CN106434898A - Method, primers and kit for quickly detecting yersinia pseudotuberculosis at constant temperature - Google Patents
Method, primers and kit for quickly detecting yersinia pseudotuberculosis at constant temperature Download PDFInfo
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Abstract
The invention discloses a method, primer group and kit for quickly detecting yersinia pseudotuberculosis at constant temperature. The method comprises the steps that genomic DNA is extracted from a sample to be detected; a constant-temperature amplification reaction is conducted by taking the genomic DNA as a template and taking the primer group capable of amplifying the specific sequences of the yersinia pseudotuberculosis as primers in an enzyme reaction system; whether the yersinia pseudotuberculosis exists in the sample to be detected or not is determined by judging whether a reaction result is positive or not. The detection method has the advantages that the high sensitivity and specificity are achieved, the detection time is short, result judging is easy, operation is convenient and rapid, the cost is low, and a wide application prospect is achieved.
Description
Technical field
The invention belongs to biological technical field, be specifically related to the side of a kind of fast constant temperature detection artificial tuberculosis yersinia genus
Method, primer and kit.
Background technology
Artificial tuberculosis yersinia genus (Yersinia pseudotuberculosis) belongs to enterobacteriaceae Yersinia ruckeri
Belonging to, being the enteric pathogenic bacteria of a kind of infecting both domestic animals and human, this bacterium can survive at low ambient temperatures, and therefore refrigerator storage food is modern society
The important infection sources that this bacterium infects can occur, gastrointestinal symptom, mesenteric lymphadenitis etc. can be caused.This bacterium infects people
In Qun to distribute based on, also can cause breaking out of different scales once in a while.Due to its atypical symptoms, easily cause diagnosis not
Bright even mistaken diagnosis and delay treatment.Therefore, for the prevention of this bacterium with detect extremely important.
Tradition artificial tuberculosis yersinia genus detection method is longer due to the detection cycle, operates relative complex, and detection efficiency is relatively
Low, it is difficult to meet modern society for food-borne pathogens detection process high flux, high sensitivity, high specific, quick, convenient
Requirement.Recently as the development of nucleic acid molecules detection technique, researcher have also been developed the detection means such as PCR, but
The method needs special detecting instrument, therefore, is not appropriate for being widely used in detection department of basic unit especially enterprise's production line
The real-time on-site detection that inside is carried out.In order to ensure food security, be badly in need of quick, simple, accurately method detect in food
Artificial tuberculosis yersinia genus.
Loop-mediated isothermal amplification technique (loop-mediated isothermal amplification, LAMP) is in recent years
A kind of novel constant-temperature nucleic acid amplification method growing up, this method is for 4 specific primers of 6 region designs of target sequence
(including upstream and downstream outer primer F3 and B3 and upstream and downstream inner primer FIP and BIP, wherein FIP is made up of F1C and F2, and BIP is by B1C
With B2 composition), utilize a kind of archaeal dna polymerase with strand-displacement activity, be incubated about 60min at constant temperature, core can be completed
Acid amplified reaction, produces macroscopic byproduct of reaction-white magnesium pyrophosphate and precipitates (see document Notomi T, Okayama
H,Masubuchi H,Yonekawa T,Watanabe K,Amino N,Hase T.Loop-mediated isothermal
amplification of DNA,Nucleic Acids Research,2000Jun 15;28(12):E63).This technology has
Not needing PCR instrument or quantitative real time PCR Instrument, can completing under constant temperature, naked eyes i.e. can determine whether reaction result, and highly sensitive,
High specificity, reaction time is short, simple operation, low cost and other advantages.
Design of primers is a step the most key in LAMP technology, and Normal practice is by the spy generally acknowledging of certain biology to be detected
Specific gene imports the online website (http of LAMP primer design://primerexplorer.jp/e), set relevant parameter raw
Become primer sets.It is to say, user is it is first necessary to guarantee the distinguished sequence that this target gene is species to be measured.With patent of invention CN
As a example by 101182575B and CN 101200760A, they are respectively directed to the special sequence of the artificial tuberculosis yersinia genus of document report
District and gyrB gene between row 16S-23S, use LAMP technology to carry out artificial tuberculosis yersinia genus detection.But, so-called " public
The specific gene recognized " is often based upon delayed knowledge, and is not based on ever-increasing microbial genome data and carries out necessity
Renewal, cause the primer obtaining based on this target-gene sequence not necessarily to can ensure that it is specific and/or logical in actual applications
The property used.Present invention table 1 illustrate primer specificity present in prior art not, the problem that can not guarantee of versatility.
It is to say, the artificial tuberculosis yersinia genus detection sequence actually not pseudoconcretion yersinia genus used in art methods
Salmonella institute is peculiar, i.e. be possible to non-artificial tuberculosis yersinia genus is regarded as artificial tuberculosis yersinia genus mistakenly.Similar asks
Topic exists in the confirmation of versatility, i.e. be possible to the part bacterial strain of missing inspection artificial tuberculosis yersinia genus.Therefore, in industry urgently
A kind of need to be able to ensure that specific and versatility artificial tuberculosis yersinia genus detection method, meet detection department pair of basic unit simultaneously
Quickly, demand easily, can carry out real-time on-site detection easily inside enterprise's production line.
