JP4475478B2 - Gene analysis method and apparatus - Google Patents

Description

[0001]
BACKGROUND OF THE INVENTION
The present invention relates to a method for analyzing gene sequence information and an apparatus therefor.
[0002]
[Prior art]
Conventionally, as a method for analyzing a gene sequence, a cloned DNA strand is cleaved with a restriction enzyme to make several hundred bp, further cleaved with an enzyme, and each base of A, T, G, C by electrophoresis. A method of obtaining an electrophoretic pattern for analyzing the base sequence is widely used.
[0003]
Recently, many nucleotides of known sequences, such as oligonucleotides and cDNAs, are immobilized on a substrate, reacted with sample DNA that has been cloned, and detected that specific adsorption has occurred. A method called a DNA chip for estimating the sequence has also been developed.
In addition, as a technique for analyzing DNA, the state in which the probe DNA is hybridized to the sample DNA by a fluorescence in situ hybridization method is observed with a fluorescence microscope. Holmes-Davis et al. [Trends in Plant Science 3 (1999) 91].
[0004]
[Problems to be solved by the invention]
Problems in the gene analysis by electrophoresis and the gene analysis by DNA chip include the complexity of the analysis operation. That is, according to this method, it is necessary to analyze a DNA sequence finely fragmented with a restriction enzyme through a number of steps and to connect the information.
[0005]
This has the problem that preparation of sample DNA takes time and cannot be applied to analysis of DNA samples that cannot be cloned, such as damaged DNA. Another problem is that the analysis is complicated.
In contrast, the Fluorescence in situ Hybridization method is a very effective method as a method for analyzing sequence information of a non-fragmented DNA sample, which requires few steps and does not require an operation for joining information. However, the conventional observation methods using a fluorescence microscope have a problem that the resolution is at most about 500 nm and the analysis can be performed only with a resolution of about 1.5 kbp.
[0006]
Genetic map analysis occupies a very important part in the genetic manipulation technique in that it specifies the target gene site. Therefore, development of a method for analyzing a genetic map quickly, efficiently and with high accuracy is strongly desired.
[0007]
[Means for Solving the Problems]
As a method for solving the problem of the Fluorescence in situ Hybridization method, in a method for determining the position of a specific gene sequence contained in a DNA strand to be measured, using a DNA strand to be measured and a probe molecule, at least DNA specific binding operation and fixation -Gene analysis method consisting of extension operation, detection operation with probe, and at least DNA fixation operation, specific binding operation, extension operation, gene analysis method consisting of detection operation with probe, and at least DNA fixation / extension operation Devised a genetic analysis method consisting of specific binding operation and probe detection, and used a near-field optical microscope probe, an atomic force microscope probe, or a tunnel microscope probe as the probe, and extended. By using the optical tweezers method, etc., the resolution and accuracy of the operation It was feasible the analysis of child array.
[0008]
DETAILED DESCRIPTION OF THE INVENTION
Hereinafter, embodiments of the present invention will be described with reference to the drawings.
1 to 3 show the basic procedure of the gene analysis method of the present invention. In FIG. 1, the DNA-specific binding operation (FIG. 1b) between the DNA strand 1 to be measured and the probe molecule 2 (FIG. 1B), the DNA to be measured The analysis procedure includes the operation of fixing the strand 1 to the substrate 3 (FIG. 1c), the operation of extending the DNA strand 1 to be measured (FIG. 1d), and the detection operation of the probe 4 (FIG. 1e). FIG. 2 shows an analysis procedure by a DNA fixing operation (FIG. 2b), a specific binding operation (FIG. 2c), an extension operation (FIG. 2d), and a detection operation by a probe (FIG. 2e). FIG. 3 shows an analysis procedure by a DNA fixing / extension operation operation (FIG. 3b), a specific binding operation (FIG. 3c), and a probe detection operation (FIG. 3d). These analysis procedures can be selected according to the technique used in each operation.
[0009]
The detection operation using the probe of this method makes it possible to analyze gene sequence information with high resolution. As the probe, a near-field optical microscope probe, an atomic force microscope probe, or a tunnel microscope probe can be used. With this probe, in addition to two-dimensional shape information, two-dimensional fluorescence information with a near-field optical microscope, electrolysis current with an electrochemical / atomic force microscope, surface potential with a surface potential / atomic force microscope, tunnel microscope Electron-excited luminescence due to can be detected, and the position of the probe molecule on the DNA strand to be measured can be identified by multidimensional information.
