CN1678743A - Method of identifying nucleic acid having polymorphism sequence site - Google Patents
Method of identifying nucleic acid having polymorphism sequence site Download PDFInfo
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- CN1678743A CN1678743A CN 03820966 CN03820966A CN1678743A CN 1678743 A CN1678743 A CN 1678743A CN 03820966 CN03820966 CN 03820966 CN 03820966 A CN03820966 A CN 03820966A CN 1678743 A CN1678743 A CN 1678743A
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- 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
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
Abstract
A method of identifying whether a nucleic acid having a polymorphism sequence site has a desired base sequence in the polymorphism sequence site or not which comprises hybridizing the following (1) and (2) with a target nucleic acid having a polymorphism sequence site and then subjecting the hybridization mixture to such reaction conditions as allowing the progress of a primer chain transfer/extension reaction: (1) an identification primer (which has a base sequence for identifying a polymorphism sequence at the 3'-terminal part) and (2) an oligonucleotide having no primer function (which is totally or partly complementary to the 5'-terminal region of the target nucleic acid compared with the above-described identification primer). According to this method, a single nucleotide difference in a nucleic acid can be quickly, conveniently and highly accurately detected.
Description
[background of invention]
Invention field
The present invention relates to a kind ofly can highly precisely detect nucleotide sequence difference, for example the nucleic acid authentication method that the difference of 1 base also can detect in the nucleotide sequence.
Correlation technique
In recent years, owing to worldwide carried out the human genome parsing, when the sequence of about 3,100,000,000 base pairs is determined, also determined the gene number the chances are ten thousand of 3-4.
Base sequence exists difference between the human individual, and the difference that exists with the frequency more than 1% in specific colony's population is called gene pleiomorphism.Show that wherein the gene base sequence has only a different SNP (single nucleotide polymorphism) of base to have association with multiple disease.For example, sick its cause of disease of Human genome is considered to the difference of a base in the gene.In addition, diseases due to habit disturbance, cancers etc. also are considered to the reason owing to the difference of a base in several genes in a plurality of genes.Therefore, the parsing of SNP is considered to very effective in the exploitation of exploring pharmaceuticals such as pharmacy target and prediction side effect.Therefore, SNP resolves and is being pushed into as global huge project.
About the effect of medicine and the individual difference of side effect, be the reason of enzyme group difference of everyone drug metabolism, recent findings, its difference also be on the gene nuance cause.In addition, all variant between the individuality at curative effect of medication, pathogeny bacterium and the viral resistance of pathogeny bacterium and virus, these also are because the nuance of individual gene causes.
Therefore, think can the ex ante analysis patient gene, select best medicine to patient's administration.And, term single gene disease not only, even for multifactorial disease, the gene diagnosis meaning is also constantly improving fast.And for the pathogeny bacterium of external factor and the gene diagnosis of virus, prediction checks that object is bound to increase from now on.
In the medical treatment of genome times afterwards comprehensively like this, can detect the nuance, the particularly difference of 1 base of the gene of human and pathogeny microorganism, be very important, estimate that importance also can strengthen from now on.
Up to now, method about the nuance that detects base sequence, particularly detect the method for the difference of 1 base, many research (Landegren have been carried out, the laboratory draft that mutation detects, the Oxford University publishes, (1996) Ahmadian etc., Biotechniques 32,1122-1137 (2002)).
But, in order to have the detection of practicality, low-cost, make method easy, shorten detection time, guarantee that all there is higher requirement aspects such as detected result is correct.Up to the present the tool inventor's understanding, does not also have the detection method of practicality.
Detect the nuance of gene, particularly during the difference of 1 base, in general, target gene fragment only contains seldom amount in sample.In this case, be necessary with someway goal gene being increased in advance.So the method for amplification gene can be enumerated PCR (polymerase chain reaction) method that resembles.
In general, for the difference of 1 base of testing goal gene, need the gene amplification stage and detect the operation (Ahmadian etc., Biotechniques 32,1122-1137 (2002)) in two stages in difference stage of 1 base of the gene that is amplified.But, the method for the operation in two stages of needs, because operation is many, can be pretty troublesome in the processing.
In order to improve the numerous and diverse of described 2 stage procedures, for example, have and use the Taqman method (Livak etc. that have fluorochrome and quencher probe, PCR Methods Appl.5,357-362 (1995)), perhaps, utilize the MALDI-TOF/MS method (Griffin etc. of DNA mass analysis with spectrometry mass, Trends Biotechnol.18,77-84 (2000)) report such as.Also have in addition as the method that need not gene amplification, use the identification of dna structure and cut off the report of the Invader method (Ryan etc., Molecular diagnosis 4,135-144 (1999)) of the enzyme of DNA.But the cost of implementing these methods is still very high, and the design of probe is also very complicated.
On the other hand, studied the method (Newton etc., Nucleic Acids Res.17,2503-2516 (1989), Okayama etc., J.Lab.Clin.Med.114,1053-113 (1989)) of the evaluation of an amplification of carrying out gene simultaneously and a base.Whether this method is in the extension of archaeal dna polymerase, complementary according to the 3 ' end and the template of primer, thereby causes extension or do not cause extension.Promptly in PCR reaction, at 3 ' end of the primer of a side, design the primer that can carry out the evaluation of 1 base, under template and the complete complementary situation of primer, carry out extension, and carry out amplified reaction between the primer of opposite side.But, under the 3 ' end and the situation of 1 base generation mispairing between template of primer, then can not begin to carry out extension from this primer, also just can't carry out and the opposite side primer between amplified reaction.So, can carry out the evaluation of 1 base by amplified reaction according to whether causing.This method behind amplified reaction, needn't be carried out other again and operate the difference of identifying 1 base.
