CN110551760A - CRISPR/Sa-SeqCas9 gene editing system and application thereof - Google Patents

Abstract

The invention belongs to the technical field of gene editing, and particularly relates to a CRISPR/Sa-SeqCas9 gene editing system and application thereof, wherein the gene editing system is a complex formed by Sa-SeqCas9 protein and sgRNA, can accurately target a DNA sequence and generate cutting to enable the DNA to generate double-strand break damage, the gene editing is to perform gene editing in cells or in vitro, Sa-SeqCas9 is fusion protein, a PAM recognition structural domain (PAM interaction, PI) of SaCas9 is replaced by a PAM recognition structural domain (SeqCas 9-PI) Sa-SeqCas9 protein of SeqCas9, the protein is 1053 amino acids, the identified PAM sequence is simple, the Sa-SeqCas9 protein has an amino acid sequence shown in SEQ ID NO:1, and the sgRNA has a nucleotide sequence shown in SEQ ID NO: 2.

Description

CRISPR/Sa-SeqCas9 gene editing system and application thereof

Technical Field

The invention belongs to the technical field of gene editing, and particularly relates to a CRISPR/Sa-SeqCas9 system capable of performing gene editing in cells and related application thereof.

Background

CRISPR/Cas9 is an acquired immune system that bacteria and archaea have evolved to protect against foreign virus or plasmid invasion. In the CRISPR/Cas9 system, after a complex is formed by crRNA (CRISPR-derived RNA), tracrRNA (trans-activating RNA) and Cas9 protein, a pam (promoter adjacentmotif) sequence for identifying a target site can form a complementary structure with a target DNA sequence, and Cas9 protein plays a role in cutting DNA, so that the DNA is subjected to breaking damage. Wherein, tracrRNA and crRNA can be fused into single-stranded guide RNA (sgRNA) through a connecting sequence. When DNA breaks and damages, two major DNA damage repair mechanisms within the cell are responsible for repair: non-homologous end-joining (NHEJ) and Homologous Recombination (HR). Deletion or insertion of a base can be caused as a result of NHEJ repair, and gene knockout can be carried out; in the case of providing a homologous template, site-directed insertion of genes and precise base substitution can be performed using HR repair.

Besides basic scientific research, the CRISPR/Cas9 also has wide clinical application prospect. When the CRISPR/Cas9 system is used for gene therapy, Cas9 and sgRNA need to be introduced into a body. The most effective delivery vector for gene therapy is AAV. However, AAV virus-packaged DNA typically does not exceed 4.5 kb. SpCas9 has been widely used because of its simple PAM sequence (recognition of NGG) and high activity. However, the SpCas9 protein has 1367 amino acids, and the sgRNA and the promoter cannot be effectively packaged into the AAV virus, so that the clinical application of the protein is limited. To overcome this problem, several small Cas9 were invented, including SaCas9(PAM sequence NNGRRT); st1Cas9(PAM sequence NNAGAW); NmCas9(PAM sequence NNNNGATT); nme2Cas9(PAM sequence NNNNCC); cjCas9(PAM sequence is NNRYAC), but these Cas9 or PAM sequences are complex (few DNA sequences can be targeted in genome), or editing efficiency is low, and wide application is difficult. The search for a small Cas9 protein, PAM sequence simple CRISPR/Cas9 system is hopeful to solve the above problems.

Disclosure of Invention

In view of the above problems, the present invention aims to provide a novel gene editing system of CRISPR/Cas9 with high editing activity, small Cas9 protein and simple PAM sequence, and applications thereof.

The CRISPR/Cas9 gene editing system provided by the invention is a complex formed by Sa-SeqCas9 protein and sgRNA, and is marked as a CRISPR/Sa-SeqCas9 gene editing system (namely, Sa-SeqCas9 protein which realizes gene editing under the coaction with single guide RNA (sgRNA)); the DNA sequence can be precisely targeted, and the cutting is generated, so that the DNA is subjected to double-strand break damage; the gene editing is gene editing in a cell or in vitro; the Sa-SeqCas9 protein is small and 1053 amino acids, the identified PAM sequence is simple (NNGRM), and the Sa-SeqCas9 protein has an amino acid sequence shown in SEQ ID NO. 1 or an amino acid sequence which is at least 80 percent identical to the amino acid sequence shown in SEQ ID NO. 1; the sgRNA has a nucleotide sequence shown in SEQ ID NO. 2, or a sgRNA sequence modified based on SEQ ID NO. 2.

