CN101824465B - Primer for analyzing gene mutation - Google Patents
Primer for analyzing gene mutation Download PDFInfo
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- CN101824465B CN101824465B CN200910207600.4A CN200910207600A CN101824465B CN 101824465 B CN101824465 B CN 101824465B CN 200910207600 A CN200910207600 A CN 200910207600A CN 101824465 B CN101824465 B CN 101824465B
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Abstract
The present invention provides a primer used for accurately and effectively detecting organism mutation. The analytical method of the gene base mutation comprises (a) a stage for amplifying a specific polynucleotide by using a forward primer and a reverse primer, (b) a stage for cutting the amplified specific polynucleotide with a restriction enzyme and producing two or more species of single chain polynucleotide fragments having a size of 2-32 bases and containing a mutated sequence and (c) a stage for measuring the molecular weight of the cut fragments.
Description
The application is 200380101469.4 (international application no PCT/KR/2003/002179), the applying date to be dividing an application of the application that on October 17th, 2003, denomination of invention " detects the method for sudden change " for application number.
Technical field
The present invention relates to the method for detection of biological body genovariation, specifically relate to a kind of primer that is used for analyzing gene mutation.Genetic analysis is used for risk assessment, diagnosis, prognosis or the disease treatment of disease.For example, make prediction disease danger become possibility, promote the prevention of disease thus to the mutation analysis of persona certa's specific gene.Through mutation analysis, can detect the virus that causes disease and whether medicine produced resistance, thereby can carry out efficacious therapy.
Background technology
The Human Genome Project makes us can more comprehensively weigh danger, diagnosis or the prognosis of disease and predicts the reaction to pharmacological agent.The analysis of the nucleotide sequence of a large amount of individualities demonstrates pleomorphism site, is referred to as SNPs (SNP).SNP appears at the variation in the chromosomal nucleotide sequence of organism with distinctive frequency.In human body, approximately SNP appears in per 1,000 base.Consider the size of human genome, millions of SNP are present in the human body.Owing to regard SNP as explain characteristic difference between the individuality means, therefore, SNP can be used for the prevention or the treatment of disease through the diagnosis cause of disease.
The SNP that is found by the Human Genome Project only shows that polymorphum is present in the human body, but does not show how those polymorphums interrelate with disease.In order to disclose the relation between SNP and the disease, need comparative analysis to show the polymorphism pattern among healthy subjects and the patient, i.e. SNP score.In order accurately to check the relation between SNP and the disease, should a large amount of SNP of correct analysis.
SNP point-score (SNP scoring method) comprises that dna sequencing, PCR-SSCP (polymerase chain reaction,PCR one single strand conformation polymorphism), allele-specific hybridization, oligonucleotide connect (oligo-ligation), micrometering preface (mini-sequencing) and enzyme cutting method.Use the method for DNA chip also to be suggested, but except the carrier that uses the immobilized oligonucleotide probe, this method and allele-specific hybridization are as broad as long on principle.
Two kinds of traditional methods that are used to carry out dna sequencing are Maxam&Gilbert Maxam-Gilbert methods, and the Sanger method of using recently.The dna sequencing method is in order to understand the nucleotide sequence of whole or portion gene, rather than detects the genovariation of specific site.Because can discern the genovariation of specific site through detecting nucleotide sequence, the dna sequencing method can be used in the SNP score.Yet owing to can read the adjacent nucleotide sequence that need not detect with target SNP, the dna sequencing method is very ineffective.
PCR-SSCP (ORITA, M.et al., Genomics, 1989,5:8874-8879) in, through the pcr amplification sequence that comprises SNP to be analyzed, be divided into strand then.After this, on polyacrylamide gel, carry out electrophoresis.Because the difference of sequence has changed the secondary structure of DNA, therefore can detect the sudden change in the sequence through difference by the electrophoretic migration speed that textural difference caused.
Allele-specific hybridization is through regulating the for example hybridization conditions of temperature, using the DNA of labelled with radioisotope and attached to the probe hybridization on the nylon membrane, detect sudden change.
Oligonucleotide connects (Nucleic Acid Research 24,3728,1996) and detects series jump through reacting under certain condition; Under this condition; If target DNA is not complementary with template DNA, then instead would not take place, whether take place thereby confirm to connect.
Micrometering preface (Genome Research 7:606,1997) is developed for the SNP score.This method is carried out the DNA polymerization under the condition of a target base of polymerizable only, discerning the polymerization base then is what.
Because polyacrylamide gel has all been used in PCR-SSCP, allele-specific hybridization, oligonucleotide link, therefore, these methods are not highly effective methods when analyzing many samples.And these methods can not be discerned the mistake that is caused by probe and non-target site mispairing.
Although the micrometering preface is simple and effective, but still can not discern the incorrect result that mistake caused of mispairing when analyzing many samples, and the micrometering preface can not be found the disappearance and the insertion of base.
For the SNP score, also developed enzyme cutting method (WO 01/90419).In enzyme cutting method, use the for example proper method amplification sequence to be analyzed of PCR.This amplified production comprises can be by the sequence of two kinds of digestion with restriction enzyme or identification.Enzyme cutting method is through detecting sequence variations with two kinds of digestion with restriction enzyme amplified productions and the molecular weight that detects endonuclease bamhi.Owing to after with the pcr amplification gene, can be obtained through the mass spectroscopy detection by the segmental molecular weight of restriction enzyme reaction gained, so enzyme cutting method has simply, advantage fast.Yet the enzyme cutting method of in patent WO 01/90419, describing can not be discerned the incorrect analysis that is caused by mistake.Although during PCR, when primer is combined on the non-target site, possibly cause incorrect analysis, can not discern this incorrect analysis.For example, the primer that is used to detect the polymorphum of CYP2C9 can combine with CYP2C8.In this case, owing to can not discern except CYP2C9, whether primer also combines with CYP2C8, and therefore, whether very difficult discovery mistake has taken place.This method can detect the replacement of a base, but can not detect base deletion or insertion.And this method can't detect the replacement of two or more adjacent bases simultaneously.
Summary of the invention
Therefore, the object of the present invention is to provide a kind of accurately and effectively method of detection of biological body sudden change that is used for.
To achieve these goals, in embodiment of the present invention, a kind of accurately and effectively method of detection of biological body sudden change that is used for is provided.
The present invention can simple and rapid detect the sudden change in many samples, and the mistake that can be caused in the combination of zone errors by primer through identification and accurately detect sudden change.And, the invention provides the method that detects two or more mutational sites, this mutational site is simultaneously adjacent within 32 bases; The present invention also provides the method that detects disappearance or insert.Particularly, when the different gene type was arranged in individuality, the sudden change that the inventive method can identify different loci was in a genotype, to exist simultaneously, still in the different gene type, mixed to exist.For example, the people has a pair of (two) karyomit(e) that comprises homologous genes information.When mutating now, it maybe or appear in two karyomit(e)s (homozygote), perhaps appears in the karyomit(e) (heterozygote).When the sudden change of two or more adjacent bases all be heterozygosis the time, those sudden changes possibly be present in the karyomit(e) simultaneously, perhaps possibly be present in the different dyeing body.Because these two kinds of situations possibly have different effects to life, therefore should they be distinguished.Receive the people under the situation of virus infection, the range gene type mixes.When the sudden change of adjacent base more than two all be heterozygosis the time, should distinguish those sudden changes is to be present in simultaneously in the genotype, still is present in the different genotype.
