CN110577972B - CRISPR/Sa-ShaCas9 gene editing system and application thereof - Google Patents

Abstract

The invention belongs to the technical field of gene editing, and particularly relates to CRISPR (clustered regularly interspaced short palindromic repeats)Sa‑ShaCas9A gene editing system and applications thereof. The gene editing system of the invention isSa‑ShaCas9A complex formed by the protein and the sgRNA can accurately target a DNA sequence and generate cutting, so that double-strand break damage occurs to the DNA; the gene editing is gene editing in a cell or in vitro;Sa‑ShaCas9for fusion proteins, the PAM recognition domain (PAM interaction, PI) of SaCas9 is replaced by the PAM recognition domain of ShaCas9 (ShaCas 9-PI),Sa‑ShaCas9the protein is small, is 1055 amino acids, and the identified PAM sequence is simpleSa‑ShaCas9The 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. The invention has wide application prospect in the field of gene editing.

Description

CRISPR/Sa-ShaCas9 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-ShaCas9 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 a CRISPR/Cas9 system, after a CRISPR (CRISPR-derived RNA), a tracrRNA (trans-activating RNA) and a Cas9 protein form a complex, a PAM (Protospace Adjacent Motif) sequence of a target site is recognized, the CRRNA and the target DNA sequence form a complementary structure, and the Cas9 protein plays a role in cutting DNA so as to break and damage the DNA. Among them, tracrRNA and crRNA can be fused into single-stranded guide RNA (sgRNA) by a linker 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 performed; 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 researches, the CRISPR/Cas9 also has wide clinical application prospects. When the CRISPR/Cas9 system is used for gene therapy, cas9 and sgRNA need to be introduced into a human body. The most effective delivery vector for gene therapy is AAV. However, AAV virus-packaged DNA typically does not exceed 4.5kb. SpCas9 is 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

Aiming at the problems, the invention aims to provide a novel CRISPR/Cas9 gene editing system which is high in editing activity, small in Cas9 protein and simple in PAM sequence and application thereof.

The CRISPR/Cas9 gene editing system provided by the invention is a complex formed by a Sa-ShaCas9 protein and a sgRNA and is marked as a CRISPR/Sa-ShaCas9 gene editing system (namely, the Sa-ShaCas9 protein which realizes gene editing by coaction with a single guide RNA (sgRNA)); the DNA sequence can be precisely targeted, and the cutting is generated, so that the double-strand break damage of the DNA is generated; the gene editing is gene editing in a cell or in vitro; the Sa-ShaCas9 protein is small and is 1053 amino acids, the identified PAM sequence is simple (NNGRM), the Sa-ShaCas9 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 cell includes a Chinese hamster ovary cell, a baby hamster kidney cell, a mouse Sertoli cell, a mouse mammary tumor cell, a buffalo rat liver cell, a rat liver tumor cell, a monkey kidney CVI line transformed by SV40, a monkey kidney cell, a canine kidney cell, a human cervical cancer cell, a human lung cell, a human liver cell, an HIH/3T3 cell, a human U2-OS osteosarcoma cell, a human A549 cell, a human K562 cell, a human HEK293T cell, a human HCT116 cell, or a human MCF-7 cell or a TRI cell.

In the invention, the Sa-ShaCas9 in the CRISPR/Cas9 system is a fusion protein, the PI domain of the SaCas9 is replaced by the PI domain of the ShaCas9, and the ShaCas9 is Staphylococcus haemolyticus Cas9. The Sa-ShaCas9 fusion protein and single guide RNA (sgRNA) act together to achieve gene editing.

In the present invention, the ShaCas9 protein belongs to Staphylococcus haemolyticus (Staphylococcus haemolyticus), and the search number of UniProt of the ShaCas9 protein is A0A2T4SLN6.

In the invention, the Sa-ShaCas9 protein comprises the Sa-ShaCas9 protein which has no cleavage activity or only has single-strand cleavage activity or has 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 PAM sequence on a Sa-ShaCas9 protein and 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-ShaCas9 protein and sgRNA complex can precisely target DNA sequences, which means that the Sa-ShaCas9 protein and sgRNA complex can recognize and bind to specific DNA sequences, or other proteins fused with the Sa-ShaCas9 protein or proteins specifically recognizing sgRNA are brought to the position of the target DNA.

In the present invention, the Sa-ShaCas9 protein and sgRNA complex or other proteins fused with the Sa-ShaCas9 protein or proteins specifically recognizing sgrnas may 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 converter 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 Cas9.

