WO2023086938A2 - Type v nucleases - Google Patents

Abstract

The present invention relates to nucleases or nucleic acids encoding the nucleases, RNA guides or nucleic acids encoding the RNA guides, processes for characterizing the nucleases and/or RNA guides, compositions comprising the nucleases and/or RNA guides, and kits and/or methods for preparing and/or using the nucleases and/or RNA guides.

Description

TYPE V NUCLEASES

CROSS-REFERENCE TO RELATED APPLICATION

The present application is entitled to priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 63/278,685, filed November 12, 2021, which is hereby incorporated by reference in its entirety herein.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

The contents of the electronic sequence listing (File Name: 381834-7008WO1 Sequence Listing.xml; Size: 5.21 megabytes; and Date of Creation: November 7, 2022) is herein incorporated by reference in its entirety.

BACKGROUND

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) genes, collectively known as CRISPR-Cas or CRISPR/Cas systems, are adaptive immune systems in archaea and bacteria that defend particular species against foreign genetic elements, e.g., phage infection. The CRISPR-Cas systems of prokaryotic adaptive immunity are an extremely diverse group of proteins effectors, non-coding elements, as well as loci architectures, some examples of which have been engineered and adapted to produce important biotechnologies.

Tire components of the system involved in host defense include one or more effector proteins capable of modifying DNA or RNA and an RNA guide element that targets these protein activities to a specific sequence on the target (e.g., phage) DNA or RNA. The RNA guide is composed of a CRISPR RNA (crRNA) and may require an additional trans-activating RNA (tracrRNA) to enable targeted nucleic acid manipulation by the effector protein(s). The crRNA consists of a direct repeat responsible for protein binding to the crRNA and a spacer sequence that is complementary to the desired nucleic acid target sequence. CRISPR systems can be reprogrammed to target alternative DNA or RNA targets by modifying the spacer sequence of the crRNA.

There remains a need for additional programmable effectors and systems for modifying nucleic acids and polynucleotides (i.e., DNA, RNA, or any hybrid, derivative, or modification) beyond the current CRISPR-Cas systems that enable novel applications through their unique properties.

SUMMARY OF THE INVENTION It is against the above background that the present invention provides certain advantages and advancements over the prior art.

Although this invention disclosed herein is not limited to specific advantages or functionalities, the present invention provides, in one aspect, a composition comprising:

(a) a nuclease or a nucleic acid encoding the nuclease, wherein the nuclease comprises an amino acid sequence with at least 80% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1; and

(b) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid.

In another aspect, the present invention provides a cell comprising a composition comprising:

(a) a nuclease or a nucleic acid encoding the nuclease, wherein the nuclease comprises an amino acid sequence with at least 80% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1; and

(b) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid.

In some aspects, the present invention provides a method of binding a composition to a target nucleic acid in a cell, the method comprising:

(a) providing the composition, wherein the composition comprises a nuclease or a nucleic acid encoding the nuclease, wherein the nuclease comprises an amino acid sequence with at least 80% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1; and an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid; and

(b) delivering the composition to the cell, wherein the cell comprises the target nucleic acid, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to the target nucleic acid.

In other aspects, the present invention provides a method of introducing an indel into a target nucleic acid in a cell, the method comprising:

(a) providing a composition comprising a nuclease or a nucleic acid encoding the nuclease, wherein the nuclease comprises an amino acid sequence with at least 80% identity to any one of SEQ ID NOs: 1- 3875 which is referred to as an effector in Column 2 of Table 1; and an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid; and

(b) delivering the composition to the cell, wherein recognition of the target nucleic acid by the composition results in a modification of the target nucleic acid.

DETAILED DESCRIPTION

Definitions

The present invention will be described with respect to particular embodiments, but the invention is not limited thereto but only by the claims. Terms as set forth hereinafter are generally to be understood in their common sense unless indicated otherwise.

Unless otherwise defined, scientific and technical terms used herein have the meanings that are commonly understood by those of ordinary skill in the art. In the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. The use of “or” means “and/or” unless stated otherwise. The use of the term “including,” as well as other forms, such as “includes” and “included,” is not limiting.

Generally, nomenclature used in connection with cell and tissue culture, molecular biology, immunology, microbiology, genetics, and protein and nucleic acid chemistry and hybridization described herein is well-known and commonly used in the art. The methods and techniques provided herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. Enzymatic reactions and purification techniques are performed according to manufacturer’s specifications, as commonly accomplished in the art or as described herein. The nomenclatures used in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Standard techniques are used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients.

That the disclosure may be more readily understood, select terms are defined below.

The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element. “About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.

As used herein, the term “catalytic residue” refers to an amino acid that activates catalysis. A catalytic residue is an amino acid that is involved (e.g., directly involved) in catalysis.

As used herein, the terms “domain” and “protein domain” refer to a distinct functional and/or structural unit of a polypeptide. In some embodiments, a domain may comprise a conserved amino acid sequence. As used herein, the term “RuvC domain” refers to a conserved domain or motif of amino acids having nuclease (e.g., endonuclease) activity. As used herein, a protein having a split RuvC domain refers to a protein having two or more RuvC motifs, at sequentially disparate sites within a sequence, that interact in a tertiary structure to form a RuvC domain.

As used herein, the term “effector” refers to a polypeptide or protein, such as an enzyme, having at least one “effector activity.” For example, effectors can include nucleases, e.g., CRISPR-associated nucleases.

As used herein, the term “effector activity” refers to a biological activity. In some embodiments, effector activity includes enzymatic activity, e.g., catalytic ability of an effector. For example, effector activity can include nuclease activity.

As used herein, the term “nuclease” refers to an enzyme capable of cleaving a phosphodiester bond. A nuclease hydrolyzes phosphodiester bonds in a nucleic acid backbone. As used herein, the term “endonuclease” refers to an enzyme capable of cleaving a phosphodiester bond between nucleotides.

As used herein, the terms “parent,” “parent polypeptide,” and “parent sequence” refer to an original polypeptide (e.g., reference or starting polypeptide) to which an alteration is made to produce a variant polypeptide of the present invention.

As used herein, the term “protospacer adjacent motif’ or “PAM” refers to a DNA sequence adjacent to a target sequence to which a complex comprising an effector and an RNA guide binds. In some embodiments, a PAM is required for enzyme activity. As used herein, the term “adjacent” includes instances in which an RNA guide of the complex specifically binds, interacts, or associates with a target sequence that is immediately adjacent to a PAM. In such instances, there are no nucleotides between the target sequence and the PAM. The term “adjacent” also includes instances in which there are a small number (e.g., 1, 2, 3, 4, or 5) of nucleotides between the target sequence, to which the targeting moiety binds, and the PAM. As used herein, the terms “reference composition,” “reference sequence,” and “reference” refer to a control, such as a negative control or a parent (e.g., a parent sequence, a parent protein, a wild-type protein, or a complex comprising a parent sequence).

