Patent Application
20120283119
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 10, 2012, is named H6808059.txt and is 872 bytes in size.
The present invention relates to biotechnology in such field as genetic diagnosis, sequence analysis of DNA, or analysis of single nucleotide polymorphism, particularly to technology in the field of genetic testing and more specifically, to potentiometric DNA microarray capable of simultaneously analyzing a plurality of different nucleic acids with high accuracy, a process for producing the microarray and a method of analyzing nucleic acids.
Rapid progress has been made in the projects of genome nucleotide sequence analysis for various living organisms including the human genome project, and enormous amounts of information on the nucleotide sequence are being accumulated. At present, the entire nucleotide sequence of the human genome is being determined. From now on, elucidation of gene functions in vivo seems likely to promote dramatic developments of gene-related technology in a wide range of fields including diagnosis of various diseases, pharmaceutical development, breeding of agricultural products, and the like. The foundation for the progress in these new fields is formed by information about gene expression and function in addition to information on nucleotide sequences. As a technology to conduct the analysis of gene function and gene expression in a large scale and to develop it to genetic testing, DNA chip or DNA microarray (hereinafter, collectively called DNA microarray) has been developed by Affymetrix Inc., Nanogen Inc., and so on. Since the majority of the present DNA microarrays utilize detection by fluorescence as the basic principle, a laser or a complex optical system is required for them, and the system becomes larger in size and expensive.
Furthermore, all DNA microarrays developed currently are discarded after only a single use as a general rule. Even if these DNA microarrays may be used repeatedly by washing, their use is limited to at most two to three times, thus giving rise to a major problem of the running cost in analyzing many samples and in the fields of gene diagnosis to test a large number of samples and the like. Particularly in the field of medicine, it is difficult for an expensive test to come into wide use in view of cost containment of medical expenses. On the other hand, high accuracy and quantitative determination are required in the field of the medicine, that is, in the field of gene diagnosis. Accordingly, a technology to satisfy both cost reduction and high accuracy is sought.
For a method to solve these problems, several DNA microarrays having a current detection system combined with oxidation-reduction labeling have been reported. Clinical Micro Sensor Systems, Inc. has developed a system in which one end of a molecule called molecular wire is immobilized on a metal electrode while the other end is bound to a nucleic acid probe, and donation and acceptance of electrons between an oxidation-reduction label and the metal electrode arising from hybridization of the nucleic acid probe with the target gene is detected as a change of electric current to detect target genes (Nature Biotechnology, vol. 16 (1998) p. 27, p. 40). Since this system does not require an expensive laser or a complex optical system, a simple and small system can be constructed. It utilizes, however, an oxidation-reduction reaction on the metal electrode as the basic principle of the detection, and therefore, the presence of an oxidizing substance or a reducing substance (e.g., ascorbic acid) in a sample induces an electric current due to its oxidation or reduction, thereby disturbing the gene detection and deteriorating accuracy of the detection. Moreover, an electrode reaction occurs progressively on the metal electrode concurrently with the current measurement. Since the electrode reaction is irreversible and is a nonequilibrium reaction, corrosion of the electrode, evolution of gas, and the like occur, resulting in instability of the current measurement and deterioration of detection accuracy particularly when the measurement is repeated.
From these backgrounds, an object of the present invention is to provide a DNA microarray that allows measurement of high accuracy using a system having a low running cost and a low price, a process for producing the DNA microarray, and a method of analyzing nucleic acids with the use of the DNA microarray.
The present invention is a DNA microarray in which a nucleic acid probe is immobilized on the surface of an insulator and then hybridized with a target gene on the surface of the insulator, and the resulting change in the electric charge density is detected. The DNA microarray is preferably the one including a system in which a nucleic acid probe is immobilized on the surface of a gate insulator of electric field effect transistor and then hybridized with a target gene on the surface of the gate insulator, and the resulting change in the electric charge density is detected by utilizing a field effect. A DNA microarray that allows a potentiometric detection of a change in the surface electric potential with a high signal to noise ratio could be realized by introducing an intercalator or by labeling nucleic acids with a molecule to form a complex with a charged particle such as ion in order to amplify the change in the surface electric charge density in addition to the charge inherent in the nucleic acids. Since a method for analyzing genes using the DNA microarray of the present invention does not require an expensive laser detection system or a complex optical detection system and detects the surface potential in an equilibrium state by immobilizing the nucleic acid probes on an insulating substrate, which is different from an amperometric detection system, the problems such as corrosion of the substrate, evolution of gas, and unstable signal values due to interference from oxidation-reduction substances are not created, thus allowing excellently stable and highly accurate detection of genes.
