WO2024040874A1

WO2024040874A1 - Mutated cas12j protein and use thereof

Info

Publication number: WO2024040874A1
Application number: PCT/CN2023/074379
Authority: WO
Inventors: 段志强
Original assignee: 山东舜丰生物科技有限公司
Priority date: 2022-08-22
Filing date: 2023-02-03
Publication date: 2024-02-29
Also published as: CN116790558A; CN115975986A; CN115975986B

Abstract

The present invention belongs to the field of nucleic acid editing, and particularly relates to the technical field of clustered regularly interspaced short palindromic repeats (CRISPRs). Specifically, the present invention provides a mutated Cas12j protein and use thereof, and the mutated Cas12j protein has wide application prospects.

Description

Mutated Cas12j protein and its applications

Cross-references to related applications

This application claims priority to Chinese patent application 202211005384.7 titled "Mutated Cas12j protein and its application" submitted on August 22, 2022. The entire content of the above application is incorporated herein by reference.

Technical field

The present invention relates to the field of gene editing, in particular to the field of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology. Specifically, the present invention relates to a mutated Cas12j protein with increased activity and its application.

Background technique

CRISPR/Cas technology is a widely used gene editing technology. It uses RNA guidance to specifically bind to target sequences on the genome and cut DNA to produce double-stranded breaks. It uses biological non-homologous end joining or homologous recombination for site-specific Gene editing.

The CRISPR/Cas9 system is the most commonly used type II CRISPR system. It recognizes the PAM motif of 3’-NGG and performs blunt-end cleavage of the target sequence. The CRISPR/Cas Type V system is a newly discovered CRISPR system that has a 5’-TTN motif and performs sticky end cleavage of target sequences, such as Cpf1, C2c1, CasX, and CasY. However, the different CRISPR/Cas currently existing have different advantages and disadvantages. For example, Cas9, C2c1 and CasX all require two RNAs for guide RNA, while Cpf1 only requires one guide RNA and can be used for multiple gene editing. CasX has a size of 980 amino acids, while the common Cas9, C2c1, CasY and Cpf1 are usually around 1300 amino acids in size. In addition, the PAM sequences of Cas9, Cpf1, CasX, and CasY are relatively complex and diverse, and C2c1 recognizes the strict 5’-TTN, so its target site is easier to predict than other systems, thereby reducing potential off-target effects.

Chinese invention patent CN111770992B discloses a Cas protein, Cas12j.19, and also discloses that this protein can perform gene editing in eukaryotic cells. However, its editing activity is not high. In order to improve the editing efficiency of this protein, this application The protein was optimized to improve its editing efficiency in eukaryotic cells.

Contents of the invention

After extensive experiments and repeated explorations, the inventors of the present application improved its editing activity and expanded its application scope through site-directed mutation of the Cas12j.19 (referred to as Cas12j19 in this application) protein.

Cas effector protein

On the one hand, the present invention provides a Cas mutant protein with improved activity or increased activity. Compared with the amino acid sequence of the parent Cas protein, the mutant protein has at the following amino acid positions corresponding to the amino acid sequence shown in SEQ ID No. 1 There is a mutation at position 100.

In one embodiment, the amino acid at position 100 is mutated to an amino acid other than E, for example, A, V, G, L, D, F, W, Y, N, S, Q, K, M, T, C , P, H, R, I; preferably, the mutation is K, Y, M, F, R, W, S, H, V, I, N, C or L.

In one embodiment, the amino acid sequence of the parent Cas protein has at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93% compared to SEQ ID No. 1 , at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% sequence identity.

In one embodiment, the parent Cas protein is a Cas protein of the Cas12 family, preferably a Cas protein of the Cas12j family, for example, Cas12j.3-Cas12j.22 disclosed in CN111770992B, etc.; in a preferred embodiment, the parent Cas protein Cas protein is Cas12j19; the amino acid sequence of Cas12j19 has at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94% compared with SEQ ID No.1 %, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, At least 99.8%, or at least 99.9%, or 100% sequence identity.

In one embodiment, the Cas mutant protein is selected from any group of I-III below:

1. Cas mutant protein obtained by mutating the amino acid sequence shown in SEQ ID No. 1 at the following amino acid positions: position 100; preferably, the amino acid at position 100 is mutated to a non-E amino acid, for example, A , V, G, L, D, F, W, Y, N, S, Q, K, M, T, C, P, H, R, I; preferably, the mutation is K, Y, M, F, R , W, S, H, V, I, N, C or L;

II. Compared with the Cas mutant protein described in I, it has the mutation site described in I; and, compared with the Cas mutant protein described in I, it has at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4% , a Cas mutant protein with at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% sequence identity;

III. Compared with the Cas mutant protein described in I, it has the mutation site described in I; and, compared with the Cas mutant protein described in I, it has a sequence with one or more amino acid substitutions, deletions or additions. ; The one or more amino acids include substitution, deletion or addition of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.

Cas proteins or Cas12j proteins from various organisms can be used as parent Cas proteins, and in some embodiments, the parent Cas proteins or Cas12j proteins have nuclease activity. In some embodiments, the parent Cas protein is a nuclease that cleaves both strands of a target duplex nucleic acid (eg, duplex DNA). In some embodiments, the parent Cas protein is a nickase, i.e., cleaves a single strand of a target duplex nucleic acid (eg, duplex DNA).

In some embodiments, the parent Cas protein is a natural wild-type Cas protein; in other embodiments, the parent Cas protein is an engineered Cas protein.

It is clear to those skilled in the art that the structure of a protein can be changed without adversely affecting its activity and functionality. For example, one or more conservative amino acid substitutions can be introduced in the amino acid sequence of the protein without affecting the activity and/or functionality of the protein molecule. Or adversely affect the three-dimensional structure. Examples and implementations of conservative amino acid substitutions will be apparent to those skilled in the art. Specifically, the amino acid residue can be replaced with another amino acid residue belonging to the same group as the site to be replaced, that is, a non-polar amino acid residue can be substituted for another non-polar amino acid residue, and a polar uncharged amino acid residue can be substituted. An amino acid residue is substituted for another polar uncharged amino acid residue, a basic amino acid residue is substituted for another basic amino acid residue, and an acidic amino acid residue is substituted for another acidic amino acid residue. Such substituted amino acid residues may or may not be composed of Encoded by the genetic code. Conservative substitutions in which one amino acid is replaced by another amino acid belonging to the same group fall within the scope of the invention as long as the substitution does not result in inactivation of the biological activity of the protein. Therefore, the protein of the present invention may contain one or more conservative substitutions in the amino acid sequence, and these conservative substitutions are preferably produced by substitutions according to Table 1. In addition, the invention also encompasses proteins that also contain one or more other non-conservative substitutions, as long as the non-conservative substitutions do not significantly affect the desired function and biological activity of the protein of the invention.

Conservative amino acid substitutions can be made at one or more predicted non-essential amino acid residues. "Non-essential" amino acid residues are amino acid residues that can be altered (deletion, substitution or replacement) without altering biological activity, whereas "essential" amino acid residues are required for biological activity. A "conservative amino acid substitution" is a substitution in which an amino acid residue is replaced by an amino acid residue with a similar side chain. Amino acid substitutions can be made in non-conserved regions of the above-mentioned Cas mutant proteins. Generally, such substitutions are not made to conserved amino acid residues, or to amino acid residues located within conserved motifs where such residues are required for protein activity. However, those skilled in the art will appreciate that functional variants may have fewer conservative or non-conservative changes in conserved regions.

Table 1

It is well known in the art that one or more amino acid residues can be altered (substituted, deleted, truncated or inserted) from the N and/or C terminus of a protein while still retaining its functional activity. Therefore, proteins that change one or more amino acid residues from the N and/or C terminus of the Cas protein while retaining its desired functional activity are also within the scope of the present invention. These changes may include those introduced by modern molecular methods such as PCR, which include PCR amplification that alters or extends the protein coding sequence by including the amino acid coding sequence among the oligonucleotides used in the PCR amplification.

It will be appreciated that proteins can be altered in a variety of ways, including amino acid substitutions, deletions, truncation and insertions, and methods for such manipulations are generally known in the art. For example, amino acid sequence variants of the above-mentioned proteins can be prepared by mutating DNA. This can also be accomplished by other forms of mutagenesis and/or by directed evolution, for example using known mutagenesis, recombination and/or shuffling methods in combination with relevant screening methods for single or multiple amino acids. Acid substitutions, deletions and/or insertions.

Those skilled in the art will understand that these minor amino acid changes in the Cas proteins of the invention can occur (eg, naturally occurring mutations) or be produced (eg, using r-DNA technology) without loss of protein function or activity. If these mutations occur in the catalytic domain, active site, or other functional domains of the protein, the properties of the polypeptide may be altered, but the polypeptide may maintain its activity. If mutations are present that are not close to the catalytic domain, active site, or other functional domains, smaller effects can be expected.

Those skilled in the art can identify the essential amino acids of the Cas mutant protein of the present invention according to methods known in the art, such as site-directed mutagenesis or analysis of protein evolution or bioinformatics systems. The catalytic domain, active site or other functional domains of a protein can also be determined by physical analysis of the structure, such as through techniques such as nuclear magnetic resonance, crystallography, electron diffraction or photoaffinity labeling, combined with putative key sites point amino acid mutations.