But for this method, its reaction is easy to be subjected to the influence of reaction conditions, for example, the amount of template, temperature, the amount of primer, and the concentration of the dNTP of response matrix etc.Therefore, usually be not easy to obtain to have reproducible data.In addition, identify the kind of base, promptly because the base of 3 ' end of primer or near the difference of base kind, the evaluation performance of this method also is subjected to very big influence (Ayyadevara etc., Anal.Biochem 284,11-18 (2000)) because also can causing sometimes, sequence identifies difficulty.
In addition, the method that other are also arranged for example, imports the method (Newton etc., Nucleic Acids Res.17,2503 (1989)) of artificial variation's (with template complementary base not) just under study for action near the 3 ' end of primer.But even this method, the optimization of primer still needs to expend certain manpower and materials, owing to identify precision also owing to the quality difference of sample, the result also can be affected sometimes.
In order to address this problem, to have inquired into the method (United States Patent (USP) the 6th, 316, No. 198 specification sheetss) that non-natural nucleic acid is imported primer, but still improved necessity has been arranged.In addition, also developed at two allyls and made the coexistence of primer specific ground basically, identified the method (McClay, Anal.Biochem., 301,2000-2006 (2002)) of 1 base by competing reaction.But this method can't fully meet the demands.
Therefore, still the wait in expectation a kind of nuance that can detect gene rapidly and easily, the particularly method of the difference of 1 base are identified precision and the high method of suitability.
[summary of the invention]
The inventor, here found, in order to identify 3 ' end parts polymorphic sequence, the primer that base sequence has been disposed in use carries out the primer extension reaction of strand displacement type, in identifying purpose nucleic acid during 1 base, add this primer, do not have the oligonucleotide of primer function, so can significantly improve the ability of 1 base identifying pleomorphism site owing to use.The present invention is promptly based on this mechanism.
The authentication method that the purpose of this invention is to provide the nucleic acid with polymorphic sequence site even sample has only trace, so long as wherein contain the nucleic acid of 1 different base, also can detect rapidly easily, and is the good method of a kind of accuracy of detection.
And the authentication method with the nucleic acid in polymorphic sequence site of the present invention is to identify in the nucleic acid with polymorphic sequence site whether the polymorphic sequence site has the method for desirable base sequence, and this method comprises:
With following (1) and (2) and purpose nucleic acid hybridization with polymorphic sequence site, these hybrids are placed under the condition that can carry out primer strand displacement extension,
(1) primers designed (here this primers designed 3 ' end parts have polymorphic sequence identify use base sequence) and
(2) do not have the primer function oligonucleotide (here this oligonucleotide is to compare with above-mentioned primers designed, with respect to territory, purpose nucleic acid 5 ' lateral areas, all or a part complementary).
Of the present inventionly be used for identifying the test kit of the nucleic acid with polymorphic sequence site is to be used to identify at the nucleic acid with polymorphic sequence site whether the polymorphic sequence site has the test kit of desirable base sequence, contain following (A) and (B):
(A) primers designed (here this primers designed 3 ' end parts have polymorphic sequence identify use base sequence) and
(B) do not have the primer function oligonucleotide (here this oligonucleotide is to compare with above-mentioned primers designed, with respect to territory, purpose nucleic acid 5 ' lateral areas, all or a part complementary).
The method according to this invention or test kit can identify rapidly and easily whether purpose nucleic acid is arbitrary type in some polymorphic sequences.This method or test kit have polymorphic sequence to identify with the method in the past of the primer of base sequence at 3 ' end to compare with only using, and the evaluation precision of polymorphism is more excellent.
[accompanying drawing summary]
Fig. 1 is the figure that shows primers designed and the pattern of the position relation of the oligonucleotide that does not have the primer function among the present invention.Among the figure, (a), (d) and (e) be the situation that primers designed overlaps with the sequence of this oligonucleotide, (b) being the situation of the sequence continuous distribution of primers designed and this oligonucleotide, (c) is the situation that the series of discrete of primers designed and this oligonucleotide distributes
Fig. 2 is the figure that shows that the mutual alignment of primers designed and this oligonucleotide concerns among the embodiment.
Fig. 3 is the figure that shows the result of embodiment 1.A in template one hurdle and the T kind of representing the base in polymorphic sequence site on the template sequence in the drawings.The kind of the primer that uses is represented on primer one hurdle, and DEO represents on one hurdle the kind of the oligonucleotide that does not have the primer function that uses.
Fig. 4 is expression embodiment 2 results' figure.In the drawings, A in template one hurdle and the T kind of representing the base in polymorphic sequence site on the template sequence.The kind of the primer that uses is represented on primer one hurdle, and DEO represents on one hurdle the kind of the oligonucleotide that does not have the primer function that uses.
Fig. 5 is expression embodiment 3 results' figure.In the drawings, A in template one hurdle and the T kind of representing the base in polymorphic sequence site on the template sequence.The kind of the primer that uses is represented on primer one hurdle, and DEO represents on one hurdle the kind of the oligonucleotide that does not have the primer function that uses.
Fig. 6 is expression embodiment 4 results' figure.In the drawings, A in template one hurdle and the T kind of representing the base in polymorphic sequence site on the template sequence.The kind of the primer that uses is represented on primer one hurdle, and DEO represents on one hurdle the kind of the oligonucleotide that does not have the primer function that uses.
[specifying of invention]
The authentication method of nucleic acid
The present invention identifies in the nucleic acid with polymorphic sequence site whether the polymorphic sequence site has the method for desirable base sequence.
" nucleic acid " in this specification sheets can be DNA or RNA, and strand or two strands can.In addition, the nucleic acid that can identify by the inventive method for the origin of nucleic acid without limits, i.e. the present invention is for coming from eukaryote, prokaryotic organism, the nucleic acid even the synthetic nucleic acid of virus can both be suitable for.