As used herein, the terms “RNA guide” or “RNA guide sequence” refer to any RNA molecule that facilitates the targeting of a polypeptide described herein to a target nucleic acid. For example, an RNA guide can be a molecule that recognizes (e.g., binds to) a target nucleic acid. An RNA guide may be designed to be complementary to a specific nucleic acid sequence. An RNA guide comprises a DNA targeting sequence and a direct repeat (DR) sequence. The terms CRISPR RNA (crRNA), pre-crRNA, mature crRNA, and gRNA are also used herein to refer to an RNA guide. As used herein, the term “pre- crRNA” refers to an unprocessed RNA molecule comprising a DR-spacer-DR sequence. As used herein, the term “mature crRNA” refers to a processed form of a pre-crRNA; a mature crRNA may comprise a DR- spacer sequence, wherein the DR is a truncated form of the DR of a pre-crRNA and/or the spacer is a truncated form of the spacer of a pre-crRNA. The RNA guide can further comprise a tracrRNA sequence. In some embodiments, the tracrRNA sequence is fused to the direct repeat sequence of the RNA guide. In some embodiments, the RNA guide is a single molecule RNA guide (e.g., an sgRNA).

As used herein, the terms “single molecule guide RNA,” “single molecule RNA guide,” “single guide RNA,” “sgRNA,” and the like are used to refer to an RNA guide (comprising a direct repeat sequence and a spacer sequence) fused to a tracrRNA. The RNA guide and tracrRNA can be transcribed together as a single transcript (e.g., with intervening linker nucleotides). The RNA guide and tracrRNA can be covalently linked (e.g., linked by intervening nucleotides). In some embodiments, the 3’ end of the RNA guide is linked to the 5’ end of the tracrRNA. In some cases, the 5’ end of the RNA guide is linked to the 3 ’ end of the tracrRNA. In some cases, the 5 ’ end of the RNA guide is linked to the 5 ’ end of the tracrRNA. In some cases, the 3’ end of the RNA guide is linked to the 3’ end of the tracrRNA.

It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, C, G), this also includes an RNA sequence (i.e., A, U, C, G), such as an RNA transcript of the DNA sequence, in which “U” replaces “T” in the sequence.

As used herein, the term “substantially identical” refers to a sequence, polynucleotide, or polypeptide, that has a certain degree of identity to a reference sequence.

As used herein, the terms “target nucleic acid” and “target sequence” refer to a nucleic acid sequence to which a targeting moiety (e.g., RNA guide) specifically binds. In some embodiments, the DNA targeting sequence of an RNA guide binds to a target nucleic acid.

As used herein, the term “targeting moiety” refers to a molecule or component (e.g., nucleic acid and/or RNA guide) that facilitates the targeting of another molecule or component to a target nucleic acid. In some embodiments, the targeting moiety specifically interacts or associates with the target nucleic acid. As used herein, the terms “trans-activating crRNA” and “tracrRNA” refer to an RNA molecule involved in or required for the binding of a targeting moiety (e.g., an RNA guide) to a target nucleic acid.

In one aspect, the present invention provides novel nucleases and methods of use thereof. In some aspects, a composition, kit, or cell comprising a nuclease of the present invention having one or more characteristics is described herein. In some aspects, a method of preparing a nuclease of the present invention is described. In some aspects, a method of delivering a composition comprising a nuclease of the present invention is described.

COMPOSITION

In some aspects, the invention described herein comprises compositions comprising a nuclease. In some embodiments, a composition of the invention includes a nuclease, and the composition has nuclease activity. In some aspects, the invention described herein comprises compositions comprising a nuclease and a targeting moiety. In some embodiments, a composition of the invention includes a nuclease and an RNA guide sequence, and the RNA guide sequence directs the nuclease activity to a site-specific target. In some embodiments, a nuclease of the composition of the present invention is a recombinant nuclease.

In some embodiments, the composition described herein comprises an RNA-guided nuclease (e.g., a nuclease comprising multiple components). In some embodiments, a nuclease of the present invention comprises enzyme activity (e.g., a protein comprising a RuvC domain or a split RuvC domain). In some embodiments, the composition comprises a targeting moiety (e.g., an RNA guide). In some embodiments, the composition comprises a ribonucleoprotein (RNP) comprising a nuclease and a targeting moiety (e.g., RNA guide).

In some embodiments, the composition of the present invention includes an effector (e.g., nuclease) described herein.

Nuclease

In various embodiments, the nuclease of the present invention is a Type V CRISPR-associated nucleases.

In some embodiments, the nuclease is an isolated or purified nuclease.

A nucleic acid sequence encoding a nuclease described herein may be substantially identical to a reference nucleic acid sequence if the nucleic acid encoding the nuclease comprises a sequence having least about 60%, least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 99.5% sequence identity to the reference nucleic acid sequence. The percent identity between two such nucleic acids can be determined manually by inspection of the two optimally aligned nucleic acid sequences or by using software programs or algorithms (e.g., BLAST, ALIGN, CLUSTAL) using standard parameters. One indication that two nucleic acid sequences are substantially identical is that the two nucleic acid molecules hybridize to each other under stringent conditions (e.g., within a range of medium to high stringency).

In some embodiments, a nuclease described herein is encoded by a nucleic acid sequence having at least about 60%, least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 99.5% sequence identity to a reference nucleic acid sequence.

A nuclease described herein may be substantially identical to a reference polypeptide if the nuclease comprises an amino acid sequence having at least about 60%, least about 65%, least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 99.5% sequence identity to the amino acid sequence of the reference polypeptide. The percent identity between two such polypeptides can be determined manually by inspection of the two optimally aligned polypeptide sequences or by using software programs or algorithms (e.g., BLAST, ALIGN, CLUSTAL) using standard parameters. One indication that two polypeptides are substantially identical is that the first polypeptide is immunologically cross-reactive with the second polypeptide. Typically, polypeptides that differ by conservative amino acid substitutions are immunologically cross-reactive. Thus, a polypeptide is substantially identical to a second polypeptide, for example, where the two peptides differ only by a conservative amino acid substitution or one or more conservative amino acid substitutions.

In some embodiments, a nuclease of the present invention comprises a polypeptide sequence having 50, 60, 65, 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 (e.g., SEQ ID NOs: 1, 6, 11, and the like). In some embodiments, a nuclease of the present invention comprises a polypeptide sequence having greater than 50, 60, 65, 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identity to, or having 100% identity to, any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1.

One skilled in the art can identify a suitable nucleic acid sequence to encode a polypeptide sequence having 50, 60, 65, 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1. In some embodiments, a nuclease of the present invention is a nuclease having a specified degree of amino acid sequence identity to one or more reference polypeptides, e.g., at least 60%, at least 65%, at least 70%, at least 75%, 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%, or even at least 99% sequence identity to the amino acid sequence of any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1. Homology or identity can be determined by amino acid sequence alignment, e.g., using a program such as BLAST, ALIGN, or CLUSTAL, as described herein. In some embodiments, a nuclease having a specified degree of amino acid sequence identity to one or more reference polypeptides retains one or more characteristics, e.g., nuclease activity, as the one or more reference polypeptides.

