contained in the reaction chamber is repetitively thermal-circulated between the high-temperature sidewall and the low-temperature sidewall using Marangoni convection generated by a surface tension gradient resulting from a temperature difference in an interface between the sample and air.
A polymer chain reaction (PCR) is a method of amplifying a particular DNA region in several tens thousands of or hundreds thousands of times by repeating a DNA synthesis reaction between two kinds of primers interposing the particular DNA region by using a DNA synthesis enzyme in a test tube. Generally, a cycle of the PCR includes denaturing double strands into a single strand, annealing two kinds of primers interposing a target region of the denatured single DNA strand, and extending the primers to produce complementary sequences on the target region.
In the PCR, the denaturing of the double strands is performed at a high temperature of 90° C., and the primer combination and the DNA synthesis are performed at relatively low temperatures of 50˜60° C. and 70˜75° C., respectively. Therefore, a thermal cycler is necessary to perform the PCR.
In the apparatus according to an embodiment of the present invention, Marangoni convection is generated by a surface tension gradient resulting from a temperature gradient in an interface between a reactive fluid and air. As a result, the fluid flows from a high-temperature region to a low-temperature region. Therefore, the apparatus according to the present invention is discriminated from a conventional apparatus using Rayleigh-Benard convection, in which a buoyancy flow from the high-temperature region to the low-temperature region is generated by a density gradient resulting from a temperature difference in the fluid.
The present invention provides the first method and apparatus adopting a principle of Marangoni convection into PCR amplification. The PCR amplification apparatus uses a surface tension flow in a container having an interface (free surface) between the fluid and the air. Therefore, the reaction chamber used in the PCR apparatus according to the present invention is preferably not closed, but is open such that an interface exists between the fluid and air.
The reaction chamber may further include a cover as far as it comprises an interface between the fluid and air. The cover may be combined with the substrate or a sidewall in a single body.
The high-temperature sidewall may be heated to a temperature appropriate to denature the reactive fluid near the high-temperature sidewall. The high-temperature sidewall may be heated by a heater to a constant temperature of 92˜97° C., preferably, 95° C.
The heater may be embodied in various ways such that the high-temperature sidewall can be heated, such as a thin film resistive heater, a heater using a heat exchanger, a radiation heater, and a hot air blasting heater. More preferably, the heater is a thin film heater made of a material selected from a group consisting of platinum, polysilicon, and tantal aluminum. Also, the heater may be installed in the inside or outside of the sidewall, and a sensor for adjusting the temperature may be provided with the heater.
The low-temperature sidewall may be cooled to a temperature appropriate to anneal the reactive fluid near the low-temperature sidewall. The low-temperature sidewall may be cooled by a cooler to a constant temperature of 44˜56° C., preferably, 50° C.
The cooler may be embodied in various ways such that the sidewall can be cooled, such as a cooling fan or a thermal cycler. Preferably, the cooler may be a Peltier device. The cooler may be installed in the inside or outside of the low-temperature sidewall, and a sensor for adjusting the temperature may be provided together with the cooler.
The sample experiences DNA denaturing near the high-temperature sidewall, and the fluid at the surface of the reactive fluid rapidly flows to the low-temperature sidewall due to Marangoni convection, where the fluid is annealed. Then, a lower region of the reactive fluid slowly flows from the low-temperature sidewall to the high-temperature sidewall, thereby generating extension, i.e., the synthesis of new DNA strands.
A gap between the high-temperature sidewall and the low-temperature sidewall may be 2 mm to 3 cm. In the conventional PCR apparatus using a buoyancy flow, since the buoyancy is proportional to the volume of a container, a driving force decreases as the size of the container decreases. However, in the PCR apparatus according to the present invention, since the surface tension is proportional to the area of the fluid surface, a sufficient driving force can be obtained even when the container is small. Therefore, the PCR apparatus according to an embodiment of the present invention can be embodied in a DNA chip, a subminiature DNA detector, or a lap-on-a-chip.
The reaction chamber may be made of a material selected from a group consisting of glass, quartz, silicon, plastic, polymer, ceramic, and metal. Preferably, the reaction chamber is made by etching a silicon wafer using photolithography, i.e., a typical semiconductor manufacturing process.
The reaction chamber may have an optical detection window. Through the optical detection window, the PCR reaction in the chamber can be optically detected using a conventional PCR detection method in a real-time manner.