In the present invention, the cells include eukaryotic cells and prokaryotic cells; the eukaryotic cells include mammalian cells and plant cells.

In the present invention, the mammalian cells include Chinese hamster ovary cells, baby hamster kidney cells, mouse Sertoli cells, mouse mammary tumor cells, buffalo rat liver cells, rat liver tumor cells, monkey kidney CVI line transformed by SV40, monkey kidney cells, canine kidney cells, human cervical cancer cells, human lung cells, human liver cells, HIH/3T3 cells, human U2-OS osteosarcoma cells, human A549 cells, human K562 cells, human HEK293T cells, human HCT116 cells, or human MCF-7 cells or TRI cells.

In the invention, Sa-SeqCas9 in the CRISPR/Cas9 system is a fusion protein, the PI domain of SaCas9 is replaced by the PI domain of SeqCas9, and SeqCas9 is Staphyloccocus equorumCas 9. The Sa-SeqCas9 fusion protein and single guide RNA (sgRNA) work together to achieve gene editing.

In the invention, the SeqCas9 protein belongs to Staphylococcus equine (Staphylococcus equorum), and the search number of the UniProt of the SeqCas9 protein is A0A1E5TL 62.

in the invention, the Sa-SeqCas9 protein comprises a Sa-SeqCas9 protein which has no cleavage activity or only single-strand cleavage activity or double-strand cleavage activity.

In the invention, the precise positioning DNA sequence comprises a sequence of 20bp or 21bp at the 5' end of the sgRNA and a target DNA sequence which can form a base complementary pairing structure.

In the invention, the accurate positioning target DNA sequence comprises a Sa-SeqCas9 protein and a PAM sequence on a sgRNA complex recognition target DNA sequence.

in the invention, the PAM sequence is NNGRM, and the target DNA sequence is:

NNNNNNNNNNNNNNNNNNNNNNNGRM(SEQ ID NO:3)。

In the invention, the Sa-SeqCas9 protein and sgRNA complex can precisely target DNA sequences, namely the Sa-SeqCas9 protein and the sgRNA complex can recognize and bind specific DNA sequences, or other proteins fused with the Sa-SeqCas9 protein or proteins specifically recognizing sgRNA are brought to the position of the target DNA.

In the present invention, the Sa-SeqCas9 protein and sgRNA complex or other protein fused with Sa-SeqCas9 protein or protein specifically recognizing sgRNA can modify and regulate the targeted DNA region, including but not limited to regulation of gene transcription level, DNA methylation regulation, DNA acetylation modification, histone acetylation modification, single base switch or chromatin imaging tracking.

In the present invention, the single base converter includes, but is not limited to, conversion between bases adenine to guanine, or cytosine to thymine, or cytosine to uracil, or other bases.

The gene editing system provided by the invention has high editing activity and has obvious advantages compared with the prior Cas 9.

The editing efficiency of the CRISPR/Sa-SeqCas9 system is detected by the techniques of gene synthesis, molecular cloning, cell transfection, PCR product deep sequencing, bioinformatics analysis and the like.

The CRISPR/Sa-SeqCas9 gene editing system provided by the invention can carry out gene editing in cells, and comprises the steps of identifying and positioning target DNA through a compound of Sa-SeqCas9 protein and sgRNA, and editing the DNA; and finally, detecting the editing efficiency.

the method comprises the following specific steps:

(1) Synthesizing a humanized Sa-SeqCas9 gene sequence; and cloning to an expression vector to obtain pAAV2_ Sa-SeqCas9_ ITR;

(2) Synthesizing oligonucleotide single-stranded DNA (deoxyribonucleic acid) corresponding to the sgRNA, namely Oligo-F and Oligo-R sequences, annealing the oligonucleotide single-stranded DNA, and connecting the oligonucleotide single-stranded DNA to a BsaI enzyme cutting site of a plasmid pAAV2_ Sa-SeqCas9_ U6_ BsaI to obtain pAAV2_ Sa-SeqCas9-hU 6-sgRNA;

(3) Delivering a vector expressing the Sa-SeqCas9 protein, sgRNA, into a cell containing a target site;

(4) And carrying out PCR amplification on the edited target site, carrying out T7EI enzyme digestion or carrying out second-generation sequencing to detect the editing efficiency.

in the present invention, any targeted sgRNA can be designed for a DNA sequence to be edited according to specific needs, and modifications well known in the art including, but not limited to, phosphorylation, shortening, lengthening, sulfurization, methylation, and hydroxylation can be performed on the sgRNA to some extent.

