WO2002024905A1 - Procede permettant de determiner la mutation genetique - Google Patents
Procede permettant de determiner la mutation genetique Download PDFInfo
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- WO2002024905A1 WO2002024905A1 PCT/JP2001/007942 JP0107942W WO0224905A1 WO 2002024905 A1 WO2002024905 A1 WO 2002024905A1 JP 0107942 W JP0107942 W JP 0107942W WO 0224905 A1 WO0224905 A1 WO 0224905A1
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- primer
- dna
- nucleic acid
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- pcr
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- 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
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6858—Allele-specific amplification
Definitions
- the present invention provides a method for easily discriminating the presence or absence of a gene mutation on a chromosome assumed in advance and the type on an allele.
- PCR-RFLP combining the polymerase chain reaction (PCR) method and restriction enzyme cleavage (Erlich et al., Science, 255, 1643, pp. 1991) ) Is a typical example.
- PCR-RFLP polymerase chain reaction
- restriction enzyme cleavage Erlich et al., Science, 255, 1643, pp. 1991
- DNA microarray method has been developed very recently (Brown et al., Nat. Gent. ⁇ 21, p. 33, 1999).
- the PCR-RFLP method cannot be said to be a rapid method because the testing process involves a restriction enzyme treatment of 3 to 24 hours.
- the DNA microarray method is extremely expensive to carry out, and is very disadvantageous in terms of processing a large number of samples. Therefore, there has been a demand for the development of a new method for discriminating gene mutations that can rapidly and inexpensively process a large amount of samples.
- the present inventors can utilize a large number of samples quickly and inexpensively by taking advantage of the PCR method as it is, and further utilizing the restrictions on primer DNA sequence design, which should be noted when performing the PCR method.
- a new method for identifying gene mutations Confronting two-pair primers PCR) that can be processed in a single step has been developed.
- the present invention provides a primer DNA having a nucleic acid corresponding to a mutant nucleic acid at the 3 ′ end, a nucleic acid corresponding to a normal nucleic acid at 3 ′, a primer DNA having an end at a 3 ′ end, and two types thereof facing the same.
- This is a method for determining the presence or absence of a predetermined gene mutation by confirming the size of a DNA fragment generated by a PCR reaction using four types of primer DNAs containing the same primer DNA.
- the present invention utilizes at least two sets of primer DNA sequences that are designed to have a desired base sequence in advance.
- the outline of the present invention is based on the target gene for which the presence or absence of a mutation is to be determined.
- Figure 1 shows an example of SNPs assuming that the base on allele X is X and the nucleic acid corresponding to base X on allele Y is Y.
- two pairs of primers DNA are designed as four types of primers DNA.
- One set is a set for which allele X is to be amplified, and another set is a set for which allele Y is to be amplified.
- one primer DNA (antisense primer 1R) is synthesized as the nucleic acid X 'complementary to the nucleic acid X, and the other end is synthesized as the nucleic acid X'. Synthesize primer 1F and combine them into one.
- a sense primer DNA (primer 1F) whose 3 end is a nucleic acid Y is synthesized, and further downstream from the primer 2F.
- the antisense primer DNA (primer 2R), which is located opposite to the primers, is synthesized to form another combination.
- the size of the specific DNA amplification product observed after each reaction is a base pair (size a ), B is a base pair (size b).
- size a and size b need to be distinguished in molecular weight by a suitable method such as gel electrophoresis. However, this may be achieved by arbitrarily adjusting the position of the primer DNA on the target gene so as to give a desired size difference.
- a PCR reaction is carried out on a gene suspected of having a mutation at the same time using the two sets of primer DNAs described above, and the size of the PCR product is confirmed. The presence or absence of mutation and the type of mutation between alleles can be determined.
- the bases that are problematic in the gene are both X alleles. Can be determined.
- the problematic base on both alleles is YY
- the size of the band confirmed after the PCR reaction is the size b and size c nodes, which means that the size b and size c
- the band is specifically amplified, it means that the base in question in the gene can be determined to be Y for both alleles. If, after the PCR reaction, three types of nodes, size a, size b, and size c, are observed, the base on the allele X becomes X based on the same principle as described above.
- c a + b-(d-1) where the base on the allele Y can be determined to be a heterozygote of Y.
- d is the sum of the number of bases of both 1R and 2F primers.
- nucleic acid X ′ is 3 and antisense primer 1R at the end is replaced with nucleic acid X3 and sense primer 2F at the end is replaced with antisense primer 1F.