[0010]
As a DNA strand to be measured, a DNA strand of 1 kbp or more can be targeted by using this method. Moreover, the DNA strand in a chromosome can also be made into a measuring object. Furthermore, it is possible to analyze damaged DNA as it is. In addition, it can be applied to plasmids, artificial chromosomes (BAC, YAC, etc.), genes in cancer cells, and the like. In particular, it can be said that the ability to target one specific limited DNA and the ability to target DNA in individual cells is a great feature.
[0011]
As the probe molecule, a molecule that specifically binds to a corresponding sequence of DNA, such as RNA, cDNA, or oligonucleotide, can be used.
By labeling this probe molecule, complementary sequence information other than shape information can be obtained. A fluorescent substance, an enzyme, etc. can be used for this label | marker. Here, as the fluorescent substance, fluorescent proteins such as GFP (Green Fluorescence Protein) and cameleon (calcium indicator protein reagent) can be used. When a plurality of types of probe molecules are used, it is possible to identify each of the probe molecules by using a plurality of types according to that. Thereby, even when a plurality of probe molecules are bound on one DNA strand, each can be identified. In addition, by using an oxidoreductase as the enzyme, the enzyme reaction product can be detected and the position can be detected. In addition, an antibody can be used. When a gene transfer check is to be performed, a protein such as a transcription factor or a restriction enzyme that specifically binds to the promoter region can be used as a probe molecule. Furthermore, gold colloid can also be used as the labeling substance. In this case, the position can be detected from the shape image. On the other hand, the double-stranded portion can be specifically stained with a fluorescent substance that intercalates in the DNA strand.
[0012]
Next, as shown in FIG. 4, the entire DNA strand is adsorbed to the substrate surface as shown in FIG. 4, or the end (fixed end 5) of the DNA strand is bound as shown in FIG. You can make it. Alternatively, fixation can be performed by binding beads to one or both ends of the DNA strand and fixing the position of the beads. 6a shows an example in which beads 6 are fixed at both ends, and FIG. 6b shows an example in which beads are fixed at one end and the other end is fixed on a substrate.
[0013]
In the fixing operation, when the entire DNA strand is adsorbed, a substrate having a hydrophobic surface can be used. In the case of a hydrophilic substrate, the DNA strand can also be fixed by adsorbing a divalent cation such as magnesium ion. In addition, by chemically modifying the substrate surface, various functional groups can be bonded to increase the ability to adsorb DNA.
[0014]
When the ends of DNA strands are bound, they can be immobilized on a substrate having a gold thin film or particles by modifying a thiol group at the DNA ends. Further, it is also possible to use a substrate in which avidin is immobilized on a thin film or particles on the substrate and immobilize a DNA strand modified with biotin at its end. In addition, such a terminal modification of DNA can be processed by using terminal transferase.
[0015]
After immobilization of the DNA strand, if necessary, as a non-specific adsorption block operation, the probe has an affinity for the substrate, and the DNA to be measured and the probe molecule react with a molecule that does not exhibit specific binding properties. Molecules can be prevented from binding non-specifically on the substrate.
For the extension of the DNA strand, the movement of the meniscus as disclosed in JP-T 9-509057 can also be used. In this case, a water flow accompanying the evaporation of the DNA aqueous solution, a water flow of the DNA aqueous solution caused by tilting or suction, or a water flow generated by blowing a gas by a blower can be used. In addition, DNA can be stretched by applying an electric field utilizing the fact that DNA extends straight by applying an electric field. When beads are bound to one or both ends of the DNA strand, the DNA strand can be extended by moving the beads with optical tweezers.
[0016]
It can be extended by using a micromanipulator. FIG. 7 shows this example. A DNA strand is bound to the micromanipulator tip 7 (FIG. 7c), and then the micromanipulator tip is moved (FIG. 7d) to extend the DNA strand. be able to.