" purpose nucleic acid " in this specification sheets is meant with the inventive method wishes the target nucleic acid self identified or the complementary strand of this target nucleic acid.
" polymorphic sequence site " in this specification sheets is meant that existence is with the lower section: be present in the base sequence of the different piece on the sequence between the nucleic acid, perhaps because the base sequence of the variation part on the nucleotide sequence that generates because of point mutation.That is, " polymorphic sequence site " is meant for the site that displacement, disappearance or the insertion of 1 base or a plurality of bases take place as the base sequence of benchmark.Therefore, according to authentication method of the present invention, can identify at pleomorphism site like this is that the nucleic acid of desirable base sequence and pleomorphism site are not the nucleic acid of such base sequence.
Here, " desirable base sequence " is meant the base sequence that is equivalent to the polymorphic sequence site that may be present in nucleotide sequence, with the mark base sequence of authentication method evaluation of the present invention.Base sequence like this can be according to identifying purpose, for example wishes the disease identified or suitably select according to the animal species of identifying object etc.
Authentication method with the nucleic acid in polymorphic sequence site of the present invention comprises, as previously described, at least use primers designed and do not have the oligonucleotide of primer function, make they and purpose nucleic acid hybridization, these materials after the hybridization are positioned under the reaction conditions of the strand displacement extension that can carry out primer.
Primers designed
" primers designed " among the present invention is that purpose nucleic acid is had the primer function, and its 3 ' end parts has the base sequence that polymorphic sequence is identified usefulness at least.At this moment, the what is called of primers designed " 3 ' end parts " is not only to guide 3 ' least significant end part of thing, since near several bases of 3 ' least significant end can, also can in the position, upper reaches of this primer.Be the scope of 1-5 base that comprises the base of least significant end from the base number of 3 ' least significant end preferably, more preferably the scope of 1-3 base most preferably is a 1-2 base.
Said here " polymorphic sequence is identified the base sequence of usefulness " is meant the base sequence that exists in the primers designed that can identify the polymorphic sequence site that exists in the purpose nucleic acid.The base sequence of usefulness " polymorphic sequence identify " is the polymorphic sequence site in purpose nucleic acid when being desirable base sequence, can be and this site complementary or non-complementary.
The polymorphic sequence that exists in the primers designed is identified the base number of usefulness, can be 2～several, also can be 1.Usually, this base number is more than 2 the time, and the evaluation of being carried out polymorphic sequence by primer is very easy, when this base number is 1, is difficult for identifying.In the present invention, even when this base number is 1, still can carry out the evaluation of polymorphic sequence at an easy rate.
Primers designed among the present invention is designed to, when polymorphic sequence in the primers designed is identified with the base sequence in base and the polymorphic sequence site of purpose nucleic acid mutually complementary the time, because the strand displacement extension of primer carries out the extension of primer, and when identifying that polymorphic sequence not complementary the time, no longer carries out the strand displacement extension of primer with the base sequence in the polymorphic sequence site of base sequence and purpose nucleic acid.
If so polymorphic sequence identifies that the base sequence of usefulness is complementary mutually with the base sequence in the polymorphic sequence site of purpose nucleic acid, cause the strand displacement extension of primer by this primers designed, primer extension can form the extension resultant, promptly with purpose nucleic acid complementary nucleic acid.
But if polymorphic sequence identifies that the base sequence of usefulness is not complementary with the base sequence in the polymorphic sequence site of purpose nucleic acid, the strand displacement extension that is caused by this primer is suppressed, and almost can't carry out the extension of primer.Therefore, also almost can't generate the extension resultant.Method in the past, even so situation is arranged, the extension of primer also can carry out a bit a little.Therefore, the tolerance range of authentication method in the past is not very high.Be in successful part of the present invention, owing to used the oligonucleotide that does not have the primer function, improved the tolerance range that to carry out extension effectively in the downstream of this primers designed.
That is to say, for primers designed, if the base sequence in the base sequence of polymorphic sequence evaluation usefulness and the polymorphic sequence site of purpose nucleic acid is complementary, primers designed and purpose nucleic acid are complementary fully, the oligonucleotide that does not have the primer function of this primer combined downstream is excluded, and can carry out the extension of primer.Relative therewith, for primers designed, if the base sequence in the base sequence of polymorphic sequence evaluation usefulness and the polymorphic sequence site of purpose nucleic acid is not complementary, the extension of primer almost can not carry out, at this moment, if the oligonucleotide that does not have the primer function in this primer downstream also exists, almost completely can suppress the carrying out of the extension of primer.The present invention utilizes this phenomenon, according to detecting the extension resultant that obtains, can identify the nucleic acid with polymorphic sequence site with high tolerance range.
Primers designed of the present invention, can be with from the polymorphic sequence site of purpose nucleic acid to all zones complementary of 3 ' end direction of purpose nucleic acid, also can be to comprise the polymorphic sequence site, and the part phase complementary shorter than above-mentioned all zones.
The chain length of primers designed of the present invention can suit according to the chain length of the purpose nucleic acid that is suitable for to select accordingly, is typically 6-100 base, preferred 10-50 base, more preferably 15-30 base.
Primers designed of the present invention can be synthetic according to the method for routine.For example, primers designed of the present invention than the polymorphic sequence site in purpose nucleic acid, can be selected the regional complementary mutually with 3 ' side of purpose nucleic acid.In addition, according to the base sequence that hope is identified, the polymorphic sequence that also can suitably select to exist in the primers designed is identified the base sequence of usefulness.