In the present invention, the CRISPR/Sa-SeqCas9 system delivered to the cell may include, but is not limited to, a plasmid expressing Sa-SeqCas9 protein or sgRNA, retrovirus, adenovirus, adeno-associated viral vector or RNA, or Sa-SeqCas9 protein, according to specific needs.

It will be appreciated by those skilled in the art that base N represents A, T, C or G, any of the four bases.

Further, in step (3), the delivery means includes, but is not limited to, liposomes, cationic polymers, nanoparticles, multifunctional envelope-type nanoparticles, and viral vectors.

Further, in step (3), the cells include, but are not limited to, human cells, animal cells, plant cells, bacterial cells, and fungal cells.

Further, in the step (2), the sgRNA has a nucleotide sequence shown in SEQ ID NO. 2, or a nucleotide sequence at least 80% identical to the nucleotide sequence shown in SEQ ID NO. 2, or modifications based on the nucleotide sequence, including but not limited to phosphorylation, shortening, lengthening, sulfurization or methylation.

More specifically, in one embodiment, oligonucleotide single-stranded DNA sequences corresponding to sgrnas, i.e., Oligo-F and Oligo-R, were synthesized as follows:

Oligo-F CACCGCTCGGAGATCATCATTGCG(SEQ ID NO:4)

Oligo-R AAACCGCAATGATGATCTCCGAGC(SEQ ID NO:5)。

more specifically, in one embodiment, it can be understood by those skilled in the art that Oligo-F and Oligo-R need to be annealed to become double-stranded DNA, and the annealing reaction system is 1. mu.L of 100. mu.M Oligo-F, 1. mu.L of 100. mu.M Oligo-R, and 28. mu.L of water, and after shaking and mixing, the mixture is placed in a PCR instrument to run an annealing program; the annealing procedure was as follows: 95 ℃ 5min, 85 ℃ 1min, 75 ℃ 1min, 65 ℃ 1min, 55 ℃ 1min, 45 ℃ 1min, 35 ℃ 1min, 25 ℃ 1min, 4 ℃ storage, cooling rate 0.3 ℃/s.

More specifically, in one embodiment, the plasmid pAAV2_ Sa-SeqCas9_ ITR requires linearization with BsaI restriction endonuclease (NEB).

More specifically, in one embodiment, the annealed Oligo-F and Oligo-R products are ligated to the linearized pAAV2_ Sa-SeqCas9_ ITR backbone vector by DNA ligase.

More specifically, in one embodiment, after transformation of the ligation products into competent cells, the correct clones were verified by Sanger sequencing and the plasmids were extracted for use.

More specifically, in one embodiment, the cell in step (3) is HEK293T comprising a target site having the nucleotide sequence shown in SEQ ID No. 6.

More particularly, in one embodimentIn an embodiment, the delivery means in step (3) is a liposome comprising2000 or PEI.

More specifically, in a specific embodiment of the first aspect of the present invention, the template for PCR in the experimental step (4) is edited HEK293T genomic DNA.

More specifically, in one embodiment, the primer sequences amplified by PCR in step (4) are:

F1-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNGCGAGAAAAGCCTTGTTT(SEQ ID NO:7)

R1-ACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTGAACTTGTGGCCGTTTAC(SEQ ID NO:8)

F2-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC(SEQ ID NO:9)

R2-CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTG(SEQ ID NO:10)。

The invention also provides a CRISPR/Sa-SeqCas9 system kit for gene editing, which comprises a Sa-SeqCas9 protein or sgRNA of a target DNA sequence or a target DNA.

The invention also provides application of the CRISPR/Sa-SeqCas9 gene editing system, which comprises gene knockout, site-specific base change, site-specific insertion, gene transcription level regulation, DNA methylation regulation, DNA acetylation modification, histone acetylation modification, single base converter or chromatin imaging tracking.

Drawings

FIG. 1 is a schematic diagram of CRISPR/Sa-SeqCas9 gene editing system cutting targeting DNA. Wherein, the grey oval represents the Sa-SeqCas9 protein, the black curved shape represents the sgRNA sequence, and the darkened region in the upper chain of the genome represents the PAM sequence NNGG.