Content of the invention
The technical problem to be solved in the present invention is to overcome primer versatility present in existing LAMP technology design of primers
With specific not enough defect, make full use of microbial genome sequence information abundant in current common data resource and phase
The sequence analysis tools answered, is designed for the primer sets of specific recognition artificial tuberculosis yersinia genus, and is formed on this basis
High sensitivity, high specific detection kit.The present invention is based on the microbial genome data resource in GenBank database
(by data on August 5th, 2013) carry out the design of artificial tuberculosis yersinia genus LAMP primer, provide a kind of fast constant temperature and expand
Increase method, primer sets and the kit of detection artificial tuberculosis yersinia genus.Use the detection method detection pseudoconcretion of the present invention
Ademilson Salmonella, has high sensitivity and a high specific, and the detection time is short, and result judges simple, simple operation, low cost excellent
Point.
The present invention proposes a kind of method of quick detection artificial tuberculosis yersinia genus bacterial strain, and described method includes following step
Suddenly:
(1) from testing sample, genomic DNA is extracted;
(2) with described genomic DNA as template, so that artificial tuberculosis yersinia genus genome specificity base sequence can be expanded
Primer sets be primer, under enzyme reaction system, carry out isothermal amplification reactions;
(3) by judging whether reaction result is positive, determine in testing sample whether there is artificial tuberculosis yersinia genus.
The method of Constant Temperature Detection artificial tuberculosis yersinia genus bacterial strain of the present invention, extracts genomic DNA from testing sample, with
Which is template, with artificial tuberculosis yersinia genus specificity amplification primer group as primer, carry out isothermal amplification reactions, then, pass through
Judge whether reaction result is positive, determine in testing sample whether there is artificial tuberculosis yersinia genus.Wherein, described enzyme reaction
System includes but is not limited to DNA polymerase reaction system.
In the present invention, it is 153946813 that described artificial tuberculosis yersinia genus genome specificity base sequence is No. GI
768567~768785bp bit sequence of artificial tuberculosis yersinia genus.
In the present invention, the described primer sets that can expand artificial tuberculosis yersinia genus genome specificity base sequence is described
A part for the nucleotide sequence of 768567~768785bp position of genome (No. GI is 153946813) or one of its complementary strand
Point.Wherein, described artificial tuberculosis yersinia genus genome specificity base sequence refers to only artificial tuberculosis yersinia genus gene
Group is specific, and the base sequence that other microbial genome do not comprise.
Wherein, the described primer sets that can expand artificial tuberculosis yersinia genus genome specific base sequence includes but is not limited to
Primer sets A, or selected from being 50% and above primer with wall scroll sequence homology in this primer sets sequence or its complementary strand sequence
Any one group of group.
Primer sets A:
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’(SEQ ID NO:1);
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’(SEQ ID NO:2);
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’
(SEQ ID NO:3);
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’
(SEQ ID NO:4).
In the present invention, the described primer sets that can expand artificial tuberculosis yersinia genus genome specific base sequence can also be wrapped
Including with wall scroll sequence homology in aforementioned each primer sets sequence or its complementary strand sequence is 50% and above primer sets, this primer
Group includes but is not limited to following primer sets B:
Primer sets B:
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’(SEQ ID NO:5) (with primers F 3_A 5 '-
GTTGTTGTATGAATTGCTGG-3 ' homology is 50%);
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’(SEQ ID NO:6);
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’
(SEQ ID NO:7);
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’
(SEQ ID NO:8).
In the inventive method, the described primer sets that can expand artificial tuberculosis yersinia genus genome specificity base sequence can
To comprise or not comprise ring primer.Described ring primer can be one or more, including primer LF and/or LB.Described energy amplification
The primer sets of artificial tuberculosis yersinia genus genome specificity base sequence is selected from following primer sets A ', any one group of B ';Or
Selected from and described primer sets A ', in B ' sequence or its complementary strand sequence wall scroll sequence homology be 50% and above primer sets it
Any one group:
Primer sets A ':
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’;
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’;
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_A:5’-TATGCTCATCCAGGCGTTTC-3’(SEQ ID NO:9);
And/or, lower lantern primer LB_A:5’-TGATGGCGATGGGGAAAATT-3’(SEQ ID NO:10);
Primer sets B ':
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’;
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’;
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_B:5’-GGGATTTCAATATGCTCATCCAG-3’(SEQ ID NO:11);
And/or, lower lantern primer LB_B:5’-TGATGGCGATGGGGAAAATT-3’(SEQ ID NO:12).
In a particular embodiment, for example, above-mentioned primer sets A ', in B ', can only comprise a upper lantern primer, or only
Comprise a lower lantern primer, or comprise a upper lantern primer and a lower lantern primer simultaneously.
