WO2016136952A1 - 核酸分子の構築方法 - Google Patents
核酸分子の構築方法 Download PDFInfo
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- WO2016136952A1 WO2016136952A1 PCT/JP2016/055850 JP2016055850W WO2016136952A1 WO 2016136952 A1 WO2016136952 A1 WO 2016136952A1 JP 2016055850 W JP2016055850 W JP 2016055850W WO 2016136952 A1 WO2016136952 A1 WO 2016136952A1
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
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- C12P19/00—Preparation of compounds containing saccharide radicals
- C12P19/26—Preparation of nitrogen-containing carbohydrates
- C12P19/28—N-glycosides
- C12P19/30—Nucleotides
- C12P19/34—Polynucleotides, e.g. nucleic acids, oligoribonucleotides
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
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- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/483—Physical analysis of biological material
- G01N33/487—Physical analysis of biological material of liquid biological material
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- G01N33/48721—Investigating individual macromolecules, e.g. by translocation through nanopores
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- C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
- C12Q2525/30—Oligonucleotides characterised by their secondary structure
- C12Q2525/301—Hairpin oligonucleotides
Definitions
- the present invention relates to a method for constructing a nucleic acid molecule for nucleic acid sequencing. More specifically, the present invention relates to a method for constructing a single-stranded nucleic acid molecule suitable for analysis by nanopore sequencing.
- Nucleic acid base sequence analysis has become very popular in recent years for the purpose of detecting genes causing genetic diseases, evaluating drug efficacy and side effects, and detecting gene mutations related to cancer diseases, etc. Yes.
- the information obtained as a result of the analysis must therefore be highly accurate.
- Patent Document 1 states that “the circular configuration of the template enables multiple repeated sequencing of the same molecule.
- the sequencing method proceeds along a completely continuous sequence, and each sequence from a complementary sequence is By repeatedly sequencing a segment, the sequence data of this segment and the sequence data within each segment can be repeatedly acquired, all or part of such sequence data is then obtained from the consensus sequence of the template and its various segments. It is useful for inducing "(paragraph number [0055]).
- Patent Document 2 discloses an adapter that contains a double-stranded nucleic acid region and can be used to create a single-stranded construct of nucleic acid for sequencing purposes.
- Patent document 2 states that “when constructs are sequenced, it is ensured that each position in the double-stranded nucleic acid is actually examined twice, not just once. This gives greater certainty in examining each position of the nucleic acid, and the overall score with a higher score for both bases at each position than would be possible with a single examination. (Paragraph number [0038]) Further, the ability to examine each position twice is also useful for distinguishing methylcytosine and thymine using probabilistic sensing.
- Patent Document 1 is a molecule in which one end of a double-stranded nucleic acid is connected by a hairpin loop, or a circular molecule in which both ends are connected by a hairpin loop.
- the molecule connected at one end improves the base determination accuracy using two results obtained by reading the sequences of the complementary strands (sense strand and antisense strand) once.
- this method can be used to detect the result between the complementary strand sequences when each nucleic acid strand has a mutation such as a mismatched base pair, or when a sequence error occurs and the complementary strand sequence is read once. Will cause a difference.
- Patent Document 2 a molecule in which one end of a double-stranded nucleic acid is connected by a hairpin loop. Similarly, by examining each complementary strand once, whether a mutation exists or a sequence error has occurred is determined. There is a problem that cannot be done. Furthermore, since a ligation reaction or the like is performed for hairpin loop formation, the construction efficiency of a nucleic acid molecule to which a hairpin loop is correctly bound is low. Although it is possible to carry out the reaction overnight (for example, 8 hours or more) in order to increase the efficiency, there is also a problem that pretreatment takes time.
- the present inventors examined a method for constructing a nucleic acid molecule having a sequence structure in which only one target base sequence is repeated in a single-stranded nucleic acid (single molecule), The present invention has been completed.
- the single-stranded structure enables analysis by nanopore sequencing, and the sequence of only the target nucleic acid that does not contain complementary strand information is repeatedly analyzed, thus addressing the problem of sequence errors and increasing accuracy. High analysis can be performed. The greater the number of times the sequence is repeated in the molecule, the better the determination accuracy.
- the present invention includes the following.
- [1] A method for constructing a single-stranded nucleic acid molecule for nucleic acid sequencing by a nanopore sequencer, Synthesizing a complementary strand of a template DNA containing a target sequence using at least one hairpin primer containing a single-stranded region on the 3 ′ side and a primer paired with the hairpin primer; The synthesized complementary strand forms a hairpin structure in the molecule and performs an extension reaction using itself as a template, and the resulting nucleic acid molecule contains both the target sequence and its complementary strand in the sequence.
- the above method A method for constructing a single-stranded nucleic acid molecule for nucleic acid sequencing by a nanopore sequencer, Synthesizing a complementary strand of a template DNA containing a target sequence using at least one hairpin primer containing a single-stranded region on the 3 ′ side and a primer paired with the hairpin primer; The synthesized complementary strand forms
- the nucleic acid molecule construction method of the present invention has the following effects.
- the target sequence is not examined only once, but the target sequence is linked to a complementary strand sequence synthesized using the sequence itself as a template. It is examined multiple times with a single-stranded nucleic acid (single molecule).
- This enables highly accurate analysis in examining the target sequence of nucleic acid. More specifically, it is possible to recognize whether there is a base difference due to a mutation or a base error due to a sequence error by repeatedly examining a single molecule synthesized using only a single-strand sequence without any complementary strand sequence information in the genome structure. It is possible to perform nucleic acid sequence analysis with high accuracy.
- the high determination accuracy of the base sequence of a single molecule makes it possible to detect abnormal cell-derived mutations that are slightly contained in a large amount of normal cell-derived genomic DNA. For example, if you want to detect DNA with cancer cell-derived mutations that are slightly contained in blood, the DNA is extracted from a certain amount of blood, and the nucleic acid molecule that contains the base sequence you want to detect is extracted using the polymerase chain reaction (PCR) method. Etc. and determine whether or not the mutation is included by determining the base sequence of the nucleic acid molecule (Couraud S.Clin Cancer Res. 2014 Sep 1; 20 (17): 4613-24. ).
- PCR polymerase chain reaction
- the final determination of a single molecule can be performed, for example, by repeatedly examining within a single molecule using only a single-stranded sequence as a template.
- the accuracy is 99.9%, it is possible to detect a slightly contained mutant DNA.
- the final determination accuracy is 99.9%, if 1,000 single molecule DNAs are detected, the frequency of occurrence of bases that differs from the main determination at the site with no mutation and the site with the mutation is 1 and 11, and this frequency difference is Since it is greatly different, it is easy to detect the presence or absence of mutation with the difference in appearance frequency. Detecting such slight mutations also means early detection of disease.
- the method of the present invention performs a polymerase chain reaction using a hairpin primer, for example, a nucleic acid molecule having a hairpin structure can be constructed with higher efficiency than in the case of linking hairpin structures by ligation. it can. Note that the probability of error in the process of repeating amplification is much lower than that of a sequence error. Therefore, it can be said that the accuracy of the analysis method using the method of the present invention is much higher than that of the conventional method.
- nucleic acid molecule construction process in the method of this invention. It is an example which shows the nucleic acid molecule construction process in the method of this invention. It is an example which shows the nucleic acid molecule construction process in the method of this invention. It is an example which shows the nucleic acid molecule construction process in the method of this invention. It is the result of comparing target sequences.