FIG. 2 is a map schematic diagram of plasmid pAAV2_ Sa-SeqCas9_ U6_ BsaI. Among them, there are AAV2 ITR, CMV enhancer, CMV promoter, SV40 NLS, Sa-SeqCas9, nucleoplasmin NLS, 3 XHA, bGH poly (A), human U6 promoter (hU6), BsaI endonuclease site, sgRNA scaffold sequence and other elements.

FIG. 3 shows the result of partial next generation sequencing after the DNA sequence of the target site has been edited. Wherein the editing result has deletion, insertion or mismatching, and the last 5bp represents a PAM sequence NNGRM.

FIG. 4 shows the cleavage of endogenous site with T7 Endonuclease I. Wherein the arrows indicate the size of the cut fragments.

Detailed Description

The present invention will be further illustrated by the following examples, which are not intended to limit the invention in any way.

reagents, methods and apparatus used in the present invention are conventional in the art unless otherwise indicated. Unless otherwise indicated, reagents and materials used in the following examples are commercially available. The experimental method not specified for the specific conditions is usually carried out under the conventional conditions or the conditions recommended by the manufacturer.

in a specific embodiment, the CRISPR/Sa-SeqCas9 system provided by the invention is a novel gene editing system, method, kit and application thereof.

In a specific embodiment of the invention, the CRISPR/Sa-SeqCas9 system enables gene editing in a cell, the method comprising the steps of:

1. Construction of plasmid pAAV2_ Sa-SeqCas9_ ITR

And (1) downloading the amino acid sequence of the Sa-SeqCas9 gene according to the retrieval number A0A1E5TL62 of the Sa-SeqCas9 gene on UniProt, wherein the amino acid sequence is shown as SEQ ID NO: 1.

And (2) carrying out codon optimization on the amino acid sequence of the Sa-SeqCas9 to obtain a coding sequence highly expressed in human cells by the Sa-SeqCas9, wherein the coding sequence is shown as SEQ ID NO: 11.

And (3) carrying out gene synthesis on the coding sequence of the obtained gene Sa-SeqCas9 in a company, and constructing the coding sequence on a pAAV2_ ITR skeleton plasmid to obtain a plasmid pAAV2_ Sa-SeqCas9_ ITR, as shown in figure 2.

2. preparation of linearized plasmid pAAV2_ Sa-SeqCas9_ ITR

Step (1), carrying out enzyme digestion linearization on the plasmid pAAV2_ Sa-SeqCas9_ ITR by using BasI restriction enzyme, wherein an enzyme digestion system comprises: mu.g of plasmid pAAV2_ Sa-SeqCas9_ ITR, 5. mu.L of 10xCutSmart buffer, 1. mu.L of the endonuclease, water to 50. mu.l, and reaction at 37 ℃ for 1 hour.

And (2) carrying out electrophoresis on the product after enzyme digestion on a 1% agarose gel at 120V for 30 minutes.

And (3) cutting off the 7423bp DNA fragment, recovering by using a glue recovery kit according to the steps provided by the manufacturer, and finally eluting by using ultrapure water.

And (4) determining the DNA concentration of the recovered linearized plasmid pAAV2_ Sa-SeqCas9_ ITR by using NanoDrop, and reserving for later use or storing at-20 ℃ for long-term storage.

3. Construction of plasmid pAAV2_ Sa-SeqCas9-hU6-sgRNA

And (1) designing a sgRNA sequence.

Step (2), adding linearized plasmids pAAV2 \ to the sense strand and antisense strand of the designed sgRNA sequence pair

The corresponding cohesive end sequences of Sa-SeqCas9_ ITR both sides, and two oligonucleotide single-stranded DNAs are synthesized by the company, and the specific sequences are as follows:

Oligo-F CACCGCTCGGAGATCATCATTGCG(SEQ ID NO:4)

Oligo-R AAACCGCAATGATGATCTCCGAGC(SEQ ID NO:5)。

And (3) annealing the oligonucleotide single-stranded DNA to obtain double-stranded DNA, wherein an annealing reaction system comprises the following steps: mu.L of 100. mu.M oligo-F, 1. mu.L of 100. mu.M oligo-R, 28. mu.L of water, shaking and mixing, placing in a PCR instrument to run an annealing program: 95 ℃ 5min, 85 ℃ 1min, 75 ℃ 1min, 65 ℃ 1min, 55 ℃ 1min, 45 ℃ 1min, 35 ℃ 1min, 25 ℃ 1min, 4 ℃ storage, cooling rate 0.3 ℃/s.

