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CN103160495A - Disconnected dependent rapid cloning method - Google Patents

Disconnected dependent rapid cloning method Download PDF

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Publication number
CN103160495A
CN103160495A CN2011104184509A CN201110418450A CN103160495A CN 103160495 A CN103160495 A CN 103160495A CN 2011104184509 A CN2011104184509 A CN 2011104184509A CN 201110418450 A CN201110418450 A CN 201110418450A CN 103160495 A CN103160495 A CN 103160495A
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dna
donor
receptor
donor dna
cloning
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张力军
徐晓昱
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Abstract

The invention relates to a rapid cloning method for donor DNA fragments. The method includes: first introducing additional sequences to the 5' ends of amplification primers so as to endow both terminals of donor DNA and both terminals of receptor DNA respectively with at least 12bp homologous sequences; then linearizing the receptor DNA, finally making the donor DNA and the linearized receptor DNA form a recombinant intermediate efficiently in vitro under catalysis of exonuclease and single-strand binding protein, and transforming the intermediate directly to a competent cell, thus finishing the cloning process from the donor DNA to the receptor DNA. With no need for an enzyme digestion treatment on the donor DNA, the method provided in the invention can realize rapid directed cloning of a single donor DNA fragment, also can realize one-step splicing cloning of a plurality of donor DNA fragments, and can be used for DNA site-directed mutagenesis. The method can provide a rapid and efficient operation platform for research in genetics, molecular biology, biochemistry and the like as well as high-throughput cloning.

Description

A kind of disconnected dependent rapid clon method
Technical field
The present invention relates to the genetically engineered field, specifically relate to a kind of method of quick clone.
Background technology
The foundation of the dependent DNA directed cloning of ligase enzyme technology is landmark achievement in the field of biology in last century.The foundation of this technology and application make people can revise within the specific limits the genetic recombination matter DNA, thereby provide possibility for exploring gene concrete function in vivo.Along with the development of biological development, particularly round pcr and the foundation of DNA site-directed mutagenesis technique, the DNA directed cloning has now become the basis of whole biology field.The DNA directed cloning refers to the donor dna fragment is cloned into specific position on receptor dna, such as multiple clone site.Traditional DNA directed cloning comprises following steps usually:
1) the primer amplification donor dna fragment of using 5 ' end to add the specific limited restriction enzyme site;
2) be connected in the T carrier after donor dna fragment amplification product purification;
3) use pre-designed restriction enzyme site with target fragment from the T carrier enzyme cutting from out and carry out purifying;
4) use with the same restriction enzyme site of step 3) the receptor dna linearizing, and carry out purifying;
5) use step 3) and 4) middle the purifying donor dna and the receptor dna that obtain carry out ligation by a certain percentage;
6) with step 5) in the connection product be converted in competent cell;
7) recombinant DNA of exact connect ion is identified, extracted to mono-clonal.
This shows, traditional DNA directed cloning is a job that takes time and effort very much, and cloning efficiency is poor, and success ratio is low.In addition, owing to usually comprising multiple restriction enzyme site in the donor dna fragment, therefore can choose the biggest obstacle that the suitable restriction enzyme that is used for the clone becomes this technical development of restriction.In today of biology develop rapidly, be accompanied by the very big development of DNA sequencing technology and synthetic biology, inefficient traditional cloning process can't satisfy and becomed more diverse and complicated clone's demand, especially can't satisfy the high-flux clone demand.
The novel cloning process based on the restructuring principle can effectively be eliminated restriction enzyme site to the restriction of Strategies For The Cloning, has many potential advantages such as suitability is wide, flux is high.At present existing several recombinant clone systems that can satisfy the high-flux clone demand come out one after another: universal support plasmid emerging system UPS, GateWay entry clones system and MAGIC cloning system.Wherein, universal support plasmid emerging system UPS, GateWay entry clones system is based on the exploitation of external locus specificity restructuring principle, and the MAGIC cloning system is based on homologous recombination and bacterium Hybridization principle in body and develop.Above three cloning systems can be completed seamless shuttle back and forth of any DNA fragment under different background, and operating process has versatility, can satisfy to a certain extent variation, high-throughout clone's demand.Yet regrettably, these disconnected dependent cloning systems all exist some self unavoidable defective.At first, compare with traditional cloning process, the other two kinds of methods except the Gateway cloning system all do not have clear superiority to initial gene clone.And Gateway clone need to complete initial gene clone with extremely expensive enzyme, and need to add the sequence that comprises recombination site of specific a section very long during design of primers.Secondly, these cloning systems require initial gene clone to carry out on fixing carrier, specify in carrier if goal gene need to be cloned into, and these systems are out of use.The 3rd, these cloning systems can only be allowed donor dna fragment of a time cloning, are not suitable for the disposable amalgamation clone of complicated many donors fragment.