- the present invention relates to a method for constructing a nucleic acid molecule for nucleic acid sequencing by a nanopore sequencer. More specifically, the present invention relates to a method for constructing a single-stranded nucleic acid molecule for nucleic acid sequencing by a nanopore sequencer, comprising at least one hairpin primer containing a single-stranded region on the 3 ′ side, and the hairpin A step of synthesizing a complementary strand of a template DNA containing a target sequence using a primer paired with a primer, and the synthesized complementary strand forms a hairpin structure in the molecule and performs an extension reaction using itself as a template. And the obtained nucleic acid molecule contains both the target sequence and its complementary strand in the sequence.
- the “target sequence” means only the sequence of one strand in the case of a double-stranded nucleic acid molecule throughout the description of the present specification.
- the complementary strand of “target sequence” is not described as “target sequence”.
- the complementary strand may be expressed as “target sequence” or “target sequence information”.
- the nanopore sequencer is a known technique, and for example, an apparatus described in WO2013 / 02181518A1 can be used preferably.
- a nanopore sequencer that detects a Raman spectrum is shown as an example, but it can be applied to all techniques for analyzing single-stranded single molecules.
- it is a nucleic acid molecule construction method applicable to a DNA sequencer that detects a blocking current or a tunnel current when passing through a nanopore or a nanopore DNA sequencer that detects fluorescence.
- the apparatus configuration is not particularly limited to the basic configuration of an upright microscope, and may be a configuration that enables signal detection of a sample by irradiation light, such as a microscope based on an inverted microscope.
- the light source emits external light (excitation light) having a wavelength capable of generating fluorescence or Raman scattered light.
- a light source 101 known in the art can be used.
- a semiconductor laser a krypton (Kr) ion laser, a neodymium (Nd) laser, an argon (Ar) ion laser, a YAG laser, a nitrogen laser, a sapphire laser, or the like can be used.
- a multiple irradiation mechanism 113 When irradiating a plurality of nanopores with external light from this light source, a multiple irradiation mechanism 113 is used.
- the multiple irradiation mechanism 113 is not limited, but a microlens array, a diffraction grating beam splitter, LCOS (Liquid crystal on silicon), or the like may be used. These are used to irradiate the nanopore with a plurality of external lights.
- a confocal lens and objective lens 102 in combination with a light source in order to irradiate and converge external light from the light source onto the microscope observation container.
- the microscope observation container 103 is installed on the XY stage 104, and the position on the horizontal plane is adjusted by the XY stage.
- the vertical position is adjusted by the Z-axis adjustment mechanism 105 so that the sample to be measured is located in the region condensed by the objective lens.
- the Z-axis adjusting mechanism may be provided on the XY stage.
- a ⁇ axis stage and a gonio stage may be used for precise adjustment. These positioning means are controlled by the drive control unit 115 and operated by the user by the computer 116.
- a filter 106 such as a notch filter, a short pass filter, a long pass filter, etc., a beam splitter 107, a diffraction grating 108, and the like corresponding to a measurement target such as a measurement wavelength region may be combined.
- a mirror 112, a pinhole, a lens 114, and an NIR (near infrared) mirror 117 may be used as required for the arrangement of optical components.
- an apparatus configuration for detecting fluorescence or Raman scattered light is known in the art, and those skilled in the art can appropriately select preferable components.
- any spectroscopic detector can be used as long as it is a detector 109 that can detect fluorescence or Raman scattered light.
- One or more one-dimensional or two-dimensional detectors can be used depending on the number and arrangement of samples in the microscope observation container to be used.
- spectral detectors include CCD (Charge Coupled Device) or Electron Multiplying CCD image sensors, CMOS (Complementary Metal Oxide Semiconductor) image sensors, image sensors of other high-sensitivity devices (such as avalanche photodiodes), etc.
- the detector preferably has a photomultiplier mechanism, for example, an image intensifier, in order to prevent a decrease in sensitivity due to an increase in detection speed.
- the detector preferably includes a large-capacity memory that can directly record image information such as Raman scattered light, whereby analysis can be performed at high speed without using a cable, a board, a computer, or the like.
- the analysis apparatus of the present invention may further include a frame buffer memory that records measurement values from the detector.
- the analysis apparatus of the present invention may be connected to a computer 116 for digitizing, calculating, and outputting the measurement value from the detector.
- an LED 110 is used as a bright-field illumination light source
- a two-dimensional detector 111 is used as a bright-field imaging device.
- the two-dimensional detector include a CCD or EMCCD image sensor and a CMOS image sensor.
- FIG. 2 shows a cross-sectional configuration of a nanopore substrate and an observation container in which the nanopore substrate is arranged.
- the observation container 201 is composed of two closed spaces, that is, a sample introduction section 204 and a sample outflow section 205 with a substrate 203 (nanopore substrate) having nanopores 202 therebetween.
- the sample introduction section 204 and the sample outflow section 205 communicate with each other through the nanopore 202.
- a molecule is put after constructing a nucleic acid molecule that is constructed by the method of the present invention described later and repeatedly contains a target sequence.
- the nucleic acid molecule may be constructed directly in the observation container.
- the observation container has a chamber part and a substrate 203 disposed therein.
- the substrate 203 includes a base, a thin film formed facing the base, and a nanopore 202 that is provided in the thin film and communicates the sample (nucleic acid molecule) introduction section 204 and the sample outflow section 205. Between the sample introduction section 204 and the sample outflow section 205.
- the substrate 203 may have an insulating layer.
- the substrate 203 is preferably a solid substrate.
- the substrate 203 can be formed of an electrical insulator material such as an inorganic material and an organic material (including a polymer material).
- the electrical insulator material constituting the substrate 203 include silicon (silicon), silicon compound, glass, quartz, polydimethylsiloxane (PDMS), polytetrafluoroethylene (PTFE), polystyrene, and polypropylene.
- the silicon compound include silicon oxynitride such as silicon nitride, silicon oxide, and silicon carbide.
- the base (base material) constituting the support portion of the substrate 203 can be made from any of these materials, but may be, for example, silicon or a silicon compound.
- the size and thickness of the substrate 203 are not particularly limited as long as the nanopore 202 can be provided.
- the substrate 203 can be manufactured by a method known in the art, or can be obtained as a commercial product.
- the substrate 203 may be formed using photolithography or electron beam lithography and techniques such as etching, laser ablation, injection molding, casting, molecular beam epitaxy, chemical vapor deposition (CVD), dielectric breakdown, electron beam or focused ion beam. Can be produced.
- the substrate 203 may be coated to avoid adsorption of off-target molecules to the surface.
- the substrate 203 has at least one nanopore 202.
- the nanopore 202 is specifically provided in the thin film, but may be provided in the base (base material) and the insulator simultaneously.
- nanopore and pore are pores having a nanometer (nm) size (that is, a diameter of 1 nm or more and less than 1 ⁇ m), penetrate the substrate 203 and have a sample introduction section 204 and a sample outflow section 205. Is a hole communicating with the.
- the substrate 203 preferably has a thin film for providing the nanopore 202. That is, the nanopore 202 can be provided on the substrate 203 simply and efficiently by forming a thin film having a material and thickness suitable for forming nano-sized holes on the substrate.
- the material of the thin film is preferably silicon oxide (SiO 2 ), silicon nitride (SiN), silicon oxynitride (SiON), metal oxide, metal silicate, or the like.
- the thin film (and possibly the entire substrate) may be substantially transparent.
- substantially transparent means that external light can be transmitted through approximately 50% or more, preferably 80% or more.
- the thin film may be a single layer or a multilayer.
- the thickness of the thin film is 1 nm to 200 nm, preferably 1 nm to 50 nm, more preferably 1 nm to 20 nm.
- the thin film can be formed on the substrate 203 by techniques known in the art, for example, by low pressure chemical vapor deposition (LPCVD).
- LPCVD low pressure chemical vapor deposition
- the thickness of the insulating layer is preferably 5 nm to 50 nm.