And (4) connecting the annealed product with the linearized plasmid pAAV2_ Sa-SeqCas9_ ITR under the action of DNA ligase according to the steps provided by the product.

Step (5), 1. mu.L of the ligation product was taken for chemical competent transformation, and the growing bacterial clones were subjected to Sanger sequencing validation.

And (6) carrying out sequencing verification on the correctly connected clone shake bacteria, and extracting a plasmid pAAV2_ Sa-SeqCas9-hU6-sgRNA for later use.

4. Plasmid pAAV2_ Sa-SeqCas9-hU6-sgRNA for transfecting and expressing Sa-SeqCas9 protein and sgRNA

Step (1), on day 0, according to transfection needs, the HEK293T cell line containing the sgRNA targeting site is plated in a 6-well plate, the cell density is about 30%, and the sequence of the target site is shown as SEQ ID NO. 6.

Step (2), day 1, transfection was performed in the following transfection system,

i. Adding 2 μ g of plasmid pAAV2_ Sa-SeqCas9-hU6-sgRNA to be transfected into 100 μ l of Opti-MEM culture medium, and gently blowing, beating and uniformly mixing;

ii. mixing2000 flick and mix evenly, suck 5 mul and add to 100 mul Opti-MEM culture medium, mix evenly gently, stand 5min at room temperature;

Will dilute2000 and diluted plasmid, gently whipping and mixing, standing at room temperature for 20min, and then adding to the medium of the cells to be transfected.

And (3) placing the cells in a 37 ℃ and 5% CO2 incubator for continuous culture.

5. Preparation of a second Generation sequencing library

and (1) collecting HEK293T cells after editing for 3 days, and extracting genomic DNA by using a DNA kit according to the steps provided by the product.

Step (2), performing first round PCR of PCR library building, performing PCR reaction by using 2xQ5 Mastermix, wherein PCR primers are shown as SEQ ID NO:7-SEQ ID NO:8, and the reaction system is as follows:

The PCR run program was as follows:

and (3) carrying out second round PCR of PCR library building, carrying out PCR reaction by using 2xQ5 Mastermix, wherein the PCR primer is shown as SEQ ID NO: 9-SEQ ID NO:10, and the reaction system is as follows:

The PCR run program was as follows:

And (4) purifying DNA fragments with the size of 366bp by using a gel recovery kit for PCR products of the second round according to the steps provided by the manufacturer, and finishing the preparation of the second generation sequencing library.

6. Analysis of the results of the second generation sequencing

Step (1), the prepared second-generation sequencing library was submitted to the company for paired-end sequencing on HiseqXTen.

Step (2) bioinformatics analysis of the next-generation sequencing results, and partial compilation results are shown in FIGS. 2 and 3.

7. Endogenous site validation

Step (1), passing a plasmid pAAV2_ Sa-SeqCas9-hU6-sgRNA expressing Sa-SeqCas9 and sgRNA through2000 were transfected into HEK293T cells according to the manufacturer's protocol, in which,

The sgRNA sequence is: GAGCTGGTGGACCTAGTACA (SEQ ID NO:12)

The specific sequence of the target site is as follows: GAGCTGGTGGACCTAGTACAATGGA, respectively; (SEQ ID NO:13)

Extracting cell genome DNA after 5 days of editing, and amplifying a target DNA sequence by using primers Test-F and Test-R through 2x Q5 Master mix; wherein:

The specific sequence of Test-F is: ATCAACCCGGAGCAGATTC (SEQ ID NO:14)

The specific sequence of Test-R is as follows: CCTCATTGTCCAGAAAGACCA (SEQ ID NO: 15);

step (3), recovering the PCR product through agarose gel, and purifying DNA fragment with size of 475 bp;

Step (4), carrying out enzyme digestion on the purified DNA fragment according to the instruction of T7 Endonuclease I, then carrying out gel running detection, wherein the result is shown in figure 4, the left side is a negative control group, and no sgRNA is generated during transfection, and T7 Endonuclease I cuts a targeting sequence and then has no cut fragment, which indicates that no editing is generated; the right panel shows the experimental group, with sgRNA at transfection, and T7 endonucleoclean I cleaved after cleavage of the targeting sequence to show that editing has occurred.