In order to analyze sudden change; Method amplification target sequence of the present invention; With the site of the products therefrom that comprises being limited property endonuclease digestion, and will be made as by the base numerical control in the fragment of digestion with restriction enzyme and be less than 32, and at least one base among them is to be produced by duplicating of template rather than primer itself; After with restriction enzyme the amplified fragments enzyme being cut, detect segmental molecular weight to analyze sudden change.
In an embodiment of the present invention, the method that detects sudden change is provided, comprising:
A) use forward primer and reverse primer amplified target polynucleotide;
B) through the target polynucleotide with the digestion with restriction enzyme amplification, generate two or more strand polynucleotide passages, this fragment comprises one or more mutant nucleotide sequences that length is 2~32 bases; And
C) molecular weight of detection endonuclease bamhi (cleaved fragment).
Preferably, the polynucleotide of said amplification are cut into a sudden change that in a strand polynucleotide passage, comprises in two or more different sudden changes, and in another strand nucleotide fragments, comprise all sudden changes.For example, when ... when A among the ATG... and G were mutant nucleotide sequence, first strand nucleotide fragments that is obtained by digestion with restriction enzyme only comprised two A in the mutant nucleotide sequence, and second strand Nucleotide comprises A and G simultaneously.
In order to analyze sudden change, method amplification target sequence of the present invention, so that it comprises such site, being limited property of the product endonuclease digestion that obtains in these sites amplifications, and endonuclease bamhi has following structure.
5’- | Primer binding sequence 1 | Restriction endonuclease recognition sequence | |
The sudden change presequence | Mutant nucleotide sequence | Sudden change back sequence | Primer binding sequence 3 | -3’ |
Said " restriction endonuclease recognition sequence " is meant can be by different restriction enzyme simultaneously or the sequence of proximity identification, this sequence can be not to cut sequence corresponding with enzyme.For example, but the equal recognition sequence GGATG of FokI and BSTFSI.But said restriction enzyme site is adjacent to respectively from the 9th/the 13rd and the 2nd/the 0th bit base of 3 ' end of recognition sequence.Two kinds of restriction enzymes that are used to discern restriction endonuclease recognition sequence can have identical or different optimum temperuture.Be preferably and have different optimum temperutures.Preferably, said restriction enzyme is the restriction enzyme with higher optimum temperuture that is selected from the restriction enzyme with low optimum temperuture of FokI, Bbv I, Bsg I, Bcg I, BpmI, BseR I, Bae I and is selected from BSTF5 I, Taq I, BsaB I, Btr I, BstAP I, Fau I, Bcl I, Pci I, Apo 1.Preferred, said restriction enzyme is Fok l and BSTF5 I.
Said restriction enzyme with low optimum temperuture comprises Bae I (25 ℃), FokI, BbvI, Bsg I, Bcg I, Bpm I, BseR I, Mmel I, Ava II (37 ℃); Said restriction enzyme with higher optimum temperuture is BSTF5 I, Taq I (65 ℃), BsaB I, Btr I, BstAP I (60 ℃), Bcl I, Pci I, Apo I (50 ℃).
One of two primers that are used for pcr amplification comprise primer binding sequence 1, restriction endonuclease recognition sequence and primer binding sequence 2, and another primer comprises primer binding sequence 3.
Said " primer binding sequence " is and nucleic acid complementary sequence as template, but said restriction endonuclease recognition sequence can be complementary with nucleic acid.Said primer binding sequence 1,2 and 3 base number should be at least four or more, to combine with template DNA.Because said primer can well combine with template DNA when 8~30 bases are long, therefore, preferred, the base number is 8~30.Said " sudden change presequence " (front sequence from mutation) is the sequence towards 5 ' end of sudden change to be detected.Said " mutant nucleotide sequence " (mutation sequence) is and the corresponding sequence of sudden change to be detected.The replacement of base, insertion and disappearance possibly take place, and wherein the number of base is generally 1, also can be two or more.Said " sudden change back sequence " (sequence behind mutation) is the sequence towards 3 ' end of mutant nucleotide sequence.
Preferably, said sudden change presequence is one or more with the base overall number of sudden change back sequence.The fragment that is cut into by restriction enzyme should comprise mutant nucleotide sequence, and segmental length is preferably 2~32 bases.Preferred, length is 12 bases.The reason of limited fragment length is, has in fragment under the situation of preferred length, and mass spectroscopy has result preferably.To such an extent as to the fragment of 32 bases is oversize can not to detect sudden change through using the mass spectrometric determination molecular weight because length surpasses, therefore above-mentioned segmental base number is preferred.And owing to only have the fragment of a mutant nucleotide sequence can not discern the combination of primer in wrong site, it is not preferred therefore the fragment of a base only being arranged.Because the identical or adjacent site of said two kinds of restriction enzymes identification is preferred, when a kind of restriction enzyme and amplified production reaction, another kind of restriction enzyme does not have activity.When with the digestion with restriction enzyme amplified fragments, consider the optimum temperuture of two kinds of restriction enzymes, can under different temperature, react continuously.In addition, can said fragment be used a kind of digestion with restriction enzyme earlier, and then use another kind of digestion with restriction enzyme.Here, the enzyme of first kind of restriction enzyme of warp is cut and should not be eliminated or damage recognition sequence or the restriction enzyme site that is present in second kind of restriction enzyme in the fragment that comprises mutant nucleotide sequence.
Brief description of drawings
From following and detailed description that accompanying drawing combines, can clearerly understand above-mentioned and further feature, aspect and the advantage of the preferred embodiment for the present invention, wherein:
Fig. 1 for when the 2741st bit base of the 4th intron of people maspin (serpinb5) gene for just often, the MALDI-TOF mass spectrum (C/C) of 7mer;
Fig. 2 for when the 2741st bit base of the 4th intron of people maspin gene for just often, the MALDI-TOF mass spectrum (C/C) of 13mer;
Fig. 3 is when the 2741st bit base of the 4th intron of people maspin gene is heterozygosis, the MALDI-TOF mass spectrum (C/T) of 7mer;
Fig. 4 is when the 2741st bit base of the 4th intron of people maspin gene is heterozygosis, the MALDI-TOF mass spectrum (C/T) of 13mer;
Fig. 5 is when the 2741st bit base of the 4th intron of people maspin gene all becomes T, the MALDI-TOF mass spectrum (T/T) of 7mer;
Fig. 6 is when the 2741st bit base of the 4th intron of people maspin gene all becomes T, the MALDI-TOF mass spectrum (T/T) of 13mer;
Fig. 7 for when the 3597th bit base of the 4th intron of people maspin gene for just often, the MALDI-TOF mass spectrum (C/C) of 7mer and 13mer;
Fig. 8 is when the 3597th bit base of the 4th intron of people maspin gene is heterozygosis, the mass spectrum of the MALDI-TOF of 7mer and 13mer (C/T); And
Fig. 9 is when the 3597th bit base of the 4th intron of people maspin gene all becomes T, the MALDI-TOF mass spectrum (T/T) of 7mer and 13mer.