Due to above-mentioned many disadvantages, these three kinds of locus specificity recombinant clone systems can't be widely used.Homologous recombination is the another kind of DNA recombinant forms that occurs in vivo.The locus specificity of comparing, the dependent restructuring of homology has great advantage.At first, the DNA restructuring that homology relies on does not need specific DNA sequence dna, only need donor dna and receptor dna to have the homologous sequence that can mate fully of certain-length to get final product at recombination site, and the locus specificity restructuring need specific DNA sequence dna to realize.Therefore, if replace the locus specificity restructuring to carry out community's DNA clone with homologous recombination, can eliminate its initial gene clone and can only carry out this restriction to specifying on carrier, make the donor dna clone have higher handiness and selectivity.Secondly, based on the Strategies For The Cloning of homologous recombination, allow the amalgamation clone who a plurality of donor fragments is carried out a step, namely complete simultaneously the connection amalgamation of a plurality of donor fragments and be cloned into receptor dna.This advantage provides a kind of solution of single step for the gene of complexity or carrier transformation.
This shows with the locus specificity restructuring and compare, the homologous recombination cloning system has unrivaled advantage.The In-FusionTM PCR clone test kit of Clontech just is based on the exploitation of homologous recombination principle and forms.Use this test kit, but donor dna PCR product Direct Cloning need not the loaded down with trivial details steps such as enzyme is cut, connection, end-filling to any receptor dna.When using this system, need to introduce at least 15 base homologous sequences at 5 ' end of PCR primer.These 15 bases must be respectively can be mated fully with 5 ' and 3 ' end of linearizing destination carrier.After the PCR reaction finished, the donor dna PCR product that purifying is crossed and linearizing receptor dna reacted 30 minutes under the catalysis of In-FusionTM recombinase, and the homologous sequence of end can merge.Reaction product directly is converted into the intestinal bacteria competence can complete clone's process.The single step clone that In-FusionTM PCR cloning system has really been realized the donor dna fragment has simplified clone's process greatly, and has significantly improved to a certain extent clone's success ratio.Yet, due to this recombinase is difficult to obtain, the cost costliness and character unstable, this system also fails to be promoted widely at present
Technology contents
For the problems referred to above, the invention provides a kind of method that realizes the directed restructuring of external DNA by DNA excision enzyme and single strand binding protein.At first design donor dna fragments specific amplimer, add respectively 12bp at least and sequence receptor dna end homology at its forward and reverse primer 5 ' end, can also add for the linearizing restriction enzyme site of donor dna if need.Use this primer pair amplification donor dna fragment, amplified production is reclaimed test kit by glue or the ethanol precipitation is carried out the purifying recovery.Secondly, receptor dna is used suitable restriction enzyme carry out linearizing and purifying recovery.At last, donor dna and linearizing receptor dna fragment can be at external efficient formation recombination intermediates under the co-catalysis of DNA excision enzyme and single strand binding protein.The direct transformed competence colibacillus cell of this recombination intermediate can be completed clone's process (seeing accompanying drawing 1).This inventive method can be used for realizing the directed cloning of single donor dna fragment, also can realize the one-step cloning of a plurality of target dna fragments, completes the seamless spliced of DNA, can also be used as the DNA rite-directed mutagenesis.The pcr amplification primer principle of design that the present invention preferably is used for single donor dna directed cloning is: forward primer: 5 '-15bp receptor dna, 5 ' end homologous sequence+restriction enzyme site+donor dna specificity forward amplimer-3 '; Reverse primer: 5 '-15bp receptor dna, 3 ' end homologous sequence+restriction enzyme site+reverse amplimer-3 ' of donor dna specificity.Described 15bp receptor dna 5 ' end homologous sequence refers to receptor dna 5 ' the last 15bp DNA sequence dna of end antisense strand end, and direction is 5 ' to 3 '; Described 15bp receptor dna 3 ' end homologous sequence refers to the proper last 15bp DNA sequence dna of adopted chain end of acceptor 3 ', and direction is 5 ' to 3 '.The length of described homologous sequence is 12bp at least, and its length is 15bp in a preference of the present invention.Described restriction enzyme site is total length or the part of receptor dna linearizing restriction enzyme digestion sites used, and direction is 5 ' to 3 '.Described donor dna specificity just (instead) refers to donor dna PCR amplimer to amplimer, and direction is 5 ' to 3 ' (seeing accompanying drawing 2).