Sequence listing

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<400> 11

atgaagcgga actacatcct gggcctggac atcggcatca ccagcgtggg ctacggcatc 60

atcgactacg agacacggga cgtgatcgat gccggcgtgc ggctgttcaa agaggccaac 120

gtggaaaaca acgagggcag gcggagcaag agaggcgcca gaaggctgaa gcggcggagg 180

cggcatagaa tccagagagt gaagaagctg ctgttcgact acaacctgct gaccgaccac 240

agcgagctga gcggcatcaa cccctacgag gccagagtga agggcctgag ccagaagctg 300

agcgaggaag agttctctgc cgccctgctg cacctggcca agagaagagg cgtgcacaac 360

gtgaacgagg tggaagagga caccggcaac gagctgtcca ccaaagagca gatcagccgg 420

aacagcaagg ccctggaaga gaaatacgtg gccgaactgc agctggaacg gctgaagaaa 480

gacggcgaag tgcggggcag catcaacaga ttcaagacca gcgactacgt gaaagaagcc 540

aaacagctgc tgaaggtgca gaaggcctac caccagctgg accagagctt catcgacacc 600

tacatcgacc tgctggaaac ccggcggacc tactatgagg gacctggcga gggcagcccc 660

ttcggctgga aggacatcaa agaatggtac gagatgctga tgggccactg cacctacttc 720

cccgaggaac tgcggagcgt gaagtacgcc tacaacgccg acctgtacaa cgccctgaac 780

gacctgaaca atctcgtgat caccagggac gagaacgaga agctggaata ttacgagaag 840

ttccagatca tcgagaacgt gttcaagcag aagaagaagc ccaccctgaa gcagatcgcc 900

aaagaaatcc tcgtgaacga agaggatatt aagggctaca gagtgaccag caccggcaag 960

cccgagttca ccaacctgaa ggtgtaccac gacatcaagg acattaccgc ccggaaagag 1020

attattgaga acgccgagct gctggatcag attgccaaga tcctgaccat ctaccagagc 1080

agcgaggaca tccaggaaga actgaccaat ctgaactccg agctgaccca ggaagagatc 1140

gagcagatct ctaatctgaa gggctatacc ggcacccaca acctgagcct gaaggccatc 1200

aacctgatcc tggacgagct gtggcacacc aacgacaacc agatcgctat cttcaaccgg 1260

ctgaagctgg tgcccaagaa ggtggacctg tcccagcaga aagagatccc caccaccctg 1320

gtggacgact tcatcctgag ccccgtcgtg aagagaagct tcatccagag catcaaagtg 1380

atcaacgcca tcatcaagaa gtacggcctg cccaacgaca tcattatcga gctggcccgc 1440

gagaagaact ccaaggacgc ccagaaaatg atcaacgaga tgcagaagcg gaacgccgcc 1500

accaacgagc ggatcgagga aatcatccgg accaccggca aagagaacgc caagtacctg 1560

atcgagaaga tcaagctgca cgacatgcag gaaggcaagt gcctgtacag cctggaagcc 1620

atccctctgg aagatctgct gaacaacccc ttcaactatg aggtggacca catcatcccc 1680

agaagcgtgt ccttcgacaa cagcttcaac aacaaggtgc tcgtgaagca ggaagaaaac 1740

agcaagaagg gcaaccggac cccattccag tacctgagca gcagcgacag caagatcagc 1800

tacgaaacct tcaagaagca catcctgaat ctggccaagg gcaagggcag aatcagcaag 1860

accaagaaag agtatctgct ggaagaacgg gacatcaaca ggttctccgt gcagaaagac 1920

ttcatcaacc ggaacctggt ggataccaga tacgccaccg ccgccctgat gaacctgctg 1980

cggagctact tcagagtgaa caacctggac gtgaaagtga agtccatcaa tggcggcttc 2040

accagctttc tgcggcggaa gtggaagttt aagaaagagc ggaacaaggg gtacaagcac 2100

cacgccgagg acgccctgat cattgccaac gccgatttca tcttcaaaga gtggaagaaa 2160

ctggacaagg ccaaaaaagt gatggaaaac cagatgttcg aggaaaagca ggccgagagc 2220

atgcccgaga tcgaaaccga gcaggagtac aaagagatct tcatcacccc ccaccagatc 2280

aagcacatta aggacttcaa ggactacaag tacagccacc gggtggacaa gaagcctaat 2340

agagagctga ttaacgacac cctgtactcc acccggaagg acgacaaggg caacaccctg 2400

atcgtgaaca atctgaacgg cctgtacgac aaggacaatg acaagctgaa aaagctgatc 2460

aacaagagcc ccgaaaagct gctgatgtac caccacgacc cccagaccta ccagaaactg 2520

aagctgatta tggaacagta cggcgacgag aagaatcccc tgtacaagta ctacgaggaa 2580