In some embodiments, a nuclease of the present invention comprises a protein with an amino acid sequence with at least about 60%, least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 99.5% sequence identity to the reference amino acid sequence of any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1. In some embodiments, a nuclease having a specified degree of amino acid sequence identity to one or more reference polypeptides retains one or more characteristics, e.g., nuclease activity, as the reference amino acid sequence.

Also provided is a nuclease of the present invention having enzymatic activity, e.g., nuclease activity, and comprising an amino acid sequence which differs from the amino acid sequences of any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 by no more than 50, no more than 40, no more than 35, no more than 30, no more than 25, no more than 20, no more than 19, no more than 18, no more than 17, no more than 16, no more than 15, no more than 14, no more than 13, no more than 12, no more than 11, no more than 10, no more than 9, no more than 8, no more than 7, no more than 6, no more than 5, no more than 4, no more than 3, no more than 2, or no more than 1 amino acid residue(s), when aligned using any of the previously described alignment methods.

In some embodiments, a nuclease of the present invention comprises a RuvC domain. In some embodiments, a nuclease of the present invention comprises a split RuvC domain or two or more partial RuvC domains. For example, a nuclease comprises RuvC motifs that are not contiguous with respect to the primary amino acid sequence of the nuclease but form a RuvC domain once the protein folds. In some embodiments, the catalytic residue of a RuvC motif is a glutamic acid residue and/or an aspartic acid residue.

In some embodiments, the invention includes an isolated, recombinant, substantially pure, or non- naturally occurring nuclease comprising a RuvC domain, wherein the nuclease has enzymatic activity, e.g., nuclease activity, wherein the nuclease comprises an amino acid sequence having at least about 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column

2 of Table 1.

In some embodiments, an effector (e.g., a nuclease) of the present invention forms a dimer. In some embodiments, the dimer is a homodimer (e.g., a homodimer comprising two identical RuvC domains). In some embodiments, the dimer is a heterodimer (e.g., a heterodimer comprising two non-identical RuvC domains). For example, in some embodiments, a first effector polypeptide of SEQ ID NO: 1 forms a homodimer with a second effector polypeptide of SEQ ID NO: 1. In other embodiments, a first effector polypeptide of SEQ ID NO: 1 forms a heterodimer with a second effector polypeptide of any one of SEQ ID NOs: 6-3875 which is referred to as an effector in Column 2 of Table 1. In some embodiments, a dimer of the present invention (e.g., a dimer comprising two RuvC domains) is capable of cleaving two target nucleic acid molecules. In some embodiments, a dimer of the present invention (e.g., a dimer comprising two RuvC domains) is capable of cleaving two sites within a single nucleic acid target. In some embodiments, a dimer of the present invention (e.g., a dimer comprising two RuvC domains) is capable of cleaving each strand of a double -stranded DNA target sequence. In some embodiments, a dimer of the present invention (e.g., a dimer comprising one active RuvC domain and one inactive RuvC domain) is capable of cleaving only a single strand of a double-stranded DNA target sequence (i.e., the dimer nicks the double-stranded DNA target).

Table 1: Amino acid and nucleotide sequences

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Biochemical Characteristics

In some embodiments, the biochemistry of a nuclease described herein is analyzed using one or more assays. In some embodiments, the biochemical characteristics of a nuclease of the present invention are analyzed in bacterial cells, as described in Example 1. In some embodiments, the biochemical characteristics of a nuclease of the present invention are analyzed in mammalian cells, as described in Example 2.

Described herein are compositions and methods relating to a nuclease of the present invention. The compositions and methods are based, in part, on the observation that cloned and expressed effectors of the present invention have nuclease activity.

In some embodiments, a nuclease and an RNA guide as described herein form a complex (e.g., an RNP). In some embodiments, the complex includes other components. In some embodiments, the complex is activated upon binding to a nucleic acid substrate that has complementarity to a spacer sequence in the RNA guide (e.g., a target nucleic acid). In some embodiments, the target nucleic acid is a double -stranded DNA (dsDNA). In some embodiments, the target nucleic acid is a single -stranded DNA (ssDNA). In some embodiments, the target nucleic acid is a single-stranded RNA (ssRNA). In some embodiments, the target nucleic acid is a double -stranded RNA (dsRNA). In some embodiments, the sequence -specificity requires a complete match of the spacer sequence in the RNA guide to the target substrate. In other embodiments, the sequence specificity requires a partial (contiguous or non-contiguous) match of the spacer sequence in the RNA guide to the target substrate.

In some embodiments, the target nucleic acid is present in a cell. In some embodiments, the target nucleic acid is present in the nucleus of the cell. In some embodiments, the target nucleic acid is endogenous to the cell. In some embodiments, the target nucleic acid is a genomic DNA. In some embodiments, the target nucleic acid is a chromosomal DNA. In one embodiment, the target nucleic acid is an extrachromosomal nucleic acid. In some embodiments, the target nucleic acid is a protein-coding gene or a functional region thereof, such as a coding region, or a regulatory element, such as a promoter, enhancer, a 5' or 3' untranslated region, etc. In some embodiments, the target nucleic acid is a non-coding gene, such as transposon, miRNA, tRNA, ribosomal RNA, ribozyme, or lincRNA. In some embodiments, the target nucleic acid is a plasmid.

In some embodiments, the target nucleic acid is exogenous to a cell. In some embodiments, the target nucleic acid is a viral nucleic acid, such as viral DNA or viral RNA. In some embodiments, the target nucleic acid is a horizontally transferred plasmid. In some embodiments, the target nucleic acid is integrated in the genome of the cell. In some embodiments, the target nucleic acid is not integrated in the genome of the cell. In some embodiments, the target nucleic acid is a plasmid in the cell. In some embodiments, the target nucleic acid is present in an extrachromosomal array.

In some embodiments, the target nucleic acid is an isolated nucleic acid, such as an isolated DNA or an isolated RNA. In some embodiments, the target nucleic acid is present in a cell-free environment. In some embodiments, the target nucleic acid is an isolated vector, such as a plasmid. In some embodiments, the target nucleic acid is an ultrapure plasmid.

In some embodiments, the complex becomes activated upon binding to the target substrate. In some embodiments, the activated complex exhibits “multiple turnover” activity, whereby upon acting on (e.g., cleaving) the target nucleic acid, the activated complex remains in an activated state. In some embodiments, the activated complex exhibits “single turnover” activity, whereby upon acting on the target nucleic acid, the complex reverts to an inactive state.

In some embodiments, a nuclease described herein binds to a target nucleic acid at a sequence defined by the region of complementarity between the RNA guide and the target nucleic acid.

In some embodiments, a nuclease described herein targets a sequence adjacent to a PAM sequence. In some embodiments, the PAM sequence of a nuclease described herein is located directly upstream of the target sequence of the target nucleic acid (e.g., directly 5’ of the target sequence). In some embodiments, the PAM sequence of a nuclease described herein is located directly 5 ’ of the non-complementary strand (e.g., non-target strand) of the target nucleic acid. As used herein, the “complementary strand” of the target hybridizes to the RNA guide. As used herein, the “non-complementary strand” of the target does not directly hybridize to the RNA.