The pcr amplification primer principle of design that the present invention preferably is used for the directed splicing clone of many donor dnas is (take two donor fragment assembly clones as example, set the splicing order and be respectively by 5 ' to 3 ' direction: donor Segment A, donor fragment B):
Donor A forward primer: 5 '-15bp receptor dna, 5 ' end homologous sequence+restriction enzyme site+donor A fragments specific forward amplimer-3 '; Donor A reverse primer: the reverse amplimer-3 ' of 5 '-donor A fragments specific; Donor B forward primer: 5 '-15bp donor A fragment, 3 ' end homologous sequence+donor B fragments specific forward amplimer-3 '; Donor B reverse primer: 5 '-15bp receptor dna, 3 ' end homologous sequence+restriction enzyme site+reverse amplimer-3 ' of donor dna specificity.Described 15bp receptor dna 5 ' end homologous sequence refers to receptor dna 5 ' the last 15bp DNA sequence dna of end antisense strand end, and direction is 5 ' to 3 '; Described 15bp donor A fragment 3 ' end homologous sequence confession under directions body A fragment 3 ' the last 15bp DNA sequence dna of end positive-sense strand, direction 5 ' to 3 '; Described 15bp receptor dna 3 ' end homologous sequence refers to the proper last 15bp DNA sequence dna of adopted chain end of acceptor 3 ', and direction is 5 ' to 3 '.The length of described homologous sequence is 12bp at least, and its length is 15bp in a preference of the present invention.Described restriction enzyme site is total length or the part of receptor dna linearizing restriction enzyme digestion sites used, and direction is 5 ' to 3 '.Described donor A fragment (B fragment) specificity just (instead) refers to donor dna PCR amplimer to amplimer, and direction is 5 ' to 3 '.
The present invention preferably is used for DNA rite-directed mutagenesis pcr amplification primer principle of design for (introducing single base mutation as example take plasmid DNA, setting take the sudden change position on M and the plasmid vector 3 ' direction with its apart the another location more than 500bp as N, be divided into two sections by 5 ' to 3 ' direction M and N two plasmid vector of naming a person for a particular job, donor MN fragment and acceptor N fragment M section): donor MN fragment forward primer and the reverse complete complementary of acceptor NM fragment reverse primer or part are complementary, and between two primers, the overlapping region is 15bp; Donor MN fragment reverse primer and acceptor NM fragment forward primer complete complementary or part are complementary, and between two primers, the overlapping region is 15bp.The single base mutation of introducing in described donor MN fragment forward primer and acceptor NM fragment reverse primer complementary region.Between described primer, the overlapping region is at least 12bp, and its length is 15bp in a preference of the present invention.
The archaeal dna polymerase that in the present invention, the amplification of donor dna fragment PCR is used can be any type of archaeal dna polymerase.In view of the requirement to the donor dna fidelity of reproduction, select high-fidelity DNA polymerase in a preference of the present invention.Described receptor dna refers to any DNA double chain link that can be used for DNA clone, includes but are not limited to following several: plasmid, BAC (bacterial artificial chromosome), YAC (artificial yeast's karyomit(e)) and Phagemid (phagemid) etc.Described receptor dna linearizing can use restriction enzyme to carry out, and also can directly use with the pcr amplification product of receptor dna as template.Donor dna fragment and linearizing receptor dna fragment need be carried out purifying and be reclaimed, the purifying mode comprise but be not limited only to following several, pillar DNA purification system, ethanol precipitation etc.In view of the DNA purity requirement, in a preference of the present invention, use the pillar DNA purification system to carry out the purifying recovery to donor dna and receptor dna.