As DNA to be analyzed, chromosomes, artificial chromosomes, sperm, DNA constituting a part of pollen, and vectors are also analyzed. When a chromosome or the like is to be measured, a specific enzyme (such as trypsin) can be used to relax a part of the structure of the chromosome and extend the DNA chain. In addition, as for chromosomes, surfactants, ultrasonic waves, centrifugal force, acids (such as acetic acid), temperature rises, etc. can be used for structural relaxation and distraction operations.
[0017]
In the detection operation, it is also possible to detect the position of the DNA strand to be measured by scanning a certain region and the detection scanning procedure along the DNA strand, thereby enabling efficient measurement.
In the detection operation, the sample DNA can be taken up by using the micro-winding mechanism, and the probe can be relatively scanned on the DNA by the movement of the DNA strand by the winding. In FIG. 8, the DNA strand is fixed to the tip 8 of the winding mechanism (FIG. 8a), and the DNA strand can be moved by rotating the rotor 8 (FIG. 8b). In this case, the direction of the DNA strand can always be kept constant by applying an electric field or the like.
[0018]
In the case of FIGS. 8A and 8B, the rotation axis of the winding mechanism is parallel to the direction of the probe tip. However, as shown in FIGS. A configuration in which the rotation axes are orthogonal can also be employed. In this case, a detection operation is performed on the axis of the winding mechanism tip. In this case, since the DNA strand once wound up is fixed in a stretched state on the rotor portion, the detection operation can be repeatedly performed by rotating the rotor.
[0019]
Next, the gene analysis apparatus of the present invention will be described.
FIG. 9 shows an example of a gene analyzing apparatus in which a near-field optical microscope and an optical tweezer operating device are combined. In FIG. 9, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The light from the optical tweezer laser 33 passes through the objective lens 32 via the galvano mirror 34 and the dichroic mirror 35 and is collected on the beads in the sample cell. The galvanometer mirror can be arbitrarily controlled via the controller 36. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The probe 40 for an optical probe microscope is disposed in the sample cell 30 and the distance from the sample surface is controlled by the displacement detection means 41, the controller 42 and the moving mechanism 31. Light for fluorescence excitation is introduced into the probe 40 from the light source 43, and the sample is irradiated from the tip of the probe. The fluorescence from the sample is transmitted through the objective lens 32, the dichroic mirror 35, and the filter 44 for fluorescence detection. It is detected by the detector 45. By performing two-dimensional scanning of the moving mechanism 31 in the X and Y directions, a shape image and a fluorescence image of the sample surface can be acquired, and gene sequence information can be analyzed. By connecting a spectroscope and a high-sensitivity CCD camera to the portion of the light detector 45, the fluorescence wavelength can be analyzed and the difference between the fluorescently labeled molecules can be identified.
[0020]
In this embodiment, an AFM type optical probe is shown, but a shear force type using a straight type optical probe is also applicable.
FIG. 10 shows an example of a gene analyzing apparatus in which an atomic force microscope and an optical tweezer operating device are combined. In FIG. 10, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The light from the optical tweezer laser 33 passes through the objective lens 32 via the galvano mirror 34 and the dichroic mirror 35 and is collected on the beads in the sample cell. The galvanometer mirror can be arbitrarily controlled via the controller 36. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The atomic force microscope probe 50 is disposed in the sample cell 30, and the distance from the sample surface is controlled by the displacement detection means 41, the controller 42, and the moving mechanism 31. By performing two-dimensional scanning of the moving mechanism 31 in the XY directions, a shape image of the sample surface can be acquired and gene sequence information can be analyzed. In addition to the shape image, a label molecule can be detected by acquiring a surface potential image or the like.
[0021]
FIG. 11 shows an example of a gene analyzing apparatus in which a tunnel microscope and an optical tweezer operating device are combined. In FIG. 11, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The light from the optical tweezer laser 33 passes through the objective lens 32 via the galvano mirror 34 and the dichroic mirror 35 and is collected on the beads in the sample cell. The galvanometer mirror can be arbitrarily controlled via the controller 36. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The tunnel microscope probe 60 is disposed in the sample cell 30, and the distance from the sample surface is controlled by the displacement detection means 61, the controller 42, and the moving mechanism 31. By performing two-dimensional scanning of the moving mechanism 31 in the XY directions, a shape image of the sample surface can be acquired and gene sequence information can be analyzed. In addition, the labeling molecule can be identified by using electron energy loss spectroscopy.