In the present invention, amino acid residues can be represented by single letters or three letters, for example: alanine (Ala, A), valine (Val, V), glycine (Gly, G), leucine (Leu, L), glutamic acid (Gln, Q), phenylalanine (Phe, F), tryptophan (Trp, W), tyrosine (Tyr, Y), aspartic acid (Asp, D), asparagine (Asn, N), glutamic acid (Glu, E), lysine (Lys, K), methionine (Met, M), serine (Ser, S), threonine (Thr, T), cysteine (Cys, C), proline (Pro, P), isoleucine (Ile, I), histidine (His, H), arginine (Arg, R).

The term "AxxB" means that amino acid A at position xx is changed to amino acid B. Unless otherwise specified, amino acid A at position xx from the N-terminus is changed to amino acid B. For example, E100R means that the E at position 100 is mutated into an R. When mutations exist at multiple amino acid sites at the same time, they can be expressed in a similar form to E328R-N369R. For example, E328R-N369R represents the mutation of E to R at position 328 and N to R at position 369.

The specific amino acid position (numbering) within the protein of the present invention is determined by comparing the amino acid sequence of the target protein with SEQ ID No. 1 using standard sequence alignment tools, such as using the Smith-Waterman algorithm or using CLUSTALW2 The algorithm aligns two sequences, with the sequences considered to be aligned when the alignment score is highest. Alignment scores can be calculated according to the method described in Wilbur, W.J. and Lipman, D.J. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA, 80: 726-730. It is preferred to use the default parameters in the ClustalW2 (1.82) algorithm: protein gap opening penalty=10.0; protein gap extension penalty=0.2; protein matrix=Gonnet; protein/DNA end gap=-1; protein/DNAGAPDIST=4. It is preferably determined by aligning the amino acid sequence of the protein to SEQ ID No. 1 using the AlignX program (part of the vectorNTI group) with default parameters suitable for multiple alignments (gap opening penalty: 10og gap extension penalty 0.05) The position of specific amino acids within the protein of the invention.

In one embodiment, the amino acid sequence of the parent Cas protein has at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94% compared to SEQ ID No. 1 , at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% sequence identity.

I. A Cas mutant protein obtained by mutating the amino acid sequence shown in SEQ ID No. 1 at any one or several of the following amino acid positions: position 100;

II. Compared with the Cas mutant protein described in I, it has the mutation site described in I; and, compared with the Cas mutant protein described in I, it has at least 80%, at least 85%, at least 90%, at least A Cas mutant protein with 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity;

III. Compared with the Cas mutant protein described in I, it has the mutation site described in I; and, compared with the Cas mutant protein described in I, it has a sequence with one or more amino acid substitutions, deletions or additions. ; the one or more Amino acids include substitutions, deletions, or additions of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids.

The biological functions of the Cas protein include, but are not limited to, the activity of binding to guide RNA, endonuclease activity, and the activity of binding to and cutting specific sites in the target sequence under the guidance of guide RNA, including but not limited to Cis cleavage activity. and Trans cleavage activity.

In the present invention, "Cas mutant protein" can also be called a mutated Cas protein or a Cas protein variant.

The present invention also provides a fusion protein, which includes the above-mentioned Cas mutant protein and other modified parts.

In one embodiment, the modifying moiety is selected from another protein or polypeptide, a detectable label, or any combination thereof.

In one embodiment, the modified moiety is selected from an epitope tag, a reporter gene sequence, a nuclear localization signal (NLS) sequence, a targeting moiety, a transcriptional activation domain (e.g., VP64), a transcriptional repression domain (e.g., KRAB domain or SID domain), a nuclease domain (e.g., Fok1), and a domain with an activity selected from: nucleotide deaminase, adenosine deaminase, cytidine deaminase, methyl enzyme activity, demethylase, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, nuclease activity, single-stranded RNA cleavage activity, double-stranded RNA cleavage activity, single-stranded DNA cleavage activity, Double-stranded DNA cleavage activity and nucleic acid binding activity; and any combination thereof. The NLS sequence is well known to those skilled in the art, and examples thereof include, but are not limited to, SV40 large T antigen, EGL-13, c-Myc and TUS protein.

In one embodiment, the NLS sequence is located at, near or close to the end (eg, N-terminus, C-terminus or both ends) of the Cas protein of the invention.

The epitope tag is well known to those skilled in the art, including but not limited to His, V5, FLAG, HA, Myc, VSV-G, Trx, etc., and those skilled in the art can select other suitable epitopes Tags (e.g., for purification, detection, or tracing).

The reporter gene sequence is well known to those skilled in the art, and examples thereof include but are not limited to GST, HRP, CAT, GFP, HcRed, DsRed, CFP, YFP, BFP, etc.

In one embodiment, the fusion protein of the present invention includes a domain capable of binding to DNA molecules or intracellular molecules, such as maltose-binding protein (MBP), DNA-binding domain (DBD) of Lex A, DBD of GAL4, etc.

In one embodiment, the fusion proteins of the invention comprise a detectable label, such as a fluorescent dye, such as FITC or DAPI.

In one embodiment, the Cas protein of the invention is coupled, conjugated or fused to the modified moiety, optionally via a linker.

In one embodiment, the modified moiety is directly linked to the N-terminus or C-terminus of the Cas protein of the invention.

In one embodiment, the modified portion is connected to the N-terminus or C-terminus of the Cas protein of the invention through a linker. Such linkers are well known in the art and examples include, but are not limited to, those containing one or more (eg, 1, 2, 3, 4 or 5) amino acids (eg, Glu or Ser) or amino acid derivatives (such as Ahx, β-Ala, GABA or Ava) linkers, or PEG, etc.

The Cas protein, protein derivative or fusion protein of the present invention is not limited by its production method. For example, it can be produced by genetic engineering methods (recombinant technology) or chemical synthesis methods.

Cas protein nucleic acid

In another aspect, the invention provides an isolated polynucleotide comprising:

(a) The polynucleotide sequence encoding the Cas mutant protein or fusion protein of the present invention;

Or, a polynucleotide complementary to the polynucleotide described in (a).

In one embodiment, the nucleotide sequence is codon-optimized for expression in prokaryotic cells. exist In one embodiment, the nucleotide sequence is codon-optimized for expression in eukaryotic cells.

In one embodiment, the cells are animal cells, eg, mammalian cells.

In one embodiment, the cells are human cells.

In one embodiment, the cells are plant cells, for example cells of cultivated plants (such as cassava, corn, sorghum, wheat or rice), algae, trees or vegetables.

In one embodiment, the polynucleotide is preferably single-stranded or double-stranded.

Guide RNA (gRNA)

On the other hand, the present invention provides a gRNA, which includes a first segment and a second segment; the first segment is also called a “skeleton region”, “protein binding segment”, “protein binding segment” Sequence", or "Direct Repeat (Direct Repeat) sequence"; the second segment is also called "targeting sequence for targeting nucleic acid" or "targeting segment for targeting nucleic acid", or "targeting target" sequence's boot sequence".

The first segment of the gRNA can interact with the Cas protein of the present invention, so that the Cas protein and the gRNA form a complex.

In a preferred embodiment, the first segment is a direct repeat sequence as described above.

The targeting sequence of the targeting nucleic acid or the targeting segment of the targeting nucleic acid of the invention comprises a nucleotide sequence complementary to a sequence in the target nucleic acid. In other words, the targeting sequence or the targeting segment of the targeting nucleic acid of the invention interacts with the target nucleic acid in a sequence-specific manner through hybridization (ie, base pairing). Thus, the targeting sequence of a targeting nucleic acid or the targeting segment of a targeting nucleic acid may be altered, or may be modified to hybridize to any desired sequence within the target nucleic acid. The nucleic acid is selected from DNA or RNA.

The percent complementarity between the targeting sequence of the targeting nucleic acid or the targeting segment of the targeting nucleic acid and the target sequence of the target nucleic acid can be at least 60% (e.g., at least 65%, at least 70%, at least 75%, at least 80% , at least 85%, at least 90%, at least 95%, at least 97%, at least 98%, at least 99% or 100%).

The "backbone region", "protein binding segment", "protein binding sequence" or "direct repeat sequence" of the gRNA of the present invention can interact with the CRISPR protein (or Cas protein). The gRNA of the present invention guides its interacting Cas protein to the specific nucleotide sequence within the target nucleic acid through the action of the targeting sequence of the targeted nucleic acid.

Preferably, the guide RNA includes a first segment and a second segment from the 5' to 3' direction.

In the present invention, the second segment can also be understood as a guide sequence that hybridizes to the target sequence.

The gRNA of the present invention can form a complex with the Cas protein.

carrier

The present invention also provides a vector, which includes the above-mentioned Cas mutant protein, isolated nucleic acid molecule or polynucleotide; preferably, it also includes a regulatory element operably connected thereto.

In one embodiment, the regulatory element is selected from one or more of the following group: enhancer, transposon, promoter, terminator, leader sequence, polyadenylation sequence, and marker gene.

In one embodiment, the vector includes a cloning vector, an expression vector, a shuttle vector, and an integration vector.

In some embodiments, the vectors included in the system are viral vectors (e.g., retroviral vectors, lentiviral vectors, adenoviral vectors, adeno-associated vectors, and herpes simplex vectors), and may also be plasmids, viruses, cosmids, Phage and other types, which are well known to those skilled in the art.

CRISPR system

The invention provides an engineered non-naturally occurring vector system, or a CRISPR-Cas system, which system includes a Cas mutant protein or a nucleic acid sequence encoding the Cas mutant protein and a nucleic acid encoding one or more guide RNAs. .

In one embodiment, the nucleic acid sequence encoding the Cas mutant protein and the nucleic acid encoding one or more guide RNAs are artificially synthesized.

In one embodiment, the nucleic acid sequence encoding the Cas mutant protein and encoding one or more guides The nucleic acid RNA does not occur naturally together.