The editing efficiency of the CRISPR/Sa-ShaCas9 system is detected by the technologies of gene synthesis, molecular cloning, cell transfection, PCR product deep sequencing, bioinformatics analysis and the like.

The CRISPR/Sa-ShaCas9 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-ShaCas9 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-ShaCas9 gene sequence; and cloning to an expression vector to obtain pAAV2_ Sa-ShaCas9_ 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-ShaCas9_ U6_ BsaI to obtain pAAV2_ Sa-ShaCas9-hU6-sgRNA;

(3) Delivering a vector expressing the Sa-ShaCas9 protein, sgRNA into a cell containing a target site;

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

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-ShaCas9 system that can be delivered to cells includes, but is not limited to, plasmids expressing the Sa-ShaCas9 protein or sgRNA, retroviruses, adenoviruses, adeno-associated viral vectors or RNA, or the Sa-ShaCas9 protein, according to specific needs.

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

Further, in step (3), the delivery means includes, but is not limited to, liposomes, cationic polymers, nanoparticles, multifunctional encapsulated 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, wherein the modifications include but are 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-ShaCas9_ ITR needs to be linearized 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-ShaCas9_ ITR backbone vector using 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 specifically, in one embodiment, the delivery means in step (3) is a liposome comprising

2000 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 for PCR amplification 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-ShaCas9 system kit for gene editing, which comprises sgRNA or targeted DNA of Sa-ShaCas9 protein or targeted DNA sequence.

The invention also provides application of the CRISPR/Sa-ShaCas9 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-ShaCas9 gene editing system cutting targeting DNA. Wherein, the grey oval represents the Sa-ShaCas9 protein, the black curved 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 representation of plasmid pAAV2_ Sa-ShaCas9_ U6_ BsaI. Wherein, the recombinant human adenovirus comprises AAV2 ITR, CMV enhancer, CMV promoter, SV40 NLS, sa-ShaCas9, nucleoplasmin NLS, 3 xHA, bGH poly (A), human U6 promoter (hU 6), 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 specific conditions is usually carried out according to conventional conditions or conditions recommended by the manufacturer.

In a specific embodiment, the CRISPR/Sa-ShaCas9 system provided by the present invention is a novel gene editing system, method, kit and application thereof.

In a specific embodiment of the invention, the CRISPR/Sa-ShaCas9 system is capable of gene editing in a cell, the method comprising the steps of:

1. construction of plasmid pAAV2_ Sa-ShaCas9_ ITR

Step (1), improving the sequence of the ShaCas9 protein downloaded according to the retrieval number A0A2T4SLN6 of the Sa-ShaCas9 gene on UniProt to obtain the Sa-ShaCas9 gene, wherein the amino acid sequence of the Sa-ShaCas9 gene is shown as SEQ ID NO: 1.

And (2) carrying out codon optimization on the amino acid sequence of the Sa-ShaCas9 to obtain a coding sequence highly expressed by the Sa-ShaCas9 in human cells, 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-ShaCas9 in a company, and constructing the coding sequence to a pAAV2_ ITR skeleton plasmid to obtain a plasmid pAAV2_ Sa-ShaCas9_ ITR, wherein the plasmid is shown in figure 2.

2. Preparation of linearized plasmid pAAV2_ Sa-ShaCas9_ ITR

Step (1), carrying out enzyme digestion linearization on the plasmid pAAV2_ Sa-ShaCas9_ ITR by using BasI restriction enzyme, wherein an enzyme digestion system comprises the following steps: mu.g of plasmid pAAV2_ Sa-ShaCas9_ ITR, 5. Mu.L of 10 xClutSmart 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 7430bp 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-ShaCas9_ ITR by using NanoDrop, and reserving for later use or storing at-20 ℃ for a long time.

3. Construction of plasmid pAAV2_ Sa-ShaCas9-hU6-sgRNA

And (1) designing a sgRNA sequence.

Step (2), respectively adding viscous terminal sequences corresponding to two sides of a linearized plasmid pAAV2_ Sa-ShaCas9_ ITR on a sense strand and an antisense strand used for a designed sgRNA sequence pair, and synthesizing two oligonucleotide single-stranded DNAs by a company, wherein the specific sequences are as follows:

Oligo-F CACCGCTCGGAGATCATCATTGCG，(SEQ ID NO:4)

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

step (3), annealing the oligonucleotide single-stranded DNA to obtain double-stranded DNA, and carrying out an annealing reaction system: after shaking and mixing 1. Mu.L of 100. Mu. Mooligo-F, 1. Mu.L of 100. Mu. Mooligo-R and 28. Mu.L of water, the mixture was placed 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-ShaCas9_ 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 to connect the correctly connected clone shake bacteria, and extracting a plasmid pAAV2_ Sa-ShaCas9-hU6-sgRNA for later use.