- any insulating material can be used for the insulating layer, for example, silicon or a silicon compound (silicon nitride, silicon oxide, etc.) is preferably used.
- the “opening” of the nanopore or the pore refers to the opening circle of the nanopore or the pore where the nanopore or the pore contacts the sample solution. In the analysis of the biopolymer, biopolymers, ions, and the like in the sample solution enter the nanopore from one opening and go out of the nanopore from the same or opposite opening.
- the size of the nanopore 202 can be selected according to the type of biopolymer to be analyzed.
- the nanopore may have a uniform diameter, but may have a different diameter depending on the site.
- the nanopore may be connected to a pore having a diameter of 1 ⁇ m or more.
- the nanopore provided in the thin film of the substrate 203 has a minimum diameter portion, that is, the smallest diameter of the nanopore has a diameter of 100 nm or less, for example, 1 nm to 100 nm, preferably 1 nm to 50 nm, for example 1 nm to 10 nm, specifically 1 nm. It is preferably 5 nm or less, 3 nm or more and 5 nm or less.
- the diameter of ssDNA is about 1.5 nm, and an appropriate range of the nanopore diameter for analyzing ssDNA is about 1.5 to 10 nm, preferably about 1.5 to 2.5 nm.
- the diameter of dsDNA double-stranded DNA
- an appropriate range of the nanopore diameter for analyzing dsDNA is about 3 nm to 10 nm, preferably about 3 nm to 5 nm.
- the nanopore diameter corresponding to the outer diameter of the biopolymer can be selected.
- the depth (length) of the nanopore 202 can be adjusted by adjusting the thickness of the substrate 203 or the thin film of the substrate 203.
- the depth of the nanopore 202 is preferably a monomer unit constituting the biopolymer to be analyzed.
- the depth of the nanopore 202 is preferably a size of one base or less, for example, about 0.3 nm or less.
- the shape of the nanopore 202 is basically circular, but may be elliptical or polygonal.
- At least one nanopore 202 can be provided on the substrate 203, and when a plurality of nanopores 202 are provided, they may be regularly arranged.
- the nanopore 202 can be formed by a method known in the art, for example, by irradiating an electron beam of a transmission electron microscope (TEM) and using a nanolithography technique or an ion beam lithography technique.
- TEM transmission electron microscope
- the chamber section includes a sample introduction section 204 and a sample outflow section 205, a substrate 203, a voltage applying means, and electrodes 213 and 214 for allowing the sample 212 to pass through the nanopore 202.
- the chamber section includes a sample introduction section 204 and a sample outflow section 205, a first electrode 213 provided in the sample introduction section 204, a second electrode 214 provided in the sample outflow section 205, first and second. Voltage application means for the other electrodes.
- An ammeter may be disposed between the first electrode 213 provided in the sample introduction section 204 and the second electrode 214 provided in the sample outflow section 205.
- the current between the first electrode 213 and the second electrode 214 may be appropriately determined in terms of determining the nanopore passage speed of the sample 212.
- an ionic liquid not including the sample 212 is used, If there is, it is preferably about 100 mV to 300 mV, but is not limited thereto.
- the electrodes 213 and 214 are made of metal, for example, platinum group such as platinum, palladium, rhodium, and ruthenium, gold, silver, copper, aluminum, nickel, etc .; graphite, for example, graphene (which may be either a single layer or multiple layers), tungsten, It can be made from tantalum or the like.
- a conductive thin film 215 may be prepared near the nanopore to generate a near field and enhance it.
- the conductive thin film 215 placed in the vicinity of the nanopore is formed in a planar shape as is apparent from the definition of the thin film.
- the thickness of the conductive thin film 215 is 0.1 nm to 10 nm, preferably 0.1 nm to 7 nm, depending on the material used. As the thickness of the conductive thin film 215 is smaller, the generated near field can be limited, and analysis with high resolution and high sensitivity becomes possible.
- the size of the conductive thin film 215 is not particularly limited, and can be appropriately selected according to the size of the solid substrate 203 and nanopore 202 to be used, the wavelength of excitation light to be used, and the like. If the conductive thin film 215 is not flat and has a bend or the like, a near field is induced at the bend and light energy leaks, and Raman scattered light is generated at a location outside the target. That is, background light increases and S / N decreases. Therefore, the conductive thin film 215 is preferably planar, in other words, the cross-sectional shape is preferably linear without bending. Forming the conductive thin film 215 in a planar shape is not only effective in reducing the background light and increasing the S / N ratio, but is also preferable from the viewpoint of uniformity of the thin film and reproducibility in production.
- the sample introduction section 204 and the sample outflow section 205 are filled with liquids 210 and 211 introduced via inflow paths 206 and 207 connected to both sections, respectively.
- the liquids 210 and 211 flow out from the outflow paths 208 and 209 connected to the sample introduction section 204 and the sample outflow section 205.
- the inflow paths 206 and 207 may be provided at positions facing each other with the substrate interposed therebetween, but the present invention is not limited to this.
- the outflow paths 208 and 209 may be provided at positions facing each other across the substrate, but are not limited thereto.
- the liquid 210 is preferably a sample solution containing a sample 212 to be analyzed.
- the liquid 210 preferably contains a large amount of ions that play a charge (hereinafter referred to as ionic liquid).
- the liquid 210 preferably contains only an ionic liquid other than the sample.
- an aqueous solution in which an electrolyte having a high degree of ionization is dissolved is preferable, and a salt solution such as an aqueous potassium chloride solution can be suitably used.
- the sample 212 has a charge in the ionic liquid.
- Sample 212 is typically a nucleic acid molecule.
- the sample introduction section 204 and the sample outflow section 205 are provided with electrodes 213 and 214 arranged to face each other with the nanopore 202 in between.
- the chamber unit also includes voltage applying means for the electrodes 213 and 214. By applying the voltage, the charged sample 212 passes from the sample introduction section 204 through the nanopore 202 and moves to the sample outflow section 205.
- the Raman scattering spectrum enhanced by the conductive thin film 215 is effectively collected by the immersion medium 216, and the Raman light is collected through the objective lens 217. To be analyzed.
- the upper part is a sample introduction section and the lower part is a sample outflow section, but the lower part may be a sample introduction section and the upper part may be a sample outflow section, and a sample passing through the nanopore may be detected.
- FIG. 3 shows an embodiment of the method of the present invention.
- One feature of the method for constructing a nucleic acid molecule of the present invention is that a target sequence of a target nucleic acid is amplified, and the target sequence is repeated and constructed in a single strand (single molecule).
- At least one of the prepared primer pairs is a primer 300 having a hairpin structure.
- the 3 ′ end side of the primer 300 is a primer sequence structure of a single-stranded region having a sequence complementary to the sequence of the template DNA containing the target sequence, and has a structure protruding from the stem portion.
- the primer 300 for amplification of the target sequence is a hairpin primer
- the primer 303 for amplification of the complementary strand of the target sequence may be a hairpin primer or may be a primer having no hairpin structure.
- the primer 303 can be used for amplification of the target sequence
- the hairpin primer 300 can be used for amplification of the complementary strand of the target sequence.
- any of the above-described aspects can be used in the method of the present invention for analyzing any one of the double-stranded nucleic acids as a target sequence, depending on the embodiment.
- the primer 303 in comparison with the hairpin primer 300, is described as a “paired primer” in this specification.
- DNA derived from a sample containing the target sequence itself can be used as it is, but the template DNA should contain a sequence capable of forming a completely complementary strand with the hairpin primer so that it can be suitably used by the method of the present invention.
- the target sequence can also be linked to the synthesized sequence.