The one or more guide RNAs target one or more target sequences in the cell. The one or more target sequences hybridize to the genomic locus of the DNA molecule encoding one or more gene products, and guide the Cas protein to the genomic locus of the DNA molecule of the one or more gene products. The Cas protein Upon reaching the target sequence location, the target sequence is modified, edited, or cleaved, whereby the expression of the one or more gene products is altered or modified.

The cells of the present invention include one or more of animals, plants or microorganisms.

In some embodiments, the Cas protein is codon-optimized for expression in cells.

In some embodiments, the Cas protein directs cleavage of one or both strands at the target sequence location.

The present invention also provides an engineered non-naturally occurring vector system. The vector system may include one or more vectors, and the one or more vectors include:

a) a first regulatory element operably linked to the gRNA,

b) a second regulatory element operably connected to the Cas protein;

wherein components (a) and (b) are located on the same or different carriers of the system.

The first and second regulatory elements include promoters (e.g., constitutive promoters or inducible promoters), enhancers (e.g., 35S promoter or 35S enhanced promoter), internal ribosome entry sites (IRES), and others. Expression control elements (eg, transcription termination signals, such as polyadenylation signals and polyU sequences).

In some embodiments, the vector in the system is a viral vector (eg, retroviral vector, lentiviral vector, adenoviral vector, adeno-associated vector, and herpes simplex vector), and may also be a plasmid, virus, cosmid, phage and other types, which are well known to those skilled in the art.

In some embodiments, the systems provided herein are in a delivery system. In some embodiments, delivery systems are nanoparticles, liposomes, exosomes, microbubbles, and gene guns.

In one embodiment, the target sequence is a DNA or RNA sequence from a prokaryotic or eukaryotic cell. In one embodiment, the target sequence is a non-naturally occurring DNA or RNA sequence.

In one embodiment, the target sequence is present within the cell. In one embodiment, the target sequence is present in the nucleus or cytoplasm (eg, organelle). In one embodiment, the cell is a eukaryotic cell. In other embodiments, the cell is a prokaryotic cell.

In one embodiment, the Cas protein is linked to one or more NLS sequences. In one embodiment, the fusion protein contains one or more NLS sequences. In one embodiment, the NLS sequence is linked to the N-terminus or C-terminus of the protein. In one embodiment, the NLS sequence is fused to the N-terminus or C-terminus of the protein.

In another aspect, the present invention relates to an engineered CRISPR system comprising the above-mentioned Cas protein and one or more guide RNAs, wherein the guide RNAs include direct repeats and spacers capable of hybridizing to target nucleic acids. sequence, the Cas protein is capable of binding the guide RNA and targeting a target nucleic acid sequence complementary to the spacer sequence.

Protein-nucleic acid complexes/compositions

In another aspect, the invention provides a complex or composition comprising:

(i) Protein component, which is selected from: the above-mentioned Cas protein, derivatized protein or fusion protein, and any combination thereof; and

(ii) A nucleic acid component comprising (a) a guide sequence capable of hybridizing to a target sequence; and (b) a direct repeat sequence capable of binding to the Cas protein of the invention.

The protein component and the nucleic acid component combine with each other to form a complex.

In one embodiment, the nucleic acid component is a guide RNA in a CRISPR-Cas system.

In one embodiment, the complex or composition is non-naturally occurring or modified. In one embodiment, at least one component of the complex or composition is non-naturally occurring or modified. In one embodiment, the first component is non-naturally occurring or modified; and/or the second component is non-naturally occurring or modified.

Activated CRISPR complex

On the other hand, the present invention also provides an activated CRISPR complex, which includes: (1) a protein component selected from: the Cas protein, derivatized protein or fusion protein of the present invention, and any combination thereof; (2) gRNA, which includes (a) a guide sequence capable of hybridizing to the target sequence; and (b) a direct repeat sequence capable of binding to the Cas protein of the invention; and (3) binding to the gRNA target sequence. Preferably, the binding is binding to the target nucleic acid through a targeting sequence on the gRNA that targets the nucleic acid.

The terms "activated CRISPR complex", "activated complex" or "ternary complex" used herein refer to the complex in which Cas protein, gRNA and target nucleic acid are combined or modified in the CRISPR system.

The Cas protein and gRNA of the present invention can form a binary complex, which is activated when combined with a nucleic acid substrate to form an activated CRISPR complex. The nucleic acid substrate and the spacer sequence (or so-called spacer sequence) in the gRNA are , complementary to the guide sequence that hybridizes to the target nucleic acid). In some embodiments, the gRNA's spacer sequence exactly matches the target substrate. In other embodiments, the spacer sequence of the gRNA matches a portion (contiguous or discontinuous) of the target substrate.

In a preferred embodiment, the activated CRISPR complex can exhibit side-branching nucleic acid cleavage activity, and the side-branching nucleic acid cleavage activity refers to the non-specific cleavage activity or random cleavage activity of single-stranded nucleic acids exhibited by the activated CRISPR complex. Cleavage activity is also called trans cleavage activity in the art.

Delivery and delivery compositions

The Cas protein, gRNA, fusion protein, nucleic acid molecule, vector, system, complex and composition of the present invention can be delivered by any method known in the art. Such methods include, but are not limited to, electroporation, lipofection, nucleofection, microinjection, sonoporation, gene gun, calcium phosphate-mediated transfection, cationic transfection, lipofection, dendrimers Transfection, heat shock transfection, nucleofection, magnetofection, lipofection, puncture transfection, optical transfection, reagent-enhanced nucleic acid uptake, and via liposomes, immunoliposomes, virus particles, artificial viruses Delivery of body etc.

Therefore, in another aspect, the present invention provides a delivery composition, which includes a delivery vector, and one or any several selected from the following: Cas protein, fusion protein, nucleic acid molecule, vector, system, Complexes and compositions.

In one embodiment, the delivery vehicle is a particle.

In one embodiment, the delivery vehicle is selected from lipid particles, sugar particles, metal particles, protein particles, liposomes, exosomes, microvesicles, gene guns or viral vectors (e.g., replication-deficient retroviruses , lentivirus, adenovirus or adeno-associated virus).

host cell

The present invention also relates to an in vitro, ex vivo or in vivo cell or cell line or their progeny, which cell or cell line or their progeny contains: Cas protein, fusion protein, nucleic acid according to the invention Molecules, protein-nucleic acid complexes, activated CRISPR complexes, vectors, delivery compositions of the invention.

In certain embodiments, the cell is a prokaryotic cell.

In certain embodiments, the cell is a eukaryotic cell. In certain embodiments, the cells are mammalian cells. In certain embodiments, the cells are human cells. In certain embodiments, the cell is a non-human mammalian cell, such as a non-human primate, bovine, ovine, porcine, canine, monkey, rabbit, rodent (eg, rat or mouse) cell. In certain embodiments, the cell is a non-mammalian eukaryotic cell, such as a cell of a poultry bird (eg, chicken), fish, or crustacean (eg, clam, shrimp). In certain embodiments, the cells are plant cells, such as those of a monocot or dicot or a cultivated plant or a food crop such as cassava, corn, sorghum, soybean, wheat, oat or rice, e.g. Algae, trees or production plants, fruits or vegetables (for example, trees such as citrus trees, nut trees; nightshades, cotton, tobacco, tomatoes, grapes, coffee, cocoa, etc.).

In certain embodiments, the cells are stem cells or stem cell lines.

In some cases, a host cell of the invention contains a genetic or genomic modification that is not present in its wild type.

Gene editing methods and applications

The Cas mutant protein, nucleic acid, the above composition, the above CIRSPR/Cas system, the above vector system, the above delivery composition or the above activated CRISPR complex or the above host cell of the present invention can be used for any one or any several of the following purposes: target To and/or edit target nucleic acid; cleave double-stranded DNA, single-stranded DNA or single-stranded RNA; non-specific cleavage and/or degradation of side branch nucleic acids; non-specific cleavage of single-stranded nucleic acids; nucleic acid detection; detection of nucleic acids in target samples; specificity Base editing of double-stranded nucleic acids; base editing of double-stranded nucleic acids; base editing of single-stranded nucleic acids. In other embodiments, it can also be used to prepare reagents or kits for any one or several of the above uses.

The invention also provides the application of the above-mentioned Cas protein, nucleic acid, above-mentioned composition, above-mentioned CIRSPR/Cas system, above-mentioned vector system, above-mentioned delivery composition or above-mentioned activated CRISPR complex in gene editing, gene targeting or gene cutting; Alternatively, use in the preparation of reagents or kits for gene editing, gene targeting or gene cleavage.

In one embodiment, the gene editing, gene targeting or gene cleavage is performed intracellularly and/or extracellularly.

The invention also provides a method for editing target nucleic acid, targeting target nucleic acid or cutting target nucleic acid. The method includes combining the target nucleic acid with the above-mentioned Cas protein, nucleic acid, above-mentioned composition, above-mentioned CIRSPR/Cas system, above-mentioned vector system, The above delivery composition or the above activated CRISPR complex is contacted. In one embodiment, the method is editing, targeting, or cleaving a target nucleic acid intracellularly or extracellularly.

The gene editing or editing target nucleic acid includes modifying genes, knocking out genes, changing the expression of gene products, repairing mutations, and/or inserting polynucleotides, and gene mutations.

The editing can be performed in prokaryotic cells and/or eukaryotic cells.

On the other hand, the present invention also provides the application of the above-mentioned Cas protein, nucleic acid, the above-mentioned composition, the above-mentioned CIRSPR/Cas system, the above-mentioned vector system, the above-mentioned delivery composition or the above-mentioned activated CRISPR complex in nucleic acid detection, or in the preparation of Use in reagents or kits for nucleic acid detection.