In some embodiments, a nuclease described herein cleaves ssDNA. In some embodiments, a nuclease described herein cleaves dsDNA. In some embodiments, a nuclease described herein is a nickase (e.g., the nuclease cleaves one strand of a double-stranded target nucleic acid).

In some embodiments, a nuclease of the present invention has enzymatic activity, e.g., nuclease activity, over a broad range of pH conditions. In some embodiments, the nuclease has enzymatic activity, e.g., nuclease activity, at a pH of from about 3.0 to about 12.0. In some embodiments, the nuclease has enzymatic activity at a pH of from about 4.0 to about 10.5. In some embodiments, the nuclease has enzymatic activity at a pH of from about 5.5 to about 8.5. In some embodiments, the nuclease has enzymatic activity at a pH of from about 6.0 to about 8.0. In some embodiments, the nuclease has enzymatic activity at a pH of about 7.0.

In some embodiments, a nuclease of the present invention has enzymatic activity, e.g., nuclease activity, at a temperature range of from about 10° C to about 100° C. In some embodiments, a nuclease of the present invention has enzymatic activity at a temperature range from about 20° C to about 90° C. In some embodiments, a nuclease of the present invention has enzymatic activity at a temperature of about 20° C to about 25° C or at a temperature of about 37° C.

In some embodiments wherein a nuclease of the present invention induces double-stranded breaks or single -stranded breaks in a target nucleic acid, (e.g. genomic DNA), the double-stranded break can stimulate cellular endogenous DNA-repair pathways, including Homology Directed Recombination (HDR), Non-Homologous End Joining (NHEJ), or Alternative Non-Homologues End-Joining (A-NHEJ). NHEJ can repair cleaved target nucleic acid without the need for a homologous template. This can result in deletion or insertion of one or more nucleotides at the target locus. HDR can occur with a homologous template, such as the donor DNA. The homologous template can comprise sequences that are homologous to sequences flanking the target nucleic acid cleavage site. In some cases, HDR can insert an exogenous polynucleotide sequence into the cleave target locus. The modifications of the target DNA due to NHEJ and/or HDR can lead to, for example, mutations, deletions, alterations, integrations, gene correction, gene replacement, gene tagging, transgene knock-in, gene disruption, and/or gene knock-outs.

In some embodiments, binding of a nuclease/RNA guide complex to a target locus in a cell recruits one or more endogenous cellular molecules or pathways other than DNA repair pathways to modify the target nucleic acid. In some embodiments, binding of a nuclease/RNA guide complex blocks access of one or more endogenous cellular molecules or pathways to the target nucleic acid, thereby modifying the target nucleic acid. For example, binding of a nuclease/RNA guide complex may block endogenous transcription or translation machinery to decrease the expression of the target nucleic acid. Variants

In some embodiments, the present invention includes variants of a nuclease described herein. In some embodiments, a nuclease described herein can be mutated at one or more amino acid residues to modify one or more functional activities. For example, in some embodiments, a nuclease of the present invention is mutated at one or more amino acid residues to modify its nuclease activity (e.g., cleavage activity). For example, in some embodiments, a nuclease may comprise one or more mutations that increase the ability of the nuclease to cleave a target nucleic acid. In some embodiments, a nuclease is mutated at one or more amino acid residues to modify its ability to functionally associate with an RNA guide. In some embodiments, a nuclease is mutated at one or more amino acid residues to modify its ability to functionally associate with a target nucleic acid.

In some embodiments, a variant nuclease has a conservative or non-conservative amino acid substitution, deletion or addition. In some embodiments, the variant nuclease has a silent substitution, deletion or addition, or a conservative substitution, none of which alter the polypeptide activity of the present invention. Typical examples of the conservative substitution include substitution whereby one amino acid is exchanged for another, such as exchange among aliphatic amino acids Ala, Vai, Leu and lie, exchange between hydroxyl residues Ser and Thr, exchange between acidic residues Asp and Glu, substitution between amide residues Asn and Gin, exchange between basic residues Lys and Arg, and substitution between aromatic residues Phe and Tyr. In some embodiments, one or more residues of a nuclease disclosed herein are mutated to an Arg residue. In some embodiments, one or more residues of a nuclease disclosed herein are mutated to a Gly residue.

A variety of methods are known in the art that are suitable for generating modified polynucleotides that encode variant nucleases of the invention, including, but not limited to, for example, site-saturation mutagenesis, scanning mutagenesis, insertional mutagenesis, deletion mutagenesis, random mutagenesis, site-directed mutagenesis, and directed-evolution, as well as various other recombinatorial approaches. Methods for making modified polynucleotides and proteins (e.g., nucleases) include DNA shuffling methodologies, methods based on non-homologous recombination of genes, such as ITCHY (See, Ostermeier et al., 7:2139-44 [1999]), SCRACHY (See, Lutz et al. 98: 11248-53 [2001]), SHIPREC (See, Sieber et al., 19:456-60 [2001]), and NRR (See, Bittker et al., 20: 1024-9 [2001]; Bittker et al., 101:7011-6 [2004]), and methods that rely on the use of oligonucleotides to insert random and targeted mutations, deletions and/or insertions (See, Ness et al., 20: 1251-5 [2002]; Coco et al., 20: 1246-50 [2002]; Zha et al., 4:34-9 [2003]; Glaser et al., 149:3903-13 [1992]).

In some embodiments, a nuclease of the present invention comprises an alteration at one or more (e.g., several) amino acids in the nuclease, wherein at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,

122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,

143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 162,

164, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183,

184, 185, 186, 187, 188, 189, 190, 191, 193, 194, 195, 196, 197, 198, 199, 200, or more amino acids are altered. In one embodiment, the alteration is relative to a parent polypeptide, wherein the alteration comprises one or more substitutions, insertions, deletions, and/or additions in the nuclease relative to the parent polypeptide.

As used herein, a “biologically active portion” is a portion that maintains the function (e.g. completely, partially, minimally) of a nuclease (e.g., a “minimal” or “core” domain). In some embodiments, a nuclease fusion protein is useful in the methods described herein. Accordingly, in some embodiments, a nucleic acid encoding the fusion nuclease is described herein. In some embodiments, all or a portion of one or more components of the nuclease fusion protein are encoded in a single nucleic acid sequence.

Although the changes described herein may be one or more amino acid changes, changes to a nuclease may also be of a substantive nature, such as fusion of polypeptides as amino- and/or carboxyl- terminal extensions. For example, nuclease may contain additional peptides, e.g., one or more peptides. Examples of additional peptides may include epitope peptides for labelling, such as a polyhistidine tag (His- tag), Myc, and FLAG. In some embodiments, a nuclease described herein can be fused to a detectable moiety such as a fluorescent protein (e.g., green fluorescent protein (GFP) or yellow fluorescent protein (YFP)).