accgggaact acctgaccaa gtactccaaa aaggacaacg gccccgtgat caagaagatt 2640

aagtattacg gcaacaaact gaacgcccat ctggacatca ccgacgacta ccccaacagc 2700

agaaacaagg tcgtgaagct gtccctgaag ccctaccgct tcgacgtgta cctggacaac 2760

ggcgtgtaca agttcgtgac cgtgaagaac ctgaacgtga taaagaagga gaactactac 2820

gaggtgaaca gcaagtgcta cgagaaggcc aagaagctga agaagataag cgaccaggcc 2880

gagttcatcg ccagcttcta caacaacgac ctgataaaga tagacggcga gctgtaccgc 2940

gtgataggcg tgaacaccga cctgataaac cgcatcgagg tgaacatggt ggacatcacc 3000

taccgcgagt acctggagaa catgaacgac aagcgcagcc cccgcatctt caagaccatc 3060

gccagcaaga cccagagcat caagaagtac agcaccgaca tcctgggcac cctgtacgag 3120

gtgaacagca agaagcaccc ccagatgata atgaagggc 3159

<210> 12

<211> 20

<212> DNA

<213> Artificial sequence

<400> 12

gagctggtgg acctagtaca 20

<210> 13

<211> 25

<212> DNA

<213> Artificial sequence

<400> 13

gagctggtgg acctagtaca atgga 25

<210> 14

<211> 19

<212> DNA

<213> Artificial sequence

<400> 14

atcaacccgg agcagattc 19

<210> 15

<211> 21

<212> DNA

<213> Artificial sequence

<400> 15

cctcattgtc cagaaagacc a 21

Claims (18)

1. A CRISPR/Cas9 gene editing system for gene editing in cells or in vitro, characterized in that the CRISPR/Cas9 system isSa-SeqCas9The protein and sgRNA complex can accurately position a target DNA sequence and generate cutting, so that double-strand break damage occurs to DNA; the above-mentionedSa-SeqCas9The protein has an amino acid sequence shown in SEQ ID NO. 1 or an amino acid sequence which is at least 80 percent identical to the amino acid sequence shown in SEQ ID NO. 1; the sgRNA has a nucleotide sequence shown in SEQ ID NO. 2, or a sgRNA sequence modified based on SEQ ID NO. 2.

2. The CRISPR/Cas9 gene editing system of claim 1, wherein the cells comprise eukaryotic cells and prokaryotic cells; the eukaryotic cells include mammalian cells and plant cells; the mammalian cells include Chinese hamster ovary cells, baby hamster kidney cells, mouse Sertoli cells, mouse mammary tumor cells, buffalo rat liver cells, rat liver tumor cells, monkey kidney CVI line transformed by SV40, monkey kidney cells, canine kidney cells, human cervical cancer cells, human lung cells, human liver cells, HIH/3T3 cells, human U2-OS osteosarcoma cells, human A549 cells, human K562 cells, human HEK293T cells, human HCT116 cells, or human MCF-7 cells or TRI cells.

3. The CRISPR/Cas9 gene editing system according to claim 1, wherein the CRISPR/Cas9 gene editing systemSa-SeqCas9Proteins comprising no cleavage activity or having only single strand cleavage activity or having double strand cleavage activitySa-SeqCas9A protein.

4. The CRISPR/Cas9 gene editing system according to claim 1, wherein the precisely positioned DNA sequence comprises a sequence of 20bp or 21bp at the 5' end of sgRNA which can form a base complementary pairing structure with a target DNA sequence.

5. The CRISPR/Cas9 gene editing system according to claim 1, wherein the precisely located targeting DNA sequence comprisesSa-SeqCas9The protein and sgRNA complex recognizes a PAM sequence on the target DNA sequence.