Preferred forms of the present invention
Below, will combine accompanying drawing to describe preferred implementation of the present invention in detail.
The sudden change of the 2741st bit base of the 4th intron of [embodiment 1] people maspin gene
Detection is known as the sudden change of the 2741st bit base (1509477, the No. 18 chromosomal the 61001755th bit bases of rs) of people maspin (serpinb5) gene of metastasis of cancer suppressor gene.
1, pcr amplification and digestion with restriction enzyme
The sequence of template DNA (5 ' → 3 ') is as follows:
GTT
TCACTTGATAAAGCAATAAAATGCTATTCAcAGCT
GCATGAGGC TACACCCTTCTTTTGAATGCAG(SEQ?ID?NO:1)
Underlined sequence is the site of hybridizing with following primer 1 and 2.The base of using lowercase to represent is " mutant nucleotide sequence ".
Primer 1:5 '-TCACTTGATAAAGCAATAAAAggatgGCTATTCA-3 ' is (SEQ ID NO:2) (34mer)
Primer 2: 5 '-CATTCAAAAGAAGGGTGTAGCCTCATGC-3 ' (28mer) (SEQ ID NO:3)
Use sequence that lowercase representes recognition sequence as FokI and BSTF5I.
With PCR damping fluid (1 *), 2mM MgSO
4, 200mM triphosphate deoxy-nucleotide (dNTP), 0.315U PlatinumTaq polymerase (Invitrogen, 10966-026), 0.5 μ M primer 1 and 0.5 μ M primer 2 and 36ng genomic dna add to 18 μ l total reaction volume.Then, under following condition, carry out the PCR reaction.
94 ℃, 2 minutes,
94 ℃, 15 seconds 55 ℃, 15 seconds 72 ℃, 30 seconds (10 circulations),
94 ℃, 15 seconds 60 ℃, 15 seconds 72 ℃, 30 seconds (35 circulations)
Isolation of genomic DNA and purifying from blood.For example; When DNA isolation from blood, can use " SDS/ Proteinase K " method (Maniatis; Molecular Cloning, A laboratory Manual, ColdSpring Harbor Laboratory Press; Cold Spring Harbor, 1989) or QIAamp DNA trace quantity reagent kit 250 (Qiagen 51106).When the concentration of DNA was hanged down, available following method concentrated this DNA.At first 3M sodium-acetate (pH 5.3) and 2.5 volume of ethanol with 1/10 volume are added in the dna solution, slowly mix.Resulting solution is placed more than 1 hour at-20 ℃, then at 4 ℃, centrifugal 15 minutes with 13000 rev/mins.After removing supernatant, add 70% ethanol, resulting solution is at 4 ℃, centrifugal 10 minutes with 13000 rev/mins.Then, drying is removed ethanol, and the zero(ppm) water of pre-determined volume is added in the gained solution.
Fragments sequence by PCR obtains (5 ' → 3 ') as follows.
TCACTTGATAAAGCAATAAAAggatgGC
TATTCA[C/T]AGCTGCATGAGGCTACACCCTTCTTTTGAATG(SEQ?ID?NO:4)
AGTGAACTATTTCGTTATTTTcctac
CGATAAGT[G/A]TCGACGTACTCCGATGTGGGAAGAAAACTTAC(SEQ?ID?NO:5)
Use site that lowercase the representes sequence as FokI and BstF5I identification, underlined site be the fragments sequence that is produced by digestion with restriction enzyme, and the base of using square brackets to represent is " mutant nucleotide sequence ".In reactant, add 1U FokI (NEB R109L), 1U BstF5I (NEB, V0031L), the 50mM Potassium ethanoate, 20mM three (methylol) aminomethane acetate (Tris-acetate), 10mM magnesium acetate, 1mM WR 34678 (DTT) (pH7.925 ℃).Gained solution reacted 2 hours in the time of 25 ℃, and then in the time of 45 ℃, reacted 2 hours.
In order to optimize enzyme reaction, when 25 ℃, 37 ℃, 45 ℃, 55 ℃ and 65 ℃, make the reaction of FokI and BstF5I and amplified production.As a result, under the situation that FokI exists, in the time of 25 ℃, carry out 70% enzyme reaction, in the time of 37 ℃, carried out surpassing 90% enzyme reaction.Under the situation that BstFSI exists, in the time of 25 ℃, enzyme reaction does not take place.Therefore, preferred, the at first reaction in the time of 25 ℃ of said amplified production, have only FokI to react this moment, then, and reaction when surpassing 37 ℃, this moment, BstF5I can react.
2, purifying and desalination
Preferably, from above-mentioned through the solution that restriction enzyme is handled purifies and separates go out dna fragmentation, then, detect this segmental molecular weight.For example, can use Nucleave Genotyping test kit (Variagenics, USA).The TEAA (triethyl ammonium acetate, pH 7.6) of 70 μ l 1M is added in this restriction enzyme reaction solution, placed 1 minute.The TEAA of 70 μ l 1M and the above-mentioned mixing solutions of 90 μ l are added on the specimen preparation plate (Sample preparation plate), and the TEAA with 85 μ 11M filters the specimen preparation plate five times then.This specimen preparation plate is centrifugal 5 minutes with 1000 rev/mins.After this, this specimen preparation plate is placed on the collecting board (collection plate), 60% Virahol with 60 μ 1 is added into wherein and filters then.When being collected in effluent in the collecting board, with this collecting board 115 ℃ the time dry 75 minutes.
3, MALDI-TOF mass spectroscopy
6 μ l MALDI matrix (22.8mg Trisodium Citrate, 148.5mg hydroxy-picolinic acid, 1.12ml acetonitrile, 7.8ml water) are added in the collecting board; Then the mixture of 4 μ l MALDI matrix and effluent is placed on chip pad plate (the Anchor chip plate of MALDI-TOF; Biflex IV, Bruker) on.Drying is 30 minutes in the time of 37 ℃, is positioned over the room temperature cooling a little while, carries out MALDI-TOF then and analyzes.This analytical procedure is with reference to the MALDI-TOF handbook.
When the 2741st bit base of the 4th intron is normal (C/C), the segmental molecular weight that obtains after enzyme is cut be 2135.4D (dalton) (7mer) and 4078.6D (13mer) (seeing Fig. 1 and 2).When the 2741st bit base of the 4th intron is heterozygosis (C/T), segmental molecular weight is 2135.4D, 2150.4D (7mer) and 4078.6D, 4062.6D (13mer) (seeing Fig. 3 and 4).When the 2741st bit base of the 4th intron becomes T (T/T) entirely, segmental molecular weight is 2150.4D (7mer) and 4062.6D (13MER) (seeing Fig. 5 and 6).
Sudden change (the rs1396782 of the 3597th bit base of the 4th intron of [embodiment 2] people maspin (serpinb5) gene; Human No. 18 chromosomal the 61002611st bit base), known this gene behaviour metastasis of cancer suppressor gene
The sequence of template DNA is as follows.