The potentiometric DNA microarray according to one aspect of the present invention comprises a plurality of the insulated gate field effect transistors on which single stranded nucleic acid probes or branched nucleic acid probes are immobilized on the surface of the gate insulators directly or via a carrier, and reference electrodes.
The potentiometric DNA microarray according to another aspect of the present invention comprises a substrate, on which a plurality of the insulated gate field effect transistors are formed and each different kind of single stranded nucleic acid probe or branched nucleic acid probe immobilized on the gate insulators over the channel regions of each of the insulated gate field effect transistors directly or via a carrier in the surface of the substrate.
The potentiometric DNA microarray according to still another aspect of the present invention comprises a first insulated gate field effect transistor on which a nucleic acid probe having a base sequence complementary to a portion of a target nucleic acid to be detected is immobilized on the surface of the gate insulator directly or via a carrier, a second insulated gate field effect transistor on which a nucleic acid probe having a base sequence noncomplementary to any portion of the target nucleic acid to be detected is immobilized on the surface of the gate insulator directly or via a carrier, and a circuit to detect and compare outputs of the first insulated gate field effect transistor and the second insulated gate field effect transistor.
The method of analyzing nucleic acids according to one aspect of the present invention comprises the steps of (a) introducing a sample solution containing at least one kind of nucleic acid onto the substrate provided with a plurality of insulated gate field effect transistors on which each different kind of single stranded nucleic acid probe or branched nucleic acid probe is immobilized on the surface of gate insulators directly or via a carrier, and subjecting to hybridization with the single stranded nucleic acid probes or branched nucleic acid probes, (b) introducing a washing solution onto the substrate to remove unreacted nucleic acids from the surface of the substrate, (c) introducing an intercalator solution onto the substrate to react with formed double stranded nucleic acids, (d) introducing the washing solution onto the substrate to remove unreacted intercalator from the surface of the substrate, and (e) introducing a buffer onto the substrate to measure outputs of the insulated gate field effect transistors.
In addition to the above steps of (a) to (e), when the method of analyzing nucleic acids further comprises the steps of (f) dissociating the nucleic acids hybridized with the single stranded nucleic acid probes or branched nucleic acid probes by heating the substrate and (g) introducing the washing solution onto the substrate to remove the nucleic acids and the intercalator dissociated from the single stranded nucleic acid probes or branched nucleic acid probes, and then the steps (a) to (e) are repeated, a plurality of measurements can be performed continuously.
The method of analyzing nucleic acids according to another aspect of the present invention comprises the steps of (a) introducing a sample solution containing nucleic acid fragments labeled with a molecule capable of incorporating charged particles onto a substrate provided with a plurality of insulated gate field effect transistors, on which each different kind of single stranded nucleic acid probe or branched nucleic acid probe is immobilized on the surface of gate insulators directly or via a carrier, to subject to hybridization with the single stranded nucleic acid probes or branched nucleic acid probes, (b) introducing a washing solution onto the substrate to remove unreacted nucleic acid fragments from the surface of the substrate, (c) introducing a solution containing an ion to form a complex with the labeling molecule onto the substrate to react with the molecule labeled on the formed double stranded nucleic acids and form a complex between the ion and the labeling molecule, and (d) measuring outputs of the insulated gate field effect transistors.
The molecule capable of incorporating charged particles may be a molecule that forms a complex selectively with a monovalent or bivalent cation or anion, for example, valinomycin, nonactin, monactin, bis(crown ether), a calixarene derivative, a non-cyclic polyether derivative, a quaternary ammonium salt, a porphyrin or a derivative of these molecules.
In this case, plural kinds of molecules capable of incorporating the charged particles are used to label different nucleic acid fragments, respectively, and the charged particles (ions) corresponding to each of the molecules are introduced onto the substrate, thereby allowing measurements of plural kinds of genes or genetic polymorphism simultaneously or one after another.
In addition to the above steps of (a) to (d), when the method of analyzing nucleic acids according to the present invention further comprises steps of (e) heating the substrate to dissociate the nucleic acid fragments hybridized with the single stranded nucleic acid probes or branched nucleic acid probes and (g) introducing the washing solution onto the substrate to remove the nucleic acid fragments dissociated from the single stranded nucleic acid probes or branched nucleic acid probes, and then the steps (a) to (d) are repeated, multiple measurements can be performed continuously.