In the present invention, the recombining reaction of donor dna fragment and receptor dna fragment is completed external under DNA excision enzyme and DNA single chain binding protein co-catalysis.Described DNA excision enzyme refers to the general name of class of enzymes that can the cutting DNA end, can be the combination of any one 5 ' → 3 ' DNA excision enzyme or several this kind excision enzymes, includes but not limited to following several: intestinal bacteria excision enzyme VII, T7 excision enzyme gene 6 etc.; Also can be the combination of any one 3 ' → 5 ' DNA excision enzyme or several this kind excision enzymes, include but not limited to following several: intestinal bacteria excision enzyme I, intestinal bacteria exonucleaseⅢ, T4 polysaccharase etc.; Also one or several combination of two class excision enzymes.Described DNA excision enzyme can derive from prokaryotic organism, for example intestinal bacteria; Also can derive from eukaryote, for example yeast, nematode, mouse, rat or people.Select the DNA excision enzyme in intestinal bacteria source in preference of the present invention.Described single strand binding protein can be any albumen that can be combined with single stranded DNA, includes but not limited to following several: intestinal bacteria SSB, eukaryote replication protein RPA, RecA, T4 gene 32 albumen etc.Described single strand binding protein can derive from prokaryotic organism, for example intestinal bacteria; Also can derive from eukaryote, for example yeast, nematode, mouse, rat or people.Select the single strand binding protein in intestinal bacteria source in preference of the present invention.
the enzyme liquid that can be used for the recombining reaction of catalysis donor dna fragment and receptor dna fragment in the present invention can be the combination of any or several excision enzyme and any or several DNA single chain binding proteins: include but not limited to following several: intestinal bacteria excision enzyme I and intestinal bacteria SSB, intestinal bacteria exonucleaseⅢ and intestinal bacteria SSB, intestinal bacteria excision enzyme VII and intestinal bacteria SSB, T7 excision enzyme gene 6 and intestinal bacteria SSB, T4 polysaccharase and intestinal bacteria SSB, intestinal bacteria excision enzyme I and RecA, intestinal bacteria exonucleaseⅢ and RecA, intestinal bacteria excision enzyme VII and RecA, T7 excision enzyme gene 6 and RecA, T4 polysaccharase and RecA etc.Select intestinal bacteria T4 polysaccharase and intestinal bacteria RecA in preference of the present invention, this combination can efficiently mediate the donor dna fragment and the receptor dna fragment is reacted in external generation homologous recombination.
In the present invention, after donor dna fragment and the purified recovery of receptor dna fragment, and after mixing, DNA excision enzyme and single strand binding protein can carry out recombining reaction.Need comprise damping fluid, salt ion and ATP in reaction system, PH can be 5.0-9.0.In preference of the present invention, the recombining reaction system comprises following component: 500mM Tris-HCL, 200mM Mg (AC) 2,10mM DTT, 1M NaAc, 1mM ATP, 10mM BSA, reaction solution PH is 8.0.Above component can replace with other similar reagent of physicochemical property, such as NaAc can replace with KAc.After donor dna and receptor dna can use respectively the DNA excision enzyme to process, remix also added single strand binding protein to carry out recombining reaction; Add DNA excision enzyme and single strand binding protein to carry out recombining reaction after also can mixing.Reaction times can be 10-60 minute, but the reaction times is too short or oversizely all will cause the recombining reaction decrease in efficiency.Temperature of reaction can be 18 ℃-50 ℃, along with the rising reaction times of temperature of reaction is answered corresponding shortening, otherwise also will cause the recombining reaction decrease in efficiency.Temperature of reaction is 30 ℃ in preference of the present invention, and the reaction times is 30 minutes.
Donor dna fragment and receptor dna fragment form recombination intermediate after recombining reaction, because of the repair mechanism that cell self has, recombination intermediate directly transformed competence colibacillus cell can be completed the homologous recombination of donor dna fragment and receptor dna fragment.One section 500bp λ DNA sequence dna of clone to the result of PUC19 plasmid can draw the following conclusions from embodiment 1: DNA excision enzyme (T4 polysaccharase) and single strand binding protein (RecA) can be in external efficient mediated dna fragment homologous recombination, thereby complete the DNA directed cloning, and clone's positive rate surpasses 90%.