The oligonucleotide that does not have the primer function
In the present invention, compare with primers designed, " oligonucleotide that does not have the primer function " is necessary for the regional complementarity of 5 ' side of purpose nucleic acid.In other words, than primers designed, this oligonucleotide is at downstream area, with the complementation of purpose nucleic acid.
Said here " not having the primer function " be meant and allow this oligonucleotide and purpose nucleic acid hybridization, though with its be positioned over primer the reaction conditions of extension under, also can not cause the state of extension from this oligonucleotide.
In the present invention, do not have the oligonucleotide and the purpose nucleic acid complementary position of primer function,,, have no particular limits as long as in the downstream than primers designed and purpose nucleic acid complementary position.Therefore,
(a) 5 ' of this oligonucleotide terminal portions has for purpose nucleic acid and can obtain sequence (with reference to Fig. 1 (a)) with the setting of 3 ' terminal portions overlaid of primers designed (perhaps repeating mutually),
(b) 5 ' of this oligonucleotide terminal portions has for purpose nucleic acid and can obtain sequence (with reference to Fig. 1 (b)) with the consecutive setting of 3 ' terminal portions of primers designed, and
(c) 5 ' of this oligonucleotide terminal portions has the sequence (with reference to Fig. 1 (c)) that can obtain the setting that 3 ' terminal portions with primers designed is separated for purpose nucleic acid.
5 ' the terminal portions of the said here oligonucleotide that does not have a primer function and the 3 ' terminal portions " overlaid " (overlapping) of primers designed, when being primers designed and the oligonucleotide that does not have the primer function and purpose nucleic acid formation complementary strand, 3 ' terminal portions of primer and 5 ' terminal portions of this oligonucleotide, for the same sequence or the same base of purpose nucleic acid, the state that has complementary sequence or base simultaneously.
In addition, at this time, the part of the 5 ' terminal portions " overlaid " of this oligonucleotide may not be complete complementary for purpose nucleic acid, and such state is also contained in " overlaid " scope.Therefore another preferred mode of the present invention is not have 5 ' terminal portions of the oligonucleotide of primer function also can have and the non-complementary base of purpose nucleic acid.At this time, 1-15 in this way of 5 ' terminal portions and the base numerical example non-complementary base of purpose nucleic acid that is present in this oligonucleotide that does not have the primer function, preferred 1-5.
Equally, " overlaid " of 3 ' terminal portions of primers designed part may not be complete complementary for purpose nucleic acid, and such state is also contained in " overlaid " scope.Therefore another preferred mode of the present invention is a primers designed, and its 3 ' terminal portions also can have and the non-complementary base of purpose nucleic acid.
In addition, " overlaid " of 3 ' terminal portions of primers designed part also can contain the base sequence that polymorphic sequence is identified usefulness, also can not contain.At this time, for " overlaid " part of 3 ' terminal portions of primers designed, polymorphic sequence identifies that the base sequence of usefulness can not be the base of 3 ' terminal least significant end.Therefore, 5 ' the terminal portions that does not have the oligonucleotide of primer function, polymorphic sequence in the primers designed is identified the base sequence of usefulness, can be only and the base sequence in the zone of 3 ' end side repeat, but the base sequence that polymorphic sequence is identified usefulness also can repeat with the sequence of the base sequence in the zone of containing 5 ' side.
So " overlaid ", comprise following any situation: 3 ' terminal portions of primers designed and the 5 ' terminal portions of oligonucleotide that do not have the primer function be for purpose nucleic acid both sides complementary situation all, and no matter which side or both sides are not complementary and have a situation of non-complementary base in the position that the complementary base is arranged originally for purpose nucleic acid.
As the example of the situation of " overlaid ", except the situation of foregoing (a), can enumerate following (d) and the situation (e) of resembling:
(d) 5 ' terminal portions that does not have an oligonucleotide of primer function has the sequence that can obtain the setting that 3 ' terminal portions with primers designed coincides for purpose nucleic acid, and 5 ' terminal portions of this oligonucleotide and purpose nucleic acid is complementary situation (with reference to Fig. 1 (d)) mutually.At this moment, 3 ' of primers designed terminal portions and purpose nucleic acid can be not complementary yet.
(e) 5 ' terminal portions that does not have an oligonucleotide of primer function does not have the sequence that can obtain the setting that 3 ' terminal portions with primers designed coincides for purpose nucleic acid, and 5 ' terminal portions of this oligonucleotide and purpose nucleic acid is complementary situation (with reference to Fig. 1 (e)) mutually.At this moment, 3 ' of primers designed terminal portions and purpose nucleic acid can be not complementary yet.
Preferred configuration of the present invention is, having for the purpose nucleic acid construct is the sequence of setting of 3 ' terminal portions overlaid (perhaps repeating mutually) of 5 ' terminal portions and primers designed that does not have the oligonucleotide of primer function, perhaps having for the purpose nucleic acid construct is the sequence that does not have the consecutive setting of 3 ' terminal portions of the 5 ' terminal portions of oligonucleotide of primer function and primers designed, when not having the oligonucleotide and the primers designed of primer function that the sequence of " overlaid " is arranged, the preferred 1-5 of base number of overlaid part is individual, more preferably 1-3.
In the present invention, do not have whole bases of the oligonucleotide of primer function to constitute, for purpose nucleic acid, do not need complete complementation, even the base of a part is not complementary also passable.But under the sort of situation, in this oligonucleotide contained and purpose nucleic acid not the ratio of complementary base wish promptly when this oligonucleotide and purpose nucleic acid specificity when combining, in strand displacement extension of the present invention, can keep and purpose nucleic acid bonded degree.