A nuclease described herein can be modified to have diminished nuclease activity, e.g., nuclease inactivation of at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or 100%, as compared to a reference nuclease. Nuclease activity can be diminished by several methods known in the art, e.g., introducing mutations into the RuvC domain (e.g, one or more catalytic residues of the RuvC domain).

In some embodiments, the nuclease described herein can be self-inactivating. See, Epstein et al., “Engineering a Self-Inactivating CRISPR System for AAV Vectors,” Mol. Ther., 24 (2016): S50, which is incorporated by reference in its entirety.

Nucleic acid molecules encoding the nucleases described herein can further be codon-optimized. The nucleic acid can be codon-optimized for use in a particular host cell, such as a bacterial cell or a mammalian cell. Targeting Moiety

In some embodiments, the composition described herein comprises a targeting moiety.

The targeting moiety may be substantially identical to a reference nucleic acid sequence if the targeting moiety comprises a sequence having least about 60%, least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 99.5% sequence identity to the reference nucleic acid sequence. The percent identity between two such nucleic acids can be determined manually by inspection of the two optimally aligned nucleic acid sequences or by using software programs or algorithms (e.g., BLAST, ALIGN, CLUSTAL) using standard parameters. One indication that two nucleic acid sequences are substantially identical is that the two nucleic acid molecules hybridize to each other under stringent conditions (e.g., within a range of medium to high stringency).

In some embodiments, the targeting moiety has at least about 60%, least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 99.5% sequence identity to the reference nucleic acid sequence.

RNA Guide Sequence

In some embodiments, the targeting moiety comprises, or is, an RNA guide sequence. In some embodiments, the RNA guide sequence directs a nuclease described herein to a particular nucleic acid sequence. Those skilled in the art reading the below examples of particular kinds of RNA guide sequences will understand that, in some embodiments, an RNA guide sequence is site-specific. That is, in some embodiments, an RNA guide sequence associates specifically with one or more target nucleic acid sequences (e.g., specific DNA or genomic DNA sequences) and not to non-targeted nucleic acid sequences (e.g., non-specific DNA or random sequences).

In some embodiments, the composition as described herein comprises an RNA guide sequence that associates with a nuclease described herein and directs a nuclease to a target nucleic acid sequence (e.g., DNA). The RNA guide sequence may associate with a nucleic acid sequence and alter functionality of a nuclease (e.g., alters affinity of the nuclease to a molecule, e.g., at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more).

The RNA guide sequence may target (e.g., associate with, be directed to, contact, or bind) one or more nucleotides of a sequence, e.g., a site-specific sequence or a site-specific target. In some embodiments, a nuclease (e.g., a nuclease plus an RNA guide) is activated upon binding to a nucleic acid substrate that is complementary to a spacer sequence in the RNA guide (e.g., a sequence-specific substrate or target nucleic acid).

In some embodiments, an RNA guide sequence comprises a spacer sequence. In some embodiments, the spacer sequence of the RNA guide sequence may be generally designed to have a length of between 15 and 50 nucleotides and be complementary to a specific nucleic acid sequence. In some embodiments, the spacer is about 15-20 nucleotides in length, about 20-25 nucleotides in length, about 25- 30 nucleotides in length, about 30-35 nucleotides in length, about 35-40 nucleotides in length, about 40-45 nucleotides in length, or about 45-50 nucleotides in length. In some particular embodiments, the RNA guide sequence may be designed to be complementary to a specific DNA strand, e.g., of a genomic locus. In some embodiments, the spacer sequence is designed to be complementary to a specific DNA strand, e.g., of a genomic locus.

In certain embodiments, the RNA guide sequence comprises a direct repeat sequence linked to a spacer sequence. In some embodiments, the RNA guide sequence includes a direct repeat sequence and a spacer sequence or a direct repeat-spacer-direct repeat sequence. In some embodiments, the RNA guide sequence includes a truncated (i.e., processed) direct repeat sequence and a spacer sequence, which is typical of processed or mature crRNA. Exemplary direct repeat sequences (e.g., exemplary unprocessed direct repeat sequences) are provided in Table 1. In some embodiments, the spacer sequence comprises from about 10 nucleotides to about 60 nucleotides. Exemplary spacer sequences are provided in Table 1. In some embodiments, a nuclease forms a complex with the RNA guide sequence, and the RNA guide sequence directs the complex to associate with site-specific target nucleic acid that is complementary to at least a portion of the RNA guide sequence.

In some embodiments, the RNA guide sequence comprises a sequence, e.g., RNA sequence, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% complementary to a target nucleic acid sequence. In some embodiments, the RNA guide sequence comprises a sequence at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% complementary to a DNA sequence. In some embodiments, the RNA guide sequence comprises a sequence at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% complementary to a target nucleic acid sequence. In some embodiments, the RNA guide sequence comprises a sequence at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% complementary to a genomic sequence. In some embodiments, the RNA guide sequence comprises a sequence complementary to or a sequence comprising at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% complementarity to a genomic sequence.

In some embodiments, an RNA guide (e.g., the spacer of the RNA guide) of the present invention binds a target adjacent to a PAM. In some embodiments, a nuclease described herein includes one or more (e.g., two, three, four, five, six, seven, eight, or more) RNA guide sequences, e.g., RNA guides.

In some embodiments, the RNA guide has an architecture similar to, for example, RNA guides described in International Publication Nos. WO 2014/093622 and WO 2015/070083, the entire contents of each of which are incorporated herein by reference.

In some embodiments, an RNA guide sequence of the present invention comprises a direct repeat sequence having 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat sequence in Column 2 of Table 1, or to a portion thereof. In some embodiments, an RNA guide of the present invention comprises a direct repeat sequence having greater than 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identity to, or having 100% identity to, any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat sequence in Column 2 of Table 1, or to a portion thereof.

In some embodiments, a CRISPR-associated protein and an RNA guide (e.g., an RNA guide comprising a direct repeat and a spacer) form a complex. In some embodiments, a CRISPR-associated protein and an RNA guide (e.g., an RNA guide comprising direct repeat-spacer-direct repeat sequence or pre-crRNA) form a complex. In some embodiments, the complex binds a target nucleic acid.

In some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1, and the direct repeat sequence comprises a nucleotide sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the nucleotide sequence of any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat in Column 2 of Table 1, or to a portion of said sequence. For example, in some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of SEQ ID NO: 1, and the direct repeat sequence comprises a nucleotide sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the nucleotide sequence of SEQ ID NO: 2 or SEQ ID NO: 3 or to a portion of the nucleotide sequence of SEQ ID NO: 2 or SEQ ID NO: 3.

Transactivating RNA (tracrRNA)

In addition to an effector protein and an RNA guide (e.g., a crRNA), some CRISPR systems also include an additional small RNA (which activates robust enzymatic activity of the effector protein) referred to as a transactivating RNA (tracrRNA). Such tracrRNAs typically include a complementary region that hybridizes to the crRNA. The crRNA-tracrRNA hybrid forms a complex with an effector resulting in the activation of programmable enzymatic activity.