- Primers having a hairpin structure having a loop portion and a stem portion are known, and examples of sequences thereof include, for example, IANAzarenko .et al. 2516-2521 Nucleic Acids Research, 1997, Vol. 25, No. 12 The example of arrangement
- a person skilled in the art can appropriately design and prepare a hairpin primer suitable for amplification once the template DNA to be amplified including the target sequence is identified.
- the primer 300 having a hairpin structure is denatured and annealed to the target sequence of the target nucleic acid (for example, human genome).
- the target nucleic acid for example, human genome
- a solution containing a target nucleic acid as a mixture of reaction solutions, a primer set sandwiching a target sequence (one or both sides being the above-described hairpin primer 300), polymerase Prepare a salt composition solution according to the polymerase.
- the DNA polymerase to be used is not limited.
- a polymerase isolated from a thermophilic bacterium represented by Taq DNA polymerase which is classified into family A (PolI type), or a super-preferred typified by KOD DNA polymerase.
- Polymerases isolated from heat archaea and those classified as family B ( ⁇ type) can be used.
- Bst DNA polymerase Bca (exo-) DNA polymerase, Klenow fragment of DNA polymerase I, ⁇ 29 phage DNA polymerase, Vent DNA polymerase, Vent (Exo- ) DNA polymerase (Vent ⁇ DNA polymerase excluding exonuclease activity), DeepVentDNA polymerase, DeepVent (Exo-) DNA polymerase (DeepVent DNA polymer excluding exonuclease activity), MS-2 phage DNA polymerase, Z- Taq DNA polymerase (manufactured by Takara Bio Inc.) and the like are generally known and can be suitably used.
- DNA polymerase mutants While having the catalytic activity required by the above-mentioned DNA polymerase, use only a part of the structure and other functions, or various mutants whose catalytic activity, stability, or heat resistance has been modified by amino acid mutation, etc. May be. As long as various DNA polymerase mutants have sequence-dependent complementary strand synthesis activity, strand displacement activity, and the like, they can be used in the present invention and are not limited to the above examples.
- the method of the present invention is a technique for increasing the reading accuracy of a sequencer by reading a sequence made by synthesis a plurality of times, a polymerase with high synthesis accuracy is preferable.
- a polymerase with high synthesis accuracy is preferable.
- the synthesis accuracy of PrimeSTAR (registered trademark) Max, PrimeSTAR (registered trademark) HS, etc. (manufactured by Takara Bio Inc.) with high synthesis accuracy is 99.995% or more. These have sufficient accuracy to detect 1-0.1% mutations so that a synthesis error at the amplification stage does not affect mutation detection.
- step (2) of FIG. 3 the mixture of (1) is heated to an appropriate denaturation temperature, each primer is annealed to the target nucleic acid, and an extension reaction is performed (step (3)).
- the extended double-stranded amplification product is dissociated under denaturing conditions, and then annealed again to each primer to be extended. This process is repeated.
- the loop part of the hairpin primer is also included in the extended double-stranded amplification product by forming a base pair (step (4)).
- a single-stranded nucleic acid having a hairpin structure can be formed by intramolecular annealing. This reaction competes with a reaction for forming a new complementary strand by intermolecular annealing with the unreacted hairpin primer 300.
- a complementary strand sequence portion 301 stem that forms a hairpin structure at the 3 ′ end is used.
- the annealing of part occurs preferentially over the annealing with the unreacted hairpin primer 300.
- the complementary strand arrangement part 301 (stem part) is given priority by designing it to be lower than the Tm value of 301 (stem part) and giving a temperature gradient so as to lower the temperature from the denaturation process to the annealing and extension process.
- the stem part of the hairpin primer has a Tm value higher than that of the single-stranded part.
- Tm melting temperature
- the complementary strand sequence part 301 when designing a sequence in which the Tm value of the single-stranded part of the hairpin primer is 60 ° C., if the Tm value of the stem part is set to 70 ° C., the complementary strand sequence part 301 will preferentially anneal and repeat the target sequence. It becomes possible to preferentially obtain a single-stranded nucleic acid having a hairpin structure.
- the state of double-stranded DNA changes at a Tm value of ⁇ 5 ° C.
- the difference in Tm value between the single chain portion and the stem portion may be set to 15 ° C. or more.
- the temperature difference may be 15 ° C. or less, more preferably about 10 ° C. Therefore, as one embodiment of the method of the present invention, the stem part of the hairpin primer 300 has a Tm value that is 5 ° C. or more, 10 ° C. or more, or 15 ° C. or more higher than the Tm value of the single-stranded part of the hairpin primer 300.
- the stem portion of the hairpin primer 300 is about 5 ° C., about 6 ° C., about 7 ° C., about 8 ° C., about 9 ° C., about 10 ° C., about 11 ° C. than the Tm value of the single-stranded portion of the hairpin primer 300. , About 12 ° C, about 13 ° C, about 14 ° C, about 15 ° C.
- betaine N, N, N-trimethylglycine
- betaine N, N, N-trimethylglycine
- it is possible to change the state of double-stranded DNA in a narrower temperature range (William A. Rees et al. Biochemistry 1993, 32,137-144), may be added to the reaction solution.
- the Tm value or the state of double-stranded DNA at each temperature varies depending on conditions such as pH and salt concentration, and also depends on the base sequence and length. It can be calculated based on the length of the sequence and the GC content. A person skilled in the art can appropriately set the Tm value of each part in the primer design, design and produce an optimal primer, and design the reaction temperature as appropriate.
- the concentration of the hairpin primer 300 decreases as the reaction cycle proceeds without performing the above-described steps, the primer 300 is depleted, so that the complementary strand arrangement unit 301 is preferentially annealed.
- the concentration may be adjusted as appropriate.
- the synthesized complementary strand sequence performs an extension reaction using itself as a template.
- the composition when the hairpin primer having the sequence structure shown in Table 1 and the polymerase and salt composition solution 100 ⁇ l is used, for example, 20 mM Tris-HCl (pH 8.5) 50 mM KCl 2 mM MgCl 2 200 ⁇ M each dNTP 5U Pfu exo -DNA polymerase (polymerase without 3'-5 'exonuclease activity) And the synthesis reaction is carried out under the following temperature conditions.
- one of the paired primers is a hairpin primer 300, but both of the paired primers may be subjected to the same reaction process using a primer having a hairpin structure.
- the time for constructing the nucleic acid molecule depends on the temperature in the synthesis reaction, the reaction time, the cycle, and the performance of the thermal-cycler, but the reaction shown in FIG. 3 is completed within approximately 30 to 90 minutes. .
- the reaction solution contains unreacted primers, etc., but using the gel filtration resin-filled spin column CHROMA SPIN Column (Takara Bio), the unreacted primer was removed in about 10 minutes, and the synthesized target sequence It is possible to take out only the nucleic acid molecule that repeats the above and proceed to the step of determining the base sequence.
- double-stranded products (5a) are mixed with single-stranded nucleic acid molecules (5b) having a hairpin structure.
- the presence of double-stranded nucleic acid molecules at the time of sequence analysis is not preferred for sequence analysis using a sequencer using nanopores (for example, 2 nm or less in diameter) that allow single-stranded DNA to pass through and detect each base. Therefore, for example, in the synthesis step shown in FIG. 3, one of the two primers used may be a primer 303 having no hairpin structure, and the sequence of the primer 303 may be an AT-rich sequence in which the complementary strand sequence is easily dissociated. .
- the structure may be such that when the product passes through the nanopore, the complementary strand sequence is dissociated by heat, alkali, or the like, and the nanopore is easily passed as single-stranded DNA.
- the reaction shown in FIG. 3 can be performed after preparing the RNA sequence at the 5 ′ end using a hybrid chimeric primer composed of DNA-RNA as the primer 303.