On the other hand, the present invention also provides a method for cutting single-stranded nucleic acids, which method includes contacting a nucleic acid population with the above-mentioned Cas protein and gRNA, wherein the nucleic acid population includes a target nucleic acid and a plurality of non-target single-stranded nucleic acids. , the Cas protein cleaves the plurality of non-target single-stranded nucleic acids.

The gRNA is capable of binding to the Cas protein.

The gRNA is capable of targeting the target nucleic acid.

The contact may be inside the cell in vitro, ex vivo or in vivo.

Preferably, the cleavage of single-stranded nucleic acid is non-specific cleavage.

On the other hand, the present invention also provides the above-mentioned Cas protein, nucleic acid, the above-mentioned composition, the above-mentioned CIRSPR/Cas system, the above-mentioned vector system, the above-mentioned delivery composition or the above-mentioned activated CRISPR complex in non-specific cutting of single-stranded nucleic acids. Application, or use in the preparation of reagents or kits for non-specific cleavage of single-stranded nucleic acids.

On the other hand, the present invention also provides a kit for gene editing, gene targeting or gene cutting, which kit includes the above-mentioned Cas protein, gRNA, nucleic acid, the above-mentioned composition, the above-mentioned CIRSPR/Cas system, the above-mentioned The vector system, the above-mentioned delivery composition, the above-mentioned activated CRISPR complex or the above-mentioned host cell.

On the other hand, the present invention also provides a kit for detecting target nucleic acid in a sample, the kit comprising: (a) Cas protein, or nucleic acid encoding the Cas protein; (b) guide RNA, or a nucleic acid encoding the guide RNA, or a precursor RNA comprising the guide RNA, or a nucleic acid encoding the precursor RNA; and (c) a single-stranded nucleic acid that is single-stranded and does not hybridize to the guide RNA Detector.

It is known in the art that precursor RNA can be cleaved or processed into the mature guide RNA described above.

On the other hand, the invention provides the above-mentioned Cas protein, nucleic acid, above-mentioned composition, above-mentioned CIRSPR/Cas system, above-mentioned vector system, above-mentioned delivery composition, above-mentioned activated CRISPR complex or above-mentioned host cell in preparation preparations or kits Purpose, the preparation or kit is used for:

(i) Gene or genome editing;

(ii) Target nucleic acid detection and/or diagnosis;

(iii) Edit target sequences in target loci to modify organisms or non-human organisms;

(iv) Treatment of disease;

(iv) Targeting target genes.

Preferably, the above-mentioned gene or genome editing is performed within or outside the cell.

Preferably, the target nucleic acid detection and/or diagnosis is performed in vitro.

Preferably, the treatment of the disease is the treatment of a condition caused by a defect in a target sequence in a target locus.

In another aspect, the invention provides a method for detecting a target nucleic acid in a sample, the method comprising contacting the sample with the Cas protein, a gRNA (guide RNA) and a single-stranded nucleic acid detector, the gRNA comprising: The Cas protein-binding region and the guide sequence for hybridizing with the target nucleic acid; detecting the detectable signal generated by the Cas protein cutting single-stranded nucleic acid detector, thereby detecting the target nucleic acid; the single-stranded nucleic acid detector does not hybridize with the gRNA .

Methods for specifically modifying target nucleic acids

On the other hand, the present invention also provides a method for specifically modifying a target nucleic acid. The method includes: combining the target nucleic acid with the above-mentioned Cas protein, nucleic acid, above-mentioned composition, above-mentioned CIRSPR/Cas system, above-mentioned carrier system, and above-mentioned delivery composition. or contact with the activated CRISPR complex described above.

The specific modification can occur in vivo or in vitro.

The specific modification can occur intracellularly or extracellularly.

In some cases, the cells are selected from prokaryotic or eukaryotic cells, for example, animal cells, plant cells, or microbial cells.

In one embodiment, the modification refers to a break in the target sequence, such as a single/double strand break in DNA, or a single strand break in RNA.

In some cases, the method further includes contacting the target nucleic acid with a donor polynucleotide, wherein the donor polynucleotide, a portion of the donor polynucleotide, a copy of the donor polynucleotide, or the donor polynucleotide Part of the copy is integrated into the target nucleic acid.

In one embodiment, the modification further includes inserting an editing template (eg, exogenous nucleic acid) into the break.

In one embodiment, the method further includes contacting an editing template with the target nucleic acid or delivering it to a cell containing the target nucleic acid. In this embodiment, the method repairs the broken target gene by homologous recombination with an exogenous template polynucleotide; in some embodiments, the repair results in a mutation that includes one or more of the target gene Insertions, deletions, or substitutions of multiple nucleotides, and in other embodiments, the mutations result in one or more amino acid changes in the protein expressed from the gene containing the target sequence.

Detection (non-specific cleavage)

On the other hand, the present invention provides a method for detecting target nucleic acid in a sample, the method comprising combining the sample with the above-mentioned Cas protein, nucleic acid, above-mentioned composition, above-mentioned CIRSPR/Cas system, above-mentioned carrier system, above-mentioned delivery composition or The above-mentioned activated CRISPR complex is in contact with the single-stranded nucleic acid detector; the detectable signal generated by the Cas protein cutting the single-stranded nucleic acid detector is detected, thereby detecting the target nucleic acid.

In the present invention, the target nucleic acid includes ribonucleotides or deoxyribonucleotides; includes single-stranded nucleic acid and double-stranded nucleic acid, such as single-stranded DNA, double-stranded DNA, single-stranded RNA, and double-stranded RNA.

In one embodiment, the target nucleic acid is derived from samples such as viruses, bacteria, microorganisms, soil, water sources, human bodies, animals, plants, etc. Preferably, the target nucleic acid is a product enriched or amplified by PCR, NASBA, RPA, SDA, LAMP, HAD, NEAR, MDA, RCA, LCR, RAM and other methods.

In one embodiment, the target nucleic acid is a viral nucleic acid, a bacterial nucleic acid, a specific nucleic acid related to a disease, such as a specific mutation site or SNP site or a nucleic acid that is different from a control; preferably, the virus is a plant Viruses or animal viruses, for example, papillomavirus, hepatovirus, herpesvirus, adenovirus, poxvirus, parvovirus, coronavirus; preferably, the virus is a coronavirus, preferably SARS, SARS-CoV2 (COVID-19) -19)、 HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, Mers-Cov.

In the present invention, the gRNA has a matching degree of at least 50% with the target sequence on the target nucleic acid, preferably at least 60%, preferably at least 70%, preferably at least 80%, preferably at least 90%.

In one embodiment, when the target sequence contains one or more characteristic sites (such as specific mutation sites or SNPs), the characteristic sites completely match the gRNA.

In one embodiment, the detection method may include one or more gRNAs with different guide sequences targeting different target sequences.

In the present invention, the single-stranded nucleic acid detector includes but is not limited to single-stranded DNA, single-stranded RNA, DNA-RNA hybrids, nucleic acid analogs, base modifications, and single-stranded nucleic acid detection containing abase spacers. devices, etc.; "nucleic acid analogs" include but are not limited to: locked nucleic acid, bridged nucleic acid, morpholine nucleic acid, ethylene glycol nucleic acid, hexitol nucleic acid, threose nucleic acid, arabinose nucleic acid, 2'oxymethyl RNA, 2' Methoxyacetyl RNA, 2' fluoro RNA, 2' amino RNA, 4' sulfur RNA, and combinations thereof, including optional ribonucleotide or deoxyribonucleotide residues.

In the present invention, the detectable signal is achieved in the following ways: vision-based detection, sensor-based detection, color detection, fluorescence signal-based detection, gold nanoparticle-based detection, fluorescence polarization, colloidal phase change/dispersion, electrochemical Chemical detection and semiconductor-based detection.

In the present invention, preferably, the two ends of the single-stranded nucleic acid detector are respectively provided with fluorescent groups and quenching groups. When the single-stranded nucleic acid detector is cleaved, it can show a detectable fluorescence signal. The fluorescent group is selected from one or more of FAM, FITC, VIC, JOE, TET, CY3, CY5, ROX, Texas Red or LC RED460; the quenching group is selected from BHQ1, BHQ2, BHQ3 , Dabcy1 or Tamra, or any one of them.

In other embodiments, the 5' end and 3' end of the single-stranded nucleic acid detector are respectively provided with different labeling molecules, and colloidal gold detection is used to detect the time before and after the single-stranded nucleic acid detector is cleaved by the Cas protein. Colloidal gold test results after being cleaved by Cas protein; the single-stranded nucleic acid detector will show different color results on the colloidal gold detection line and quality control line before being cleaved by Cas protein and after being cleaved by Cas protein.

In some embodiments, the method of detecting a target nucleic acid may further include comparing the level of the detectable signal to a reference signal level and determining the amount of the target nucleic acid in the sample based on the level of the detectable signal.

In some embodiments, the method of detecting a target nucleic acid may further include using an RNA reporter nucleic acid and a DNA reporter nucleic acid on different channels (e.g., fluorescent colors), and by measuring signal levels of the RNA and DNA reporter molecules, and by measuring The amount of target nucleic acid in the RNA and DNA reporter molecules is used to determine the level of detectable signal, and the level of detectable signal is sampled based on combining (eg, using a minimum or product).

In one embodiment, the target gene is present within the cell.

In one embodiment, the cell is a prokaryotic cell.

In one embodiment, the cell is a eukaryotic cell.

In one embodiment, the cells are animal cells.