In some embodiments, the RNA guide further comprises a trans-activating RNA (tracrRNA). In some embodiments, the RNA guide forms a complex (e.g., a duplex) with the tracrRNA. In some embodiments, an RNA guide is fused to a tracrRNA. The term single-guide RNA (sgRNA) is used herein to refer to an RNA guide -tracrRNA fusion. In some embodiments, the RNA guide-tracrRNA duplex or sgRNA binds to a CRISPR-associated protein.

TracrRNA sequences can be identified by searching genomic sequences flanking CRISPR arrays for short sequence motifs that are homologous to the direct repeat portion of the crRNA. Search methods include exact or degenerate sequence matching for the complete direct repeat (DR) or DR subsequences. For example, a DR of length n nucleotides can be decomposed into a set of overlapping 6-10 nt kmers. These kmers can be aligned to sequences flanking a CRISPR locus, and regions of homology with 1 or more kmer alignments can be identified as DR homology regions for experimental validation as tracrRNAs. Exemplary kmers are provided in Table 1 and referred to as “direct repeat homology” sequences and exemplary DR homology regions are provided in Table 1 and referred to as “direct repeat homologycontaining” sequences.

Alternatively, RNA cofold free energy can be calculated for the complete DR or DR subsequences and short kmer sequences from the genomic sequence flanking the elements of a CRISPR system. Flanking sequence elements with low minimum free energy structures can be identified as DR homology regions for experimental validation as tracrRNAs.

TracrRNA elements frequently occur within close proximity to CRISPR associated genes or a CRISPR array. As an alternative to searching for DR homology regions to identify tracrRNA elements, non-coding sequences flanking CRISPR associated proteins or the CRISPR array can be isolated by cloning or gene synthesis for direct experimental validation of tracrRNAs.

Experimental validation of tracrRNA elements can be performed using small RNA sequencing of the host organism for a CRISPR system or synthetic sequences expressed heterologously in non-native species. Alignment of small RNA sequences from the originating genomic locus can be used to identify expressed RNA products containing DR homology regions and sterotyped processing typical of complete tracrRNA elements.

Complete tracrRNA candidates identified by RNA sequencing can be validated in vitro or in vivo by expressing the crRNA and effector in combination with or without the tracrRNA candidate, and monitoring the activation of effector enzymatic activity. In engineered constructs, the expression of tracrRNAs can be driven by promoters including, but not limited to U6, Ul, and Hl promoters for expression in mammalian cells or J23119 promoter for expression in bacteria.

In some embodiments, a tracrRNA can be fused with a crRNA and expressed as a single RNA guide.

In some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of any one of SEQ ID NOs: 1-3875 referred to as an effector in Column 2 of Table 1, and the tracrRNA sequence comprises a nucleotide sequence, or an RNA transcript thereof, having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to a portion of, or to a portion of the reverse complement of, any one of SEQ ID NOs: 1-3875 referred to as a non-coding sequence in Column 2 of Table 1. For example, in some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of SEQ ID NO: 1, and the tracrRNA sequence comprises a nucleotide sequence, or an RNA transcript thereof, having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to a portion of SEQ ID NO: 5, or to a portion of the reverse complement of SEQ ID NO: 5. In some embodiments, the tracrRNA sequence is encoded by a nucleotide sequence having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to a portion of, or to a portion of the reverse complement of, any one of SEQ ID NOs: 1-3875 referred to as a non-coding sequence in Column 2 of Table 1. In some embodiments, the tracrRNA sequence comprises an RNA transcript of a nucleotide sequence having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to a portion of, or to a portion of the reverse complement of, any one of SEQ ID NOs: 1-3875 referred to as a non-coding sequence in Column 2 of Table 1.

In some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,

96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of any one of SEQ ID NOs: 1-3875 referred to as an effector in Column 2 of Table 1, and the tracrRNA sequence comprises a nucleotide sequence, or an RNA transcript thereof, having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%,

88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to any one of SEQ

ID NOs: 1-3875 referred to as a direct repeat homology-containing sequence in Column 2 of Table 1, to a portion thereof, to the reverse complement thereof, or to a portion of the reverse complement thereof. For example, in some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of SEQ ID NO: 11, and the tracrRNA sequence comprises a nucleotide sequence, or an RNA transcript thereof, having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to SEQ ID NO: 18, to a portion of SEQ ID NO: 18, to the reverse complement of SEQ ID NO: 18, or to a portion of the reverse complement of SEQ ID NO: 18. In some embodiments, the tracrRNA sequence is encoded by a nucleotide sequence having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to any one of SEQ ID NOs: 1-3875 referred to as a direct repeat homology-containing sequence in Column 2 of Table 1, to a portion thereof, to the reverse complement thereof, or to a portion of the reverse complement thereof. In some embodiments, the tracrRNA sequence comprises an RNA transcript of a nucleotide sequence having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to any one of SEQ ID NOs: 1-3875 referred to as a direct repeat homology-containing sequence in Column 2 of Table 1, to a portion thereof, to the reverse complement thereof, or to a portion of the reverse complement thereof.

In some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of any one of SEQ ID NOs: 1-3875 referred to as an effector in Column 2 of Table 1, and the tracrRNA sequence comprises a nucleotide sequence having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to any one or more of SEQ ID NOs: 1-3875 referred to as a direct repeat homology sequence in Column 2 of Table 1. For example, in some embodiments, the CRISPR-associated protein comprises an amino acid sequence that is at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identical to the amino acid sequence of SEQ ID NO: 11, and the tracrRNA sequence comprises a nucleotide sequence having at least 80% (e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) identity to SEQ ID NO: 16 and/or SEQ ID NO: 17.

Novel RNA Modulators of Enzymatic Activity In addition to the effector protein and an RNA guide (e.g., a crRNA), some CRISPR systems may also include an additional small RNA to activate or modulate the effector activity, referred to herein as an RNA modulator.

RNA modulators are expected to occur within close proximity to CRISPR-associated genes or a CRISPR array. To identify and validate RNA modulators, non-coding sequences flanking CRISPR- associated proteins or the CRISPR array can be isolated by cloning or gene synthesis for direct experimental validation.

Experimental validation of RNA modulators can be performed using small RNA sequencing of the host organism for a CRISPR system or synthetic sequences expressed heterologously in non-native species. Alignment of small RNA sequences to the originating genomic locus can be used to identify expressed RNA products containing DR homology regions and sterotyped processing.

Candidate RNA modulators identified by RNA sequencing can be validated in vitro or in vivo by expressing a crRNA and an effector in combination with or without the candidate RNA modulator and monitoring alterations in effector enzymatic activity.

In engineered constructs, RNA modulators can be driven by promoters including U6, Ul, and Hl promoters for expression in mammalian cells, or J23119 promoter for expression in bacteria.

In some embodiments, the RNA modulators can be artificially fused with either a crRNA, a tracrRNA, or both and expressed as a single RNA element.