In the inventive method, in a specific embodiments (primer containing ring), the enzyme reaction system of described constant-temperature amplification is:
1 × BstDNA polymeric enzyme reaction buffer solution, 2-9mmol/L Mg2+(MgSO4Or MgCl2), 1.0-1.6mmol/L dNTP, 0.8-
FIP and the BIP primer of 2.0 μm of ol/L, F3 and the B3 primer of 0.15-0.3 μm of ol/L, LF and/or LB of 0.4-1.0 μm of ol/L draws
Thing, 0.16-0.64U/ μ L Bst archaeal dna polymerase and 0-1.5mol/L glycine betaine.(draw without ring in another specific embodiments
Thing) in, the enzyme reaction system of described constant-temperature amplification is:1 × Bst DNA polymerase reaction buffer solution, 2-9mmol/L Mg2+
(MgSO4Or MgCl2), FIP and the BIP primer of 1.0-1.6mmol/L dNTP, 0.8-2.0 μm of ol/L, 0.15-0.3 μm of ol/L's
F3 and B3 primer, 0.16-0.64U/ μ L Bst archaeal dna polymerase and 0-1.5mol/L glycine betaine.Ring primer is favorably improved reaction
Efficiency.For example, 1 × Bst DNA polymerase reaction buffer solution can select 1 × Thermopol reaction buffer, comprises
20mmol/L Tris-HCl (pH8.8), 10mmol/L KCl, 10mmol/L (NH4)2SO4,0.1%Triton X-100,2mM
MgSO4.MgSO in 1 × Bst DNA polymerase reaction buffer solution4With the magnesium ion Mg in enzyme reaction system2+Do merging treatment.
In the inventive method, the response procedures of described isothermal amplification reactions hatches 10~90min, preferably for 1. 60~65 DEG C
Ground is 10~60min;2. 80 DEG C terminate reaction 2~20min.The present invention does not limit and realizes this by other suitable response procedures
Invention detection method.
In the inventive method, detection method includes but is not limited to electrophoresis detection, Turbidity measurement or color developing detection etc..Described electricity
Swimming detection, preferably gel electrophoresis assays, can be Ago-Gel, it is also possible to be polyacrylamide gel.Electrophoresis detection
In result, band as stepped in electrophoretogram expression characteristics, then testing sample is that artificial tuberculosis yersinia genus is positive, containing false knot
Core Yersinia ruckeri;Band as stepped in electrophoretogram not expression characteristics, then testing sample is that artificial tuberculosis yersinia genus is negative.
Described Turbidity measurement, is to detect by an unaided eye or transmissometer detection turbidity, and detection pipe occurs substantially muddy, then testing sample is false knot
Core Yersinia ruckeri is positive, containing artificial tuberculosis yersinia genus;As muddy in having no, then testing sample is artificial tuberculosis yersinia genus
Negative.Also can visually observe whether have precipitation at the bottom of reaction tube after centrifugal, if there being precipitation at the bottom of reaction tube, then testing sample is vacation
Tuberculosis Yersinia ruckeri is positive, containing artificial tuberculosis yersinia genus;Do not precipitate as at the bottom of reaction tube, then testing sample is pseudoconcretion
Yersinia ruckeri is negative.
Described color developing detection, is addition developer, including but not limited to calcein (50 μM) or SYBR in reaction tube
GreenI (30-50 ×), or hydroxynaphthol blue (i.e. HNB, 120-150 μM).Make when using calcein or SYBR Green I
During for developer, as after reaction, color is orange, then testing sample is that artificial tuberculosis yersinia genus is negative;As after reaction, color is
Green, then testing sample is that artificial tuberculosis yersinia genus is positive, containing artificial tuberculosis yersinia genus.Make when using hydroxynaphthol blue
During for developer, as after reaction, color is pansy, then testing sample is that artificial tuberculosis yersinia genus is negative;Such as face after reaction
Look is sky blue, then testing sample is that artificial tuberculosis yersinia genus is positive.Described color developing detection, except above by visually observing
Outside reaction result, it is also possible to carry out real-time or end point determination reaction result by detecting instrument, set feminine gender instead by rational
The threshold value answered, when the result of testing sample reaction is less than or equal to this threshold value, then testing sample is artificial tuberculosis yersinia genus
Negative;When the result of testing sample reaction is more than this threshold value, then testing sample is that artificial tuberculosis yersinia genus is positive.Described inspection
Survey instrument include but is not limited to sepectrophotofluorometer, quantitative real time PCR Instrument, constant-temperature amplification micro-fluidic chip foranalysis of nucleic acids instrument and
Genie II isothermal duplication fluorescence detecting system etc..