In one embodiment, the cells are human cells.

In one embodiment, the target gene is present in a nucleic acid molecule (eg, a plasmid) in vitro.

In one embodiment, the target gene is present in a plasmid.

Definition of Terms

In the present invention, unless otherwise stated, scientific and technical terms used herein have the meanings commonly understood by those skilled in the art. Moreover, the procedures used in this article such as molecular genetics, nucleic acid chemistry, chemistry, molecular biology, biochemistry, cell culture, microbiology, cell biology, genomics and recombinant DNA are routine procedures widely used in the corresponding fields. . Meanwhile, in order to better understand the present invention, definitions of relevant terms and explain.

Nucleic acid cleavage or cleavage of nucleic acids herein includes: DNA or RNA cleavage in the target nucleic acid produced by the Cas enzyme described herein (Cis cleavage), DNA or RNA cleavage in side nucleic acid substrates (single-stranded nucleic acid substrates) ( That is, non-specific or non-targeted, Trans cleavage). In some embodiments, the cleavage is a double-stranded DNA break. In some embodiments, the cleavage is a single-stranded DNA break or a single-stranded RNA break.

CRISPR system

As used herein, the term "Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) (CRISPR-Cas) system" or "CRISPR system" is used interchangeably and has the skill in the art. It is generally understood that it generally includes transcripts or other elements related to the expression of CRISPR-related ("Cas") genes, or transcripts or other elements capable of directing the activity of the Cas gene.

CRISPR/Cas complex

As used herein, the term "CRISPR/Cas complex" refers to a complex formed by binding of guide RNA (guide RNA) or mature crRNA to Cas protein, which includes a guide sequence that hybridizes to the target sequence and is Protein-bound direct repeats allow the complex to recognize and cleave polynucleotides that hybridize to the guide RNA or mature crRNA.

Guide RNA (guideRNA, gRNA)

As used herein, the terms "guide RNA (gRNA)," "mature crRNA," and "guide sequence" are used interchangeably and have meanings commonly understood by those skilled in the art. Generally speaking, a guide RNA may comprise, consist essentially of, or consist of direct repeats and a leader sequence.

In some cases, a guide sequence is any polynucleotide sequence that has sufficient complementarity to a target sequence to hybridize to the target sequence and direct specific binding of the CRISPR/Cas complex to the target sequence. In one embodiment, when optimally aligned, the degree of complementarity between a guide sequence and its corresponding target sequence is at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or At least 99%. Determining the optimal alignment is within the ability of one of ordinary skill in the art. For example, there are public and commercially available alignment algorithms and programs such as, but not limited to, ClustalW, Smith-Waterman in matlab, Bowtie, Geneious, Biopython, and SeqMan.

target sequence

"Target sequence" refers to a polynucleotide targeted by a guide sequence in a gRNA, e.g., a sequence complementary to the guide sequence, wherein hybridization between the target sequence and the guide sequence will facilitate the CRISPR/Cas complex (including Cas protein and gRNA) formation. Perfect complementarity is not required, as long as sufficient complementarity exists to cause hybridization and promote the formation of a CRISPR/Cas complex.

The target sequence can comprise any polynucleotide, such as DNA or RNA. In some cases, the target sequence is located intracellularly or extracellularly. In some cases, the target sequence is located in the nucleus or cytoplasm of the cell. In some cases, the target sequence may be located in an organelle of a eukaryotic cell such as a mitochondria or chloroplast. The sequence or template that can be used for recombination into a target locus containing the target sequence is called an "editing template" or "editing polynucleotide" or "editing sequence." In one embodiment, the editing template is an exogenous nucleic acid. In one embodiment, the recombination is homologous recombination.

In the present invention, a "target sequence" or "target polynucleotide" or "target nucleic acid" may be any polynucleotide endogenous or exogenous to a cell (eg, a eukaryotic cell). For example, the target polynucleotide may be a polynucleotide present in the nucleus of a eukaryotic cell. The target polynucleotide can be a sequence encoding a gene product (eg, a protein) or a non-coding sequence (eg, a regulatory polynucleotide or useless DNA). In some cases, the target sequence should be associated with a protospacer adjacent motif (PAM).

Single-stranded nucleic acid detector

The single-stranded nucleic acid detector of the present invention refers to a sequence containing 2-200 nucleotides, preferably, having 2-150 nucleotides. Nucleotides are preferably 3-100 nucleotides, preferably 3-30 nucleotides, preferably 4-20 nucleotides, and more preferably 5-15 nucleotides. Preferred are single-stranded DNA molecules, single-stranded RNA molecules or single-stranded DNA-RNA hybrids.

The two ends of the single-stranded nucleic acid detector include different reporting groups or labeling molecules. When it is in the initial state (that is, when it is not cleaved), it does not present a reporting signal. When the single-stranded nucleic acid detector is cleaved, it displays a reporting signal. A detectable signal is produced, that is, there is a detectable difference after cutting and before cutting.

In one embodiment, the reporter group or labeling molecule includes a fluorescent group and a quenching group, and the fluorescent group is selected from FAM, FITC, VIC, JOE, TET, CY3, CY5, ROX, Texas Red Or one or any several of LC RED460; the quenching group is selected from one or any of several BHQ1, BHQ2, BHQ3, Dabcy1 or Tamra.

In one embodiment, the single-stranded nucleic acid detector has a first molecule (such as FAM or FITC) connected to the 5' end and a second molecule (such as biotin) connected to the 3' end. The reaction system containing a single-stranded nucleic acid detector is used in conjunction with a flow strip to detect target nucleic acids (preferably, colloidal gold detection method). The flow strip is designed to have two capture lines. The sample contact end (colloidal gold) is provided with an antibody that binds the first molecule (i.e., the first molecule antibody), and the first line (control line) contains an antibody that binds the third molecule. An antibody with one molecule of antibody contains a second molecule of antibody (that is, a second molecule of antibody, such as avidin) that binds to the second molecule at the second line (test line). As the reaction flows along the strip, the first molecule of antibody binds to the first molecule and carries the cleaved or uncleaved oligonucleotide to the capture line. The cleaved reporter will bind to the first molecule of antibody at the first capture line. antibody, while the uncleaved reporter will bind a second antibody molecule at the second capture line. The binding of reporter groups in each line will result in a strong readout/signal (eg color). As more reporters are cleaved, more signal will accumulate at the first capture line, and less signal will appear at the second line. In certain aspects, the invention relates to the use of a flow strip as described herein for detecting nucleic acids. In certain aspects, the invention relates to methods of detecting nucleic acids using flow strips as defined herein, such as (lateral) flow tests or (lateral) flow immunochromatographic assays. In some aspects, the molecules in the single-stranded nucleic acid detector can be replaced with each other, or the position of the molecules can be changed. As long as the reporting principle is the same or similar to the present invention, the improved methods are also included in the present invention.

The detection method of the present invention can be used for quantitative detection of target nucleic acids to be detected. The quantitative detection index can be quantified based on the signal strength of the reporter group, such as the luminescence intensity of the fluorescent group, or the width of the color band.

Wild type

As used herein, the term "wild type" has the meaning commonly understood by those skilled in the art to mean the typical form of an organism, strain, gene, or characteristics that distinguish it from mutant or variant forms as it occurs in nature, It is isolated from sources in nature and has not been intentionally modified by man.

derivatization

As used herein, the term "derivatization" refers to the chemical modification of an amino acid, polypeptide, or protein to which one or more substituents have been covalently linked. Substituents may also be called side chains.

A derivatized protein is a derivative of the protein. Generally, derivatization of the protein does not adversely affect the desired activity of the protein (e.g., binding activity to guide RNA, endonuclease activity, binding to a target sequence under the guidance of guide RNA) Specific site binding and cleavage activity), that is to say, the protein derivatives have the same activity as the protein.

derivatized protein

Also known as "protein derivatives", refers to modified forms of proteins, for example, in which one or more amino acids of the protein can be deleted, inserted, modified and/or substituted.

non-naturally occurring

As used herein, the terms "non-naturally occurring" or "engineered" are used interchangeably and mean the involvement of man. When these terms are used to describe a nucleic acid molecule or polypeptide, it is meant that the nucleic acid molecule or polypeptide is at least substantially free from at least one other component with which it is associated in nature or as found in nature.

Orthologue, ortholog

As used herein, the term "orthologue, ortholog" has the meaning commonly understood by those skilled in the art. As further guidance, an "ortholog" of a protein as used herein refers to a protein belonging to a different species that performs the same or similar function as the protein of which it is an ortholog.