- the RNA that forms the DNA-RNA hybrid duplex is cleaved using RNaseH enzyme, etc., to create a site where the end of the reaction product becomes single-stranded DNA, and it can be easily integrated into the nanopore. You may let it pass from the location of strand DNA.
- the negatively charged DNA is electrically drawn to the anode side via the nanopore. Double-stranded DNA is formed with hydrogen bonds and may be drawn in while dissociating the hydrogen bonds.
- the speed of passing through the nanopore is slow, and it is possible to pass through a portion that becomes a sufficient detection field over a sufficient time. That is, the speed at which DNA passes through the nanopores can be controlled by adjusting the heat, alkali, or pulling force of the hydrogen bonding force that forms a double strand.
- the method of the present invention synthesizes a complementary strand sequence based only on the target sequence (double-stranded single DNA strand), and subsequently synthesizes the complementary strand sequence of the synthesized sequence to produce a single-stranded nucleic acid.
- Molecules are constructed and used to detect them with a nanopore sequencer. This is because if it is difficult to decipher the base sequence by analyzing only one strand of the target sequence, for example, if there is a signal that is similar between bases, even if the signal obtained is uncertain, Can be obtained.
- the sequence information of only one strand of the same target sequence is read twice, so it has high accuracy with the information read twice. It shows that nucleic acid sequence analysis is possible. Even if the device to be detected (for example, a detector or a lens) is not an expensive and high-accuracy object, a device that can obtain sufficient accuracy by reading multiple times, that is, a burden on the device (for example, functional) ) And the method of the present invention is also a method that allows the device for sequencing to be an inexpensive or miniaturized device.
- Analysis with a nanopore sequencer can be performed from the 5 'side or the 3' side in the case of single-stranded nucleic acid molecules.
- the hairpin amplification product shown in FIG. 3 (5b) is first analyzed from the sequence information of the primer, and then read from the 5 ′ side.
- the target sequence, hairpin primer sequence, target sequence (complementary sequence), and primer sequence (complementary sequence) are analyzed in this order.
- the base sequence information derived from each primer sequence and the signal information of the base sequence are known, a peak is obtained in advance with which signal (wavelength, wave number or current value). Since it is known in which order the peak corresponding to the signal corresponding to each base is obtained, detection calibration can be performed in real time. For example, when detecting Raman scattered light, spectral information based on known Raman scattered light can be obtained sequentially, so if the information obtained from the spectral peak cannot be obtained at the position of the element that is originally obtained, for example, the position of the detecting element is calibrated. May be.
- a plurality of Raman spectrum peaks obtained from a known array part can be used not only for position calibration of the above-described element but also for detection of contamination and carryover.
- the sequence of the hairpin portion of the hairpin primer 300 used for analysis is changed for each sample.
- the sequence of the hairpin portion of the hairpin primer 300 used for analysis is changed for each sample.
- contamination between samples and the previous time at the time of analysis are analyzed.
- the analysis sample can be recognized and analyzed.
- calibration may be performed using a current value obtained from each base of each known primer sequence and a background signal value.
- a current value obtained from each base of each known primer sequence For example, it is particularly effective when the background signal value fluctuates during measurement.
- the signal value immediately before the nucleic acid passes is used as the background signal value, and the current value changes greatly when the nucleic acid molecule is incorporated. Therefore, the current value is measured by subtracting the background signal value before the nucleic acid molecule is incorporated.
- a known base sequence aligned with ACGT is measured in order, after subtracting the background signal value from the signal intensity of each base, the signal intensity ratio or signal change due to the known sequence is used as a reference value, and is obtained at the target sequence part.
- the base may be determined by comparing the obtained signal value with the reference value.
- the calibration method is not limited to these. This is a method of calibrating or analyzing based on a known signal value or signal information obtained from a known arrangement, or an actual measurement signal obtained from a known arrangement obtained from a known arrangement. A person skilled in the art can appropriately modify the method of the present invention based on the above description.
- the example of determining the nucleic acid base sequence by detecting Raman scattered light has been mainly shown.
- the method of the present invention is not limited to this, for example, a nucleic acid base for detecting a blocking current when passing through a nanopore.
- Sequencing method (US2011 / 0229877, US2011 / 0177498, etc.), nucleobase sequencing method to detect tunneling current generated when passing through nanopore (JP 2014-20837), single molecule nucleobase sequencing using droplet (WO2014111723A, WO2014053854A), a nucleobase sequencing method that detects a single molecule of a fluorescently labeled pyrophosphate [PPi] moiety released from a nucleotide triphosphate [NTP] when a polymerase extension product is produced ( Patent No. 4638043) can use the nucleic acid molecule obtained by the method of the present invention. Even if the target sequence reading accuracy is low, multiple target sequence information is included in the molecule. Therefore, it is possible to show a highly accurate analysis result by analyzing one molecule, and the burden on the detection device side (for example, functional Can be reduced.
- Example 1 the nucleic acid molecule constructed when the hairpin primer is used in only one of the molecules shown in (4) and (5b) of FIG. In this example, about half of the molecules capable of detecting the target sequence shown in FIG. 3 (5b) twice are constructed, but the total number of constructed molecules can detect the target sequence twice. How to build a simple molecule.
- FIG. 4 shows the procedure.
- a process similar to that shown in FIG. 3 is performed before the process shown in FIG.
- a difference from the process shown in FIG. 3 is that the amplification process shown in FIG. 3 is performed by biotinylating the primer 303 that forms a pair with the hairpin primer 300.
- a spacer (for example, a base or the like) of about 5 carbon atoms may be included in order to reduce an amplification obstacle in the synthesis using a polymerase generated by the biotin three-dimensional structure accompanying the biotinylation of the primer.
- biotinylated primer 300 for example, 40 ⁇ l of the reaction product amplified in the step shown in FIG. 3 is mixed with magnetic beads (eg, Dynabeads® M-280 Streptavidin) provided with streptavidin, and suspended. Incubate for 15 minutes at room temperature to allow amplification product to bind to magnetic beads.
- magnetic beads eg, Dynabeads® M-280 Streptavidin
- a magnet is installed outside the reaction vessel, and only the supernatant is removed while the magnetic beads are attracted and fixed to the magnet side across the reaction vessel, and the washing solution is added and suspended, drawn by the magnet, and the supernatant is removed.
- Perform the washing operation When this washing operation is performed, the washing solution is kept at 60 ° C. or higher or 95 ° C. or higher, so that the DNA strand existing in the complementary strand of the DNA strand bound to the magnetic beads is washed away along with the dissociation of the double-stranded DNA, and magnetic It is possible to isolate only the DNA strand bound to the bead, ie the molecule extended from the biotinylated primer. Alternatively, the same effect can be obtained by washing while dissociating the double-stranded DNA with an alkaline solution.
- a molecule is constructed in which the total number of molecules can detect the target sequence twice. For example, add a solution of the following composition when the reaction solution is 100 ⁇ l to the isolated DNA strand, 20 mM Tris-HCl (pH 8.5) 50 mM KCl 2 mM MgCl 2 200 ⁇ M each dNTP 5U Pfu exo -DNA polymerase (polymerase without 3'-5 'exonuclease activity) The reaction is carried out under the following temperature conditions.
- the hairpin structure is constructed by annealing at 30 ° C. for 30 seconds and at 60 ° C. for 45 seconds to anneal the sequence portion having the complementary strand at the 3 ′ end, and the elongation reaction is carried out by heating at 72 ° C. for 90 seconds or more.
- reaction conditions are not limited to the above reaction conditions, and the temperature, time, cycle, etc. may be changed depending on the target sequence or primer sequence.
- purification process which removes a salt and an enzyme between the reaction of each process was not described, you may implement if needed depending on the case.