The process for producing the potentiometric DNA microarray according to one aspect of the present invention comprises the steps of: forming a silicon film on a first surface of the insulating substrate; dividing the silicon film into a plurality of silicon film formation areas by patterning of the silicon film; forming a plurality of pn junctions working as source and drain regions of the field effect transistors, a heater, and a temperature sensor, respectively, in each of the silicon film formation areas; carrying out wiring for signal from the source and drain regions with the region between the source and drain regions serving as a channel; and immobilizing nucleic acid probes directly or via a carrier at the sites corresponding to the channels of the field effect transistors on a second surface opposite to the surface where the silicon film is formed on the insulating substrate.
The process for producing the potentiometric DNA microarray according to another aspect of the present invention comprises the steps of: forming a silicon film on a surface of the insulating substrate; dividing the silicon film into a plurality of silicon film formation areas by patterning of the silicon film; forming a plurality of pn junctions working as the source and drain regions of the field effect transistors, a heater, and a temperature sensor, respectively, in each of the silicon film formation areas; carrying out wiring for signal from the source and drain regions with the region between the source and drain regions serving as a channel; forming an insulating film on the surface where the wiring for signal is carried out; and immobilizing nucleic acid probes directly or via a carrier at the sites corresponding to the channels of the field effect transistors on the surface of the insulating film.
The present invention is explained below in detail with reference to the accompanying drawings. The same functional portions are designated by the same reference numerals in the following illustrations.
It is configured such that a nucleic acid probe 3 is immobilized on the surface of a gate insulator 2 of an insulated gate FET 1. For the nucleic acid probe is used an oligonucleotide, cDNA, or DNA fragment branched in the middle, each generally composed of 300 nucleotides or less and capable of hybridizing with a target gene to be measured under appropriate conditions. In the case of an oligonucleotide, it is preferably a nucleic acid fragment with a length of 80 bases or less. For the gate insulator, a material such as silicon dioxide (SiO2), silicon nitride (SiN), aluminum oxide (Al203), or tantalum oxide (Ta205) is used alone or in combination, and
generally a bilayer structure in which silicon nitride (SiN), aluminum oxide (Al203), and tantalum oxide (Ta205) are layered on top of silicon dioxide (Si02) is employed to keep performance of a transistor better.
In order to immobilize the nucleic acid probe on the surface of the insulator, one of the terminal ends of the nucleic acid probe is chemically modified to contain an amino group (NH2 group), a thiol group (SH group), biotin, or the like. When a nucleic acid probe chemically modified to contain an amino group is used, the surface of the insulator is modified with a chemical such as aminopropylethoxysilane or polylysine to introduce an amino group onto the surface of the insulating film, and then the latter group is reacted with glutaraldehyde or phenylene diisocyanate (PDC) to immobilize the nucleic acid probe chemically modified to contain the amino group on the surface of the insulator. When the nucleic acid probe chemically modified to contain the thiol group is immobilized on the surface of the insulator, a gold thin film is formed on the insulator and the nucleic acid probe is immobilized by taking advantage of an affinity between thiol group and gold. Furthermore, when the nucleic acid probe chemically modified to contain biotin is immobilized, streptoavidin is introduced onto the surface of the insulator and the nucleic acid probe is immobilized by taking advantage of an affinity between biotin and streptoavidin on the surface of the gate insulator. At the time of a practical immobilization, a solution containing the nucleic acid probe is dropped or spotted only on the surface of the gate insulator on FET channel, thereby immobilizing the nucleic acid probe only on the gate insulator of the channel portion.
On the other hand, by forming a fixed carrier on the surface of the gate insulator of FET, the nucleic acid probe may be immobilized on the surface or in the inside of the fixed carrier in an indirect way. The materials that can be used for the fixed carrier include agarose, polyacrylamide, polyhydroxyethyl methacrylate (pHEMA), and the like. The fixed carrier may be chemically modified to contain an amino group or streptoavidin, and as described above, the nucleic acid probe may be immobilized by using glutaraldehyde or PDC, or by taking advantage of an affinity with biotin, respectively, on the fixed carrier. In this way, the nucleic acid probe may also be formed indirectly on the gate insulator of FET via the fixed carrier.