The invention has the advantages that:
1. cloning efficiency is high, and clone's number is many and positive rate is high;
2. step is simple, need not to the donor dna fragment shuttle back and forth clone or enzyme cut processing;
3. the donor dna fragment does not need restriction enzyme to process, and has therefore thoroughly eliminated the restriction that the inherent restriction enzyme site of donor dna is selected for Strategies For The Cloning;
4. the inventive method not only can be used as the quick clone of single donor dna fragment, and can be used for realizing the seamless spliced and single step clone of a plurality of donor dna fragments.
Above-mentioned explanation is not limited only to the present invention and described embodiment, and those skilled in the art can implement and use technical solutions according to the invention by modifying, adjust, changing, and these technical schemes all fall within the scope of protection of the present invention.
Description of drawings
Fig. 1: present patent application methods experiment schematic flow sheet.
Fig. 2: present patent application method design of primers schematic diagram.
Fig. 3: embodiment 1 mono-clonal PCR qualification result electrophorogram.
The M:DL2000 molecular weight standard, 2.0kbp, 1.0kbp, 0.75kbp, 0.5kbp, 0.25kbp, 0.1kbp; 1-14:14 different mono-clonal bacterium colony PCR products, positive colony amplified production size should be 700bp.
Fig. 4: embodiment 1 mono-clonal EcoRI and BamHI double digestion product electrophorogram.
The M:DL2000 molecular weight standard, 2.0kbp, 1.0kbp, 0.75kbp, 0.5kbp, 0.25kbp, 0.1kbp; 1-8:8 different mono-clonal enzymes are cut product, and positive colony should produce 2.6kbp and two bands of a spectrum of 500bp.
Embodiment
The term that uses in the present invention unless other explanation is arranged, generally has the implication that those of ordinary skills understand usually.
Below in conjunction with specific embodiment, and comparable data is described the present invention in further detail.Should be understood that these embodiment just in order to demonstrate the invention, but not limit the scope of the invention by any way.
In following embodiment, various processes and the method do not described in detail are ordinary methods as known in the art.The source of all reagent, trade(brand)name and be necessary to list its moiety person are all indicated when occurring first, thereafter identical reagent used if no special instructions, all identical with the content of indicating first.
Experiment reagent used and plasmid in embodiment, its source is as follows:
1.λDNA。Available from U.S. Promega company;
2.PrimeSTAR HS DNA Polymerase。Available from Japanese Takara company;
3. restriction enzyme EcoRI, BamHI.Available from Japanese Takara company;
4.T4 polysaccharase, intestinal bacteria RecA.Available from NEB company;
5. glue reclaims test kit.Available from sky, Beijing root company limited;
6. the inorganic salt that use in the experiment are all available from U.S. Sigma company.
Embodiment 1. with the sequence directed cloning of one section 500bp of λ DNA to the carrier PUC19 between EcoRI and BamHI.
1. design primer
At first design cloned sequence pcr amplification primer
Forward primer: 5 '-ATCAGTCATTTCTCGCACATTG-3 ', (SEQ ID NO.1)
Reverse primer: 5 '-TTACGGGGTTGGAGGTCA-3 ', (SEQ ID NO.2)
15bp carrier homologous sequence and restriction enzyme site that forward primer 5 ' end needs to add are: 5 '-AAAACGACGGCCAGT GAATTC(EcoRI)-3 ', (SEQ ID NO.3)
15bp carrier homologous sequence and restriction enzyme site that reverse primer 5 ' end needs to add are: 5 '-GACGATATCTCTAGA GGATCC(BamHI)-3 ', (SEQ ID NO.4)
Therefore the forward primer ultimate sequence is: 5 '-AAAACGACGGCCAGT GAATTCATCAGTCATTTCTCGCACATTG-3 ', (SEQ ID NO.5)
The reverse primer ultimate sequence is: 5 '-GACGATATCTCTAGA GGATCCTTACGGGGTTGGAGGTCA-3 ', (SEQ ID NO.6)
2.PCR amplification
The pcr amplification system:
PrimeSTAR 0.5 μl
5X PrimeSTAR Buffer 10 μl
λDNA(1ng/ul) 1 μl
Forward primer (10um) 1 μl
Reverse primer (10um) 1 μl
Sterile purified water 36.5 μl
Amount to 50 μl
The PCR reaction conditions is: at first 94 ℃ of sex change are 5 minutes, and cycling condition is: 98 ℃ 10 seconds, 68 degree 30 seconds, totally 35 circulations.Thoroughly extended 10 minutes at 72 ℃ at last.Use instrument to be 2720 model PCR instrument of AB company.Reaction product is carried out glue and is reclaimed after 1% agarose electrophoresis.