In the present invention " oligonucleotide that does not have the primer function " is the function of short of primer, has no particular limits.Deoxy-oligonucleotide, the ribose oligonucleotide can, its mosaic also can.In addition, this oligonucleotide can contain modified base, also can contain the nucleic acid construct (for example, the modified base of non-natural type, the sugared structure of non-natural type) of non-natural type.In addition, as this oligonucleotide, also can use PNA with different main chains etc.
Preferred configuration of the present invention is not have the oligonucleotide of primer function to be, does not have the oligonucleotide of primer function and the bonded melting temperature(Tm) between the purpose nucleic acid than the melting temperature(Tm) height between primers designed and the purpose nucleic acid.For example, there are not the oligonucleotide of primer function and the bonded melting temperature(Tm) between the purpose nucleic acid can be than the high 1-15 of melting temperature(Tm) between primers designed and the purpose nucleic acid ℃.If this oligonucleotide has such melting temperature(Tm), when causing extension, there is not the oligonucleotide of primer function to combine with purpose nucleic acid by primers designed.Thus, when not matching between the base sequence of the polymorphic sequence of 3 ' terminal portions of primers designed evaluation usefulness and the polymorphic sequence site of purpose nucleic acid, the extension of primer is bound to be suppressed.
In the present invention, there is not the sequence of the purpose nucleic acid that the oligonucleotide of primer function can identify according to hope suitably to select.The oligonucleotide that does not have the primer function, for example, also can be synthetic according to the method for routine, also the nucleic acid that hope is identified can be prepared with additive method, cut off arbitrarily again and obtain.
In addition, can make this oligonucleotide not have the primer function to the ordinary method (for example, United States Patent (USP) the 5th, 849, the method for No. 497 specification sheets records) that this oligonucleotide is suitable for.In addition; according to the hydroxyl of the Nucleotide of the synthetic 3 ' terminal portions that waits the oligonucleotide that obtains (for example with protecting group arbitrarily; phosphate) modify, or import and purpose nucleic acid complementary base not at this 3 ' terminal portions, oligonucleotide has not just had the function of primer.
Therefore, another preferred configuration of the present invention is the oligonucleotide that does not have the primer function, and the hydroxyl of the Nucleotide of its 3 ' terminal portions can be modified by phosphate.
In addition, another preferred configuration of the present invention does not have the oligonucleotide of primer function, can have and the non-complementary base of purpose nucleic acid at its 3 ' terminal portions.At this time, 3 ' terminal portions of the oligonucleotide that does not have the primer function that exist with the base numerical example non-complementary base of purpose nucleic acid as can being 1-30, preferred 3-10.
In the present invention, do not have the chain length of the oligonucleotide of primer function suitably to select, wishes minimumly to contain 10 more than the base, preferably 15-50 base, more preferably 25-35 base according to the chain length of the purpose nucleic acid that is suitable for.
The amount of the used oligonucleotide that does not have the primer function can suit according to the amount of purpose nucleic acid to select among the present invention, when primers designed and the complete complementation of purpose nucleic acid, is the amount that does not suppress the extension of primer.And preferably its in extension can with all purpose nucleic acid bonded amounts.Under such situation, the amount of this oligonucleotide is compared with the amount of purpose nucleic acid, wants excessive existence at least.
More preferably form of the present invention is that the amount of the relative primers designed of amount of this oligonucleotide is the 0.1-5 equivalent, preferred 1-3 equivalent, more preferably 1-1.5 equivalent.
Other
In the present invention, make primers designed and do not have the oligonucleotide and the purpose nucleic acid hybridization of primer function, method routinely, for example, with they design temperature conditions suitably together, easy handling.
In this manual, said " being positioned under the reaction conditions that the strand displacement extension of primer can carry out " be meant can carry out primer the reaction conditions of strand displacement extension, for example, in the presence of the enzyme of regulation, under the temperature condition and/or in the presence of the matrix, place the primer of hybridization etc.The representative instance of reaction conditions like this is known in those skilled in the art, in the present invention, according to purpose nucleic acid, primer etc., can suitably adjust top condition.For example, according to the enzyme that uses, design temperature condition that can be suitable.
As enzyme used herein, the preferred substitutional template dependency of complementary strand nucleic acid synthetic enzyme.Enzyme like this can use reversed transcriptive enzyme when purpose nucleic acid is RNA, and, when purpose nucleic acid is DNA, can use archaeal dna polymerase.At this moment operable DNA or RNA polymerase importantly do not have 5 ' → 3 ' exonuclease activity and 3 ' → 5 ' exonuclease activity, but have the strand displacement activity.
As described RNA polymerase, that for example can enumerate has a M-MLV reversed transcriptive enzyme etc.
In addition, for natural enzyme, can manually remove these activity with 5 ' → 3 ' exonuclease activity and 3 ' → 5 ' exonuclease activity.Therefore, as archaeal dna polymerase, can use and remove active enzyme.In the present invention, as the enzyme that can use, for example, that can enumerate has the big fragment of Bst archaeal dna polymerase (New England Biolabs corporate system), a Stoffel fragment archaeal dna polymerase (ア プ ラ イ De バ イ オ シ ス テ system ズ corporate system) etc.
Method of the present invention preferably is suitable for the method that promptly can carry out the evaluation of 1 base by 1 extension.Method like this for example can be enumerated 1 base extension method (SBE method) (Syvanen etc., Genomics, 8,684-692 (1990)).This method is the method for carrying out primer extension reaction for the DNA by the amplification of PCR method.Promptly this method is utilize primer 3 ' terminal and complementary or not complementary fully by the purpose nucleic acid that pcr amplification obtained, thereby can the decision extension carry out.The used method according to the present invention can improve the identification capacity of SBE method, in addition, can shorten the time of condition enactment.The SBE method is the method for extensively popularizing, and can form better authentication method yet combine with the present invention.