When a number of genes containing a target gene to be measured are present in a sample and when a nucleic acid probe having a base sequence complementary to the target gene is immobilized on the gate insulator of FET for gene detection, the target gene and the nucleic acid probe hybridize with each other under appropriate reaction conditions to form a complex of the target gene and the nucleic acid probe. Under an appropriate condition for pH of a buffer solution used for the reaction, nucleic acids are charged negative. Accordingly, the formation of the complex by hybridization induces a change in electric charge density in the vicinity of the gate insulator of FET, thereby changing the surface potential of the gate insulator. This change behaves equally as a gate voltage change of FET, resulting in a change of conductivity of the channel. Therefore, the formation of the complex, that is, the presence of the target gene, can be detected as a change in drain current passing between a source 4 and a drain 5.
This genetic testing system is provided with a reference FET 6 in addition to the Genetic FET 1 shown in
Such a differential measurement allows to accurately detect only the output change caused by the hybridization of the target gene and the nucleic acid probe by
compensating for an output change occurring from changes in ambient temperature and light due to the difference in electric properties of FET or by offsetting an output change arising from non-specific adsorption of charged particles in the sample on the gate insulator. Since the Genetic FET and the reference FET are desired to be uniform in their electric properties, it is desirable to use a pair of FET integrated on the same substrate.
In order to stably measure the surface potentials of the Genetic FET and the reference FET, a reference electrode 8 that serves as a reference for the potential measurement is provided. The reference electrode conventionally used is the one that a silver-silver chloride electrode or a calomel electrode is dipped into an internal solution for the electrode having a specified composition and concentration, and the electrode is constructed such that the internal solution and a sample solution make contact with each other via a liquid junction formed with salt bridge or porous material. The surface potentials of the Genetic FET 1 and the reference FET 6 are measured with their respective drive circuits 9, and both of the outputs are input to a signal processing circuit 11 via the differential measurement circuit 10. When a plurality of Genetic FETs are integrated to measure a plurality of genes at the same time, the reference FET may be used in common to perform the differential measurements between different Genetic FETs and the common reference FET.
that is different from the base sequences complementary to the first and second genes is immobilized on the surface of the gate insulator of the reference FET.
A specific example is explained below. It is known that there exist single nucleotide polymorphisms (SNPs) in alcohol dehydrogenase-related gene. A first and a second nucleic acid probes each having a length of 17 bases in which the base at a SNP position is interposed between 8 common bases were synthesized. The base sequences of these probes are shown below.
The ninth position from the 5′ terminus is the site of the SNP. In the first nucleic acid probe, the base is A at the SNP site, while in the second nucleic acid probe, the base is G at the site. The first and the second nucleic acid probes are immobilized on the first and the second gates of FETs, respectively. A nucleic acid probe that has a base sequence different from the first and the second nucleic acid probes, for example, a nucleic acid probe of 17 bases composed exclusively of A, is immobilized on the gate of the reference FET. Alternatively, a nucleic acid probe may not be immobilized on the gate of the reference FET. The 5′ termini of the above nucleic acid probes are modified to contain amino groups, respectively. On the other hand, the gate insulating film of FET in the present example is made of silicon nitride, and the surface of the silicone nitride is chemically modified using γ-aminopropyltriethoxysilane to introduce an amino group thereon. The amino group of the nucleic acid probe and that of the silicone nitride are reacted with a bifunctional reagent such as glutaraldehyde to immobilize the nucleic acid probe on the surface of silicone nitride through the formation of a Schiff base bond.
The human genome was extracted from white blood cells in the blood, and a region of 100 base length that contains the SNP site was amplified to serve as a sample to be tested. The sample was introduced to the first and the second Genetic FETs and the reference FET, followed by hybridization for 8 hours at 45 degrees C. After the hybridization, these FETs were washed with a buffer to remove unreacted sample, and then ethidium bromide was introduced as an intercalator to them. The measurement was first conducted by introducing the buffer to the first and the second Genetic FETs and the reference FET, and the output voltage of each of these FETs, the differential output between the first Genetic FET and the reference FET and that between the second Genetic FET and the reference FET were measured. After these measurements, the sample was introduced, hybridized, and washed, followed by introduction of the intercalator, and then the output voltage of each of these FETs, the differential output between the first Genetic FET and the reference FET, and that between the second Genetic FET and the reference FET were measured. The changes in the output voltage before and after the introduction of the sample and the intercalator were measured.