[0022]
In the above apparatus configuration, an XY stage with a large stroke is further provided, and by moving within the sample surface, measurement of long DNA strands of several tens of microns or more can be supported. It is also possible to perform chain measurements on the same sample substrate.
Next, FIG. 12 shows an example of a gene analysis device that combines a near-field optical microscope and a micromanipulator operation device. In FIG. 12, a sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. A micromanipulator operation device 71 for performing the distraction operation is installed with the tip 7 inserted into the sample cell 30. The probe 40 for an optical probe microscope is disposed in the sample cell 30 and the distance from the sample surface is controlled by the displacement detection means 41, the controller 42 and the moving mechanism 31. Light for fluorescence excitation is introduced into the probe 40 from the light source 43, and the sample is irradiated from the tip of the probe. The fluorescence from the sample is transmitted through the objective lens 32, the dichroic mirror 35, and the filter 44 for fluorescence detection. It is detected by the detector 45. By performing two-dimensional scanning of the moving mechanism 31 in the X and Y directions, a shape image and a fluorescence image of the sample surface can be acquired, and gene sequence information can be analyzed. By connecting a spectroscope and a high-sensitivity CCD camera to the portion of the light detector 45, the fluorescence wavelength can be analyzed and the difference between the fluorescently labeled molecules can be identified.
[0023]
In this embodiment, an AFM type optical probe is shown, but a shear force type using a straight type optical probe is also applicable.
FIG. 13 shows an example of a gene analyzing apparatus in which an atomic force microscope and an optical tweezer operating device are combined. In FIG. 13, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. A micromanipulator operation device 71 for performing the distraction operation is installed with the tip 7 inserted into the sample cell 30. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The atomic force microscope probe 50 is disposed in the sample cell 30, and the distance from the sample surface is controlled by the displacement detection means 41, the controller 42, and the moving mechanism 31. By performing two-dimensional scanning of the moving mechanism 31 in the XY directions, a shape image of the sample surface can be acquired and gene sequence information can be analyzed. In addition to the shape image, a label molecule can be detected by acquiring a surface potential image or the like.
[0024]
FIG. 14 shows an example of a gene analyzing apparatus in which a tunnel microscope and an optical tweezer operating device are combined. In FIG. 14, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. A micromanipulator operation device 71 for performing the distraction operation is installed with the tip 7 inserted into the sample cell 30. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The tunnel microscope probe 60 is disposed in the sample cell 30, and the distance from the sample surface is controlled by the displacement detection means 61, the controller 42, and the moving mechanism 31. By performing two-dimensional scanning of the moving mechanism 31 in the XY directions, a shape image of the sample surface can be acquired and gene sequence information can be analyzed.
[0025]
In addition to the general micromanipulator operating device shown in the present embodiment, it is possible to produce a millimeter level micromanipulator by micromachine technology. In this case, the entire drive portion is inserted into the sample cell. Can also be used.
On the other hand, FIG. 15 shows an example of a gene analyzing apparatus that combines a near-field optical microscope and a micro-winding device. In FIG. 15, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The driving unit 81 and the rotor of the micro winding mechanism manufactured by the micromachine technique are inserted into the sample cell 30 and controlled by the controller 82. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. A micromanipulator operation device 71 for performing the distraction operation is installed with the tip 7 inserted into the sample cell 30. The probe 40 for an optical probe microscope is disposed in the sample cell 30 and the distance from the sample surface is controlled by the displacement detection means 41, the controller 42 and the moving mechanism 31. Light for fluorescence excitation is introduced into the probe 40 from the light source 43, and the sample is irradiated from the tip of the probe. The fluorescence from the sample is transmitted through the objective lens 32, the dichroic mirror 35, and the filter 44 for fluorescence detection. It is detected by the detector 45. By performing two-dimensional scanning of the moving mechanism 31 in the X and Y directions, a shape image and a fluorescence image of the sample surface can be acquired, and gene sequence information can be analyzed. By connecting a spectroscope and a high-sensitivity CCD camera to the portion of the light detector 45, the fluorescence wavelength can be analyzed and the difference between the fluorescently labeled molecules can be identified.
[0026]
In this embodiment, an AFM type optical probe is shown, but a shear force type using a straight type optical probe is also applicable.