CTG
GAGTATTATCCTTGCAGGCTTGATATGAAGcTTGAAAT
TTCTCC CCAAAGAGATTTAGTTAACAGGCAAA(SEQ?ID?NO:6)
Underlined sequence is the site of hybridizing with following primer 3 and 4.Sport " mutant nucleotide sequence " with what lowercase was represented.
Primer 3:5 '-GAGTATTATCCTTGCAGGCTTggatgATATGAAG-3 ' is (SEQ ID NO:7) (34mer)
Primer 4:5 '-GCCTGTTAACTAAATCTCTTTGGGGAGAA-3 ' is (SEQ ID NO:8) (29mer)
In above-mentioned primer, the site that the use lowercase is represented is not for to be present in the sequence in the template DNA, but FokI and BstF5I can discern them.This comprises the experimental technique of PCR reaction identical with described in the embodiment 1.
Fragments sequence through PCR obtains (5 ' → 3 ') as follows.
GAGTATTATCCTTGCAGGCTTggatgAT
ATGAAG[C/T]TTGAAATTTCTCCCCAAAGAGATTTAGTTAACAGGC(SEQ?ID?NO:9)
CTCATAATAGGAACGTCCGAAcctac
TATACTTC[G/A]AACTTTAAAGAGGGGTTTCTCTAAATCAATTGTCCG(SEQ?ID?NO:10)
The site of using lowercase to represent in the above-mentioned sequence is the restriction enzyme enzyme recognition sequence, the fragments sequence of underlined site for obtaining by digestion with restriction enzyme, and the base of representing with square brackets ([]) is " mutant nucleotide sequence ".With 1U FokI (NEB R109L), 1U BstF5I (NEB, V0031L), 50mM Potassium ethanoate, 20mM Tris-acetate, 10mM magnesium acetate, 1mM DTT (7.925 ℃ of pH).Resulting solution reacted 2 hours in the time of 25 ℃, and then in the time of 45 ℃, reacted 2 hours.
When the 3597th bit base of the 4th intron is normal (C/C), cutting the segmental molecular weight that obtains by enzyme is 2209.4D (7mer) and 3988.6D (13MER) (see figure 7).When the 3597th bit base of the 4th intron is heterozygosis (C/T), segmental molecular weight is 2209.4D, 2224.4D (7mer) and 3988.6D, 3972.6D (13mer) (see figure 8).When the 3597th bit base of the 4th intron becomes T (T/T) entirely, segmental molecular weight is 2224.4D (7mer) and 3972.6D (13mer) (see figure 9).
The base mutation in tyrosine-methionine(Met)-aspartic acid-aspartic acid (YMDD) site of [embodiment 3] hepatitis b virus dna polymerase
Detect the YMDD site mutation, this sudden change is arranged in the archaeal dna polymerase of the hepatitis B virus that causes human hepatitis B.The YMDD site mutation can produce the resistance to the lamivudine that is used for treating hepatitis B (1amivudine).Known, as methionine(Met) (M), promptly No. 552 codon when becoming Xie Ansuan (V) or Isoleucine (I), produced the resistance to lamivudine.
1, pcr amplification and digestion with restriction enzyme
(Qiagen CA), isolates hepatitis B virus DNA from 0.2ml serum, then 2 μ l DNA are used for pcr amplification to use QIAamp blood test kit.
The sequence of template DNA (5 ' → 3 ') is as follows.
TTCCCCCACTGTTTGGCTTTCAGTTATATG
GATGATGTGGTATTGG GGGCCAAGTCTGTA(SEQ?ID?NO:11)
Underlined sequence is the site of hybridizing with following primer 5 and 6.
Primer 5 (SEQ ID NO:12):
5′-TTCCCCCACTGTTTGGCTggatgTCAGTTAT-3′(31mer)
Primer 6 (SEQ ID NO:13):
5′-TACAGACTTGGCCCCCAATACCACAT
GATC-3′(30mer)
In primer 5, use sequence that lowercase the representes recognition sequence as FokI and BstF5I, this sequence is not included in the template DNA, but artificial the insertion.The sequence that underlines in primer 6 is the sequence through the manual change, to prevent the identification of FokI.
Through using 18 μ l to comprise 20mM Tris hydrochloride buffer (Tris-HCl; PH 8.4), 50mM Repone K, 0.2mM dNTP, 0.4U PlatinumTaq polymerase (Invitrogen; 10966-026), the reaction solution of 10pmol primer 5 and 10pmol primer 6, under following condition, carrying out the PCR reaction.
94 ℃, 2 minutes
94 ℃, 15 seconds 50 ℃, 15 seconds 72 ℃, 30 seconds (10 circulations),
94 ℃, 15 seconds 55 ℃, 15 seconds 72 ℃, 30 seconds (35 circulations)
Fragments sequence (5 ' → 3 ') by PCR obtains is as follows.
TTCCCCCACTGTTTGGCTggatgTC
AGTTATATGGATCATGTGGTATTGGGGGCCAAGTCTGTA(SEQ?ID?NO:14)
AAGGGGGTGACAAACCGAcctac
AGTCAATATACCTAGTACACCATAACCCCCGGTTCAGACAT(SEQ?ID?NO:15)
The site of using lowercase to represent is FokI and the discernible sequence of BstF5I, the fragments sequence of underlined site for being obtained by digestion with restriction enzyme.(NEB V0031L) mixes with 10 μ l reaction solutions (50mM Potassium ethanoate, 20mMTris-acetate, 10mM magnesium acetate, 1mM DTT) with PCR product and 1U FokI (NEBR109L), 1U BstF5I.This mixing solutions reacted 2 hours in the time of 37 ℃, in the time of 45 ℃, reacted 2 hours then.At first, this PCR product was cut 2 hours with the FokI enzyme 37 ℃ the time, in the time of 45 ℃, cut 2 hours then with the BstF5I enzyme.
2, purifying and desalination and MALDI-TOF mass spectroscopy
According to carrying out this experiment with embodiment 1 identical method.
Cut the segmental theoretical length that obtains by enzyme and accurately accord with value, show and be lower than 0.1% difference (seeing table 1) according to the actual molecular weight analyzing and testing.
Table 1
The guess value and the observed value of the PDT16 quality that obtains by the digestion with restriction enzyme of PCR product
Infer fragments sequence | Infer segmental quality (Da) | Observe segmental quality (Da) | ||||
Genotype codon No.552 | 7mer 13mer | 7mer 13mer | 7mer 13mer | |||
YMDD?aTg YVDD?aTg YIDD?aTt YIDD?aTc YIDD?aTa | AGTTATa?TCcAtATAACTGA AGTTATg?TCcAcATAACTGA AGTTATa?TCaAtATAACTGA AGTTATa?TCgAtATAACTGA AGTTATa?TCtAtATAACTGA | 2199.43997.6 2215.43982.6 2199.44021.6 2199.44037.6 2199.44012.6 | 2199.63998.0 2215.93982.6 2199.64021.8 2199.64038.0 2199.64012.6 |
In last table, resolving power (remove observation quality and infer the difference between the quality with inferring quality) is lower than 0.1%.