In a sample having the base sequence corresponding to the first nucleic acid probe (Normal), the differential output between the first Genetic FET and the reference FET was 5.0 mV. On the other hand, the differential output between the second Genetic FET and the reference FET was 0.5 mV, showing a significant difference from the above. It is desirable that a series of these measurements are performed at the same time, while successive measurements are also allowed when performed within the same test time period. In another sample having the base sequence corresponding to the second nucleic acid probe (Mutant), the differential output between the first Genetic FET and the reference FET was 0.3 mV. On the other hand, the differential output between the second Genetic FET and the reference FET was 4.0 mV, showing again a significant difference from the above. In still another sample having the base sequences corresponding to the first and the second nucleic acid probes half-and-half (Hetero), the differential output between the first Genetic FET and the reference FET was 2.3 mV, while the differential output between the second Genetic FET and the reference FET was 2.0 mV, showing approximately one to one ratio between Normal and Mutant. From the foregoing, the SNP analysis according to the present invention allowed to discriminate three kinds of samples of Normal/Normal homo-type, Mutant/Mutant homo-type, and Normal/Mutant hetero-type. When an intercalator is used, it is unnecessary to label the DNA sample by chemically linking a labeling compound.
When the detection was carried out only by the charge inherent in the target DNA alone without using the intercalator as shown in
The molecule (ligand) that is used to form a complex with the ion includes valinomycin, nonactin, monactin, bis(crown ether), calixarene derivatives, non-cyclic polyether derivatives, quaternary ammonium salts, and the like. For example, when the target gene is labeled with Bis(12-crown-4), a property of Bis(12-crown-4) to form a complex selectively with sodium ion may be utilized. That is, the labeled target gene is hybridized with the nucleic acid probe on the gate insulator, and then, a buffer containing sodium ion is introduced onto the DNA microarray to allow a selective complex formation between Bis(12-crown-4) and sodium ion, which causes a local change in the electric charge density on the surface of the gate insulator. This change is detected by the FET.
The present example was specifically applied to an SNP analysis, which is explained below. Using the alcohol dehydrogenase-related gene shown in Example 3, two nucleic acid probes shown below were immobilized on the gate insulators of the first and second Genetic FETs, respectively.
A nucleic acid probe that has a sequence different from those of the first and the second nucleic acid probes, for example, a nucleic acid probe of 17 base length composed exclusively of A, is immobilized on the gate of the reference FET. A DNA sample was extracted from white blood cells in the blood, and a region of 100 base length that contains the SNP site was amplified, and then Normal DNA and Mutant DNA were labeled with bis(crown ether) and valinomycin, respectively.
The sample from Normal DNA was introduced to the first and second Genetic FETs and the reference FET, followed by hybridization for 8 hours at 45 degrees C. After the hybridization, these FETs were washed with a buffer to remove unreacted sample, and an aqueous solution of 50 mM NaCl was introduced thereto, followed by the measurements of the output voltage of each of the first and the second Genetic FETs and the reference FET, the differential output between the first Genetic FET and the reference FET and that between the second Genetic FET and the reference FET. The differential output between the first Genetic FET and the reference FET was 4.0 mV, while the differential output between the second Genetic FET and the reference FET was 0.2 mV. After these measurements, an aqueous solution of 50 mM KCl was introduced, and the measurements of the outputs were carried out similarly, resulting in that the differential output between the first Genetic FET and the reference FET was 0.1 mV and that the differential output between the second Genetic FET and the reference FET was 0.3 mV. Thus, it was confirmed that Normal DNA in the sample hybridized only with the first nucleic acid probe, showing a selective response of the first Genetic FET.
On the other hand, a sample of Mutant DNA was measured in a way similar to the above. When a solution of 50 mM NaCl was introduced, the differential output between the first Genetic FET and the reference FET was 0.1 mV, while the differential output between the second Genetic FET and the reference FET was 0.2 mV. After an aqueous solution of 50 mM KCl was introduced, the differential output between the first Genetic PET and the reference FET was 0.1 mV, while the differential output between the second Genetic FET and the reference FET was 5.0 mV, confirming that Mutant DNA in the sample hybridized only with the second nucleic acid probe showing a selective response of the second Genetic FET. In another sample containing Normal and Mutant DNAs half-and-half (Hetero), when an aqueous solution of 50 mM NaCl was introduced, the differential output between the first Genetic FET and the reference FET was 2.3 mV, while the differential output between the second Genetic FET and the reference FET was 0.1 mV. After an aqueous solution of 50 mM KCl was introduced, the differential output between the first Genetic FET and the reference FET was 0.1 mV, while the differential output between the second Genetic FET and the reference FET was 2.5 mV, showing approximately one to one ratio between Normal and Mutant.