- Combination of primer 2R and anti-primer having nucleic acid Y at the 3 'end instead of sense primer 2F having nucleic acid Y at the 3' end for allele Y The present invention can also be carried out by combining 1R and sense primer 1F and performing a PCR reaction in the coexistence of these.
- the size of the transcript is also size a, size b, and size c. When the size c is YY type, the size a and the size c are respectively confirmed.
- nucleic acid corresponding to the mutant nucleic acid and the nucleic acid corresponding to the normal nucleic acid according to the present invention mean the mutant nucleic acid and the normal nucleic acid or the nucleic acid complementary thereto as in the above two examples.
- the PCR reaction and the confirmation of the molecular weight of the PCR product are completed in two steps, and the PCR product is treated with the restriction enzyme over several hours.
- the time required for discrimination can be significantly reduced.
- the PCR-RFLP method there is a restriction that a restriction enzyme site must be designed in advance so that a fragment having a molecular weight difference required for fractionation after restriction enzyme treatment is generated. Therefore, it may be difficult to design an appropriate primer DNA depending on the nucleotide sequence of the target gene, but the PCR-CTPP method of the present invention has no such restrictions at all. It also has an advantage in the flexibility of primer-DNA design.
- the present invention does not require cleavage of a PCR product with a restriction enzyme, it is not affected by various artificial by-products due to the restriction enzyme treatment, and the determination can be performed reliably. Can be done.
- the PCR-CTPPP method of the present invention has an advantage even compared to the DNA microarray method. In other words, no special equipment is required, and the cost difference when processing a large amount of specimens is significantly lower than that of the DNA microarray method.
- the present invention is useful for discrimination of so-called polymorphism, but can also be used for discrimination of a causative gene or a cancer gene of a specific disease, and mutation is substitution, addition, or deletion. Any of the above is applicable.
- DNA containing the target gene to be discriminated can be subjected to a PCR reaction from blood or other tissues collected from a patient or a healthy person by a method commonly used by those skilled in the art in the field to which the present invention belongs.
- the present invention can be carried out using this as a sample as long as it is prepared as a DNA of the order.
- the design of the primer DNA used in the method of the present invention is based on three terminal Besides the determination of the nucleic acid in step 1 and that the difference between the molecular weight (base pair number) of the amplified DNA product and the PCR product when using the primer DNA is appropriate. There are no separate restrictions.
- the size difference between the DNA product and the size of the PCR product can be appropriately determined depending on the sensitivity of the method for detecting the amplified product, but it is sufficient if there are tens to hundreds of base pairs in general. In the case of using a high-sensitivity detection method such as capillary-electrophoresis, the difference may be several base pairs.
- Such a primer DNA design can be easily performed by a general person skilled in the art to which the present invention belongs based on the nucleotide sequence of the gene to be identified and the position of the mutation. It is something.
- the preparation of the primer DNA itself can be easily performed using a so-called automatic DNA synthesizer or other general-purpose equipment or a synthesis method.
- the PCR reaction in the present invention can also be performed under general reaction conditions that do not include special reagents or reaction steps, and commercially available PCR reactions can be used.
- PCR reaction is performed using the primer D N
- each primer set It is also possible to carry out the PCR reaction step by step.
- the PCR product can be detected by any method available to those skilled in the art, such as agarose gel electrophoresis, polyacrylamide gel electrophoresis, or capillary electrophoresis. , High-performance liquid chromatography (HPLC) or gas chromatography, such as chromatography, mass spectrometry (GC-MS), etc. . Gel electrophoresis is preferred as a simpler method.
- Example 1-Adrenoreceptor-2 (BAR-2) Polymorphism Detection of Adrenoceptor 2 (BAR-2), which has been reported to be involved in obesity and / or metabolic dysfunction Testing for polymorphism was performed.
- the nucleobase changes from C to G, and the 27th glutamine of the receptor protein is mutated to glutamic acid.
- a peripheral blood sample of 7 ml was prepared from 20 patients who gave written consent.
- chromosomal DNA was extracted from the buffy coat fraction and used as the chromosomal DNA in the following tests.
- the primer DNA of SEQ ID NO: 1 was synthesized as the primer DNA for the allele of the normal nucleic acid C, and the primer DNA of SEQ ID NO: 2 was synthesized as the antisense primer DNA.
- the primer DNA of SEQ ID NO: 3 was synthesized as the sense primer DNA for the allele of the mutant nucleic acid G, and the primer DNA of SEQ ID NO: 4 was synthesized as the antisense primer: DNA.