[embodiment 4] hepatitis C viruss (HCV) 5 ' NCR (non-coding region) site mutation
When Interferon, rabbit was used for the treatment of chronic hepatitis C, the difference of the result of treatment of performance depended on the genotype of hepatitis C in the human body.Therefore, the genotype of hepatitis C virus in should first human body before using Interferon, rabbit.In order to find genotype, the detection of 5 ' NCR sudden change is useful.In an embodiment of the present invention, the method for the 5 ' NCR site mutation that is used to analyze hepatitis C virus is disclosed.
1, rt polymerase chain reaction,PCR (RT PCR)
(Qiagen CA) isolates the RNA of hepatitis C virus from 0.14ml serum, then 10 μ l RNA are used for the RT pcr amplification to use QIAamp viral RNA trace quantity reagent kit.
The reaction solution that comprises 0.2mM dNTP, 0.4 μ M primer 2 and 10 μ l RNA reacted 5 minutes in the time of 65 ℃, placed on ice then 1 minute.With reaction solution and 20mM Tris HCl (pH 8.4), 50mM KCl, 4mM DTT, 0.4 μ M primer 1,100U SuperScript III ribonuclease H-reversed transcriptive enzyme (Invitrogen; 18080-044), 20U RNaseOUT (Invitrogen; 10777-019), (Invitrogen 10966-026) mixes 0.4U PlatinumTaq polymerase.Then, the solution with 25 μ l gained carries out RT PCR under following condition.
50 ℃, 45 minutes,
94 ℃, 2 seconds,
94 ℃, 15 seconds 55 ℃, 15 seconds 72 ℃, 30 seconds (35 circulations)
72 ℃, 5 minutes
The sequence of template DNA (5 ' → 3 ') is as follows.
GCAGAAAGCGTCTAGCCATGGCGTTAGTATGAGT (omitting)
ACTGCCTGATAGGGTGCTTGCGAG(SEQ ID NO:16)
Underlined sequence is the site of hybridizing with primer 7 and 8.
Primer 7 (SEQ ID NO:17): 5 '-GCAGAAAGCGTCTAGCCATGGCGT-3 ' is (24mer)
Primer 8 (SEQ ID NO:18): 5 '-CTCGCAAGCACCCTATCAGGCAGT-3 ' is (24mer)
2, nest-type PRC (Nested PCR) and digestion with restriction enzyme
Above-mentioned RT PCR reaction solution is diluted to 1/50 of original content.With 2 μ l diluents and 18 μ l comprise 20mM Tris HCl (pH 8.4), 50mM KCl, 0.2mM dNTP, 0.4U PlatinumTaq polymerase (Invitrogen, 10966-026), 10pmol primer 9 and 10,10pmol primer 11 and 12 and the reaction solution of 10pmol primer 13 and 14 mix.Carrying out following three types PCR reaction and restriction enzyme with this mixing solutions handles.Primer 9 and 10 is used to react 1, and primer 11 and 12 is used to react 2, and primer 13 and 14 is used to react 3.The PCR temperature of reaction and the time of said three kinds of reactions are described below.
94 ℃, 5 minutes,
94 ℃, 30 seconds 55 ℃, 30 seconds 72 ℃, 30 seconds (35 circulations)
72 ℃, 5 minutes
1) reaction 1
Use primer 9 and 10, in RT-PCR solution, carry out this pcr amplification.The sequence of template DNA (5 ' → 3 ') is as follows.
CGTCTAGCCATGGCGTTAGTATGAGTGTCGTGCAGCCTCCAGGACCC... (omit) ... CTGCTAGCCGAGTAGTGTTGGGTCGCGAAAG
GCCTTGTGGTACTGCCTGATAGGG(SEQ ID NO:19)
Underlined sequence is the site of hybridizing with following primer 9 and 10.
Primer 9 (SEQ ID NO:20):
5′-CGTCTAGCCATGGCGTTAGggatgATGAGTGT-3′(32mer)
Primer 10 (SEQ ID NO:21):
5′-CCCTATCAGGCAGTACCACAAGGC-3′(24mer)
Fragments sequence (5 ' → 3 ') as follows by the pcr amplification generation.
CGTCTAGCCATGGCGTTAGggatgAT
GAGTGTCGTGCAGCCTCCAGGACCC... (omit)
GCAGATCGGTACCGCAATCcctac
TACTCACAGCACGTCGGAGGTCCTGGG... (omit)
...CTGCTAGCCGAGTAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGG(SEQ?ID?NO:22)
...GACGATCGGCTCATCACAACCCAGCGCTTTCCGGAACACCATGACGGACTATCCC(SEQ?ID?NO:23)
The site of using lowercase to represent is FokI and the discernible sequence of BstF5I.Underlined site is the fragments sequence (7mer and 13mer) that is produced by restriction enzyme.(NEB V0031L) mixes with 10 μ l reaction solutions (50mM Potassium ethanoate, 20mM Tris-acetate, 10mM magnesium acetate, 1mM DTT) with PCR product and 1U FokI (NEB R109L), 1U BstF5I.This mixing solutions reacted 2 hours in the time of 37 ℃, in the time of 45 ℃, reacted 2 hours then.The PCR product was cut 2 hours with the FokI enzyme 37 ℃ the time, in the time of 45 ℃, cut 2 hours then with the BstF5I enzyme.
2) reaction 2
Use primer 11 and 12, in RT-PCR solution, carry out this pcr amplification.The sequence of template DNA (5 ' → 3 ') is as follows.
GTGGTCTGCGGAACCGGTGAGTACACCGGAATTGCCAGGACGACCGGGTCC... (omit)
...CCCGCAAGACTG
CTAGCCGAGTAGRGTTGGGTRGCGAA(SEQID?NO:24)
Underlined sequence is the site of hybridizing with following primer 11 and 12.
Primer 11 (SEQ ID NO:25):
5′-GTGGTCTGtccaacCGGTGAGTACACCGGAAT-3′(32mer)
Primer 12 (SEQ ID NO:26):
5′-TTCGCRACCCAACRCTACtccaacggtcCGGCTAG-3′(35MER)
The represented base of R is VITAMIN B4 (A) or guanine (G).Use comprises the mixture of two kinds of primers of each base.
Fragments sequence (5 ' → 3 ') as follows by this PCR generation.
GTGGTCTGtccaacCGGTGAGTACACCGGAATTG
CCAGGACGACCGGGTCC... (omit)
CACCAGACaggttgGCCACTCATGTGGCCTTA
ACGGTCCTGCTGGCCC AGG... (omit)
...CCCCGC
AAGACTGCTAGCCGgaccgttggaGTAGRGTTGGGTRGCGAA(SEQ?ID?NO:27)
...GGGG
CGTTCTGACGATCGGCctggcaacctCATCRCAACCCARCGCTT(SEQ?ID?NO:28)
The site of using lowercase to represent is MmeI and the discernible sequence of AvaII, and underlined site is the fragments sequence (13mer, 18mer, 24mer, 19mer) that produces with digestion with restriction enzyme.PCR product and 1.5U MmeI (NEB R0637L), 50 μ M SAM (S-adenosine-L-methionine(Met)) and 10 μ l, 1 * reaction solution (pH 7.9 for 50mM Potassium ethanoate, 20mM Tris-acetate, 10mM magnesium acetate, 1mMDTT) are mixed.This mixed solution reacted 2 hours in the time of 37 ℃, and (NEB R0153S) adds wherein with 1.5U AvaII then.The solution of gained reacted 2 hours in the time of 37 ℃.MmeI and AvaII can add in the mixed solution simultaneously.