From the foregoing, the SNP analysis according to the present invention allowed to discriminate three kinds of samples of Normal/Normal homo-type, Mutant/Mutant homo-type, and Normal/Mutant hetero-type. In the present example, the processes of the SNP analysis involve two selective processes of chemical reactions that are hybridization and ion-ligand complex formation. Therefore, the SNP analysis can be performed with high accuracy.
Besides the SNP analysis, it is also possible to perform an expression analysis by immobilizing many kinds of nucleic acid probes on the gates of FETs, and labeling a target sample and its reference sample with valinomycin and bis(crown ether), respectively.
Next, etching of oxidized film and formation of doping regions are carried out as shown in
Next, metal wiring for electrodes is carried out as shown in
Finally, DNA probes are immobilized as shown in
On the surface of the insulating glass surface 17, a solution is introduced onto the surface where the nucleic acid probes 3 are formed. Therefore, the solution may sometimes contact with wiring and signal wires for an electronic device such as transistor to develop a short-circuit, resulting in a faulty operation. In the present invention, the wiring 25 is formed on the surface opposite to the surface with which the solution makes contact and on which the nucleic acid probes 3 are formed, and signal wires are designed to be connected to the opposite surface. Accordingly, the problem of the faulty operation caused by contacting with the solution is eliminated, and a measurement system with high reliability can be provided.
silicon film is p-type, n-type doping regions are formed, and when the silicon film is n-type, p-type doping regions are formed. These doping regions served for the source and drain regions 21 of FETs, the heater 22, or the temperature sensor 23. Each doping region is bonded to external drive circuit via the electric wiring 25.
In the present example, two FETs are formed in one piece of the silicon film formation area 19 as shown in
A perspective view from the backside of the DNA array depicted in
Another example of the present invention is explained using
In the same way as in
In the present example, the radiation fins 27 of grid pattern are formed of silicon film so as to surround each of the silicon film formation areas 19, the purpose of which is to carry out hybridization and washing at the optimal temperature for each reaction according to Tms of the nucleic acid probes formed on each Genetic FET, thereby improving accuracy of temperature control for each of the silicon film formation areas 19. The radiation fin 27 has good thermal conductivity because of being made of silicon film and can efficiently radiate heat generated in the adjacent silicon film formation areas 19, reduce effects on the adjacent silicon film formation areas, and control the temperature of each of the silicon film formation areas 19 independently. In the present example, the size of one piece of the silicon film formation area 19 is 1 mm square, the distance between the silicon film formation area 19 and the radiation fin 27 is 0.5 mm, and the width of the radiation fin is 0.5 mm. By employing this structure, the temperature of each of the silicon film formation areas 19 could be controlled from room temperature to 95 degrees C. with a precision of one degree C.
The thin film gate type Genetic FET chip of the present example has a structure in which the glass substrate of the gate regions for the Genetic FET and the reference FET in the DNA microarray explained in Example 5 is made thinner. The thickness of the glass substrate in the thin film gate regions 28 is preferably in the range of from 0.01 to 1 μm and was 0.1 μm in the present example. This structure can make the transconductance of the FET larger and detect a change in electric charge occurring on the gate with high sensitivity. In addition to making only the gate region of the FET a thinner film, it is also possible to make the whole glass substrate of the silicon film formation area a thinner film, thereby allowing the recessed area formed by being made thinner to be used as a reaction cell.
Examples 5, 6, and 7 are structured such that the nucleic acid probes 3 are formed on the glass surface opposite to the silicon film formation area 19, whereas the nucleic acid probes 3 in the present example were immobilized on a second insulating film 29 formed on an oxidized silicon film, i.e. an insulating film 2 formed on the silicon film formation areas 19. The material usable for the second insulating film 29 includes silicon nitride, aluminum oxide, and tantalum oxide. This example enables precise control of the thickness of the gate insulating film of FET and detection of a change in electric charge occurring on the gate with high sensitivity by making the transconductance of the FET larger.