FIG. 16 shows an example of a gene analyzing apparatus in which an atomic force microscope and a micro winding device are combined. In FIG. 16, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The driving unit 81 and the rotor of the micro winding mechanism manufactured by the micromachine technique are inserted into the sample cell 30 and controlled by the controller 82. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The atomic force microscope probe 50 is disposed in the sample cell 30, and the distance from the sample surface is controlled by the displacement detection means 41, the controller 42, and the moving mechanism 31. By performing two-dimensional scanning of the moving mechanism 31 in the XY directions, a shape image of the sample surface can be acquired and gene sequence information can be analyzed. In addition to the shape image, a label molecule can be detected by acquiring a surface potential image or the like.
[0027]
FIG. 17 shows an example of a gene analyzing apparatus in which a tunnel microscope and a micro winding device are combined. In FIG. 17, the sample cell 30 is held by a moving mechanism 31 that can be displaced in the XYZ directions, and an objective lens 32 is disposed below the moving mechanism 31. The driving unit 81 and the rotor of the micro winding mechanism manufactured by the micromachine technique are inserted into the sample cell 30 and controlled by the controller 82. The state of the sample can be observed through the switchable mirror 37, for example, through an eyepiece lens 38, or by a CCD camera. The tunnel microscope probe 60 is disposed in the sample cell 30, and the distance from the sample surface is controlled by the displacement detection means 61, the controller 42, and the moving mechanism 31. By performing two-dimensional scanning of the moving mechanism 31 in the XY directions, a shape image of the sample surface can be acquired and gene sequence information can be analyzed.
[0028]
The rotor used in this apparatus can be made of a transparent material such as glass so that it can be easily observed under a microscope.
[0029]
【The invention's effect】
The gene analysis method and apparatus of the present invention makes it possible to analyze a genetic map at a much faster and practical resolution than the sequencing method, and far exceeds the limit of 1 kbp that can be analyzed at a time by the sequencing method. It is also possible to analyze a DNA strand having a size exceeding 100 mm. According to the method of the present invention, it is possible to improve the measurement accuracy by performing shape measurement in addition to the improvement of the resolution even in the conventional FISH method. Furthermore, it has become possible to analyze DNA damage that could not be applied by the conventional sequencing method.
[Brief description of the drawings]
FIG. 1 is an explanatory diagram showing a gene analysis method of the present invention.
FIG. 2 is an explanatory diagram showing a gene analysis method of the present invention.
FIG. 3 is an explanatory diagram showing the gene analysis method of the present invention.
FIG. 4 is an explanatory view showing a fixing operation in the present invention.
FIG. 5 is an explanatory view showing a fixing operation in the present invention.
FIG. 6 is an explanatory view showing a fixing operation in the present invention.
FIG. 7 is an explanatory view showing a distraction operation in the present invention.
FIG. 8 is an explanatory view showing a distraction operation in the present invention.
FIG. 9 is a schematic view showing a gene analyzing apparatus of the present invention.
FIG. 10 is a schematic diagram showing a gene analyzing apparatus of the present invention.
FIG. 11 is a schematic diagram showing a gene analyzing apparatus of the present invention.
FIG. 12 is a schematic diagram showing a gene analyzing apparatus of the present invention.
FIG. 13 is a schematic diagram showing a gene analyzing apparatus of the present invention.
FIG. 14 is a schematic diagram showing a gene analysis apparatus of the present invention.
FIG. 15 is a schematic diagram showing a gene analyzing apparatus of the present invention.
FIG. 16 is a schematic diagram showing a gene analyzing apparatus of the present invention.
FIG. 17 is a schematic diagram showing a gene analysis apparatus of the present invention.