4. Plasmid pAAV2_ Sa-ShaCas9-hU6-sgRNA for transfecting and expressing Sa-ShaCas9 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 mu g of plasmid pAAV2_ Sa-ShaCas9-hU6-sgRNA to be transfected into 100 mu l of Opti-MEM culture medium, and gently blowing, beating and uniformly mixing;

ii. Subjecting to

2000 flick and mix evenly, absorb 5 muAdding l into 100 μ l of Opti-MEM culture medium, mixing, and standing at room temperature for 5min;

will dilute

2000 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 an incubator at 37 ℃ and 5% CO2 for continuous culture.

5. Preparation of a second Generation sequencing library

And (1) collecting the HEK293T cells after editing for 3 days, and extracting the 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 PCR primers are 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 the PCR products of the second round according to the steps provided by the manufacturer, and preparing 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 secondary sequencing results, and partial editing results are shown in fig. 2 and 3.

7. Endogenous site validation

Step (1), passing the plasmid pAAV2_ Sa-ShaCas9-hU6-sgRNA expressing Sa-ShaCas9 and sgRNA through

2000 were transfected into HEK293T cells according to the manufacturer's protocol, in which,

the sgRNA sequence is: AGTGAGGGAACAAAGTGGAC, (SEQ ID NO: 12)

The specific sequence of the target site is as follows: AGTGAGGGAACAAAGTGGACATGC; (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 a 2x Q5 Master mix; wherein:

the specific sequence of Test-F is: GCTGCTTTCCTGCTGTCTTC, (SEQ ID NO: 14)

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

Recovering the PCR product through agarose gel, and purifying the DNA fragment with the size of 284 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 sgRNA is not generated during transfection, and no cut fragment is generated after the T7 Endonuclease I cuts the target sequence, which indicates that no editing is generated; the right panel is the experimental group, sgRNA was present during transfection, and the T7 endonucleolytic I cleaved after cleavage of the targeting sequence, indicating that editing has occurred.

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<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 8

actggagttc agacgtgtgc tcttccgatc tctgaacttg tggccgttta c 51

<210> 9

<211> 45

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 9

aatgatacgg cgaccaccga gatctacact ctttccctac acgac 45

<210> 10

<211> 52

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 10

caagcagaag acggcatacg agatcactgt gtgactggag ttcagacgtg tg 52

<210> 11

<211> 3165

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<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 agctaccgct tcgacgtgta cctgaccgac 2760

aagggctaca agttcgtgag catcacctac ctggacgtgc tgaagaagga gaactactac 2820

tacatcagcg aggccaagta cgacaagctg aagctgaaca agggcatcga cgacaaggcc 2880

aagttcatcg gcagcttcta ctacaacgac ctgatagagc tggacggcga ggtgtacacc 2940

gtgataggcg tgaacaacga caagaacaac gtgatagagc tgaacctgcc cgagatacgc 3000

tacaaggagt actgcgagat aaacaacatc aagggcagcg gcaggctgcg catcaccatc 3060

ggcaagaagg tgaacagcat ccgcaagctg agcaccgacg tgctgggcaa ccgctactac 3120

cagagcttcg ccaagaagcc ccagctggtg ttcaagaagg gcatc 3165

<210> 12

<211> 21

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 12

agtgagggga acaaagtgga c 21

<210> 13

<211> 26

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 13

agtgagggga acaaagtgga catggc 26

<210> 14

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 14

gctgctttcc tgctgtcttc 20

<210> 15

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 15

aaggaggtct ctgtctgtgc 20

Claims (16)

1. A CRISPR/Cas9 gene editing system is used for gene editing in cells or in vitro and is characterized in that the CRISPR/Cas9 system is a Sa-ShaCas9 protein and sgRNA complex, can accurately position a target DNA sequence and generate cutting, so that double strand break damage occurs to DNA; the Sa-ShaCas9 protein is an amino acid sequence shown as SEQ ID NO: 1; the sgRNA is a nucleotide sequence shown in 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 cell includes a Chinese hamster ovary cell, a baby hamster kidney cell, a mouse Sertoli cell, a mouse mammary tumor cell, a buffalo rat liver cell, a rat liver tumor cell, a monkey kidney CVI line transformed by SV40, a monkey kidney cell, a canine kidney cell, a human cervical cancer cell, a human lung cell, a human liver cell, an HIH/3T3 cell, a human U2-OS osteosarcoma cell, a human A549 cell, a human K562 cell, a human HEK293T cell, a human HCT116 cell, or a human MCF-7 cell or a TRI cell.