An optimal way of the present invention is that method of the present invention can be combined enforcement with the SBE method.
The present invention is and the combined amplification of carrying out exponential relationship of known gene amplification method to be easy to detect owing to extend resultant, so better effects if.As such TRAP, for example, can enumerate PCR method (Polfs etc., PCR:Clinical Diagnostics and Research, Springer-Verlag (1992)), NASBA method (Gabrielle etc., J.General.Microbiol.139,2423-2429 (1993)), TMA method (Kacian etc., United States Patent (USP) the 5th, 399, No. 491), SDA method (Walker etc., Nucleic Acids Res.20,1691-1696 (1992)), LAMP method (Notomi etc., Nucleic Acids Res.28, e63 (2000)) or ICAN method (Mukai etc., No. 00/56877, International Application No. WO).Method of the present invention no matter be non-isothermal or isothermal, can utilize the method for primer extension reaction combined with all.
Therefore, optimal way of the present invention is the operation that method of the present invention also comprises primer strand displacement extension amplification extension resultant.This TRAP can be the nucleic acid amplification that is selected from above-mentioned PCR method, NASBA method, TMA method, SDA method, LAMP method or ICAN method.
Optimal way of the present invention is that method of the present invention also comprises the detection operation by the existence of the primer strand displacement extension resultant that extension generated.Therefore, for example,, can judge in the polymorphic sequence site it is desirable base sequence if detect the extension resultant.
The existence of extension resultant can be by detecting with general nucleic acid detection method.
Therefore, for example, the present invention and above-mentioned SBE method when combined, are used fluorescently-labeled mononucleotide triphosphoric acid,, can identify the difference (Syvanen etc., Genomics, 8,684-692 (1990)) of 1 base by the mononucleotide specialization that will enter.In addition, when the present invention and the combination of PCR method, for example, in fluorescigenic material, add the amplified material that obtains,, can detect the difference of 1 base at an easy rate according to whether fluorescing.These detection methods also can be suitable for (Foy etc. in other cases, ClinicalChem.47,990-1000 (2002)), thus, can detect the nuance (for example difference of several bases) of the nucleotide sequence in the sample easily, perhaps the difference of 1 base.
Another mode of the present invention is provided for identifying comprises following (A) and (B) constitutes, and whether the polymorphic sequence site has the test kit of desirable base in the nucleic acid that the polymorphic sequence site is arranged:
(A) primers designed (here this primers designed has polymorphic sequence evaluation base sequence in 3 ' end parts), and
(B) do not have the primer function oligonucleotide (here this oligonucleotide is to compare with above-mentioned primers designed, with respect to the territory, 5 ' lateral areas of purpose nucleic acid, all or a part complementary).
Preferred mode of the present invention is that this test kit also comprises following (C) and constitutes:
(C) the substitutional template dependency of complementary strand nucleic acid synthetic enzyme.
Other optimal ways of the present invention are above-mentioned test kits, contain the matrix monokaryon guanosine triphosphate of extension and/or are suitable for the damping fluid of the enzyme reaction of above-mentioned enzyme.
Here, the matrix monokaryon guanosine triphosphate as extension typically refers to 4 kinds of deoxynucleotide triphosphoric acids (dNTP), as the damping fluid of the enzyme reaction that is suitable for above-mentioned enzyme, can suitably be selected from known damping fluid according to used enzyme.
[embodiment]
Below, by embodiment the present invention is specifically described, but the present invention is not limited to this.
Used in the present embodiment oligonucleotide is by ABI 392 automatic dna synthesizers (ア プ ラ イ De バ イ オ シ ス テ system corporate system) synthetic.When 3 ' end of oligonucleotide imports phosphoric acid, use 3 ' phosphorylation CPG (グ レ Application リ サ one チ corporate system).
The synthetic oligonucleotide by the polyacrylamide gel electrophoresis purifying, uses behind deprotection then.
As the template of amplification, use separately and contain the segmental plasmid of Pst I that has A allyl group or the allylic beta-globin gene of T (pBR322-β respectively does for oneself
A, pER322-β
S(Ikuta etc., Nucleic Acids Res.15,797-811)).
Primer extension reaction carries out according to implementing the PCR method.Here as archaeal dna polymerase, use Stoffel fragment archaeal dna polymerase Stoffel fragment DNA polymerase (ア プ ラ イ De バ イ オ シ ス テ system corporate system), reaction unit uses Thermal Cycler 9700 (RocheDiagnostics corporate systems).The amplified reaction resultant is that reaction solution is carried out 3% agarose gel electrophoresis, and ethidium bromide staining is confirmed.
The oligonucleotide that uses, promptly primer and the oligonucleotide that do not have a primer function are as shown below.Following underscore partly is expression and the corresponding base of A-allyl group or the allylic position of T-, and 3 ' terminal p represents phosphoric acid.
Primer (primers designed) (chain identical) with template:
BGT:5 ' ATG GTG CAC CTG ACT CCT GT (sequence number 1)
BGA:5 ' ATG GTG CAC CTG ACT CCT GA (sequence number 2)
Primer (with the template complementary):
ASP6:5 ' TGT CTT GTA ACC TTG ATA CC (sequence number 3)
The oligonucleotide that does not have the primer function:
DEO-1A:5 '
AGG AGA AGT CTG CCG TTA CTGp (sequence number 4)
DEO-2A:5 '
AGG AGA AGT CTG CCG TTA CTG CCC TGT GGGp (sequence number 5)
DEO-3A:5 ' G
AG GAG AAG TCT GCC GTT ACT GCCC TGT GGGp (sequence number 6)
DEO-1T:5 '
TGG AGA AGT CTG CCG TTA CTGp (sequence number 7)
DEO-2T:5 '
TGG AGA AGT CTG CCG TTA CTG CCC TGT GGGp (sequence number 8)
DEO-3T:5 ' G
TG GAG AAG TCT GCC GTT ACT GCC CTG TGGGp (sequence number 9)
DEO-4:5 ' GGA GAA GTC TGC CGT TAC TGC CCT GTG GGGCp (sequence number 10)
DEO-5:5 ' TGC CGT TAC TGC CCT GTG GGGC AAGG TGAACp sequence number 11)
These primers and do not have between the oligonucleotide of primer function the position relation as shown in Figure 2.