The DNA microarray chip having at least the Genetic FET and the reference FET is mounted on a flow cell 30, which is connected to a flow channel 31. A hybridization solution 32 and a washing solution 33 flow into the flow channel 31 via a valve 34. These solutions can be introduced into the flow cell 30 by driving a pump 35. A sample and an intercalator are dispensed into the valve 34 by a dispenser 36, and then introduced into the flow cell 30 to react with the Genetic FET and the reference FET. After the reaction, spent solution is sent to a liquid waste bottle 37 by the pump 35. The outputs of the Genetic FET and the reference FET after the reaction are processed and computed by a signal processing circuit 38.
The structure of the flow cell 30 is shown in
The measurement system of Genetic FET of the present construction employs a flow system for the measurement, and therefore, a number of samples can be handled continuously and automatically, which is advantageous for a high-throughput measurement. When the intercalator described in Example 3 is used, the measurement is conducted by the following steps:
(1) Introduction of a washing solution into the flow cell.
(2) Introduction of a hybridization solution into the flow cell (replacement of the washing solution).
(3) Setting of the temperature of each of the silicon film formation areas to the optimal temperature for each nucleic acid probe.
(4) Measurement of the outputs of the Genetic FET and the reference FET and computation of the difference.
(5) Dispensing of a sample to the valve and subsequent introduction to the flow cell with the hybridization solution.
(6) Hybridization in the flow cell.
(7) Introduction of a buffer to the flow cell to remove unreacted sample.
(8) Introduction of an intercalator solution into the flow cell and reaction.
(9) Introduction of the buffer to remove unreacted intercalator solution.
(10) Measurement of the outputs of the Genetic FET and the reference FET, and computation of the difference.
(11) Setting of the temperature of each of the silicon film formation areas to 95 degrees C.
(12) Introduction of the washing solution to wash the inside of the flow cell.
The above sequence for the measurement is shown in
When SNP is analyzed using the molecules (ligands) to form complexes with ions as described in Example 4, the measurement is conducted by the following steps:
(1) Introduction of a washing solution into the flow cell.
(2) Introduction of a hybridization solution into the flow cell (replacement of the washing solution).
(3) Setting of the temperature of each of the silicon film formation areas to the optimal temperature for each nucleic acid probe.
(4) Measurement of the outputs of the Genetic FET and the reference FET and computation of the difference.
(5) Dispensing of a sample to the valve and subsequent introduction to the flow cell with the hybridization solution.
(6) Hybridization in the flow cell.
(7) Introduction of a buffer to the flow cell to remove unreacted sample.
(8) Introduction of a solution of 50 mM NaCl into the flow cell and reaction.
(9) Measurement of the outputs of the Genetic FET and the reference FET and computation of the difference.
(10) Introduction of a solution of 50 mM KCl into the flow cell and reaction.
(11) Measurement of the outputs of the Genetic FET and the reference FET and computation of the difference.
Judgment of Normal/Normal, Mutant/Mutant, and Normal/Mutant from the information on the nucleic acid probe for each FET and the differential outputs in NaCl and KCl.
(12) Introduction of the buffer to remove the KCl solution.
(13) Setting of the temperature of each of the silicon film formation areas to 95 degrees C.
(14) Introduction of the washing solution to wash the inside of the flow cell.
The present invention provides a DNA microarray system in which nucleic acid probes are immobilized on the surface of the gate insulator of FET and then hybridized with a target gene on the surface of the gate insulator of FET, and a change in the surface electric charge density is detected by using the field effect. The DNA microarray that allows a potentiometric detection of a change in the surface electric potential with a high signal to noise ratio can be realized by introducing an intercalator or labeling nucleic acids with molecules to form complexes with charged particles such as ions in order to amplify the change in the surface electric charge density in addition to the charge inherent in the nucleic acids. The DNA microarray of the present invention does not require an expensive laser detection system or a complex optical detection system, and detects the surface potential in an equilibrium state by immobilizing the nucleic acid probes on an insulating substrate, which is different from an amperometric detection system. Therefore, the problems such as corrosion of the substrate, evolution of gas, and unstable signal values due to interference from oxidation-reduction substances do not arise, thus allowing excellently stable and highly accurate detection of genes.
This application is a divisional application of U.S. application Ser. No. 10/499,005, filed Jun. 18, 2004, the entire disclosure of which is incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 10499005 | Jun 2004 | US |
| Child | 13493534 | US |