In some embodiments wherein an effector of the present invention forms a dimer, the dimer forms a complex with one or more RNA guide sequences. In some embodiments wherein an effector of the present invention forms a dimer, the dimer forms a complex with one or more tracrRNA sequences. In some embodiments, the dimer forms a complex with one tracrRNA sequence and one RNA guide sequence. In some embodiments, the dimer forms a complex with one tracrRNA sequence and two RNA guide sequences. In some embodiments, the dimer forms a complex with two tracrRNA sequences and one RNA guide sequence. In some embodiments, the dimer forms a complex with two tracrRNA sequences and two RNA guide sequences. In some embodiments, the dimer forms a complex with one sgRNA sequence. In some embodiments, the dimer forms a complex with two sgRNA sequences.

In some embodiments, a homodimer comprising two identical RuvC domains forms a complex with one tracrRNA sequence and one RNA guide sequence. In some embodiments, a heterodimer comprising two non-identical RuvC domains forms a complex with one tracrRNA sequence and one RNA guide sequence. In some embodiments, a homodimer comprising two identical RuvC domains forms a complex with one tracrRNA sequence and two RNA guide sequences. In some embodiments, a heterodimer comprising two non-identical RuvC domains forms a complex with one tracrRNA sequence and two RNA guide sequences. In some embodiments, a homodimer comprising two identical RuvC domains forms a complex with two tracrRNA sequences and one RNA guide sequence. In some embodiments, a heterodimer comprising two non-identical RuvC domains forms a complex with two tracrRNA sequences and one RNA guide sequence. In some embodiments, a homodimer comprising two identical RuvC domains forms a complex with two tracrRNA sequences and two RNA guide sequences. In some embodiments, a heterodimer comprising two non-identical RuvC domains forms a complex with two tracrRNA sequences and two RNA guide sequences. In some embodiments, a homodimer comprising two identical RuvC domains forms a complex with one sgRNA sequence. In some embodiments, a heterodimer comprising two non-identical RuvC domains forms a complex with one sgRNA sequence. In some embodiments, a homodimer comprising two identical RuvC domains forms a complex with two sgRNA sequences. In some embodiments, a heterodimer comprising two non-identical RuvC domains forms a complex with two sgRNA sequences.

Unless otherwise noted, all compositions and nucleases provided herein are made in reference to the active level of that composition or nuclease, and are exclusive of impurities, for example, residual solvents or by-products, which may be present in commercially available sources. Nuclease component weights are based on total active protein. All percentages and ratios are calculated by weight unless otherwise indicated. All percentages and ratios are calculated based on the total composition unless otherwise indicated. In the exemplified composition, the nuclease levels are expressed by pure enzyme by weight of the total composition and unless otherwise specified, the ingredients are expressed by weight of the total compositions.

Modifications

The RNA guide sequence, tracrRNA sequence, sgRNA sequence, or any of the nucleic acid sequences encoding a nuclease may include one or more covalent modifications with respect to a reference sequence, in particular the parent polyribonucleotide, which are included within the scope of this invention.

Exemplary modifications can include any modification to the sugar, the nucleobase, the intemucleoside linkage (e.g. to a linking phosphate/to a phosphodiester linkage/to the phosphodiester backbone), and any combination thereof. Some of the exemplary modifications provided herein are described in detail below.

The RNA guide sequence, tracrRNA sequence, sgRNA sequence, or any of the nucleic acid sequences encoding components of a nuclease may include any useful modification, such as to the sugar, the nucleobase, or the intemucleoside linkage (e.g. to a linking phosphate/to a phosphodiester linkage/to the phosphodiester backbone). One or more atoms of a pyrimidine nucleobase may be replaced or substituted with optionally substituted amino, optionally substituted thiol, optionally substituted alkyl (e.g., methyl or ethyl), or halo (e.g., chloro or fluoro). In certain embodiments, modifications (e.g., one or more modifications) are present in each of the sugar and the intemucleoside linkage. Modifications may be modifications of ribonucleic acids (RNAs) to deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs) or hybrids thereof). Additional modifications are described herein.

In some embodiments, the modification may include a chemical or cellular induced modification. For example, some nonlimiting examples of intracellular RNA modifications are described by Lewis and Pan in “RNA modifications and structures cooperate to guide RNA-protein interactions” from Nat Reviews Mol Cell Biol, 2017, 18:202-210.

Different sugar modifications, nucleotide modifications, and/or intemucleoside linkages (e.g., backbone structures) may exist at various positions in the sequence. One of ordinary skill in the art will appreciate that the nucleotide analogs or other modification(s) may be located at any position(s) of the sequence, such that the function of the sequence is not substantially decreased. The sequence may include from about 1% to about 100% modified nucleotides (either in relation to overall nucleotide content, or in relation to one or more types of nucleotide, i.e. any one or more of A, G, U or C) or any intervening percentage (e.g., from l% to 20%>, from l% to 25%, from l% to 50%, from l% to 60%, from l% to 70%, from 1% to 80%, from 1% to 90%, from 1% to 95%, from 10% to 20%, from 10% to 25%, from 10% to 50%, from 10% to 60%, from 10% to 70%, from 10% to 80%, from 10% to 90%, from 10% to 95%, from 10% to 100%, from 20% to 25%, from 20% to 50%, from 20% to 60%, from 20% to 70%, from 20% to 80%, from 20% to 90%, from 20% to 95%, from 20% to 100%, from 50% to 60%, from 50% to 70%, from 50% to 80%, from 50% to 90%, from 50% to 95%, from 50% to 100%, from 70% to 80%, from 70% to 90%, from 70% to 95%, from 70% to 100%, from 80% to 90%, from 80% to 95%, from 80% to 100%, from 90% to 95%, from 90% to 100%, and from 95% to 100%).

In some embodiments, sugar modifications (e.g., at the 2’ position or 4’ position) or replacement of the sugar at one or more ribonucleotides of the sequence may, as well as backbone modifications, include modification or replacement of the phosphodiester linkages. Specific examples of a sequence include, but are not limited to, sequences including modified backbones or no natural intemucleoside linkages such as intemucleoside modifications, including modification or replacement of the phosphodiester linkages. Sequences having modified backbones include, among others, those that do not have a phosphoms atom in the backbone. For the purposes of this application, and as sometimes referenced in the art, modified RNAs that do not have a phosphoms atom in their intemucleoside backbone can also be considered to be oligonucleosides. In particular embodiments, a sequence will include ribonucleotides with a phosphoms atom in its intemucleoside backbone.

Modified sequence backbones may include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates such as 3 ’-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates such as 3 ’-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3 ’-5’ linkages, 2 ’-5’ linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3’-5’ to 5’-3’ or 2’-5’ to 5’-2’. Various salts, mixed salts and free acid forms are also included. In some embodiments, the sequence may be negatively or positively charged.