Example 1
Use primer bGT (0.5 μ M), primer ASP6 (0.5 μ M), do not have the oligonucleotide (0.5 μ M) of primer function and as the plasmid pBR322-β of template
A(the A allyl group, 300pg) or plasmid pBR322-β
S(the T allyl group 300pg) carries out amplified reaction.Contain the 4 kind deoxynucleotide triphosphoric acids (each 200 μ Ms) corresponding of adding in the reaction solution of above-mentioned each composition, reaction buffer (Stoffel fragment archaeal dna polymerase with damping fluid (ア プ ラ イ De バ イ オ シ ス テ system corporate system)) with A, G, T and C, and adding archaeal dna polymerase (Stoffel fragment archaeal dna polymerase) (1.5 unit) (ア プ ラ イ De バ イ オ シ ス テ system corporate system), the total amount of reaction solution is 50 μ L.Reaction solution is placed certain temperature condition, make it carry out amplified reaction.A circulation of temperature condition is 94 ℃ (15 seconds), 55 ℃ (15 seconds), 72 ℃ (30 seconds) successively, during reaction this circulation is carried out 40 times.
The reaction solution 10 μ L that obtain carry out 3% agarose gel electrophoresis, are analyzed.
The result as shown in Figure 3.
The polymorphic sequence of primer bGT is identified when the polymorphic sequence site in site and the template is complementary, has been increased nucleic acid specificity.On the other hand, the polymorphic sequence of primer bGT is identified when the polymorphic sequence site in site and the template is not complementary, can be seen the amplification of nucleic acid hardly.Therefore, can identify desirable nucleic acid clearly with polymorphic sequence site.
When using DEO-3A or DEO-3T, identification capacity is very good.
Example 2
A circulation of the temperature condition except will implement amplified reaction the time is made as 94 ℃ (15 seconds), 50 ℃ (15 seconds), 72 ℃ (30 seconds), carries out reaction and the analysis same with example 1.
This example in addition is to reduce primer specificity, the annealing temperature that has reduced wittingly.
The result as shown in Figure 4.
Because the annealing temperature that has reduced, the specificity of primer all is lowered, but when using DEO-3A or DEO-3T, the identification capacity of desirable nucleic acid is very good.
Example 3
Except using primer bGA replacement primer bGT, carry out same reaction and analysis with example 1.
The result as shown in Figure 5.
Found that the effect of identifying when using any oligonucleotide that does not have the primer function is good.
Example 4
Except using primer bGA to replace primer bGT, and a circulation of the temperature condition will implement amplified reaction the time is made as 94 ℃ (15 seconds), 50 ℃ (15 seconds), 72 ℃ (30 seconds), in addition, carries out identical reaction and analysis with example 1.
This example in addition is to reduce primer specificity, the annealing temperature that has reduced wittingly.
The result as shown in Figure 6.
Found that also the effect of identifying when using any oligonucleotide that does not have the primer function is good.
Sequence table
<110>Wakunaga?Pharmaceutical?Co.，Ltd.
＜120〉has the authentication method of the nucleic acid in polymorphic sequence site
<130>143669Q1
<140>
<141>
<160>11
<170>PatentIn?Ver.2.1
<210>1
<211>20
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: primer
<400>1
atggtgcacc?tgactcctgt 20
<210>2
<211>20
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: primer
<400>2
atggtgcacc?tgactcctga 20
<210>3
<211>20
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: primer
<400>3
tgtcttgtaa?ccttgatacc 20
<210>4
<211>21
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>4
aggagaagtc?tgccgttact?g 21
<210>5
<211>30
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>5
aggagaagtc?tgccgttact?gccctgtggg 30
<210>6
<211>31
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>6
gaggagaagt?ctgccgttac?tgccctgtgg?g 31
<210>7
<211>21
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>7
tggagaagtc?tgccgttact?g 21
<210>8
<211>30
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>8
tggagaagtc?tgccgttact?gccctgtggg 30
<210>9
<211>31
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>9
gtggagaagt?ctgccgttac?tgccctgtgg?g 31
<210>10
<211>31
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>10
ggagaagtct?gccgttactg?ccctgtgggg?c 31
<210>11
<211>31
<212>DNA
＜213〉artificial sequence
<220>
＜223〉artificial sequence description: synthetic oligonucleotide
<400>11
tgccgt?tact?gccctgtggg?gcaaggtgaa?c 31
Claims (20)
1. identify in nucleic acid whether the polymorphic sequence site has the method for desirable base sequence, and this method comprises for one kind with polymorphic sequence site
With following (1) and (2) and purpose nucleic acid hybridization with polymorphic sequence site, they are placed under the reaction conditions that can carry out primer strand displacement extension, wherein,
(1) primers designed (here this primers designed 3 ' end parts have polymorphic sequence identify use base sequence) and
(2) do not have the primer function oligonucleotide (here this oligonucleotide is to compare with above-mentioned primers designed, with respect to the territory, 5 ' lateral areas of purpose nucleic acid all or a part complementary).