[Explanation of symbols]
DESCRIPTION OF SYMBOLS 1 DNA strand 2 Probe molecule 3 Substrate 4 Probe 5 DNA fixed end 6 Bead 7 Micromanipulator tip 8 Winding mechanism tip 30 Sample cell 31 Moving mechanism 32 Objective lens 33 Laser for optical tweezer 34 Galvano mirror 35 Dichroic mirror 36 Controller 37 Mirror 38 Eyepiece 40 Optical probe microscope probe 41 Displacement detection means 42 Controller 43 Light source 44 Fluorescence detection filter 45 Photo detector 50 Atomic force microscope probe 60 Tunnel microscope probe 61 Displacement detection means 71 Micromanipulator operation device 81 Micro winding mechanism drive unit 82 Controller

Claims (7)

In a gene analysis apparatus for determining the position of a specific gene sequence contained in the DNA strand using a DNA strand that specifically binds a probe molecule,
A sample cell capable of accommodating the DNA strand;
A light source that generates light for excitation;
An optical probe disposed in the sample cell;
A moving mechanism that holds the sample cell and can be displaced in a three-dimensional direction;
Displacement detecting means for detecting the distance between the tip of the optical probe and the surface of the DNA strand;
A controller for a moving mechanism that controls the distance between the tip of the optical probe and the surface of the DNA strand by controlling the moving mechanism;
A micro-winding mechanism having a rotatable rotor inserted into the sample cell and capable of winding the DNA strand stretched by application of an electric field;
A rotor controller for controlling rotation of the rotor;
Light from the light source is introduced into the tip of the optical probe, the DNA strand is irradiated with light from the tip of the optical probe, and fluorescence from the DNA strand is converted into an objective lens, a dichroic mirror, and a fluorescence detection filter. A photodetector to detect via,
A gene analyzing apparatus comprising: In a gene analysis apparatus for determining the position of a specific gene sequence contained in the DNA strand using a DNA strand that specifically binds a probe molecule,
A sample cell capable of accommodating the DNA strand;
An atomic force microscope probe disposed in the sample cell;
A moving mechanism that holds the sample cell and can be displaced in a three-dimensional direction;
A displacement detecting means for detecting a distance between the tip of the atomic force microscope probe and the surface of the DNA strand;
A controller for a moving mechanism that controls the distance between the tip of the atomic force microscope probe and the surface of the DNA strand by controlling the moving mechanism;
A micro-winding mechanism having a rotatable rotor inserted into the sample cell and capable of winding the DNA strand stretched by application of an electric field;
A rotor controller for controlling rotation of the rotor;
A gene analyzing apparatus comprising: In a gene analysis apparatus for determining the position of a specific gene sequence contained in the DNA strand using a DNA strand that specifically binds a probe molecule,
A sample cell capable of accommodating the DNA strand;
A tunneling microscope probe disposed in the sample cell;
A moving mechanism that holds the sample cell and can be displaced in a three-dimensional direction;
A displacement detecting means for detecting the distance between the tip of the tunnel microscope probe and the surface of the DNA strand, and detecting a shape image of the surface of the DNA strand by two-dimensional scanning of the moving mechanism;
A controller for a moving mechanism that controls the distance between the tip of the tunnel microscope probe and the surface of the DNA strand by controlling the moving mechanism;
A micro-winding mechanism having a rotatable rotor inserted into the sample cell and capable of winding the DNA strand stretched by application of an electric field;
A rotor controller for controlling rotation of the rotor;
A gene analyzing apparatus comprising: A specific binding operation for specifically binding a probe molecule to a DNA strand; a fixing operation for fixing the DNA strand specifically bound to the probe molecule; an extension operation for extending the DNA strand fixed by the fixing operation; In a detection operation for detecting the DNA strand extended by the extension operation by scanning a probe of a scanning probe microscope, and a gene analysis method for obtaining the position of a specific gene sequence contained in the DNA strand,
In the fixing operation, the DNA strand specifically bound to the probe molecule is fixed on the rotor of a micro winding mechanism having a rotatable rotor,
The gene stretching method is characterized by extending the DNA strand fixed on the rotor by applying an electric field, rotating the rotor, and winding the stretched DNA strand onto the rotor. The detection operation is characterized in that the DNA strand extended in the extension operation is wound on the rotor, and the probe relatively scans the DNA strand by movement of the DNA strand by winding. The gene analysis method according to claim 4. In the fixing operation, a thiol group is modified at the end of the DNA chain to which the probe molecule is specifically bound, and a gold thin film or gold fine particle is fixed on the rotor, and the thiol group and the gold thin film or the gold fine particle The gene analysis method according to claim 4 or 5, wherein the gene is fixed by binding. The immobilization operation is characterized in that biotin is modified at the end of the DNA strand to which the probe molecule is specifically bound, avidin is immobilized on the rotor, and immobilization is performed by binding the biotin and the avidin. The gene analysis method according to claim 4 or 5.

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