- 30 ng to 100 ng of the chromosomal DNA prepared above was combined with 0.15 mM dNTP, 25 pmol of each primer DNA, and 0.5 unit of Evening Kara Shuzo T aq (R) enzyme, 1 5 m M of M g C l 2 and including 2.
- CC type normal homozygous in which two kinds of PCR products of 279 base pairs and 204 base pairs are observed, and 279 base pairs, 204 base pairs, 11 Heterotype (CG type) in which three types of PCR products of 0 base pairs are observed, and mutant homo type (GG type) in which two types of PCR products of 279 base pairs and 110 base pairs are observed )
- CG type Heterotype
- GG type mutant homo type
- IL-1B IL-1B
- the primer DNA of SEQ ID NO: 5 was synthesized as the sense primer DNA for the allele of the normal nucleic acid C, and the primer DNA of SEQ ID NO: 6 was synthesized as the antisense primer DNA.
- a primer DNA of SEQ ID NO: 7 was synthesized as a primer DNA for an allele of a different nucleic acid T, and a primer DNA of SEQ ID NO: 8 was synthesized as an antisense primer DNA. From 30 ng of chromosomal DNA prepared in Example 1: LOO ng to 0.15 mM dNTP, 25 pmol of each primer DNA, 0.5 unit Evenings Kara Shuzo Ltd.
- T aq (TM) enzyme was added PCR reactions 1 2 containing 5 mM of M g C l 2.
- the reaction solution 2 5 ⁇ 1 comprising 1 0 XPCR buffer.
- the reaction conditions were denaturation at 94 ° C for 5 minutes, followed by 25 cycles of 60 seconds at 94 ° C, 60 seconds at 54 ° C, and 60 seconds at 72 ° C. Finally, a final extension reaction is performed at 72 ° C for 5 minutes.
- PCR products were visualized by 2% agarose gel and ethidium bromide staining. Figure 3 shows the results.
- CC type normal homozygous in which two kinds of PCR products, 240 base pairs and 155 base pairs, are observed, 240 base pairs, 155 base pairs, and 125 base pairs Hetero-type (CT type) in which three types of PCR products of 2 base pairs are observed, and mutant homo-type (TT type) in which two types of PCR products of 240 base pairs and 122 base pairs are observed )
- CT type Tero-type
- TT type mutant homo-type
- FIG. 1 is a diagram schematically illustrating the principle and scheme of the method of the present invention.
- FIG. 2 is an electrophoresis photograph of the PCR reaction product performed in Example 1.
- Lane M is a 100 base pair size marker
- lane 2, 4, 6, 7, 9, 11, 11, 12, 15, 17, 20 are normal.
- lanes 1, 5, 8, 13, 13, 14, 18 , 19 are heterotypes (CG type)
- lanes 3, 10, and 16 are mutant homotypes (GG type).
- FIG. 3 is an electrophoresis photograph of the PCR reaction product performed in Example 2.
- Lane M is a 100 base pair size marker
- lanes 13, 15, and 18 are normal heterotype (CC type)
- lanes 1, 2, 4, 5, 7, 9, 9 and 1 0 and 14 are heterozygous (CT type)
- lanes 3, 6, 8, 11, 12, 16, 17, 19 and 20 are mutant homozygous (TT type) . .