3. The CRISPR/Cas9 gene editing system of claim 1, wherein the Sa-ShaCas9 protein comprises a Sa-ShaCas9 protein with no cleavage activity or with only single strand cleavage activity or with double strand cleavage activity.

4. The CRISPR/Cas9 gene editing system of 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 of claim 1, wherein the precisely located targeting DNA sequence comprises a Sa-ShaCas9 protein and sgRNA complex recognizing a PAM sequence on the targeting DNA sequence.

6. The CRISPR/Cas9 gene editing system of 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 of claim 1, wherein the sgRNA can be phosphorylated, sulfurized, methylated, or hydroxylated modified.

8. The CRISPR/Cas9 gene editing system of claim 1, wherein the ability of Sa-ShaCas9 protein and sgRNA complex to precisely target DNA sequences means that Sa-ShaCas9 protein and sgRNA complex can recognize and bind to specific DNA sequences or to bring other proteins fused to Sa-ShaCas9 protein or proteins specifically recognizing sgrnas to the location of the targeted DNA.

9. The CRISPR/Cas9 gene editing system of claim 8, wherein the Sa-ShaCas9 protein and sgRNA complex or other protein fused to Sa-ShaCas9 protein or protein specifically recognizing sgRNA can modify and regulate targeted DNA regions including regulation of gene transcription level, single base switch or chromatin imaging tracking.

10. The CRISPR/Cas9 gene editing system of 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. A method of gene editing for non-therapeutic purposes by the CRISPR/Cas9 gene editing system of any of claims 1 to 10 in a cell comprising editing DNA by recognition of a targeting DNA by a complex of the Sa-ShaCas9 protein and sgRNA; finally, detecting the editing efficiency; the method comprises the following specific steps:

(1) Synthesizing a humanized ShaCas9-PI gene sequence; and cloning to an expression vector to obtain pAAV2_ Sa-ShaCas9_ ITR;

(2) Synthesizing oligonucleotide single-stranded DNA (deoxyribonucleic acid) corresponding to sgRNA (ribonucleic acid), namely Oligo-F and Oligo-R sequences, annealing, and connecting to a BsaI enzyme digestion site of a plasmid pAAV2_ Sa-ShaCas9_ U6_ BsaI to obtain pAAV2_ Sa-ShaCas9-hU6-sgRNA;

(3) Delivering a vector expressing the Sa-ShaCas9 protein, sgRNA into a cell containing a target site;

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

12. The method of claim 11 wherein the pAAV2_ Sa-ShaCas9-hU6-sgRNA is an adeno-associated viral backbone plasmid comprising AAV2 ITR, CMV enhancer, CMV promoter, SV40 NLS, sa-ShaCas9, 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/Sa-ShaCas9 system delivered to the cells comprises a plasmid, retrovirus, adenovirus, adeno-associated viral vector or RNA, or Sa-ShaCas9 protein that expresses the Sa-ShaCas9 protein or sgRNA.

14. The method of claim 11, wherein the sgRNA is synthesized with corresponding single-stranded oligonucleotide DNA sequences, i.e., oligo-F and Oligo-R sequences are shown in SEQ ID NO 4 and SEQ ID NO 5;

the target site of the cell in the step (3) has a nucleotide sequence shown by SEQ ID NO. 6;

the template of PCR in the step (4) is edited DNA; the primer sequences for PCR amplification are: SEQ ID NO. 7, 8, 9, 10.

15. Kit of the CRISPR/Sa-ShaCas9 gene editing system according to any of claims 1 to 10 comprising sgrnas or targeting DNAs of the Sa-ShaCas9 protein or targeting DNA sequence.

16. Use of the CRISPR/Sa-ShaCas9 gene editing system according to any of claims 1 to 10, comprising gene knockout, site-directed base change, site-directed insertion, regulation of gene transcription level, single base switch or chromatin imaging tracking.

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