3) reaction 3
Use primer 13 and 14, in RT-PCR solution, carry out this pcr amplification.The sequence of template DNA (5 ' → 3 ') is as follows.
GACIGGGTCCTTTCTTGGATCAACCCGCTCAATGCCTGGAG
ATTTG GGCGTGCCCCCGC(SEQ?ID?NO:29)
Underlined sequence is the site of hybridizing with following primer 13 and 14.
Primer 13 (SEQ ID NO:30):
5′-GACIGGGTCCTggatgTCTTGGA-3′(23mer)
Primer 14 (SEQ ID NO:31):
5′-GCGGGGGCACggatgCCCAAAT-3′(22mer)
The represented base of I is an inosine.
Fragments sequence (5 ' → 3) as follows by this PCR generation.
GACIGGGTCCTggatgTC
TTGGATC?
AACCCGCTCAATGC CTGGAGATTTGGG?catccGTGCCCCCGC(SEQ?ID?NO:32)
CTGICCCAGGAcctac
AGAACCTAGTTGG?
GCGAGTTACGGACC?
TCTA AACCCgtaggCACGGGGGCG(SEQ?ID?NO:33)
The site of using lowercase to represent is FokI and the discernible sequence of BstF5I, and underlined site is the fragments sequence that produces with digestion with restriction enzyme.The fragment that generates is 2 7mer, 2 13mer, and 2 14mer.(NEB V0031L) mixes with 10 μ l reaction solutions (50mM Potassium ethanoate, 20mM Tris-acetate, 10mM Potassium ethanoate, 1mM DTT) with PCR product and 1U FokI (NEB R109L), 1U BstF5I.This mixed solution reacted 2 hours in the time of 37 ℃, in the time of 45 ℃, reacted 2 hours then.This fragment was at first cut 2 hours with the FokI enzyme 37 ℃ the time, cut 2 hours with the BstF5I enzyme at 45 ℃ then.
2, purifying and desalination and MALDI-TOF mass spectroscopy
Adopt the PCR and the restriction enzyme reaction solution of three types of the method purifying identical, then the detection molecules amount with embodiment 1.
By the segmental length of reaction 1 (table 2), reaction 2 (tables 3) and reaction 3 (tables 4) generation shown in table 2~4.Confirm the genotype of hepatitis C according to the fragment length that obtains by ready reckoner, shown in table 2~4.
Table 2
Genotype | 7mer | 13mer |
1a | 2216.4 | 3983.6 |
1b | 2216.4 | 3983.6 |
1c | 2216.4 | 3983.6 |
3a | 2216.4 | 3983.6 |
3b | 2216.4 | 3983.6 |
3c | 2216.4 | 3983.6 |
3d | 2216.4 | 3983.6 |
3e | 2216.4 | 3983.6 |
3f | 2216.4 | 3983.6 |
6b | 2216.4 | 3983.6 |
7a | 2216.4 | 3983.6 |
7b | 2216.4 | 3983.6 |
7c | 2216.4 | 3983.6 |
2′ | 2216.4 | 3989.6 |
5a | 2216.4 | 3989.6 |
1b | 2216.4 | 3998.6 |
1d | 2216.4 | 3998.6 |
1e | 2216.4 | 3998.6 |
1f | 2216.4 | 3998.6 |
2a | 2216.4 | 3998.6 |
2b | 2216.4 | 3998.6 |
2c | 2216.4 | 3998.6 |
2d | 2216.4 | 3998.6 |
2e | 2216.4 | 3998.6 |
2′ | 2216.4 | 3998.6 |
4h | 2216.4 | 3998.6 |
6a | 2216.4 | 3998.6 |
7d | 2216.4 | 3998.6 |
1b | 2231.4 | 3967.6 |
4g | 2231.4 | 3967.6 |
4k | 2231.4 | 3967.6 |
2a | 2231.4 | 3982.6 |
4a | 2231.4 | 3982.6 |
4b | 2231.4 | 3982.6 |
4c | 2231.4 | 3982.6 |
4d | 2231.4 | 3982.6 |
4e | 2231.4 | 3982.6 |
4e′ | 2231.4 | 3982.6 |
4f | 2231.4 | 3982.6 |
4f’ | 2231.4 | 3982.6 |
Table 3
Genotype | 13mer | 18mer | Genotype | 14mer | 19mer |
1a | 4049.6 | 5556.6 | 2a | 4337.8 | 5891.8 |
1b | 4049.6 | 5556.6 | 2e | 4337.8 | 5891.8 |
1c | 4049.6 | 5556.6 | 4b | 4337.8 | 5891.8 |
1d | 4049.6 | 5556.6 | 4e′ | 4337.8 | 5891.8 |
1e | 4049.6 | 5556.6 | 1a | 4352.8 | 5875.8 |
1f | 4049.6 | 5556.6 | 1c | 4352.8 | 5875.8 |
6b | 4049.6 | 5556.6 | 1d | 4352.8 | 5875.8 |
7a | 4049.6 | 5556.6 | 1e | 4352.8 | 5875.8 |
7b | 4049.6 | 5556.6 | 2a | 4352.8 | 5875.8 |
4a | 4049.6 | 5572.6 | 2b | 4352.8 | 5875.8 |
6a | 4064.6 | 5540.6 | 2c | 4352.8 | 5875.8 |
7c | 4064.6 | 5540.6 | 2d | 4352.8 | 5875.8 |
7d | 4064.6 | 5540.6 | 2′-1 | 4352.8 | 5875.8 |
4f | 4065.6 | 5541.6 | 2′-2 | 4352.8 | 5875.8 |
4e′ | 4064.6 | 5556.6 | 3a | 4352.8 | 5875.8 |
4f | 4065.6 | 5557.6 | 3b | 4352.8 | 5875.8 |
4g | 4065.6 | 5557.6 | 3d | 4352.8 | 5875.8 |
5a | 4080.6 | 5525.6 | 3e | 4352.8 | 5875.8 |
3b | 4080.6 | 5541.6 | 4c | 4352.8 | 5875.8 |
4b | 4080.6 | 5541.6 | 4d | 4352.8 | 5875.8 |
4c | 4080.6 | 5541.6 | 4f | 4352.8 | 5875.8 |
4d | 4080.6 | 5541.6 | 4f | 4352.8 | 5875.8 |
4e | 4080.6 | 5541.6 | 4g | 4352.8 | 5875.8 |
4h | 4080.6 | 5541.6 | 6a | 4352.8 | 5875.8 |
4k | 4080.6 | 5541.6 | 6b | 4352.8 | 5875.8 |
2d | 4088.6 | 5515.6 | 7c | 4353.8 | 5876.8 |
2b | 4088.6 | 5530.6 | 1b | 4368.8 | 5860.8 |
3f | 4096.6 | 5526.6 | 1f | 4368.8 | 5860.8 |
2a | 4104.6 | 5500.6 | 3c | 4368.8 | 5860.8 |
2c | 4104.6 | 5500.6 | 3f | 4368.8 | 5860.8 |
2e | 4104.6 | 5500.6 | 4a | 4368.8 | 5860.8 |
2′ | 4104.6 | 5500.6 | 4e | 4368.8 | 5860.8 |
2′ | 4104.6 | 5500.6 | 4h | 4368.8 | 5860.8 |
3a | 4111.6 | 5510.6 | 4k | 4368.8 | 5860.8 |
3c | 4111.6 | 5510.6 | 5a | 4368.8 | 5860.8 |
3d | 4111.6 | 5510.6 | 7a | 4368.8 | 5860.8 |
3e | 4111.6 | 5510.6 | 7b | 4368.8 | 5860.8 |
7d | 4368.8 | 5860.8 |
Table 4
Industrial applicability
In an embodiment of the invention, can discern the improper analysis that the mistake in the method for conventional sense sudden change causes, and can detect 32 various sudden changes simultaneously with interior adjacent base.When the individuality with sudden change had the range gene type, the sudden change that can distinguish different loci was to be present in simultaneously in the genotype, still mixed to be present in the plural genotype.In addition, can detect the sudden change that causes by genetically deficient or insertion.