3.PUC19 carrier linearizing
1 μ g PUC19 plasmid uses 1 μ l EcoRI and 1 μ l BamHI, cuts 2 hours at 37 ℃ of lower enzymes.Product carries out glue and reclaims after 1% agarose electrophoresis.
4. vitro recombination reaction
The following reaction system of configuration in ice-water bath:
Figure BSA00000636202900091
The 10X reaction buffer comprises following component: 5M Tris-HCL, 2M Mg (AC) 2, 100mM DTT, 10M NaAc, 100mM BSA, PH is 8.0.Reaction mixture reacts under 30 ℃ and was placed on the ice-water bath stopped reaction in 30 minutes.
5. transform the intestinal bacteria competence
The recombining reaction system is added (CaCL in 200ul bacillus coli DH 5 alpha competent cell 2Method is made, and efficient approximately has 10 6~10 7Cfu/ug), be coated on the dull and stereotyped upper 37 ℃ of incubated overnight of LB of ammonia benzyl resistance after conversion.
6. clone identification
Grow on the LB flat board of incubated overnight~1000 mono-clonals.Identify through bacterium colony PCR, positive rate is 100% (14/14) (seeing accompanying drawing 2).After getting wherein 8 mono-clonals and extracting plasmid, enzyme is cut evaluations (EcoRI+BamHI), is all correctly to clone (8/8) (seeing accompanying drawing 3).Get wherein that 4 positive colonies send order-checking, sequence is all consistent with expection.
The sequence (Segment A) of one section 500bp of embodiment 2. clone λ DNA and the sequence of one section 700bp (fragment B), two DNA fragmentations are sequentially seamless spliced, and directed cloning is to the carrier PUC19 between EcoRI and BamHI.
1. design primer
Segment A forward amplimer is: 5 '-ATCAGTCATTTCTCGCACATTG-3 ', (SEQ ID NO.7)
The reverse amplimer of Segment A is: 5 '-TTACGGGGTTGGAGGTCA-3 ', (SEQ ID NO.8)
15bp carrier homologous sequence and restriction enzyme site that Segment A forward primer 5 ' end needs to add are:
5’-AAAACGACGGCCAGT GAATTC(EcoRI)-3’,(SEQ ID NO.9)
Segment A reverse primer 5 ' end needs the 15bp and the fragment B 5 ' that add to hold the sequence of homology to be:
5’-GAAGCGGCGCAATAT-3’,(SEQ ID NO.10)
Therefore Segment A forward primer ultimate sequence is: 5 '-AAAACGACGGCCAGT GAATTCATCAGTCATTTCTCGCACATTG-3 ', (SEQ ID NO.11)
The reverse primer ultimate sequence is: 5 '-GAAGCGGCGCAATATTTACGGGGTTGGAGGTCA-3 ', (SEQ ID NO.12)
Fragment B forward amplimer is: 5 '-ATATTGCGCCGCTTCAGGATGC-3 ', (SEQ ID NO.13)
The reverse amplimer of fragment B is: 5 '-TCACATTCAAACATTAATTT-3 ', (SEQ ID NO.14)
The 15bp homologous sequence that needs because of Segment A and fragment B restructuring has been included in the Segment A reverse primer, and fragment B forward amplimer 5 ' end need not to introduce additional sequences.
15bp carrier homologous sequence and restriction enzyme site that fragment B reverse primer 5 ' end needs to add are:
5’-GACGATATCTCTAGA GGATCC(BamHI)-3’,(SEQ ID NO.15)
Therefore fragment B reverse primer ultimate sequence is: 5 '-GACGATATCTCTAGA GGATCCTCACATTCAAACATTAATTT-3 ', (SEQ ID NO.16)
2.PCR amplification
The pcr amplification system:
PrimeSTAR 0.5 μl
5X PrimeSTAR Buffer 10 μl
λDNA(1ng/ul) 1 μl
Forward primer (10um) 1 μl
Reverse primer (10um) 1 μl
Sterile purified water 36.5 μl
Amount to 50 μl
The PCR reaction conditions is: at first 94 ℃ of sex change are 5 minutes, and cycling condition is: 98 ℃ 10 seconds, 68 degree 30 seconds, totally 35 circulations.Thoroughly extended 10 minutes at 72 ℃ at last.Use instrument to be 2720 model PCR instrument of AB company.Reaction product is carried out respectively glue and is reclaimed after 1% agarose electrophoresis.