- the magnetic beads When performing nanopore sequencing, if the sequencing efficiency is reduced by the bound magnetic beads, the magnetic beads may be separated from the nucleic acid molecule. For example, a spacer region provided between the primer and biotin may be cleaved. As a cleavage method, for example, a restriction enzyme cleavage sequence may be included in advance in the base sequence of the spacer region, and cleavage may be performed before sequencing. Thereby, nanopore sequencing can be performed using a sample obtained by separating a DNA strand and a magnetic bead.
- FIG. 5 shows the procedure.
- This embodiment is characterized in that the 5 ′ end of the hairpin primer is phosphorylated before use, and the DNA strand phosphorylated at the 5 ′ end after the construction of the target nucleic acid molecule is degraded.
- Degradation is not particularly limited, but for example, ⁇ exonuclease is used.
- the process similar to FIG. 3 is performed before the process shown in FIG.
- the difference from the process shown in FIG. 3 is that the 5 ′ end of the hairpin primer 300 is phosphorylated, and the amplification process shown in FIG. 3 is performed without phosphorylating the paired primer 303.
- salts and primers in the amplification reaction solution are removed.
- the removal method is not limited, but for example, NucleoSpin (registered trademark) Gel and PCR Clean-up (manufactured by Takara Bio Inc.), which is a commercially available kit that is purified by immobilizing an amplification product on a silica membrane and centrifuging it, may be used.
- Lambda exonuclease is an enzyme that is characterized by digesting from the phosphorylated 5 'end of double-stranded DNA and releasing mononucleotides. Double-stranded DNA phosphorylated at the 5 'end is a good substrate. Using this property, ⁇ exonuclease (manufactured by NEB) was added to the amplification product, and the reaction solution was adjusted with a buffer composition of 67 mM glycine-KOH (pH 9.4), 2.5 mM MgCl 2 , 50 ⁇ g / ml BSA, and 37 Incubate at 30 ° C for 30 minutes.
- the solution subjected to the ⁇ exonuclease reaction is adjusted to a solution having the following composition, for example. 20 mM Tris-HCl (pH 8.5) 50 mM KCl 2 mM MgCl 2 200 ⁇ M each dNTP 5U Pfu exo -DNA polymerase (polymerase without 3'-5 'exonuclease activity)
- the reaction is carried out under the following temperature conditions with the above composition.
- the higher-order structure is loosened by heating at 94 ° C for 5 minutes.
- the hairpin structure is constructed by annealing the sequence portion having the complementary strand at the 3 ′ end at 95 ° C. for 30 seconds and at 60 ° C. for 45 seconds.
- This reaction is not limited to the reaction conditions shown above. The temperature, time, cycle and the like may be changed depending on the target sequence and the sequence of the hairpin structure.
- the nucleic acid molecule prepared in the present example can detect the target sequence twice during sequencing, and a highly accurate base sequence can be obtained.
- FIG. 6 shows the procedure.
- the process similar to FIG. 3 is performed before the process shown in FIG.
- the difference from the process shown in FIG. 3 is that the 3 ′ end of the reaction product is 1 base of adenine by performing the step of “90 seconds at 72 ° C.” in the extension reaction for a sufficiently long time (for example, 5 minutes or longer).
- a protruding structure can be intentionally formed.
- TA cloning is performed on the reaction product thus formed by linking an adapter 601 having a terminal structure with a protruding thymine base at the 3 'end and a hairpin structure.
- this adapter 601 is formed between a portion (double-stranded DNA) that binds (ligates) with the reaction product in the previous step and a portion that forms a hairpin loop (for example, a sequence as shown in Table 1).
- a hairpin loop for example, a sequence as shown in Table 1
- it has a structure that is connected only by a single strand. This has a structure in which the 3 'end from the hairpin loop to the portion binding to the reaction product is interrupted.
- the connection with the adapter 601 by TA cloning is shown, but the connection method is not limited to this.
- a cloning system using topoisomerase for example, StrataClone PCR cloning system using Cre recombinase derived from DNA topoisomerase I ⁇ ⁇ and bacteriophage P1 (Agilent) or TOPO (registered trademark) ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ Cloning (Life Technologies), etc. Ligation may be performed using cloning techniques.
- the ligated reaction product is subjected to an extension reaction using a strand displacement polymerase.
- This reaction is incubated at a temperature (for example, 60 ° C.) capable of forming a base pair bond to a complementary base sequence from the 3 ′ end of the adapter 601 and maintaining the enzyme activity at which the strand displacement reaction occurs. .
- the incubation time may be adjusted depending on the base length for the extension reaction.
- the conditions that cause base pair binding at various places are generally set to, for example, the melting temperature or lower, and are the same as those used in the PCR method and the LAMP method.
- the elongation due to this strand displacement reaction may include buffering agents that give a pH suitable for the enzyme, salt components used for maintaining the catalytic activity and annealing of the enzyme, enzyme protecting agents, and melting temperature adjusting agents as necessary. May be carried out under the condition of coexistence.
- a neutral to weakly alkaline buffering agent such as Tris-HCl may be used. Adjust the pH according to the characteristics of the enzyme (DNA polymerase) used.
- As the salt component KCl, NaCl, (NH 4 ) 2 SO 4, or the like may be appropriately added in order to maintain the activity of the enzyme and adjust the melting temperature of the nucleic acid.
- saccharides or bovine serum albumin may be used for protecting the enzyme.
- Dimethyl sulfoxide (DMSO) and formamide are generally used to adjust the melting temperature.
- a melting temperature adjusting agent for these, annealing from the 3 ′ end can be adjusted under limited temperature conditions.
- betaine N, N, N-trimethylglycine
- proline, trimethylamine N-oxide and the like are known as melting temperature adjusting agents. By causing destabilization of double-stranded DNA, strand displacement efficiency can be improved.
- the amount of betaine added is preferably about 0.2 to 3.0 M, more preferably about 0.5 to 1.5 M in the reaction solution, and the promotion of the nucleic acid amplification reaction of the present invention can be expected. Since these melting temperature adjusting agents act in the direction of lowering the melting temperature, conditions for giving an appropriate reaction are set empirically in consideration of other reaction conditions such as salt concentration and reaction temperature.
- the extension reaction may proceed as long as the reaction takes place.
- the 3 'end structure that leads the extension reaction undergoes self-annealing, or the reaction jumps to its own base sequence in the vicinity.
- ddNTP (dideoxynucleoside triphosphate) may be included at a certain concentration in addition to dNTP (deoxynucleoside triphosphate) as a substrate for DNA polymerase. good.
- the length of the template to be amplified can be limited by the concentration of ddNTP contained. For example, if the extension reaction continues via a loop structure, the extension reaction can be stopped by incorporating ddNTP during the strand displacement reaction by containing a high concentration of ddNTP.
- ddNTP concentration may be adjusted according to the required extension product length. Depending on the concentration adjustment of ddNTP, it is possible to repeat the target sequence information more than 4 times. However, excessive repeat structure results in the formation of higher order structure, which can affect the passage of nanopores. The number of repetitions may be properly used depending on the configuration of the sing.
- Extension due to the progress of the strand displacement reaction without limitation can be controlled using ddNTP as described above, but the control method is not limited thereto.
- the strand displacement polymerase reaction stops at the abasic site. Therefore, the length of the nucleic acid molecule produced by abasic control can be controlled.
- the hairpin loop structure portion of the adapter 601 can contain a molecule that inhibits the elongation reaction by polymerase.
- a molecule that inhibits the elongation reaction by polymerase By preparing the inhibitor molecule, it is possible to inhibit the elongation reaction by the polymerase during the elongation reaction and to prevent the elongation without restriction.