6. The CRISPR/Cas9 gene editing system according to claim 5, wherein the PAM sequence is NNGRM and the targeting DNA sequence is shown in SEQ ID NO 3.

7. The CRISPR/Cas9 gene editing system according to claim 1, wherein the sgRNA can be phosphorylated, shortened, lengthened, sulfurized, methylated, or hydroxylated modified.

8. The CRISPR/Cas9 gene editing system according to claim 1, wherein the CRISPR/Cas9 gene editing systemSa-SeqCas9Protein and sgRNA complex can precisely target DNA sequenceSa-SeqCas9the complex of protein and sgRNA can recognize and bind to a specific DNA sequence, or to be bound toSa-SeqCas9Other proteins of the protein fusion or proteins that specifically recognize the sgRNA are brought into position to target the DNA.

9. the CRISPR/Cas9 gene editing system according to claim 8, wherein the CRISPR/Cas9 gene editing systemSa-SeqCas9Protein and sgRNA complexes or withSa-SeqCas9Other proteins of the protein fusion or proteins that specifically recognize the sgrnas can modify and regulate targeted DNA regions, including regulation of gene transcription levels, DNA methylation regulation, DNA acetylation modification, histone acetylation modification, single base converters, or chromatin imaging tracking.

10. The CRISPR/Cas9 gene editing system according to claim 9, wherein the single base switch comprises a switch between bases adenine to guanine, cytosine to thymine, cytosine to uracil or other bases.

11. CRISPR/according to one of claims 1 to 10Sa-SeqCas9A method for gene editing in a cell by a gene editing system comprisingSa-SeqCas9Identifying and positioning the target DNA by the compound of the protein and the sgRNA, and editing the DNA; finally, detecting the editing efficiency; the method comprises the following specific steps:

(1) Synthetic humanizationSeqCas9-PIA gene sequence; and cloning the gene into an expression vector to obtain pAAV2 \ uSa- SeqCas9_ITR；

(2) Single-stranded oligonucleotides DNA corresponding to sgRNA, i.e., Oligo-F and Oligo-R sequences, were synthesized, annealed and ligated to plasmid pAAV2 \\ uSa-SeqCas9BsaI cleavage site of U6 BsaI to obtain pAAV 2USa-SeqCas9-hU6-sgRNA；

(3) will expressSa-SeqCas9The protein, vector of sgRNA, is delivered into a cell containing the target site;

(4) And carrying out PCR amplification on the edited target site, carrying out T7EI enzyme digestion or carrying out second-generation sequencing to detect the editing efficiency.

12. The method of claim 11 wherein said pAAV2 \uSa-SeqCas9-hU6-sgRNA is an adeno-associated virus backbone plasmid comprising AAV2 ITR, CMV enhancer, CMV promoter, SV40 NLS, Sa-SeqCas9, nucleoplasmin NLS, 3 xha, bGH poly (a), human U6 promoter, BsaI endonuclease site, sgRNA scaffold sequence.

13. the method of claim 11, wherein the CRISPR ∑ is delivered to a cellSa-SeqCas9The system includes an expressionSa-SeqCas9Plasmids, retroviruses, adenoviruses, adeno-associated viral vectors or RNAs or of proteins or sgRNAsSa-SeqCas9a protein.

14. The method of claim 11, wherein the sequences of single-stranded oligonucleotides corresponding to sgrnas, i.e., Oligo-F and Oligo-R, are shown in SEQ ID NOs 4 and 5, are synthesized.

15. The method according to claim 11, wherein the target site of the cell in step (3) has the nucleotide sequence shown as SEQ ID NO 6.

16. The method according to claim 11, wherein the template for PCR in step (4) is edited DNA; the primer sequences for PCR amplification are: SEQ ID NO7, SEQ ID NO8, SEQ ID NO9, SEQ ID NO 10.

17. CRISPR/according to one of claims 1 to 10Sa-SeqCas9a kit for a gene editing system, the kit comprisingSa-SeqCas9sgRNA or targeting DNA of a protein or targeting DNA sequence.

18. CRISPR/according to one of claims 1 to 10Sa-SeqCas9Applications of gene editing systems, including gene knockout, site-directed base alteration, site-directed insertion, regulation of gene transcription levels, regulation of DNA methylation, DNA acetylation modification, histone acetylation modification, single base converters, or chromatin imaging tracking.