In described color developing detection, according to calcein or hydroxynaphthol blue as developer, can be anti-at constant-temperature amplification
Added before should, it is also possible to add after isothermal amplification reactions completes, it is therefore preferable to add before isothermal amplification reactions, permissible
The effective possibility reducing reaction pollution.According to SYBR Green I as developer, then complete in isothermal amplification reactions
Add afterwards.According to calcein as developer, then while adding 50 μM of calceins in enzyme reaction system, add
0.6-1mM[Mn2+], for example, the MnCl of 0.6-1mM2.
Present invention also offers for the primer in the method for Constant Temperature Detection artificial tuberculosis yersinia genus bacterial strain.Described primer
Including the primer sets of artificial tuberculosis yersinia genus genome specific base sequence can be expanded, it includes but is not limited to, described primer
Sequence be the nucleotide sequence of 768567~768785bp position of the artificial tuberculosis yersinia genus genome that No. GI is 153946813
A part or the part of its complementary strand.
Wherein, the described primer sets that can expand artificial tuberculosis yersinia genus genome specificity base sequence is selected from following
Any one group of primer sets, or selected from being 50% with wall scroll sequence homology in described each primer sets sequence or its complementary strand sequence
And above arbitrary primer sets.Wherein, described primer sets includes but is not limited to following primer sets A.Described with aforementioned primer sets sequence
In row or its complementary strand sequence, wall scroll sequence homology is 50% and above primer sets includes but is not limited to following primer sets B.
Primer sets A:
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’;
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’;
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’.
Primer sets B:
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’;
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’;
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’.
The present invention in the primer in described Constant Temperature Detection artificial tuberculosis yersinia genus method, described can expand pseudoconcretion
The primer sets of Yersinia ruckeri genome specificity base sequence can also comprise or not comprise one or more ring primer;Described
Ring primer is LF and/or LB.The described primer sets that can expand artificial tuberculosis yersinia genus genome specificity base sequence is selected from
Following primer sets A ', any one group of B ';Or be selected from and described primer sets A ', wall scroll sequence in B ' sequence or its complementary strand sequence
Homology is 50% and any one group of above primer sets:
Primer sets A ':
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’;
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’;
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_A:5’-TATGCTCATCCAGGCGTTTC-3’;
And/or, lower lantern primer LB_A:5’-TGATGGCGATGGGGAAAATT-3’;
Primer sets B ':
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’;
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’;
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_B:5’-GGGATTTCAATATGCTCATCCAG-3’;
And/or, lower lantern primer LB_B:5’-TGATGGCGATGGGGAAAATT-3’.
In a particular embodiment, above-mentioned primer sets A ', in B ', can only comprise a upper lantern primer, or only comprise
Article one, lower lantern primer, or comprise a upper lantern primer and a lower lantern primer simultaneously.In one embodiment, institute
State primer and be respectively the primer shown in FIP, BIP, F3, B3, LF and LB or single with aforementioned primer sequence or its complementary strand sequence
Bar primer homology is 50% and above primer.
The present invention also provides a kind of for the kit in above-mentioned Constant Temperature Detection artificial tuberculosis yersinia genus bacterial strain method, its
Including the described primer sets that can expand artificial tuberculosis yersinia genus genome specific base sequence.In kit of the present invention, described
The primer sets of artificial tuberculosis yersinia genus genome specificity base sequence can be expanded, including but not limited to genome (No. GI:
153946813) part for nucleotide sequence for 768567~768785bp position or a part for its complementary strand are drawn as described
Thing sequence;Described primer includes but is not limited to described primer sets A.Also including but not limited to with aforementioned primer sequence or it is complementary
In chain-ordering, wall scroll sequence homology is 50% and above primer sets is as primer;Including but not limited to primer sets B.
In kit of the present invention, the described primer sets that can expand artificial tuberculosis yersinia genus genome specificity base sequence
Can comprise or not comprise one or more ring primer;Ring primer is as optional component.Described ring primer is LF and/or LB.Bag
The primer sets of the LF and/or LB of primer containing ring includes but is not limited to primer sets A ', B ' etc..In a particular embodiment, present invention examination
Agent box can comprise LF and/or the LB ring primer of 0.4-1.0 μm of ol/L.In one embodiment, the sequence of primer sets
Be respectively the primer shown in FIP, BIP, F3, B3, LF and LB or with foregoing sequences or its complementary strand sequence wall scroll primer homology
It is 50% and above primer.
In kit of the present invention, also include Bst DNA polymerase buffer liquid, Bst archaeal dna polymerase, dNTP solution, Mg2+
(MgSO4Or MgCl2) and glycine betaine in one or more.In one embodiment, kit enzyme reaction system of the present invention
Comprise 1 × Bst DNA polymerase reaction buffer solution, 2-9mmol/L Mg2+(MgSO4Or MgCl2), 1.0-1.6mmol/LdNTP,
FIP and the BIP primer of 0.8-2.0 μm of ol/L, F3 and the B3 primer of 0.15-0.3 μm of ol/L, 0.16-0.64U/ μ L Bst DNA
Polymerase and the glycine betaine of 0-1.5mol/L.For example, 1 × Bst DNA polymerase reaction buffer solution can select 1 ×
Thermopol reaction buffer, comprises 20mmol/L Tris-HCl (pH 8.8), 10mmol/L KCl, 10mmol/L (NH4)2SO4,0.1%TritonX-100,2mM MgSO4.MgSO in 1 × Bst DNA polymerase reaction buffer solution4With enzyme reaction body
Magnesium ion Mg in system2+Do merging treatment.