Identity

As used herein, the term "identity" is used to refer to the match of sequences between two polypeptides or between two nucleic acids. When a position in both sequences being compared is occupied by the same base or amino acid monomer subunit (for example, a position in each of two DNA molecules is occupied by adenine, or two A certain position in each polypeptide is occupied by lysine), then the molecules are identical at that position. "Percent identity" between two sequences is a function of the number of matching positions common to the two sequences divided by the number of positions compared × 100. For example, if 6 out of 10 positions of two sequences match, then the two sequences are 60% identical. For example, the DNA sequences CTGACT and CAGGTT share 50% identity (matching at 3 positions out of a total of 6 positions). Typically, comparisons are made when two sequences are aligned to yield maximum identity. Such alignment can be accomplished using, for example, the method of Needleman et al. (1970) J. Mol. Biol. 48:443-453, which can be conveniently performed by a computer program such as the Align program (DNAstar, Inc.). It is also possible to use the PAM120 weight residue table using the algorithm of E. Meyers and W. Miller (Comput. Appl Biosci., 4:11-17 (1988)) integrated into the ALIGN program (version 2.0). , a gap length penalty of 12 and a gap penalty of 4 to determine the percent identity between two amino acid sequences. Alternatively, the Needleman and Wunsch (J MoI Biol. 48:444-453 (1970)) algorithm can be used using the Blossum 62 matrix or PAM250 matrix with a gap weight of 16, 14, 12, 10, 8, 6 or 4 and a length weight of 1, 2, 3, 4, 5 or 6 to determine the percent identity between two amino acid sequences .

carrier

The term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid molecule to which it is linked. Vectors include, but are not limited to, single-stranded, double-stranded, or partially double-stranded nucleic acid molecules; nucleic acid molecules including one or more free ends, no free ends (eg, circular); including DNA, RNA, or both. Nucleic acid molecules; and a wide variety of other polynucleotides known in the art. The vector can be introduced into the host cell through transformation, transduction or transfection, so that the genetic material elements it carries can be expressed in the host cell. A vector can be introduced into a host cell to thereby produce a transcript, protein, or peptide, including from a protein, fusion protein, isolated nucleic acid molecule, etc. as described herein (e.g., a CRISPR transcript, such as a nucleic acid transcript , protein, or enzyme). A vector can contain a variety of expression-controlling elements, including, but not limited to, promoter sequences, transcription initiation sequences, enhancer sequences, selection elements, and reporter genes. In addition, the vector may also contain an origin of replication site.

One type of vector is a "plasmid," which refers to a circular double-stranded DNA circle into which additional DNA segments can be inserted, such as by standard molecular cloning techniques.

Another type of vector is a viral vector, in which virus-derived DNA or RNA sequences are present in packaging viruses (e.g., retroviruses, replication-deficient retroviruses, adenoviruses, replication-deficient adenoviruses, and adeno-associated virus) vector. Viral vectors also contain polynucleotides carried by the virus for transfection into a host cell. Certain vectors (eg, bacterial vectors with bacterial origins of replication and episomal mammalian vectors) are capable of autonomous replication in the host cells into which they are introduced.

Other vectors (eg, non-episomal mammalian vectors) integrate into the genome of a host cell upon introduction to the host cell and are thereby replicated with the host genome. Furthermore, certain vectors are capable of directing the expression of genes to which they are operably linked. Such vectors are referred to herein as "expression vectors."

host cell

As used herein, the term "host cell" refers to a cell that can be used to introduce a vector, which includes, but is not limited to, prokaryotic cells such as E. coli or Bacillus subtilis, such as microbial cells, fungal cells, animal cells, and plants. eukaryotic cells.

Those skilled in the art will understand that the design of the expression vector may depend on factors such as the choice of host cell to be transformed, the desired level of expression, and the like.

regulatory elements

As used herein, the term "regulatory element" is intended to include promoters, enhancers, internal ribosome entry sites (IRES), and other expression control elements (e.g., transcription termination signals, such as polyadenylation signals and PolyU sequence), for detailed description please refer to Goeddel, "GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY" 185, Academic Press, San Diego , California (1990). In some cases, regulatory elements include those that direct constitutive expression of a nucleotide sequence in many types of host cells as well as those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). Tissue-specific promoters may primarily direct expression in the desired tissue of interest, such as muscle, neurons, bone, skin, blood, a specific organ (e.g., liver, pancreas), or a specific cell type (e.g., lymphocytes). In some cases, regulatory elements may also direct expression in a timing-dependent manner (eg, in a cell cycle-dependent or developmental stage-dependent manner), which may or may not be tissue or cell type specific. In some cases, the term "regulatory element" encompasses enhancer elements such as WPRE; CMV enhancer; the R-U 5' fragment in the LTR of HTLV-I ((Mol. Cell. Biol., pp. 8( 1), pp. 466-472, 1988); the SV40 enhancer; and the intron sequence between exons 2 and 3 of rabbit β-globin (Proc. Natl. Acad. Sci. USA., Volume 78(3), pages 1527-31, 1981).

Promoter

As used herein, the term "promoter" has a meaning known to those skilled in the art, which refers to a non-coding nucleotide sequence located upstream of a gene that can initiate the expression of a downstream gene. A constitutive promoter is a nucleotide sequence that, when operably linked to a polynucleotide encoding or defining the gene product, results in the gene product in the cell under most or all physiological conditions of the cell. of production. An inducible promoter is a nucleotide sequence that, when operably linked to a polynucleotide encoding or defining a gene product, results in essentially only when an inducer corresponding to said promoter is present in the cell. The gene product is produced within the cell. A tissue-specific promoter is a nucleotide sequence that, when operably linked to a polynucleotide encoding or defining a gene product, results in essentially only cells of the tissue type to which the promoter corresponds. Gene products are produced in cells.

NLS

A "nuclear localization signal" or "nuclear localization sequence" (NLS) is an amino acid sequence that "tags" a protein for import into the nucleus via nuclear transport, ie, proteins with an NLS are transported to the nucleus. Typically, NLS contain positively charged Lys or Arg residues exposed on the protein surface. Exemplary nuclear localization sequences include, but are not limited to, NLS from: SV40 large T antigen, EGL-13, c-Myc, and TUS proteins. In some embodiments, the NLS includes the PKKKRKV sequence. In some embodiments, the NLS includes the sequence AVKRPAATKKAGQAKKKKLD. In some embodiments, the NLS includes the PAAKRVKLD sequence. In some embodiments, the NLS includes the sequence MSRRRKANPTKLSENAKKLAKEVEN. In some embodiments, the NLS includes the KLKIKRPVK sequence. Other nuclear localization sequences include, but are not limited to, the acidic M9 domain of hnRNP A1, the sequences KIPIK and PY-NLS in the yeast transcriptional repressor Matα2.

operably connected

As used herein, the term "operably linked" is intended to mean that a nucleotide sequence of interest is linked to the one or more regulatory elements (e.g., , in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).

complementarity

As used herein, the term "complementarity" refers to the ability of a nucleic acid to form one or more hydrogen bonds with another nucleic acid sequence by means of traditional Watson-Crick or other non-traditional types. Percent complementarity represents the percentage of residues (e.g., out of 10) in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence. 5, 6, 7, 8, 9, and 10 of them are 50%, 60%, 70%, 80%, 90%, and 100% complementary). "Perfectly complementary" means that all contiguous residues of one nucleic acid sequence form hydrogen bonds with the same number of contiguous residues of a second nucleic acid sequence. As used herein, "substantially complementary" means that in a system having At least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98 over a region of 30, 35, 40, 45, 50 or more nucleotides %, 99%, or 100% complementarity, or refers to two nucleic acids that hybridize under stringent conditions.

strict conditions

As used herein, "stringent conditions" for hybridization refer to conditions under which a nucleic acid having complementarity to a target sequence hybridizes primarily to the target sequence and does not substantially hybridize to non-target sequences. Stringent conditions are often sequence dependent and vary depending on many factors. In general, the longer the sequence, the higher the temperature at which the sequence will hybridize specifically to its target sequence.

hybridization

The term "hybrid" or "complementary" or "substantially complementary" means that a nucleic acid (e.g., RNA, DNA) contains nucleotide sequences that enable it to bind non-covalently, i.e., in a sequence-specific, antiparallel manner ( That is, a nucleic acid specifically binds a complementary nucleic acid) to form base pairs and/or G/U base pairs, "annealing" or "hybridization" with another nucleic acid.

Hybridization requires that the two nucleic acids contain complementary sequences, although mismatches between bases may exist. Suitable conditions for hybridization between two nucleic acids depend on the length and degree of complementarity of the nucleic acids, variables well known in the art. Typically, hybridizable nucleic acids are 8 nucleotides or more in length (e.g., 10 nucleotides or more, 12 nucleotides or more, 15 nucleotides or more, 20 nucleotides or more). nucleotides or more, 22 nucleotides or more, 25 nucleotides or more, or 30 nucleotides or more).

It will be understood that the sequence of a polynucleotide does not need to be 100% complementary to the sequence of its target nucleic acid in order to hybridize specifically. The polynucleotide may comprise 60% or higher, 65% or higher, 70% or higher, 75% or higher, 80% or higher, 85% or higher, 90% or higher, 95% or Higher, 98% or higher, 99% or higher, 99.5% or higher, or the sequence complementarity of the target region in the target nucleic acid sequence to which it hybridizes is 100%.

Hybridization of the target sequence to the gRNA represents at least 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96% of the nucleic acid sequence of the target sequence and the gRNA , 97%, 98%, 99% or 100% can hybridize and form a complex; or there are at least 12, 15, 16, 17, 18, 19, 20 nucleic acid sequences representing the target sequence and gRNA. One, 21, 22 or more bases can complement each other and hybridize to form a complex.

Express

As used herein, the term "expression" refers to the process by which a DNA template is transcribed into a polynucleotide (eg, into mRNA or other RNA transcript) and/or the transcribed mRNA is subsequently translated into a peptide, The process of polypeptide or protein. Transcripts and encoded polypeptides may collectively be referred to as "gene products." If the polynucleotide is derived from genomic DNA, expression can include splicing of mRNA in eukaryotic cells.

Connector

As used herein, the term "linker" refers to a linear polypeptide formed by multiple amino acid residues linked by peptide bonds. The linker of the present invention can be a synthetic amino acid sequence or a naturally occurring polypeptide sequence, such as a polypeptide with hinge region function. Such linker polypeptides are well known in the art (see, e.g., Holliger, P. et al. (1993) Proc. Natl. Acad. Sci. USA 90:6444-6448; Poljak, R.J. et al. (1994) Structure 2:1121- 1123).

treat

As used herein, the term "treating" means treating or curing a condition, delaying the onset of symptoms of a condition, and/or delaying the progression of a condition.