So far, detailed description the present invention.Yet, should be appreciated that because from this detailed description; To those skilled in the art, the variations and modifications that do not exceed spirit and scope of the invention are conspicuous, therefore; Detailed description and specific embodiment that this has shown the preferred embodiment for the present invention only are exemplary.
Sequence table
< 110>Genematrix Inc.; Liu Wangdun
< 120>detect the method for suddenling change
<130>PCT03-058
<150>KR2002-0063832
<151>2002-10-18
<150>KR2003-0061066
<151>2003-09-02
<160>33
<170>KopatentIn?1.71
<210>1
<211>69
<212>DNA
< 213>people
<400>1
gtttcacttg?ataaagcaat?aaaatgctat?tcacagctgc?atgaggctac?acccttcttt 60
tgaatgcag 69
<210>2
<211>34
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer of maspin gene the 4th intron
<400>2
tcacttgata?aagcaataaa?aggatggcta?ttca 34
<210>3
<211>28
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer of maspin gene the 4th intron
<400>3
cattcaaaag?aagggtgtag?cctcatgc 28
<210>4
<211>68
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>4
tcacttgata?aagcaataaa?aggatggcta?ttcactagct?gcatgaggct?acacccttct 60
tttgaatg 68
<210>5
<211>68
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>5
agtgaactat?ttcgttattt?tcctaccgat?aagtgatcga?cgtactccga?tgtgggaaga 60
aaacttac 68
<210>6
<211>73
<212>DNA
< 213>people
<400>6
ctggagtatt?atccttgcag?gcttgatatg?aagcttgaaa?tttctcccca?aagagattta 60
gttaacaggc?aaa 73
<210>7
<211>34
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer of maspin gene the 4th intron
<400>7
gagtattatc?cttgcaggct?tggatgatat?gaag 34
<210>8
<211>29
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer of maspin gene the 4th intron
<400>8
gcctgttaac?taaatctctt?tggggagaa 29
<210>9
<211>72
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>9
gagtattatc?cttgcaggct?tggatgatat?gaagctttga?aatttctccc?caaagagatt 60
tagttaacag?gc 72
<210>10
<211>72
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>10
ctcataatag?gaacgtccga?acctactata?cttcgaaact?ttaaagaggg?gtttctctaa 60
atcaattgtc?cg 72
<210>11
<211>60
<212>DNA
< 213>hepatitis B virus
<400>11
ttcccccact?gtttggcttt?cagttatatg?gatgatgtgg?tattgggggc?caagtctgta 60
60
<210>12
<211>31
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer of hepatitis B virus
<400>12
ttcccccact?gtttggctgg?atgtcagtta?t 31
<210>13
<211>30
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer of hepatitis B virus
<400>13
tacagacttg?gcccccaata?ccacatgatc 30
<210>14
<211>64
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>14
ttcccccact?gtttggctgg?atgtcagtta?tatggatcat?gtggtattgg?gggccaagtc 60
tgta 64
<210>15
<211>64
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>15
aagggggtga?caaaccgacc?tacagtcaat?atacctagta?caccataacc?cccggttcag 60
acat 64
<210>16
<211>244
<212>DNA
< 213>artificial sequence
<220>
< 223>5 ' of hepatitis C virus non-coding region
<400>16
gcagaaagcg?tctagccatg?gcgttagtat?gagtgtcgtg?cagcctccag?gaccccccct 60
cccgggagag?ccatagtggt?ctgcggaacc?ggtgagtaca?ccggaattgc?caggacgacc 120
gggtcctttc?ttggatcaac?ccgctcaatg?cctggagatt?tgggcgtgcc?cccgcaagac 180
tgctagccga?gtagtgttgg?gtcgcgaaag?gccttgtggt?actgcctgat?agggtgcttg 240
cgag 244
<210>17
<211>24
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer of hepatitis C virus 5 ' non-coding region
<400>17
gcagaaagcg?tctagccatg?gcgt 24
<210>18
<211>24
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer of hepatitis C virus 5 ' non-coding region
<400>18
ccctatcagg?cagtaccaca?aggc 24
<210>19
<211>226
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>19
cgtctagcca?tggcgttagt?atgagtgtcg?tgcagcctcc?aggacccccc?ctcccgggag 60
agccatagtg?gtctgcggaa?ccggtgagta?caccggaatt?gccaggacga?ccgggtcctt 120
tcttggatca?acccgctcaa?tgcctggaga?tttgggcgtg?cccccgcaag?actgctagcc 180
gagtagtgtt?gggtcgcgaa?aggccttgtg?gtactgcctg?ataggg 226
<210>20
<211>32
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer
<400>20
cgtctagcca?tggcgttagg?gatgatgagt?gt 32
<210>21
<211>24
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer
<400>21
ccctatcagg?cagtaccaca?aggc 24
<210>22
<211>230
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR primer of gained
<400>22
cgtctagcca?tggcgttagg?gatgatgagt?gtcgtgcagc?ctccaggacc?ccccctcccg 60
ggagagccat?agtggtctgc?ggaaccggtg?agtacaccgg?aattgccagg?acgaccgggt 120
cctttcttgg?atcaacccgc?tcaatgcctg?gagatttggg?cgtgcccccg?caagactgct 180
agccgagtag?tgttgggtcg?cgaaaggcct?tgtggtactg?cctgataggg 230
<210>23
<211>230
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>23
gcagatcggt?accgcaatcc?ctactactca?cagcacgtcg?gaggtcctgg?gggggagggc 60
cctctcggta?tcaccagacg?ccttggccac?tcatgtggcc?ttaacggtcc?tgctggccca 120
ggaaagaacc?tagttgggcg?agttacggac?ctctaaaccc?gcacgggggc?gttctgacga 180
tcggctcatc?acaacccagc?gctttccgga?acaccatgac?ggactatccc 230
<210>24
<211>133
<212>DNA
< 213>artificial sequence
<220>
< 223>template DNA
<400>24
gtggtctgcg?gaaccggtga?gtacaccgga?attgccagga?cgaccgggtc?ctttcttgga 60
tcaacccgct?caatgcctgg?agatttgggc?gtgcccccgc?aagactgcta?gccgagtagr 120
gttgggtrgc?gaa 133
<210>25
<211>32
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer
<400>25
gtggtctgtc?caaccggtga?gtacaccgga?at 32
<210>26
<211>35
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer
<400>26
ttcgcraccc?aacrctactc?caacggtccg?gctag 35
<210>27
<211>142
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>27
gtggtctgtc?caaccggtga?gtacaccgga?attgccagga?cgaccgggtc?ctttcttgga 60
tcaacccgct?caatgcctgg?agatttgggc?gtgcccccgc?aagactgcta?gccggaccgt 120
tggagtagrg?ttgggtrgcg?aa 142
<210>28
<211>142
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<400>28
caccagacag?gttggccact?catgtggcct?taacggtcct?gctggcccag?gaaagttcct 60
agttgggcga?gttacggacc?tctaaacccg?cacgggggcg?ttctgacgat?cggcctggca 120