2. the method for claim 1, following design primers designed, so that the polymorphic sequence of primers designed is identified the mutual added time of base sequence with the polymorphic sequence site of base sequence and purpose nucleic acid, because the strand displacement extension of primer causes the extension of primer, and this polymorphic sequence is identified when the base sequence in the polymorphic sequence site of using base sequence and purpose nucleic acid is not complementary, does not cause primer strand displacement extension.
3. method as claimed in claim 1 or 2, polymorphic sequence identifies that the base number with base sequence is 1 in the primers designed.
4. as each described method of claim 1-3, aforementioned purpose nucleic acid is the complementary strand of target nucleic acid.
5. as each described method of claim 1-4, comprise the step of the extension resultant amplification that will generate by primer strand displacement extension.
6. method as claimed in claim 5, the amplification of extension resultant are to be undertaken by the nucleic acid amplification method that is selected from PCR method, NASBA method, TMA method, SDA method, LAMP method or ICAN method.
7. as each described method of claim 1-6, also comprise the operation of detection by the existence of the extension resultant of primer strand displacement extension generation.
8. method as claimed in claim 5 also comprises after the amplification step of the extension resultant that is generated by primer strand displacement extension, detects the step of the existence of this extension resultant.
9. as each described method of claim 1-8, wherein do not have 5 ' terminal portions of the oligonucleotide of primer function to have and to obtain sequence with the setting of 3 ' the terminal portions overlaid (perhaps repeating mutually) of primers designed for purpose nucleic acid.
10. method as claimed in claim 9, not having the base number of 3 ' the terminal portions overlaid part of the 5 ' terminal portions of oligonucleotide of primer function and primers designed is 1-5.
11., wherein do not have 5 ' terminal portions of this oligonucleotide of primer function to have and to obtain sequence with the consecutive setting of 3 ' terminal portions of primers designed for purpose nucleic acid as each described method of claim 1-8.
12., have and purpose nucleic acid complementary base not at 5 ' terminal portions of the oligonucleotide that does not have the primer function as each described method of claim 1-11.
13., do not have the hydroxyl of 3 ' terminal Nucleotide of the oligonucleotide of primer function to be modified by phosphate as each described method of claim 1-11.
14., have and purpose nucleic acid complementary base not at 3 ' terminal portions of the oligonucleotide that does not have the primer function as each described method of claim 1-11.
15. as each described method of claim 1-14, do not have the oligonucleotide of primer function, in its sequence, contain modified base or non-natural nucleic acid construct.
16., do not have the oligonucleotide of primer function and the bonded melting temperature(Tm) between the purpose nucleic acid than the bonded melting temperature(Tm) height between primers designed and the purpose nucleic acid as each described method of claim 1-15.
17. as each described method of claim 1-16, primer strand displacement extension is the reaction that is caused by the substitutional template dependency of complementary strand nucleic acid synthetic enzyme.
18. method as claimed in claim 17, template dependency nucleic acid synthetic enzyme is an archaeal dna polymerase.
19. method as claimed in claim 17, template dependency nucleic acid synthetic enzyme is a reversed transcriptive enzyme.
20. a test kit, it is to be used for identifying at the nucleic acid with polymorphic sequence site whether the polymorphic sequence site has desirable base, and this test kit comprises following (A) and (B):
(A) primers designed (here this primers designed 3 ' end parts have polymorphic sequence identify use base sequence) and
(B) do not have the primer function oligonucleotide (here this oligonucleotide is to compare with above-mentioned primers designed, with respect to the territory, 5 ' lateral areas of purpose nucleic acid all or a part complementary).
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| JP2002261683 | 2002-09-06 | ||
| JP261683/2002 | 2002-09-06 |
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| Publication Number | Publication Date |
|---|---|
| CN1678743A true CN1678743A (en) | 2005-10-05 |
| CN100471952C CN100471952C (en) | 2009-03-25 |
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| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CNB038209667A Expired - Fee Related CN100471952C (en) | 2002-09-06 | 2003-09-05 | Method of identifying nucleic acid having polymorphism sequence site |
Country Status (4)
| Country | Link |
|---|---|
| JP (1) | JP4406366B2 (en) |
| CN (1) | CN100471952C (en) |
| AU (1) | AU2003261970A1 (en) |
| WO (1) | WO2004022743A1 (en) |
Families Citing this family (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2007181435A (en) * | 2006-01-10 | 2007-07-19 | Univ Kinki | Method for judging contamination with tissue or secretion of genetically modified animal |
| JP2010246400A (en) * | 2009-04-10 | 2010-11-04 | Olympus Corp | Polymorphism identification method |
| RS62334B1 (en) * | 2014-09-16 | 2021-10-29 | Sangamo Therapeutics Inc | Methods and compositions for nuclease-mediated genome engineering and correction in hematopoietic stem cells |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5849497A (en) * | 1997-04-03 | 1998-12-15 | The Research Foundation Of State University Of New York | Specific inhibition of the polymerase chain reaction using a non-extendable oligonucleotide blocker |
-
2003
- 2003-09-05 WO PCT/JP2003/011377 patent/WO2004022743A1/en active Application Filing
- 2003-09-05 JP JP2004534177A patent/JP4406366B2/en not_active Expired - Fee Related
- 2003-09-05 AU AU2003261970A patent/AU2003261970A1/en not_active Abandoned
- 2003-09-05 CN CNB038209667A patent/CN100471952C/en not_active Expired - Fee Related
Also Published As
| Publication number | Publication date |
|---|---|
| JPWO2004022743A1 (en) | 2005-12-22 |
| WO2004022743A1 (en) | 2004-03-18 |
| JP4406366B2 (en) | 2010-01-27 |
| AU2003261970A1 (en) | 2004-03-29 |
| CN100471952C (en) | 2009-03-25 |
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