According to another aspect of the present invention, there is provided a polymerase chain reaction method comprising: putting a sample into the reaction chamber of any one of the above-described polymerase chain reaction apparatuses, maintaining temperatures of the high-temperature sidewall and the low-temperature sidewall constant; and repetitively thermal-circulating the sample contained in the reaction chamber between the high-temperature sidewall and the low-temperature sidewall using Marangoni convection.
The sample may include a typical template DNA, oligonucleotide primers, four dNTP's (i.e., dATP, dCTP, dGTP, and dTTP), a thermostable DNA polymerase, and a reactive buffer.
The high-temperature sidewall may be maintained at a constant temperature of 92˜97° C., appropriate for denaturing the DNA sample, and the low-temperature sidewall may be maintained at a constant temperature of 48˜54° C., appropriate for annealing the sample.
The sample may contain a fluorescent material to detect amplification of a nucleic acid in a real-time manner. The amplification sample may be a plasmid DNA. A driving fluid may be produced by adding primers, dNDP, a base, and a buffer solution containing a DNA polymerization enzyme into an initial sample. Distinct amplification DNA bands are visible when the fluorescent material in the DNA sample that has been amplified using the PCR reaction is detected.
According to still another aspect of the present invention, there is provided a method of manufacturing a PCR apparatus including a photolithographic process. In the method, photolithography is applied to a first substrate to form the pattern of a flow path and a PCR chamber on its upper surface. The first substrate may be made of a material selected from a group consisting of silicon, glass, polycarbonate, polydimethylsiloxane, and polymethylmetaacrylate. The first substrate may be etched to have a desired thickness by wet etching or dry etching such as a reactive ion etching. If necessary, the photolithographic process and the etching process may be repeated several times to allow the flow path and the chamber to have varying depths. A hydrophobic treatment is applied to the upper portion of a second substrate, which is a cover for preventing evaporation of the DNA reaction fluid in the PCR chamber to resist wetting. After patterns of an inlet and an outlet for the sample are formed on the first substrate through photolithography, the inlet and the outlet are finished by sound-blasting. If it is necessary to form an electrode structure on the second substrate, electrode patterns are formed through photolithography and are obtained using a lift-off procedure. Subsequently, the first and second substrates are bonded using a method such as anodic bonding, fluorine bonding, thermal bonding, or polymer film bonding.
According to still another aspect of the present invention, there is provided a lab-on-a-chip comprising any one of the above-described polymerase chain reaction apparatuses and an electrophoresis performing unit connected to the polymerase chain reaction apparatus in a fluidic manner.
When the sample in the chip passes through the PCR apparatus, the DNA is amplified. When the sample passes through the electrophoresis performing unit, the DNA is separated depending on its molecular amount or charge to detect target DNA.
The substrates may be made of a material selected from a group consisting of glass, quartz, silicon, plastic, polymer, ceramic, or metal. The electrophoresis unit may have multiple channels performing capillary electrophoresis. The PCR amplification apparatus and the electrophoresis performing unit may be formed on a substrate through photolithography.
According to still another aspect of the present invention, there is provided an inkjet spotter comprising: any one of the above-described polymerase chain reaction apparatuses formed on a substrate; a restrictor connected to the polymerase chain reaction apparatus in a fluidic manner; an ejecting chamber storing a DNA solution from the polymerase chain reaction apparatus via the restrictor; an ejecting driving element providing a driving force of the DNA solution ejection; and a nozzle ejecting the DNA solution from the ejecting chamber.
The inkjet spotter according to the present invention may be similar to a typical inkjet spotter used to manufacture a conventional DNA micro-array except for a PCT apparatus. The ejecting driving element may be a thermal type (similar to that disclosed in U.S Pat. No. 4,438,191), a Piezo type (similar to that disclosed in U.S. Pat. No. 5,748,214), or an electric field type (similar to that disclosed in U.S. Pat. No. 4,752,783).
Hereinafter, exemplary embodiments according to the present invention will be described in detail with reference to the accompanying drawings.