- the structure of the inhibitor molecule is not particularly limited as long as it can inhibit the elongation reaction by polymerase, but preferably contains, for example, a nucleic acid derivative or a non-nucleic acid derivative.
- nucleic acid derivative in addition to the above abasic, a nucleic acid having a structure that sterically inhibits the progress of polymerase, such as a strong higher-order structure that is not dissociated by a strand displacement enzyme or a pseudoknot structure, an L-type nucleic acid, 3- Deoxy-2-hydroxy-dN, modified base nucleic acid, damaged base nucleic acid, phosphate binding site modified nucleic acid, RNA, 2′-OMe-N, BNA (LNA), and derivatives thereof.
- a nucleic acid having a structure that sterically inhibits the progress of polymerase such as a strong higher-order structure that is not dissociated by a strand displacement enzyme or a pseudoknot structure
- L-type nucleic acid 3- Deoxy-2-hydroxy-dN, modified base nucleic acid, damaged base nucleic acid, phosphate binding site modified nucleic acid, RNA, 2′-OMe-N, BNA (LNA), and derivatives thereof.
- the nucleic acid molecule prepared in this example can detect the target sequence four times during sequencing, and can determine the base sequence with higher accuracy.
- the nucleic acid molecules constructed in Example 4 can be mixed with nucleic acid molecules that repeat the target sequence twice or four times.
- a method for constructing a nucleic acid molecule in which the total number of molecules repeats the target sequence four times will be described.
- FIG. 7 shows the procedure.
- the generated reaction product is a nucleic acid molecule in which the total number of molecules contains the target sequence repeated twice, and using this, a nucleic acid molecule that repeats the target sequence four times is constructed.
- connection method with the adapter is not particularly limited.
- an extension reaction using a strand displacement polymerase is performed.
- incubation is performed at a temperature capable of forming a base pair bond to a complementary base sequence from the 3 ′ end and maintaining an enzyme activity in which a strand displacement reaction occurs.
- the conditions that cause base pair binding at various places are generally set to, for example, the melting temperature or lower, and are the same as those used in the PCR method and the LAMP method.
- the strand displacement reaction shown here the reaction is performed in consideration of the same points as the strand displacement reaction shown in Example 4.
- the nucleic acid molecule prepared in this example can detect the target sequence four times during sequencing, and can determine the base sequence with higher accuracy.
- Example 6 describes a construction method that also takes into account the efficient introduction of the nucleic acid molecules constructed in Examples 1 to 5 into the nanopore.
- the terminal structure of the nucleic acid molecule constructed by the methods of Examples 1 to 5 is in the form of double-stranded DNA.
- the double-stranded single-stranded DNA is used. By dissociating into two, the efficiency of introduction into the nanopore with the diameter size of single-stranded DNA is improved.
- the ends of the molecules generated by the nucleic acid molecule construction methods shown in Examples 1 to 5 are, for example, double-stranded DNA having the sequence of the primer 303 that makes a pair with the hairpin primer 300 in the reaction shown in FIG. It has a structure, and as it is, it does not easily enter the nanopore which is the diameter size of single-stranded DNA. Therefore, by changing the sequence of the primer 303 to a sequence 701 (FIG. 7) rich in the sequence of AT (adenine and thymine) that tends to become a single-stranded DNA upon denaturation, the single-stranded DNA can be easily converted into a base sequence. It becomes easy to introduce into the nanopore structure.
- the reaction shown in FIG. 3 is performed as a DNA-RNA chimeric primer having RNA at the 5 'end of the hairpin primer 300, and the reactions shown in the respective examples are performed.
- RNaseH a ribonuclease
- RNaseH a ribonuclease
- the hairpin primer 300 is provided with a random sequence 801, whereby the nucleic acid molecule derived from the amplification is recognized by the random sequence 801, and the determination accuracy of the sequence of the derived nucleic acid molecule is increased. Will be explained.
- the hairpin primer 300 is given a random sequence 801.
- this random sequence 801 is used as the location of the double-stranded forming sequence of the hairpin primer 300.
- a 10-base-pair random sequence is formed in the double-stranded sequence (stem part) at a location other than the sequence that is complementary to the target sequence, it is 4 to the 10th power (1,048,576) with 4 types of bases.
- a hairpin primer having a random sequence of can be prepared. As a result, in the steps of FIGS.
- nucleic acid molecule amplified using a nucleic acid molecule replicated with a certain random sequence 801 as a template is as shown in FIG. 8C (5).
- an exponentially amplified nucleic acid molecule can be obtained while maintaining the sequence from which amplification was derived and the random sequence.
- the nucleic acid molecules amplified from the hairpin primers 803 to 805 having different random sequences constitute a group of nucleic acid molecules having different random sequences (FIG. 8C).
- the sequence of the nucleic acid molecule derived from the amplification is recognized by recognizing the corresponding portion (random sequence 801 and its complementary sequence 802) of the double-stranded formation sequence of the hairpin primer 300 together with the target sequence.
- random sequence 801 and its complementary sequence 802 the corresponding portion of the double-stranded formation sequence of the hairpin primer 300 together with the target sequence.
- FIG. 9 shows an example of the result of comparing the sequence analysis results of a plurality of nucleic acid molecules (01 to 05) having the same random sequence 901 and comparing the target sequences.
- results that differ between the molecules can be detected. In that case, if it is a reading error at the time of sequence analysis, the presence of a base different from the reference sequence is indicated at random positions of some of the nucleic acid molecules (bases surrounded by a square in the figure). For example, if the amplified nucleic acid molecule 01 is analyzed as “G” and the other nucleic acid molecules 02 to 05 are analyzed as “C”, this is determined as a reading error (“C” in the reference sequence).
- This method is particularly effective in detecting the abnormal cell-derived mutations slightly contained in the large amount of normal cell-derived genomic DNA described above.
- the base length of the random sequence 801 is 10 bases, it is not limited to this.
- the ratio of detection targets is small, by increasing the base length of the random sequence, more types of hairpin primers can be used in the reaction, and the detection targets (for example, abnormal cell-derived nucleic acids) and others ( It is possible to amplify without using a hairpin primer having the same random sequence in a normal cell-derived nucleic acid. That is, it is preferable that the hairpin primer has a random sequence species equal to or greater than the number of mutations in the target sequence.
- the position of the random sequence 801 is defined as a double-strand forming sequence, but a random sequence including the loop portion of the hairpin may be formed.
- the base length of the stem part of the hairpin primer can be in the range of 8 to 20 bases, for example, 16 to 18 bases.