3.PUC19 carrier linearizing
1 μ g PUC19 plasmid uses 1 μ l EcoRI and 1 μ l BamHI, cuts 2 hours at 37 ℃ of lower enzymes.Product carries out glue and reclaims after 1% agarose electrophoresis.
4. vitro recombination reaction
The following reaction system of configuration in ice-water bath:
Figure BSA00000636202900111
The 10X reaction buffer comprises following component: 5M Tris-HCL, 2M Mg (AC) 2, 100mM DTT, 10M NaAc, 100mM BSA, PH is 8.0.Reaction mixture reacts under 30 ℃ and was placed on the ice-water bath stopped reaction in 30 minutes.
5. transform the intestinal bacteria competence
The recombining reaction system is added (CaCL in 200ul bacillus coli DH 5 alpha competent cell 2Method is made, and efficient approximately has 10 6~10 7Cfu/ug), be coated on the dull and stereotyped upper 37 ℃ of incubated overnight of LB of ammonia benzyl resistance after conversion.
6. clone identification
Grow on the LB flat board of incubated overnight~400 mono-clonals.Identify through bacterium colony PCR, positive rate is 89% (16/18).After getting wherein 6 mono-clonals and extracting plasmid, enzyme is cut evaluations (EcoRI+BamHI), is all correctly to clone (6/6).Get wherein that 4 positive colonies send order-checking, sequence is all consistent with expection.
Embodiment 3. introduces respectively the point mutation of T to G and G to A 967 and 2361 of PUC19 plasmid.
Experimental strategy is: plasmid is divided into two sections of 2362-967 (Segment A) and 968-2361 (fragment B) increases with PCR respectively, required point mutation is introduced when design of primers.The reverse amplimer of Segment A and the complete reverse complemental of fragment B forward amplimer, and all introduce 967 T to the point mutation of G; The complete reverse complemental of reverse amplimer of the forward amplimer of Segment A and fragment B, and all introduce the G of 2631 to the point mutation of A.
1. design primer
Segment A forward amplimer: 5 '-CTTTTACTTTCACCA ACGTTTCTGGGTGAG-3 ', (SEQ ID NO.17)
The reverse amplimer of Segment A: 5 '-GCTTCCAGGGGGAA CCGCCTGGTATCTTTA-3 ', (SEQ ID NO.18)
Fragment B forward amplimer: 5 '-TAAAGATACCAGGCG GTTCCCCCTGGAAGC-3 ', (SEQ ID NO.19)
The reverse amplimer of fragment B: 5 '-CTCACCCAGAAACG TTGGTGAAAGTAAAAG-3 ', (SEQ ID NO.20)
The base of underscore mark is the point mutation of introducing in primer.
2.PCR amplification
The pcr amplification system:
PrimeSTAR 0.5 μl
5X PrimeSTAR Buffer 10 μl
λDNA(1ng/ul) 1 μl
Forward primer (10um) 1 μl
Reverse primer (10um) 1 μl
Sterile purified water 36.5 μl
Amount to 50 μl
The PCR reaction conditions is: at first 94 ℃ of sex change are 5 minutes, and cycling condition is: 98 ℃ 10 seconds, 68 degree 2 minutes, totally 35 circulations.Thoroughly extended 10 minutes at 72 ℃ at last.Use instrument to be 2720 model PCR instrument of AB company.Reaction product is carried out respectively glue and is reclaimed after 1% agarose electrophoresis.
3. vitro recombination reaction
The following reaction system of configuration in ice-water bath:
Figure BSA00000636202900131
The 10X reaction buffer comprises following component: 5M Tris-HCL, 2M Mg (AC) 2, 100mM DTT, 10M NaAc, 100mM BSA, PH is 8.0.Reaction mixture reacts under 30 ℃ and was placed on the ice-water bath stopped reaction in 30 minutes.