acctcatcrc?aacccarcgc?tt 142
<210>29
<211>59
<212>DNA
< 213>artificial sequence
<220>
< 223>template DNA
<220>
The base of < 221>modifying
<222>(4)
<223>i
<400>29
gacngggtcc?tttcttggat?caacccgctc?aatgcctgga?gatttgggcg?tgcccccgc 59
<210>30
<211>23
<212>DNA
< 213>artificial sequence
<220>
< 223>forward primer
<220>
< 221>base of modified
<222>(4)
<223>i
<400>30
gacngggtcc?tggatgtctt?gga 23
<210>31
<211>22
<212>DNA
< 213>artificial sequence
<220>
< 223>reverse primer
<400>31
gcgggggcac?ggatgcccaa?at 22
<210>32
<211>67
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<220>
The base of < 221>modifying
<222>(4)
<223>i
<400>32
gacngggtcc?tggatgtctt?ggatcaaccc?gctcaatgcc?tggagatttg?ggcatccgtg 60
cccccgc 67
<210>33
<211>67
<212>DNA
< 213>artificial sequence
<220>
< 223>the PCR fragment of gained
<220>
The base of < 221>modifying
<222>(4)
<223>i
<400>33
ctgncccagg?acctacagaa?cctagttggg?cgagttacgg?acctctaaac?ccgtaggcac 60
gggggcg 67
Claims (1)
1. primer that is used for analyzing gene mutation; Comprise primer binding sequence 1, restriction endonuclease recognition sequence and primer binding sequence 2; Wherein, Cut the polynucleotide passage that obtains through two or more enzymes of discerning the restriction enzyme of said restriction endonuclease recognition sequence and comprise a mutant nucleotide sequence, and said segmental size is 2~32 bases
Wherein said primer is selected from: the SEQ ID NOS.2 and 3 of the 2741st bit base sudden change that is used to detect the 4th intron of people maspin gene; Be used to detect the SEQ ID NOS.7 and 8 of the 3597th base mutation of the 4th intron of people maspin gene; Be used to detect the SEQ ID NOS.12 and 13 of the base mutation in the tyrosine-aspartic acid of hepatitis b virus dna polymerase-propylhomoserin site, east, Tianmen; Be used to detect the SEQ ID NOS.20 and 21 of hepatitis C virus 5 ' non-coding region base mutation; Be used to detect the SEQ ID NOS.25 and 26 of hepatitis C virus 5 ' non-coding region base mutation; And the SEQ ID NOS.30 and 31 that is used to detect hepatitis C virus 5 ' non-coding region base mutation, and
Wherein said restriction enzyme is FokI and BstF5I, perhaps Mme I and Ava II.
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KR20020063832 | 2002-10-18 | ||
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KR20030061066A KR100642829B1 (en) | 2002-10-18 | 2003-09-02 | Method for detecting base mutation |
KR10-2003-0061066 | 2003-09-02 |
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CN2003801014694A Division CN101027407B (en) | 2002-10-18 | 2003-10-17 | Method for detecting mutation |
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CN200910207600.4A Expired - Fee Related CN101824465B (en) | 2002-10-18 | 2003-10-17 | Primer for analyzing gene mutation |
CN2003801014694A Expired - Fee Related CN101027407B (en) | 2002-10-18 | 2003-10-17 | Method for detecting mutation |
CN2009102088016A Pending CN101962672A (en) | 2002-10-18 | 2003-10-17 | Method for detecting mutation |
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CN2003801014694A Expired - Fee Related CN101027407B (en) | 2002-10-18 | 2003-10-17 | Method for detecting mutation |
CN2009102088016A Pending CN101962672A (en) | 2002-10-18 | 2003-10-17 | Method for detecting mutation |
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KR (1) | KR100642829B1 (en) |
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JP2009201457A (en) * | 2008-02-29 | 2009-09-10 | Jsr Corp | Set of primer and probe, kit for detecting hepatitis c virus rna by real-time detection pcr and method for detecting hepatitis c virus rna by real-time detection pcr |
CN101597638B (en) * | 2008-06-04 | 2011-12-28 | 博奥生物有限公司 | Method and special kit for detecting gene multi-mutant site |
KR101025450B1 (en) * | 2008-08-06 | 2011-04-04 | (주)진매트릭스 | Method for detecting multiple base mutations |
KR101287431B1 (en) | 2010-05-07 | 2013-07-19 | (주)진매트릭스 | Primer composition for amplifying genetic region having various genetic variations in target genes, method for amplifying the target genes using the same, PCR amplification kit comprising the same and method for analyzing the genotype of the target genes |
KR20130110811A (en) * | 2012-03-30 | 2013-10-10 | (주)진매트릭스 | Method for detecting mutations in drug-resistant related genes of hiv using restriction fragments mass polymorphism |
KR101915701B1 (en) * | 2016-06-16 | 2018-11-07 | 한국한의학연구원 | Method for measuring mutation rate |
Citations (1)
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CN1340705A (en) * | 2000-08-25 | 2002-03-20 | 程新建 | Method for detecting mutation of allelic gene point |
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CN1340705A (en) * | 2000-08-25 | 2002-03-20 | 程新建 | Method for detecting mutation of allelic gene point |
Non-Patent Citations (2)
Title |
---|
Georgios Amexis等.Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorptiony ionization time-of-flight mass spectrometry.《PNAS》.2001,第98卷(第21期),12097-12102. * |
Kenneth H. Buetow等.High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorptionyionization time-of-flight mass spectrometry.《PNAS》.2001,第98卷(第2期),581-584. * |
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JP2007209354A (en) | 2007-08-23 |
CN101824465A (en) | 2010-09-08 |
JP4020845B2 (en) | 2007-12-12 |
HK1113589A1 (en) | 2008-10-10 |
CN101027407A (en) | 2007-08-29 |
JP4073471B2 (en) | 2008-04-09 |
CN101027407B (en) | 2012-05-23 |
JP2004135659A (en) | 2004-05-13 |
KR20040034382A (en) | 2004-04-28 |
KR100642829B1 (en) | 2006-11-10 |
CN101962672A (en) | 2011-02-02 |
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