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Abstract
Description
[1]ナノポアシーケンサによる核酸配列決定の為の一本鎖核酸分子の構築方法であって、
3'側に一本鎖領域を含む少なくとも一つのヘアピンプライマーと、該ヘアピンプライマーと対をなすプライマーとを用いて標的配列を含む鋳型DNAの相補鎖を合成する工程と、
合成された相補鎖が分子内にヘアピン構造を形成して自己を鋳型に伸長反応を行うようにする工程と
を含み、得られた核酸分子が標的配列及びその相補鎖の双方を配列中に含むものである、上記方法。
[2]前記ヘアピンプライマーのステム部が、前記一本鎖部のTm値より高いTm値を有する、[1]に記載の方法。
[3]反応の進行によるヘアピンプライマーの減少と共に、合成された相補鎖配列が自己を鋳型に伸長反応を行う、[1]に記載の方法。
[4]ヘアピンプライマーの5'末端を使用前にリン酸化し、目的の核酸分子の構築後に5'末端がリン酸化したDNA鎖を分解する工程を更に含む、[1]に記載の方法。
[5]λエキソヌクレアーゼを使用して前記分解を行う、[4]に記載の方法。
[6]5'末端がリン酸化したDNA鎖の分解後、その相補鎖の3'末端からヘアピン構造を介して自己アニールする伸長反応を行う、[4]に記載の方法。
[7]ヘアピンループ構造をもつアダプタを前記生成物と連結し、鎖置換反応を行って核酸分子を伸長させる工程を更に含む、[1]に記載の方法。
[8]ヘアピンループ構造をもつアダプタを前記生成物と連結し、鎖置換反応を行って核酸分子を伸長させる、[6]に記載の方法。
[9]前記対をなすプライマーから形成された末端を固定化し、相補鎖DNAを解離させた後に伸長反応を行う、[1]に記載の方法。
[10]前記アダプタのループ構造部が、伸長反応阻害分子を含む、[7]又は[8]に記載の方法。
[11]前記対をなすプライマーがDNAとRNAのキメラ構造を有し、伸長反応後にRNAを分解する工程を更に含む、[1]に記載の方法。
[12][1]に記載の方法によって得られた核酸分子の塩基配列をナノポアシーケンサによって解析することを含む、核酸塩基配列決定方法。
[13]配列決定工程において、核酸分子中に含まれる既知の塩基配列から得られる信号を元に検出器の校正を行う、[12]に記載の方法。
[14]配列決定工程において、核酸分子中に含まれる既知の塩基配列から得られる信号を元に解析を行う、[12]に記載の方法。
[15]二本鎖形成した反応物を用い、ナノポアを通過する反応物の速度を制御する、[12]に記載の方法。
[16]前記ヘアピンプライマーがランダム配列を有する、[1]に記載の方法。
[17]前記ヘアピンプライマーが前記標的配列の変異の数以上のランダム配列種を有する、[16]に記載の方法。
20mM Tris-HCl (pH8.5)
50mM KCl
2mM MgCl2
200μM 各dNTP
5U Pfuexo-DNAポリメラーゼ (3’-5’エキソヌクレアーゼ活性を持たないポリメラーゼ)
と調製し、以下の温度条件で合成反応を行う。
20mM Tris-HCl (pH8.5)
50mM KCl
2mM MgCl2
200μM 各dNTP
5U Pfuexo-DNAポリメラーゼ(3’-5’エキソヌクレアーゼ活性のないポリメラーゼ)
以下の温度条件で反応を行う。
20mM Tris-HCl (pH8.5)
50mM KCl
2mM MgCl2
200μM 各dNTP
5U Pfuexo-DNAポリメラーゼ(3’-5’エキソヌクレアーゼ活性のないポリメラーゼ)
上記の組成で以下の温度条件で反応を行う。94℃で5分の加熱で高次構造をほぐす。その後95℃で30秒、60℃で45秒により3’末端の相補鎖をもつ配列箇所がアニールすることによりヘアピン構造を構築し、72℃で90秒以上の加熱により伸長反応を行う。この反応は、上記に示した反応条件に限定されない。標的とする配列やヘアピン構造の配列により温度、時間、サイクル等は変えてもよい。
101 光源
102 対物レンズ
103 顕微鏡観察容器
104 XYステージ
105 Z軸調整機構
106 フィルタ
107 ビームスプリッター
108 回折格子
109 検出器
110 LED
111 二次元検出器
112 ミラー
113 多重照射機構
114 レンズ
115 駆動制御部
116 コンピュータ
117 NIR(近赤外)ミラー
201 観察容器
202 ナノポア
203 基板
204 試料導入区画
205 試料流出区画
206 流入路
207 流入路
208 流出路
209 流出路
210 液体
211 液体
212 試料
213 電極
214 電極
215 導電性薄膜
216 液浸媒体
217 対物レンズ
300 ヘアピンプライマー
300a ヘアピンプライマー300の伸長産物
301 ヘアピン構造を形成させる相補鎖配列部
302 ヘアピンプライマーにおける相補鎖配列部
303 プライマー
303a プライマー303の伸長産物
303b プライマー303の伸長産物
303c プライマー303の伸長産物
303d プライマー303の伸長産物
601 ヘアピンアダプタ
701 AT(アデニンとチミン)の配列に富んだ配列
801 ランダム配列
802 ランダム配列の相補配列
803 異なるランダム配列を有するヘアピンプライマー
804 異なるランダム配列を有するヘアピンプライマー
805 異なるランダム配列を有するヘアピンプライマー
901 ランダム配列
902 核酸分子01~05で共通して異なる塩基
Claims (17)
- ナノポアシーケンサによる核酸配列決定の為の一本鎖核酸分子の構築方法であって、
3'側に一本鎖領域を含む少なくとも一つのヘアピンプライマーと、対をなすプライマーとを用いて標的配列を含む鋳型DNAの相補鎖を合成する工程と、
合成された相補鎖が分子内にヘアピン構造を形成して自己を鋳型に伸長反応を行うようにする工程と
を含み、得られた核酸分子が標的配列及びその相補鎖の双方を配列中に含むものである、上記方法。 - 前記ヘアピンプライマーのステム部が、前記一本鎖部のTm値より高いTm値を有する、請求項1に記載の方法。
- 反応の進行によるヘアピンプライマーの減少と共に、合成された相補鎖配列が自己を鋳型に伸長反応を行う、請求項1に記載の方法。
- ヘアピンプライマーの5'末端を使用前にリン酸化し、目的の核酸分子の構築後にヘアピンプライマー5'末端がリン酸化したDNA鎖を分解する工程を更に含む、請求項1に記載の方法。
- λエキソヌクレアーゼを使用して前記分解を行う、請求項4に記載の方法。
- 5'末端がリン酸化したDNA鎖の分解後、その相補鎖の3'末端からヘアピン構造を介して自己アニールする伸長反応を行う、請求項4に記載の方法。
- ヘアピンループ構造をもつアダプタを前記生成物と連結し、鎖置換反応を行って核酸分子を伸長させる工程を更に含む、請求項1に記載の方法。
- ヘアピンループ構造をもつアダプタを前記生成物と連結し、鎖置換反応を行って核酸分子を伸長させる、請求項6に記載の方法。
- 前記対をなすプライマーから形成された末端を固定化し、相補鎖DNAを解離させた後に伸長反応を行う、請求項1に記載の方法。
- 前記アダプタのループ構造部が、伸長反応阻害分子を含む、請求項7又は8に記載の方法。
- 前記対をなすプライマーがDNAとRNAのキメラ構造を有し、伸長反応後にRNAを分解する工程を更に含む、請求項1に記載の方法。
- 請求項1に記載の方法によって得られた核酸分子の塩基配列をナノポアシーケンサによって解析することを含む、核酸塩基配列決定方法。
- 配列決定工程において、核酸分子中に含まれる既知の塩基配列から得られる信号を元に検出器の校正を行う、請求項12に記載の方法。
- 配列決定工程において、核酸分子中に含まれる既知の塩基配列から得られる信号を元に解析を行う、請求項12に記載の方法。
- 二本鎖形成した反応物を用い、ナノポアを通過する反応物の速度を制御する、請求項12に記載の方法。
- 前記ヘアピンプライマーがランダム配列を有する、請求項1に記載の方法。
- 前記ヘアピンプライマーが前記標的配列の変異の数以上のランダム配列種を有する、請求項16に記載の方法。
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WO2020105318A1 (ja) * | 2018-11-21 | 2020-05-28 | 株式会社日立製作所 | 生体分子分析装置及び生体分子分析方法 |
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AU2012288629B2 (en) | 2011-07-25 | 2017-02-02 | Oxford Nanopore Technologies Limited | Hairpin loop method for double strand polynucleotide sequencing using transmembrane pores |
GB201314695D0 (en) | 2013-08-16 | 2013-10-02 | Oxford Nanopore Tech Ltd | Method |
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