In kit of the present invention, also comprise positive control template.In one embodiment, described positive control template
Include but is not limited to complete genome DNA, portion gene group DNA of artificial tuberculosis yersinia genus, or comprise pseudoconcretion pestis
Bacterium complete genome DNA or the carrier of portion gene group DNA.
In kit of the present invention, also comprising negative control template, described negative control template includes but is not limited to distilled water.
In kit of the present invention, also comprising developer, developer includes but is not limited to calcein, SYBR Green I or
Hydroxynaphthol blue.When developer is calcein, kit also comprises [Mn2+], for example, MnCl2.
In kit of the present invention, also comprise distilled water.
In kit of the present invention, also comprise nucleic acid extraction reagent.
The invention allows for a kind of carrier, described carrier comprises selected from primer sets A, B, A ', any one group of primer of B '.
This carrier has the specific DNA sequence dna of artificial tuberculosis yersinia genus owing to containing, therefore can be applicable to microbial taxonomy,
The research field such as comparative genomics, evolution, and the application such as microorganism detection.This carrier can be but not limited to plasmid
Carrier (such as pBR322, pUC18, pUC19, pBluescript M13, Ti-plasmids etc.), viral vectors (such as bacteriophage lambda etc.) and people
Make chromosome vector (such as Bacterial artificial chromosome BAC, yeast artificial chromosome YAC etc.).For example, primer sets A is comprised arbitrarily
Article one, carrier pBR322-A, the carrier pBR322-B ... of any one primer comprising primer sets B of primer comprises primer sets
The carrier pBR322-B ' of any one the primer of B '.Carrier bacteriophage lambda-the A of any one the primer comprising primer sets A, comprise
Carrier bacteriophage lambda-the B ... of any one primer of primer sets B comprise primer sets B ' the carrier λ of any one primer bite
Thalline-B ' etc..
The invention allows for selected from primer sets A, B, A ', the primer of any one group of B ' is at Constant Temperature Detection pseudoconcretion Yale
Application in gloomy Salmonella.
The invention allows for application in Constant Temperature Detection artificial tuberculosis yersinia genus for the described kit.
The invention allows for application in Constant Temperature Detection artificial tuberculosis yersinia genus for the described carrier.
The present invention is that technical field of food safety detection provides a kind of simple and quick sensitive detection pseudoconcretion yersinia genus
The method of Salmonella, primer/primer sets, detection reagent/kit, have greater significance to the food security of China.The present invention has
Benefit effect includes:Artificial tuberculosis yersinia genus detection method of the present invention is used to have high specificity, highly sensitive, detection time
Short, result judges simple, simple operation, low cost and other advantages.Compared with conventional at present detection method, the constant temperature that the present invention uses
TRAP, can be carried out under constant temperature, only need to use simple thermostat, it is not necessary to the expensive instrument in PCR experiment,
Do not need to carry out amplified production the steps such as electrophoresis detection, thus, it is very suitable for being widely used in various circles of society and include that basic unit eats
Product safety detection department promotes the use of, even if also may be used in the environment of molecular biology professional knowledge and skills base relative deficiency
Fully application.Above-mentioned each optimum condition can be combined based on common sense in the field, all belong to scope.
Brief description
Fig. 1 shows the specific of the embodiment of the present invention 7 artificial tuberculosis yersinia genus Constant Temperature Detection method.
Fig. 2 shows the sensitivity of the embodiment of the present invention 8 artificial tuberculosis yersinia genus detection method.
Detailed description of the invention
Being combined to lower specific embodiments and the drawings, the present invention is described in further detail, the protection content of the present invention
It is not limited to following example.Under the spirit and scope without departing substantially from inventive concept, those skilled in the art it is conceivable that change
Change and advantage is all included in the present invention, and with appending claims as protection domain.Implement the present invention process,
Condition, reagent, experimental technique etc., outside the lower content mentioned specially, be universal knowledege and the common knowledge of this area,
The present invention is not particularly limited content.
Embodiment 1-6 artificial tuberculosis yersinia genus isothermal reaction system and detection method
Detect according to following (1)~(3) step:
(1) extraction of genomic DNA
Derive from Chinese medicine bacteria culture preservation administrative center, numbering for the artificial tuberculosis yersinia genus bacterial classification of detection
CMCC53504.Taking 1mL bacterial cultures uses the bacterial nucleic acid of Beijing Tian Gen bio-engineering corporation to extract kit extraction gene
Group DNA, DNA OD260/OD280Being 1.8, concentration is 18.94ng/ μ L.