Subject

As used herein, the term "subject" includes, but is not limited to, various animals, plants, and microorganisms.

animal

For example, mammals, such as bovines, equids, ovines, porcines, canines, felines, leporids, rodents (e.g., mice or rats), non-human primates animal (e.g., macaque or cynomolgus monkey) or human. In certain embodiments, the subject (eg, a human) has a disorder (eg, a disorder resulting from a defect in a disease-associated gene).

plant

The term "plant" is understood to mean any differentiated multicellular organism capable of photosynthesis and includes crop plants at any stage of maturity or development, in particular monocots or dicots, vegetable crops including artichokes, kohlrabi, Arugula, leeks, asparagus, lettuce (e.g., head, leaf, romaine), bok choy, yam, melons (e.g., melon, watermelon, crenshaw ), honeydew, romaine melon), rapeseed crops (e.g. Brussels sprouts, cabbage, cauliflower, broccoli, kale, kale, Chinese cabbage, bok choy), cardoons, carrots, napa, Okra, onions, celery, parsley, chickpeas, parsnips, chicory, peppers, potatoes, gourds (e.g., zucchini, cucumbers, courgettes, pumpkins, pumpkins), radishes, dried onions, rutabaga, Purple eggplant (also called eggplant), salsify, endive, shallots, chicory, garlic, spinach, green onions, pumpkin, greens, beets (sugar beets and fodder beets), sweet potatoes, chard, Wasabi, tomatoes, turnips, and spices; fruit and/or vine crops such as apples, apricots, cherries, nectarines, peaches, pears, plums, prunes, cherries, quinces, almonds, chestnuts, hazelnuts, pecans, Pistachios, walnuts, citrus, blueberries, boysenberries, cranberries, currants, loganberries, raspberries, strawberries, blackberries, grapes, avocados, bananas, kiwis, persimmons, pomegranates, pineapples , tropical fruits, pome fruits, melons, mangoes, papayas, and lychees; field crops, such as clover, alfalfa, evening primrose, alfalfa, corn/maize (feed corn, sweet corn, popcorn), hops, lotus root Barley, peanuts, rice, safflower, small cereal crops (barley, oats, rye, wheat, etc.), sorghum, tobacco, kapok, leguminous plants (beans, lentils, peas, soybeans), oil-bearing plants (rapeseed, rape, etc.) mustard, poppy, olive, sunflower, coconut, castor plant, cocoa beans, groundnut), Arabidopsis, fiber plants (cotton, flax, jute), Lauraceae (cinnamon, camphor), or a plant such as coffee , sugar cane, tea, and natural rubber plants; and/or bedding plants, such as flowering plants, cacti, succulents and/or ornamental plants, and trees such as forests (broadleaf and evergreen trees, such as conifers), fruit trees, ornamental trees, and nut-bearing trees, as well as shrubs and other seedlings.

Beneficial effects of the invention

The present invention improves the activity of Cas12j19 protein through mutation and has broad application prospects.

The embodiments of the present invention will be described in detail below with reference to the drawings and examples, but those skilled in the art will understand that the following drawings and examples are only used to illustrate the present invention and do not limit the scope of the present invention. Various objects and advantageous aspects of the present invention will become apparent to those skilled in the art from the accompanying drawings and the following detailed description of preferred embodiments.

Description of drawings

Figure 1. Verification results of single-site amino acid mutation Cas protein editing efficiency.

Figure 2. Verification results of the editing efficiency of mutated E100R protein and wild-type Cas12j19 in soybean. The abscissa represents different target positions, and the ordinate represents editing efficiency.

Figure 3. Verification results of Cas protein editing efficiency of single-site amino acid saturation mutation.

Detailed ways

The following examples are only used to describe the present invention but not to limit the present invention. Unless otherwise indicated, the experiments and methods described in the examples were performed essentially according to conventional methods well known in the art and described in various references. For example, for conventional techniques such as immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA used in the present invention, see Sambrook, Fritsch ) and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, 2nd ed. (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY ) (edited by F.M. Ausubel et al., (1987)); "METHODS IN ENZYMOLOGY" series (Academic Publishing Company): "PCR 2: A PRACTICAL APPROACH" ) (edited by M.J. MacPherson, B.D. Hames and G.R. Taylor (1995)), Harlow and Lane (1988) "Antibodies: "ANTIBODIES, A LABORATORY MANUAL", and "ANIMAL CELL CULTURE" (edited by R.I. Freshney (1987)).

In addition, if the specific conditions are not specified in the examples, the conventional conditions or the conditions recommended by the manufacturer shall be followed. If the manufacturer of the reagents or instruments used is not indicated, they are all conventional products that can be purchased commercially. Those skilled in the art will appreciate that the examples describe the invention by way of example and are not intended to limit the scope of the invention as claimed. All publications and other references mentioned herein are incorporated by reference in their entirety.

Example 1. Obtaining Cas mutant protein

For the known Cas protein (Cas12j.19 in CN111770992B, in this example, it is called Cas12i19), the applicant used bioinformatics to predict the key amino acid positions that may affect its biological function, and assigned the amino acid positions to Point mutations were performed to obtain Cas mutant proteins with improved editing activity. Specifically, the Cas12j19 coding sequence was codon optimized and synthesized. The amino acid sequence of wild-type Cas12j19 is shown in SEQ ID No. 1, and its nucleic acid sequence is shown in SEQ ID No. 2. The potential Cas12j19 was analyzed through bioinformatics methods. Site-directed mutagenesis of amino acids that bind to the target sequence.

SEQ ID No.1:

SEQ ID No.2:

Variants of Cas proteins were generated by PCR-based site-directed mutagenesis. The specific method is to divide the DNA sequence design of Cas12j19 protein into two parts centered on the mutation site, design two pairs of primers to amplify the two parts of the DNA sequence respectively, and introduce the sequence that needs to be mutated on the primers, and finally use Gibson cloning. Load both fragments into pcDNA3.3-eGFP vector. The combination of mutants is constructed by splitting the DNA of the Cas12j19 protein into multiple segments and using PCR and Gibson clone. Fragment amplification kit: TransStart FastPfu DNA Polymerase (containing 2.5mM dNTPs), please refer to the instruction manual for specific experimental procedures. Glue recovery kit: Gel DNA Extraction Mini Kit, please refer to the instruction manual for detailed experimental procedures. The kit used for vector construction: pEASY-Basic Seamless Cloning and Assembly Kit (CU201-03). Please refer to the instruction manual for specific experimental procedures. The mutated amino acid sites involved and the primer sequences used are shown in the following table:

Based on the above amino acid mutation sites, the wild-type protein (WT) of Cas12j19 and the proteins with mutations in the above amino acid single sites (named after the mutation type) were obtained: D50R, E100R and N103D, which are relative to SEQ ID No.1 In the sequence shown, the 50th amino acid from the N terminus is mutated to R, the 100th amino acid from the N terminus is mutated to R, and the 103rd amino acid from the N terminus is mutated to D.

Example 2. Verification of editing activity of Cas mutant protein

Different Cas proteins obtained in Example 1 were used to verify their gene editing activity in animal cells, and the target was designed for the Chinese hamster ovary cell (CHO) FUT8 gene, FUT8-3: ATGGAGGCTGTCTACAATGGGG A, the italicized part is the PAM sequence, and the remaining regions is the target area. The vector pcDNA3.3 was modified to contain EGFP fluorescent protein and PuroR resistance gene. The SV40NLS-Cas-XX fusion protein was inserted through the restriction site XbaI and PstI; the U6 promoter and gRNA sequence were inserted through the restriction site Mfe1. The CMV promoter drives the expression of the fusion protein SV40NLS-Ca s-XX-NLS-GFP. The protein Cas-XX-NLS and the protein GFP are connected using the connecting peptide T2A. Promoter EF-1α drives puromycin resistance gene expression. Plating: Plate the CHO cells until the confluence is 70-80%. The number of cells seeded in the 12-well plate is 8*10^4 cells/well. Transfection: Plate for 24 hours for transfection. Add 6.25 μl Hieff Trans ^TM liposome nucleic acid transfection reagent to 100 μl opti-MEM and mix well. Add 2.5ug plasmid to 100 μl opti-MEM and mix well. Mix the diluted Hieff Trans ^TM liposome nucleic acid transfection reagent and the diluted plasmid evenly, and incubate at room temperature for 20 minutes. The incubated mixture was added to the culture medium on which cells were plated for transfection. After 48 hours of transfection, the cells were digested with trypsin-EDTA (0.05%), and cells with GFP signal were sorted using flow cytometry (FACS).

Extract DNA, PCR amplify near the editing area, and send to hiTOM for sequencing: cells are collected after trypsin digestion, and genomic DNA is extracted using a cell/tissue genomic DNA extraction kit (Biotech). Amplify the region near the target site from genomic DNA. PCR products were subjected to hiTOM sequencing. Sequencing data analysis, counting the sequence types and proportions within the range of 15nt upstream and 10nt downstream of the target position, counting the sequences with SNV frequency greater than/equal to 1% or non-SNV mutation frequency greater than/equal to 0.06%, to obtain Cas-XX The editing efficiency of the protein at the target position. CHO cell F UT8 gene target sequence: FUT8-Cas-XX-g3: ATGGAGGCTGTCTACAATGGGGA, the italicized part is the PAM sequence, and the rest of the region is the targeting region. The gRNA sequence is: The bolded region is the targeting region, and the other regions are DR (direct repeat sequence) regions.