The Marangoni convection flow occurs from the high-temperature sidewall 1, which has a temperature of about 95° C., toward the low-temperature sidewall 2, which has a temperature of about 50° C. The DNA sample contained in the fluid is denatured at about 94° C. near the high-temperature sidewall 1, flows along the interface between the fluid and air toward the low-temperature sidewall 2, and annealed at about 55° C. near the low-temperature sidewall 2. Accordingly, the DNA sample flows along the bottom of the chamber, either adiabatically or at a constant temperature of 72° C. to generate extension. The denaturing, annealing, and extension constitute a thermal cycle. According to the present invention, the time required to complete one thermal cycle can be as low as 5 seconds or less. However, an excessively short cycle may result in insufficient DNA amplification. Therefore, an appropriate time period for one cycle is within a range from 5 seconds to 30 seconds. The time for performing a cycle can be adjusted by controlling the size of the reaction chamber and the surface tension of the reaction fluid using an electric field on a surface active agent.
A method of manufacturing the PCR apparatus will now be described.
First, a flow path and a PCR chamber pattern are formed on a first substrate through photolithography. The first substrate may be made of a material selected from a group consisting of silicon, glass, polycarbonate, polydimethylsiloxane, and polymethylmetaacrylate. Wet etching or dry etching such as reactive ion etching may be used to form the first substrate to a desired thickness. If required, the photolithographic process and the etching process may be repeated several times to provide the flow path and the chamber with varying depths. In the case of a silicon substrate, a silicon oxide film, which will be used as a DNA absorption protection film as well as an electric insulation film, having a thickness of several hundreds of nanometers, is deposited by wet etching after the final etching process. Electrodes on the bottom of the first substrate are patterned using photolithography, a thin film made of platinum, tantal aluminum, or polysilicon, which will be used as a thin film heater, is coated thereon, and then the first electrodes are completed by performing a lift-off procedure. Then, a hydrophobic treatment is applied to the upper surface of a second substrate, which is a cover for preventing evaporation of the DNA reaction fluid from the PCR chamber, to resist wetting. After the pattern of the inlet and outlet for the sample are formed in the first substrate through photolithography, the first substrate is sand-blasted to finish the inlet and outlet. If it is necessary to form an electrode structure on the second substrate, the electrode patterns are formed through photolithography and performing a lift-off procedure. Subsequently, the first and second substrates are bonded using a method such as anodic bonding, fluorine bonding, thermal bonding, or polymer film bonding.
The present invention will now be fully described using examples. The examples should be considered in descriptive sense only and are not for purposes of limitation. Therefore, the scope of the invention is not defined by the following embodiments.
Thermal-flow fields in the Marangoni PCR chamber have been analyzed using a commercial professional numerical analysis tool, FLOW3D (www.flow3d.com), specialized for a surface flow analysis. In the analysis, it was assumed that the sidewalls were maintained at temperatures of 95° C. and 50° C., respectively. Also, it was assumed that a buffer solution had a thermal conductivity of 0.656 W/m K, a specific heat of 4187 J/Kg K, and a surface tension coefficient of 72 dyne/cm. It was also assumed that the buffer solution had a contact angle of 90° by supposing that a hydrophobic treatment was used. Further, a surface tension coefficient based on the temperature was 0.16 dyne/cm K, corresponding to that of water.
Similar to the Example 1, thermal-flow fields in the Marangoni PCR chamber have been analyzed by using FLOW3D. It was assumed that the fluid was divided into 25×25×20 grids in x, y, and z directions. Also, it was assumed that the conditions such as boundary conditions and material properties were similar to those of the two-dimensional analysis.
An inkjet spotter having a PCR apparatus according to an embodiment of the present invention is manufactured.
In the conventional PCR amplification, DNA amplification was accomplished by cyclically heating and cooling a chamber containing a DNA buffer solution. Therefore, it was difficult to control temperature, there was high power consumption, and it takes a long time to complete a cycle of amplification. However, according to the present invention, the PCR amplification is automatically accomplished by a surface tension flow generated by Marangoni convection resulting from a temperature difference in an interface between a fluid and air when sidewalls of the chamber are maintained at a predetermined temperature difference. As a result, it is possible to reduce power consumption, simplify the configuration of a temperature control circuit, and reduce the time for an amplification cycle.
While the present invention has been particularly shown and described with reference to exemplary embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the spirit and scope of the invention as defined by the appended claims. The exemplary embodiments should be considered in descriptive sense only and not for purposes of limitation. Therefore, the scope of the invention is defined not by the detailed description of the invention but by the appended claims, and all differences within the scope will be construed as being included in the present invention.
Number | Date | Country | Kind |
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10-2004-0073920 | Sep 2004 | KR | national |