(2) with artificial tuberculosis yersinia genus genomic DNA to be measured as template, be respectively adopted autogamy kit (be shown in Table 2,
Table 3), and according to condition described in table 3, prepare reaction system, with artificial tuberculosis yersinia genus specificity amplification primer group for drawing
Thing, carries out isothermal amplification reactions.Primer in embodiment 1~6 is respectively primer sets A, and A ' (1 ring primer), (2 ring draws A '
Thing), B, B ' (2 ring primer), B ' (1 ring primer).
(3) according to condition described in table 3, by electrophoresis detection, Turbidity measurement or color developing detection, amplification is carried out true
Recognize.
As can be seen from Table 3, detection method and the primer sets being used and reaction system thereof can be right well
Artificial tuberculosis yersinia genus specific fragment carries out expanding and obtains testing result.Additionally, when using detector to detect,
Shorten the reaction time to also there being good Detection results (such as embodiment 6) during 10min.Therefore, present invention could apply to detection
Whether sample contains artificial tuberculosis yersinia genus.
Embodiment 7 artificial tuberculosis yersinia genus specific detection
Collect non-artificial tuberculosis yersinia genus 29 strain (in table 4 and Fig. 1 1~24,26~30), by these bacterial strains and false knot
Core pestis strain (in table 4 and Fig. 1 25) is cultivated respectively, takes 1mL bacterium solution, uses kit IA, extracts bacterium
DNA, and with reference to the reaction system of embodiment 1 and condition, carry out LAMP amplification (primer sets is A) respectively and add developer sight
Examine.
Its testing result is as shown in table 4 and Fig. 1, and in Fig. 1,1-24 is respectively staphylococcus aureus, Staphylococcus aureus
The golden yellow subspecies of bacterium, MRSE, Rhodococcus equi, bacillus cereus, gill fungus sample bacillus, listeria monocytogenes,
Ying Nuoke Listeria, listeria ivanovii, intestines salmonella intestines subspecies, Bacterium enteritidis, salmonella typhimurium, B-mode
Salmonella paratyphi, shigella dysenteriae, Shigella bogdii, shigella flexneri, ETEC (contain clostridium botulinum
A type gene), pathogenic ETEC, Diarrheogenil Escherichia coli, product enterotoxin ETEC, enterotoxigenic big
Intestines Escherichia, hemorrhagic ETEC, the rugged Cronobacter sakazakii of slope and yersinia enterocolitica, 26-30 is respectively
For Vibrio vulnificus, vibrio parahaemolytious, Freund vibrios, comma bacillus and Song Shi Shigella, NTC:Negative control, 25:Pseudoconcretion
Yersinia ruckeri.In Fig. 1, only the product after artificial tuberculosis yersinia genus bacterial strain amplified reaction is rendered as bright green, for the positive
As a result, as shown in No. 25 pipe.And the product after other non-artificial tuberculosis yersinia genus bacterial strains and negative control amplified reaction is equal
It is rendered as orange, is negative findings, as the 1st~No. 24,26~No. 30 is managed and shown in NTC negative control pipe.
By Fig. 1 and Biao 4 result it can be seen that detection kit of the present invention and detection method have good pseudoconcretion Yale
Gloomy Salmonella strain specificity, i.e. the only artificial tuberculosis yersinia genus bacterial strain amplification positive, other non-artificial tuberculosis yersinia genus bacterium
Strain is feminine gender.
Preparation detection kit, the primer using in kit is respectively primer sets B, primer sets A ', B ', by above-mentioned special
Property detection method, respectively obtains same testing result, i.e. non-artificial tuberculosis yersinia genus bacterial strain and negative control amplified reaction
After product be negative findings, the product after artificial tuberculosis yersinia genus bacterial strain amplified reaction is positive findings.
Additionally, according to method described in table 1, respectively to primer sets A, primer sets B, primer sets A ', B ' is specifically carried out
Theory analysis, it was found that in the case that each bar primer at most allows three mispairing, each primer sets has five and draws at most simultaneously
Thing comparison, on non-artificial tuberculosis yersinia genus, shows the specific all preferable of each primer sets.
Embodiment 8 sensitivity technique
As described in Example 1 extract bacterium CMCC 53504 DNA, use kit IB, and according to 50ng, 5ng,
500pg, 50pg, 5pg, 500fg, 50fg DNA ladder degree adds reaction system, and other reaction conditions are with reference to the side of table 3 embodiment 1
Method carries out LAMP amplification (primer sets is A) respectively and adds developer to observe.As in figure 2 it is shown, 1-7 be respectively 50ng, 5ng,
500pg, 50pg, 5pg, 500fg and 50fg, ntc:Negative control.The product that in Fig. 2,50ng, 5ng, 500pg are processed presents
For bright green, being positive findings, 50pg, 5pg, 500fg, 50fg are processed and the product of negative control is rendered as orange, are
Negative findings.Testing result shows, minimum in each reaction tube (is approximately equivalent to 10 containing 500pg5Individual bacterium) DNA when still can quilt
Detection.