Figure 1 shows the editing activity of wild-type Cas12j19 protein (WT, shown in SEQ ID No. 1) and mutant proteins with single amino acid site mutations. As shown in Figure 1, compared with WT, mutations at the E100R amino acid site can significantly improve the editing efficiency of Cas12j19 protein, while mutations in D50R and N103D will reduce the editing efficiency of Cas12j19 protein.

Example 3. Verification of editing activity of Cas mutant protein in soybean

Multiple targets were designed for the FAD gene and BADH gene in the soybean genome. The target information is shown in Table 2. The designed targets were constructed into vectors containing the Cas mutant protein E100R in Example 1, which were used as verification vectors. With high editing efficiency, the constructed vector was used for transient transformation of soybean seedlings with Agrobacterium rhizogenes.

(1) Soybean seed germination: Mix nutrient soil and vermiculite in a ratio of 2:1, spread it flat on the plug tray, and place the soybean seeds. Sow the seeds into the plug tray at a depth of 0.5cm, pour an appropriate amount of water to prepare for germination.

(2) Preparation of bacterial plate and bacterial liquid: Take 500-600 μl of Agrobacterium rhizogenes K599 glycerol bacterial liquid and apply it on the plate. At the same time, take 50 μl of bacterial liquid and add TY culture medium containing the corresponding antibiotics, and culture at 28°C overnight.

(3) Agrobacterium rhizogenes infects soybeans: Use a blade to cut an inclined wound 1cm from the hypocotyls of the cotyledons of soybean seedlings that have grown for 7-14 days, and dip the wound into the wound to inoculate it with Agrobacterium rhizogenes. The hypocotyls of the inoculated seedlings were then directly planted in a humid sterile vermiculite culture box, and each plant was poured with 10 ml of K599 infection suspension, and then maintained at high humidity for 16 days to promote soybean hairy root growth.

After the hairy roots grow, the DNA of the soybean hairy roots is extracted using the TPS method, and the corresponding fragments are amplified using detection primers. The primer information is shown in Table 3. The amplified products are sequenced by the Sanger method, and the editing efficiency is determined based on the sequencing results.

Table 2. Sequence information of targets

Table 3. Sequence information of detection primers

The results are shown in Figure 2. It was detected that the editing efficiencies of wild-type Cas12j19 and mutated E100R were significantly different at different target sites. The mutated E100R protein was detected at target sites BADH2-6, FAD-1A-1, BADH1-5, FAD-1B-2 and FAD-1B-3 showed significant editing activity, and wild-type Cas12j19 had no editing activity detected at each target site; compared with wild-type Cas12j19, the mutated E100R protein edited at each target site Efficiencies are significantly improved.

Example 4. Perform saturation mutation on position 100 of wild-type Cas12j19 and verify its editing activity

Using the wild-type Cas12j19 protein as a template, refer to the method for obtaining the mutant protein in Example 1, design corresponding point primers, generate variants of the Cas protein through site-directed mutagenesis based on PCR, and obtain mutations at position 100 into multiple amino acid types. Cas protein variants of (A, V, G, L, D, F, W, Y, N, S, Q, K, M, T, C, P, H, or I).

The method of verifying the editing activities of different Cas proteins in animal cells in Example 2 was used to verify the activity of each of the above Cas protein variants in animal cells. The results are shown in Figure 3. A saturation mutation was performed on the 100th amino acid position of the wild-type Cas protein. Different types of amino acids after mutation have different editing activities in animal cells. The 100th position was mutated to K, Y, M. When F, W, S, H, V, I, N, the editing efficiency of the Cas protein variant is significantly higher than that of wild-type Cas12j19. After the amino acid mutation is C or L, the activity is basically the same as that of wild-type Cas12j19. When the amino acid mutation is Q, The editing activity after G, T, D, and P is lower than that of wild-type Cas12j19. When the amino acid type is mutated to A, the Cas protein variant loses its editing activity.

Although the specific embodiments of the present invention have been described in detail, those skilled in the art will understand that various modifications and changes can be made to the details based on all teachings that have been published, and these changes are within the protection scope of the present invention. . The full scope of the present invention is given by the appended claims and any equivalents thereof.

Claims

A Cas mutant protein, compared with the amino acid sequence of the parent Cas protein, there is a mutation at the following amino acid position corresponding to the amino acid sequence shown in SEQ ID No. 1: No. 100; preferably, the The 100th amino acid is mutated to any one of K, Y, M, F, R, W, S, H, V, I, N, C, and L.
The Cas mutant protein according to claim 1, wherein the parent Cas protein is a Cas12j family protein.
The Cas mutant protein according to claim 1 or 2, characterized in that the Cas mutant protein is selected from any group of the following I-III:

I. Cas mutant protein obtained by mutating the amino acid sequence shown in SEQ ID No. 1 at the following amino acid positions: the 100th amino acid;

II. Compared with the Cas mutant protein described in I, it has the mutation site described in I; and, compared with the Cas mutant protein described in I, it has at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4% , a Cas mutant protein with at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% sequence identity;

III. Compared with the Cas mutant protein described in I, it has the mutation site described in I; and, compared with the Cas mutant protein described in I, it has a sequence with one or more amino acid substitutions, deletions or additions. ; The one or more amino acids include substitution, deletion or addition of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.
A fusion protein, the fusion protein includes the Cas mutant protein according to any one of claims 1-3 and other modified parts; preferably, the modified part is selected from another protein or polypeptide, a detectable label or its random combination.
An isolated polynucleotide, characterized in that the polynucleotide is a polynucleotide sequence encoding the Cas mutant protein of any one of claims 1-3, or a polynucleotide encoding the fusion protein of claim 4 sequence.
A vector, characterized in that the vector contains the polynucleotide of claim 5 and a regulatory element operably connected thereto.
A CRISPR-Cas system, characterized in that the system includes the Cas mutant protein according to any one of claims 1-3 and at least one gRNA;

The gRNA is capable of binding to the Cas mutant protein of any one of claims 1-3.
A composition, characterized in that the composition contains:

(i) Protein component, which is selected from: the Cas mutant protein described in any one of claims 1-3 or the fusion protein described in claim 4;

(ii) a nucleic acid component, which is gRNA, and the gRNA is capable of binding to the Cas mutant protein of any one of claims 1-3;

The protein component and the nucleic acid component combine with each other to form a complex.
An activated CRISPR complex comprising:

(i) Protein component, which is selected from: the Cas mutant protein described in any one of claims 1-3 or the fusion protein described in claim 4;

(ii) a nucleic acid component, which is a gRNA, which includes a direct repeat sequence capable of binding the Cas mutant protein of any one of claims 1-3 and a guide sequence capable of targeting a target sequence;

(iii) Binding to a target sequence on the gRNA described in (ii).
An engineered host cell, characterized in that the host cell contains the Cas mutant protein of any one of claims 1-3, or the fusion protein of claim 4, or the polynucleoside of claim 5 acid, or right The vector of claim 6, or the CRISPR-Cas system of claim 7, or the composition of claim 8, or the activated CRISPR complex of claim 9.
The Cas mutant protein of any one of claims 1-3, or the fusion protein of claim 4, or the polynucleotide of claim 5, or the vector of claim 6, or the vector of claim 7 The CRISPR-Cas system, or the composition of claim 8, or the activated CRISPR complex of claim 9, or the host cell of claim 10 in gene editing, gene targeting or gene cutting. Application; or use in the preparation of reagents or kits for gene editing, gene targeting or gene cleavage.
The Cas mutant protein of any one of claims 1-3, or the fusion protein of claim 4, or the polynucleotide of claim 5, or the vector of claim 6, or the vector of claim 7 The CRISPR-Cas system, or the composition of claim 8, or the activated CRISPR complex of claim 9, or the host cell of claim 10 is selected from any one or any several of the following: application:

Targeting and/or editing of target nucleic acids; cleavage of double-stranded DNA, single-stranded DNA or single-stranded RNA; non-specific cleavage and/or degradation of side nucleic acids; non-specific cleavage of single-stranded nucleic acids; nucleic acid detection; specific editing of double-stranded nucleic acids ;Base editing double-stranded nucleic acid;Base editing single-stranded nucleic acid.
A method for editing a target nucleic acid, targeting a target nucleic acid, or cutting a target nucleic acid, the method comprising combining the target nucleic acid with the Cas mutant protein of any one of claims 1-3, or the fusion protein of claim 4, or The polynucleotide of claim 5, or the vector of claim 6, or the CRISPR-Cas system of claim 7, or the composition of claim 8, or the activated CRISPR-Cas system of claim 9 The CRISPR complex, or the host cell of claim 10 is contacted.
A kit for gene editing, gene targeting or gene cutting, the kit comprising the Cas mutant protein of any one of claims 1-3, or the fusion protein of claim 4, or claim 5 The polynucleotide, or the vector of claim 6, or the CRISPR-Cas system of claim 7, or the composition of claim 8, or the activated CRISPR complex of claim 9 , or the host cell of claim 10.
The Cas mutant protein of any one of claims 1-3, or the fusion protein of claim 4, or the polynucleotide of claim 5, or the vector of claim 6, or the vector of claim 7 The CRISPR-Cas system, or the composition of claim 8, or the activated CRISPR complex of claim 9, or the use of the host cell of claim 10 in preparing a preparation or kit, Preparations or kits for:

(i) Gene or genome editing;

(ii) Target nucleic acid detection and/or diagnosis;

(iii) Edit target sequences in target loci to modify organisms;

(iv) Treatment of disease;

(v) targeting target genes;

(vi) Cut the target gene.