4. transform the intestinal bacteria competence
The recombining reaction system is added (CaCL in 200ul bacillus coli DH 5 alpha competent cell 2Method is made, and efficient approximately has 10 6~10 7Cfu/ug), be coated on the dull and stereotyped upper 37 ℃ of incubated overnight of LB of ammonia benzyl resistance after conversion.
5. clone identification
Grow on the LB flat board of incubated overnight~800 mono-clonals.Identify through bacterium colony PCR, positive rate is 100% (8/8).Get wherein 2 positive colony complete sequences surveys logical, sequence is all consistent with expection.
Figure ISA00000636203100011
Figure ISA00000636203100021
Figure ISA00000636203100031
Figure ISA00000636203100061

Claims (10)

1. one kind is utilized the external homologous recombination reaction of exonuclease and single strand binding protein mediation the donor dna fragment to be carried out the method for quick clone, it is characterized in that: first make donor dna two ends and receptor dna two ends that the homologous sequence of 12bp at least be arranged respectively by introducing appended sequence at amplimer 5 ' end, again with the receptor dna linearizing, donor dna and linearizing receptor dna can be at external efficient formation recombination intermediates under the catalysis of exonuclease and single strand binding protein, the direct transformed competence colibacillus cell of this intermediate just can be completed donor dna to clone's process of receptor dna.
2. the method for claim 1 it is characterized in that a kind of method of quick clone, wherein donor dna need not restriction endonuclease just process can Direct Cloning to receptor dna.
3. method as claimed in claim 2, is characterized in that, described donor dna needs to introduce appended sequence at pcr amplification primer 5 ' end.
4. method as claimed in claim 3, is characterized in that, the pcr amplification forward primer 5 ' end of donor dna need add 12bp receptor dna 5 ' end homologous sequence at least, the i.e. last 12bp DNA sequence dna of its 5 ' end antisense strand end; Donor dna pcr amplification reverse primer 5 ' end need add 12bp receptor dna 3 ' end homologous sequence at least, i.e. its 3 ' proper last 12bp DNA sequence dna of adopted chain end.
5. method as claimed in claim 2, is characterized in that, described receptor dna need to carry out linearizing.
6. method as claimed in claim 5, is characterized in that, described linearizing is to use the DNA restriction enzyme to carry out, or directly uses receptor dna total length pcr amplification product.
7. the method for claim 1, it is characterized in that, described DNA excision enzyme is 5 ' DNA excision enzyme, or 3 ' DNA excision enzyme, include but are not limited to following several: intestinal bacteria excision enzyme VII, T7 excision enzyme gene 6, intestinal bacteria excision enzyme I, intestinal bacteria exonucleaseⅢ, T4 polysaccharase.
8. the method for claim 1, it is characterized in that, described single strand binding protein refer to can with the albumen of single stranded DNA (ssDNA) combination, include but are not limited to following several: intestinal bacteria SSB, eukaryote replication protein RPA, RecA, T4 gene 32 albumen.
9. the method for claim 1, is characterized in that, comprises at least a DNA excision enzyme and at least a single strand binding protein in the enzyme liquid of the outer homologous recombination reaction of catalytic body.
10. the method for claim 1, is characterized in that, after donor dna and receptor dna used respectively exonuclease to process, remix also added single strand binding protein to carry out recombining reaction; Or with donor dna with add simultaneously DNA excision enzyme and single strand binding protein to carry out recombining reaction after receptor dna mixes.
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CN104178477A (en) * 2013-05-28 2014-12-03 中国人民解放军军事医学科学院生物工程研究所 Gene synthesis method
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CN104195161A (en) * 2014-09-12 2014-12-10 刘喜朋 Preparing method for DNA recombinase based on controllable DNA polymerase and exonuclease activity and application thereof
CN104195161B (en) * 2014-09-12 2020-06-09 刘喜朋 Preparation method and application of DNA recombinase based on controllable DNA polymerase and exonuclease activity
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CN107760706A (en) * 2017-10-11 2018-03-06 吴江近岸蛋白质科技有限公司 The application of DNA excision enzymes and the method for seamless clone
CN109439684A (en) * 2018-12-27 2019-03-08 尚科生物医药(上海)有限公司 A method of improving foreign gene efficiency of evolution in eukaryocyte
CN109439684B (en) * 2018-12-27 2023-09-01 尚科生物医药(上海)有限公司 Method for improving evolution efficiency of exogenous gene in eukaryotic cells

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