By above-mentioned detection method, other Step By Conditions ibid, use primer sets B, primer sets A respectively ', B ', each reaction
In pipe, the DNA of as little as 5pg~500fg still can be detected.
Embodiment 9 versatility detects
According to method described in table 1, respectively to primer sets A, primer sets B, primer sets A ', the versatility of B ' carries out theoretical point
Analysis, it was found that the primer region of each primer sets and 4 strain artificial tuberculosis yersinia genus (No. GI is respectively 51594359,
153946813,170022262 and 186893344) coupling completely, may be used for above-mentioned 4 strain pseudoconcretion pestis in theory
The detection of bacteria strain, shows that the versatility of each primer sets is all preferable.
The versatility of primer and specifically analysis in the existing detection method of table 1 artificial tuberculosis yersinia genus
Note:A) 4 genome (GI difference by the sequence between primers F in patent 3 and B3 and artificial tuberculosis yersinia genus
It is 153946813,51594359,170022262 and 186893344) carry out Bowtie comparison, determine detection region at No. GI
Position in 153946813 genomes.B) detection regional sequence is carried out in common data base resource Blast comparison, primer
It is good that region is mated completely for versatility.C) detection regional sequence is carried out in common data base resource Blast comparison, guiding region
Territory matching degree is higher, specifically poorer;If primer can not simultaneously comparison in non-artificial tuberculosis yersinia genus strain, show special
Property is good.
The kit species of table 2 Constant Temperature Detection artificial tuberculosis yersinia genus and mainly comprise composition
Reaction condition in the method for table 3 embodiment 1-6 Constant Temperature Detection of the present invention artificial tuberculosis yersinia genus and detection knot
Really
Table 4 tests bacterial strain uses therefor and testing result
Note:a)CGMCC:China General Microbiological DSMZ, CICC:Chinese industrial Microbiological Culture Collection manages
Center, CMCC:Chinese medicine bacteria culture preservation administrative center.b)+:Positive findings ,-:Negative findings.
Claims (19)
1. the method for a fast constant temperature detection artificial tuberculosis yersinia genus, it is characterised in that comprise the following steps:
(1) from testing sample, genomic DNA is extracted;
(2) with described genomic DNA as template, so that drawing of artificial tuberculosis yersinia genus genome specificity base sequence can be expanded
Thing group, as primer, carries out isothermal amplification reactions under enzyme reaction system;
(3) by judging whether reaction result is positive, determine in testing sample whether there is artificial tuberculosis yersinia genus;
Wherein, described artificial tuberculosis yersinia genus genome specificity base sequence is the pseudoconcretion that No. GI is 153946813
768567~768785bp bit sequence of Ademilson Salmonella genome.
2. the method for claim 1, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specificity
The primer sets sequence of base sequence is artificial tuberculosis yersinia genus genome 768567~768785bp that No. GI is 153946813
A part for the nucleotide sequence of position or a part for its complementary strand.
3. method as claimed in claim 2, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specificity
The primer sets of base sequence is primer sets A;Or be selected from and wall scroll sequence homology in described primer sets A sequence or its complementary strand sequence
Property is 50% and above primer sets;
Primer sets A:
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’(SEQ ID NO:1);
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’(SEQ ID NO:2);
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’(SEQ ID
NO:3);
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’(SEQ ID
NO:4).
4. method as claimed in claim 3, it is characterised in that with wall scroll in described primer sets A sequence or its complementary strand sequence
Sequence homology is 50% and above primer sets includes following primer sets B:
Primer sets B:
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’(SEQ ID NO:5);
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’(SEQ ID NO:6);
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’(SEQ ID
NO:7);
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’(SEQ ID
NO:8).
5. method as claimed in claim 2, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specificity
The primer sets of base sequence also comprises one or more ring primer;Described ring primer is LF and/or LB.
6. method as claimed in claim 5, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specificity
The primer sets of base sequence is selected from following primer sets A ', any one group of B ';Or selected from and described primer sets A ', B ' sequence or its
In complementary strand sequence, wall scroll sequence homology is 50% and any one group of above primer sets:
Primer sets A ':
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’;
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’;
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_A:5’-TATGCTCATCCAGGCGTTTC-3’(SEQ ID NO:9);
And/or, lower lantern primer LB_A:5’-TGATGGCGATGGGGAAAATT-3’(SEQ ID NO:10);
Primer sets B ':
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’;
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’;
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_B:5’-GGGATTTCAATATGCTCATCCAG-3’(SEQ ID NO:11);
And/or, lower lantern primer LB_B:5’-TGATGGCGATGGGGAAAATT-3’(SEQ ID NO:12).