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- Wood Science & Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
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- Immunology (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Analytical Chemistry (AREA)
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- Biotechnology (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
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- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| AU2001286218A AU2001286218A1 (en) | 2000-09-19 | 2001-09-13 | Method of judging gene mutation |
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| JP2000-283996 | 2000-09-19 | ||
| JP2000283996A JP2001137000A (ja) | 2000-09-19 | 2000-09-19 | 遺伝子変異の判別方法 |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| WO2002024905A1 true WO2002024905A1 (fr) | 2002-03-28 |
Family
ID=18768281
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/JP2001/007942 Ceased WO2002024905A1 (fr) | 2000-09-19 | 2001-09-13 | Procede permettant de determiner la mutation genetique |
Country Status (3)
| Country | Link |
|---|---|
| JP (1) | JP2001137000A (fr) |
| AU (1) | AU2001286218A1 (fr) |
| WO (1) | WO2002024905A1 (fr) |
Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2008066164A1 (fr) * | 2006-11-30 | 2008-06-05 | Arkray, Inc. | Ensemble d'amorces utilisé dans l'amplification du gène de l'obésité, réactif utilisé dans l'amplification du gène de l'obésité comprenant ledit ensemble d'amorce et son utilisation |
Families Citing this family (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2001137000A (ja) * | 2000-09-19 | 2001-05-22 | Nobuyuki Hamashima | 遺伝子変異の判別方法 |
| JP4491276B2 (ja) * | 2004-05-17 | 2010-06-30 | 日本製粉株式会社 | 標的dna配列において一塩基変異多型の存在を検出する方法及びキット |
| WO2006030872A1 (fr) * | 2004-09-15 | 2006-03-23 | Celltec Projet Management Co., Ltd. | Procédé et appareil de mesure de taux de mutation |
| JP4650420B2 (ja) * | 2005-03-30 | 2011-03-16 | 東洋紡績株式会社 | 塩基判定方法及び塩基判定用キット |
Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP0530794A1 (fr) * | 1991-09-06 | 1993-03-10 | Roche Diagnostics GmbH | Méthode pour la détection d'acides nucléiques ayant une séquence similaire |
| JPH06167492A (ja) * | 1992-11-30 | 1994-06-14 | Otsuka Pharmaceut Co Ltd | 変異癌遺伝子の検出測定方法 |
| JPH0889297A (ja) * | 1994-09-26 | 1996-04-09 | S R L:Kk | Dna点突然変異の検出方法及び試薬 |
| JPH10276779A (ja) * | 1997-04-01 | 1998-10-20 | Sumitomo Metal Ind Ltd | 遺伝子プローブとdnaポリメラーゼを用いた変異検出方法 |
| JP2001137000A (ja) * | 2000-09-19 | 2001-05-22 | Nobuyuki Hamashima | 遺伝子変異の判別方法 |
-
2000
- 2000-09-19 JP JP2000283996A patent/JP2001137000A/ja active Pending
-
2001
- 2001-09-13 AU AU2001286218A patent/AU2001286218A1/en not_active Abandoned
- 2001-09-13 WO PCT/JP2001/007942 patent/WO2002024905A1/fr not_active Ceased
Patent Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP0530794A1 (fr) * | 1991-09-06 | 1993-03-10 | Roche Diagnostics GmbH | Méthode pour la détection d'acides nucléiques ayant une séquence similaire |
| JPH06167492A (ja) * | 1992-11-30 | 1994-06-14 | Otsuka Pharmaceut Co Ltd | 変異癌遺伝子の検出測定方法 |
| JPH0889297A (ja) * | 1994-09-26 | 1996-04-09 | S R L:Kk | Dna点突然変異の検出方法及び試薬 |
| JPH10276779A (ja) * | 1997-04-01 | 1998-10-20 | Sumitomo Metal Ind Ltd | 遺伝子プローブとdnaポリメラーゼを用いた変異検出方法 |
| JP2001137000A (ja) * | 2000-09-19 | 2001-05-22 | Nobuyuki Hamashima | 遺伝子変異の判別方法 |
Non-Patent Citations (4)
| Title |
|---|
| BROWN P.O. ET AL.: "Exploring the new world of the genome with DNA microarrays", NAT. GENET., vol. 21, no. 1 (SUPPL.), 1999, pages 33 - 37, XP002907408 * |
| ERLICH H.A. ET AL.: "Recent advances in the polymerase chain reaction", SCIENCE, vol. 252, 1991, pages 1643 - 1651, XP002907409 * |
| HAMAJIMA N. ET AL.: "Polymerase chain reaction with confronting two-pair primers for polymorphism genotyping", JPN. J. CANCER RES., vol. 91, no. 9, 25 September 2000 (2000-09-25), pages 865 - 868, XP002907406 * |
| KENSHI HAYASHI: "Jikken igaku bessatsu; Bio-manual UP series PCR-hou no saishin gijutsu", 15 October 1996, KABUSHIKI KAISHA YOUDOSHA, XP002907407 * |
Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2008066164A1 (fr) * | 2006-11-30 | 2008-06-05 | Arkray, Inc. | Ensemble d'amorces utilisé dans l'amplification du gène de l'obésité, réactif utilisé dans l'amplification du gène de l'obésité comprenant ledit ensemble d'amorce et son utilisation |
| US8021845B2 (en) | 2006-11-30 | 2011-09-20 | Arkray, Inc. | Probes for detecting obesity gene |
| JP5279492B2 (ja) * | 2006-11-30 | 2013-09-04 | アークレイ株式会社 | 肥満遺伝子増幅用プライマーセット、それを含む肥満遺伝子増幅用試薬およびその用途 |
Also Published As
| Publication number | Publication date |
|---|---|
| AU2001286218A1 (en) | 2002-04-02 |
| JP2001137000A (ja) | 2001-05-22 |
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