7. the method for claim 1, it is characterised in that in step (2), described enzyme reaction system includes:1×Bst
DNA polymerase reaction buffer solution, 2-9mmol/L Mg2+, FIP and BIP of 1.0-1.6mmol/L dNTP, 0.8-2.0 μm of ol/L
Primer, F3 and the B3 primer of 0.15-0.3 μm of ol/L, 0.16-0.64U/ μ L Bst archaeal dna polymerase, the beet of 0-1.5mol/L
Alkali, including or do not include LF and/or the LB primer of 0.4-1.0 μm of ol/L.
8. the method for claim 1, it is characterised in that the response procedures of described isothermal amplification reactions is:1. 60~65
DEG C hatch 10~90min;2. 80 DEG C terminate reaction 2~20min.
9. for the primer in Constant Temperature Detection artificial tuberculosis yersinia genus method as claimed in claim 1, it is characterised in that described
Primer includes the primer sets that can expand artificial tuberculosis yersinia genus genome specificity base sequence, and its sequence is No. GI and is
A part for the nucleotide sequence of 768567~768785bp position of the artificial tuberculosis yersinia genus genome of 153946813 or it is mutual
Mend a part for chain.
10. primer as claimed in claim 9, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specific
The primer sets of property base sequence is primer sets A;Or with wall scroll sequence homology in described primer sets A sequence or its complementary strand sequence
It is 50% and above primer sets;
Primer sets A:
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’;
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’;
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’.
11. primers as claimed in claim 10, it is characterised in that single with described primer sets A sequence or its complementary strand sequence
Bar sequence homology is 50% and above primer sets includes following primer sets B:
Primer sets B:
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’;
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’;
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’.
12. primers as claimed in claim 9, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specific
The primer sets of property base sequence also comprises one or more ring primer;Described ring primer is LF and/or LB.
13. primers as claimed in claim 12, it is characterised in that described can expand artificial tuberculosis yersinia genus genome specific
Property base sequence primer sets be selected from following primer sets A ', any one group of B ';Or selected from and described primer sets A ', B ' sequence or
In its complementary strand sequence, wall scroll sequence homology is 50% and any one group of above primer sets:
Primer sets A ':
Upstream outer primer F3_A:5’-GTTGTTGTATGAATTGCTGG-3’;
Downstream outer primer B3_A:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_A:5’-GTAACGCTGAAATACCGAACTGTAAATGGTTGATGAAGGTGG-3’;
Downstream inner primer BIP_A:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_A:5’-TATGCTCATCCAGGCGTTTC-3’;
And/or, lower lantern primer LB_A:5’-TGATGGCGATGGGGAAAATT-3’;
Primer sets B ':
Upstream outer primer F3_B:5’-GAATTGCTGGAAATGGTTG-3’;
Downstream outer primer B3_B:5’-GCGGATAACTCCTGTTCT-3’;
Upstream inner primer FIP_B:5’-GTAACGCTGAAATACCGAACTGTATGAAGGTGGTTTGAAACG-3’;
Downstream inner primer BIP_B:5’-CACCTTTATCTCTGATAATTTCCGCCTTTCCAGCTCATGTTGAT-3’;
Upper lantern primer LF_B:5’-GGGATTTCAATATGCTCATCCAG-3’;
And/or, lower lantern primer LB_B:5’-TGATGGCGATGGGGAAAATT-3’.
14. 1 kinds of kits for Constant Temperature Detection artificial tuberculosis yersinia genus, it is characterised in that described kit includes such as power
Profit requires the primer described in any one of 9~13.
15. kits as claimed in claim 14, it is characterised in that its also include Bst DNA polymerase reaction buffer solution,
Bst archaeal dna polymerase, dNTP solution, Mg2+, one or more in glycine betaine.
16. 1 kinds of kits for Constant Temperature Detection artificial tuberculosis yersinia genus, it is characterised in that the enzyme reaction of described kit
System includes:1 × Bst DNA polymerase reaction buffer solution, 2-9mmol/L Mg2+, 1.0-1.6mmol/L dNTP, 0.8-2.0 μ
FIP and the BIP primer of mol/L, F3 and the B3 primer of 0.15-0.3 μm of ol/L, including or do not include the LF of 0.4-1.0 μm of ol/L
And/or LB primer, 0.16-0.64U/ μ L Bst archaeal dna polymerase, and the glycine betaine of 0-1.5mol/L.
17. 1 kinds of carriers, it is characterised in that described carrier comprises the primer as described in any one of claim 9~13.
Application in Constant Temperature Detection artificial tuberculosis yersinia genus for 18. primers, it is characterised in that described primer is for such as claim
Primer described in any one of 9~13.
19. kits as described in any one of claim 14~16 or carrier as claimed in claim 17 are in Constant Temperature Detection
Application in artificial tuberculosis yersinia genus.
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CN202010036128.9A CN111020046A (en) | 2015-09-02 | 2016-08-30 | Nucleic acid rapid constant temperature detection method for yersinia pseudotuberculosis and application |
CN202010035792.1A CN111100906A (en) | 2015-09-02 | 2016-08-30 | Rapid constant-temperature detection method, primer group and kit for yersinia pseudotuberculosis |
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