The modified nucleotides, which may be incorporated into the sequence, can be modified on the intemucleoside linkage (e.g., phosphate backbone). Herein, in the context of the polynucleotide backbone, the phrases “phosphate” and “phosphodiester” are used interchangeably. Backbone phosphate groups can be modified by replacing one or more of the oxygen atoms with a different substituent. Further, the modified nucleosides and nucleotides can include the wholesale replacement of an unmodified phosphate moiety with another intemucleoside linkage as described herein. Examples of modified phosphate groups include, but are not limited to, phosphorothioate, phosphoroselenates, boranophosphates, boranophosphate esters, hydrogen phosphonates, phosphoramidates, phosphorodiamidates, alkyl or aryl phosphonates, and phosphotriesters. Phosphorodithioates have both non-linking oxygens replaced by sulfur. The phosphate linker can also be modified by the replacement of a linking oxygen with nitrogen (bridged phosphoramidates), sulfur (bridged phosphorothioates), and carbon (bridged methylene-phosphonates).

The a-thio substituted phosphate moiety is provided to confer stability to RNA and DNA polymers through the unnatural phosphorothioate backbone linkages. Phosphorothioate DNA and RNA have increased nuclease resistance and subsequently a longer half-life in a cellular environment.

In specific embodiments, a modified nucleoside includes an alpha-thio-nucleoside (e.g., 5’-O-(l- thiophosphate)-adenosine, 5 ’-O-( 1 -thiophosphate)-cytidine (a-thio-cytidine), 5 ’-O-( 1 -thiophosphate)- guanosine, 5’-O-(l-thiophosphate)-uridine, or 5’-O-(l-thiophosphate)-pseudouridine).

Other intemucleoside linkages that may be employed according to the present invention, including intemucleoside linkages which do not contain a phosphorous atom, are described herein.

In some embodiments, the sequence may include one or more cytotoxic nucleosides. For example, cytotoxic nucleosides may be incorporated into sequence, such as bifunctional modification. Cytotoxic nucleoside may include, but are not limited to, adenosine arabinoside, 5 -azacytidine, 4’-thio-aracytidine, cyclopentenylcytosine, cladribine, clofarabine, cytarabine, cytosine arabinoside, l-(2-C-cyano-2-deoxy- beta-D-arabino-pentofuranosyl)-cytosine, decitabine, 5-fluorouracil, fludarabine, floxuridine, gemcitabine, a combination of tegafur and uracil, tegafur ((RS)-5 -fluoro- l-(tetrahydrofuran-2-yl)pyrimidine- 2,4(lH,3H)-dione), troxacitabine, tezacitabine, 2 ’-deoxy-2’ -methylidenecytidine (DMDC), and 6- mercaptopurine. Additional examples include fludarabine phosphate, N4-behenoyl-l-beta-D- arabinofuranosylcytosine, N4-octadecyl- 1 -beta-D-arabinofuranosylcytosine, N4-palmitoyl- 1 -(2-C-cyano- 2-deoxy-beta-D-arabino-pentofuranosyl) cytosine, and P-4055 (cytarabine 5’-elaidic acid ester).

In some embodiments, the sequence includes one or more post-transcriptional modifications (e.g., capping, cleavage, polyadenylation, splicing, poly-A sequence, methylation, acylation, phosphorylation, methylation of lysine and arginine residues, acetylation, and nitrosylation of thiol groups and tyrosine residues, etc.). The one or more post-transcriptional modifications can be any post-transcriptional modification, such as any of the more than one hundred different nucleoside modifications that have been identified in RNA (Rozenski, J, Crain, P, and McCloskey, J. (1999). The RNA Modification Database: 1999 update. Nucl Acids Res 27: 196-197) In some embodiments, the first isolated nucleic acid comprises messenger RNA (mRNA). In some embodiments, the mRNA comprises at least one nucleoside selected from the group consisting of pyridin-4-one ribonucleoside, 5 -aza-uridine, 2-thio-5 -aza-uridine, 2- thiouridine, 4-thio-pseudouridine, 2-thio-pseudouridine, 5 -hydroxyuridine, 3 -methyluridine, 5- carboxymethyl -uridine, 1 -carboxymethyl-pseudouridine, 5 -propynyl-uridine, 1 -propynyl -pseudouridine, 5-taurinomethyluridine, I-taurinomethyl -pseudouridine, 5-taurinomethyl-2-thio-uridine, I-taurinomethyl- 4-thio-uridine, 5-methyl -uridine, 1 -methyl -pseudouridine, 4-thio-l -methyl -pseudouridine, 2-thio-l- methyl-pseudouridine, 1 -methyl- 1 -deaza-pseudouridine, 2-thio- 1 -methyl- 1 -deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2- methoxyuridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, and 4-methoxy-2-thio- pseudouridine. In some embodiments, the mRNA comprises at least one nucleoside selected from the group consisting of 5 -aza-cytidine, pseudoisocytidine, 3-methyl-cytidine, N4-acetylcytidine, 5 -formylcytidine, N4-methylcytidine, 5 -hydroxymethylcytidine, I-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo- pseudoisocytidine, 2-thio-cytidine, 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-l -methylpseudoisocytidine, 4-thio- 1 -methyl- 1 -deaza-pseudoisocytidine, 1 -methyl- 1 -deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy- cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, and 4-methoxy- I-methyl- pseudoisocytidine. In some embodiments, the mRNA comprises at least one nucleoside selected from the group consisting of 2-aminopurine, 2, 6-diaminopurine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza- 2-aminopurine, 7-deaza-8-aza-2-aminopurine, 7-deaza-2, 6-diaminopurine, 7-deaza-8-aza-2,6- diaminopurine, 1 -methyladenosine, N6-methyladenosine, N6-isopentenyladenosine, N6-(cis- hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine, N6- glycinylcarbamoyladenosine, N6-threonylcarbamoyladenosine, 2-methylthio-N6-threonyl carbamoyladenosine, N6,N6-dimethyladenosine, 7-methyladenine, 2-methylthio-adenine, and 2-methoxy- adenine. In some embodiments, mRNA comprises at least one nucleoside selected from the group consisting of inosine, 1 -methyl -inosine, wyosine, wybutosine, 7-deaza-guanosine, 7-deaza-8-aza- guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl- guanosine, 6-thio-7-methyl-guanosine, 7-methylinosine, 6-methoxy-guanosine, 1-methylguanosine, N2- methylguanosine, N2,N2-dimethylguanosine, 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, l-methyl-6- thio-guanosine, N2-methyl-6-thio-guanosine, and N2,N2-dimethyl-6-thio-guanosine.

The sequence may or may not be uniformly modified along the entire length of the molecule. For example, one or more or all types of nucleotide (e.g., naturally-occurring nucleotides, purine or pyrimidine, or any one or more or all of A, G, U, C, I, pU) may or may not be uniformly modified in the sequence, or in a given predetermined sequence region thereof. In some embodiments, the sequence includes a pseudouridine. In some embodiments, the sequence includes an inosine, which may aid in the immune system characterizing the sequence as endogenous versus viral RNAs. The incorporation of inosine may also mediate improved RNA stability/reduced degradation. See for example, Yu, Z. et al. (2015) RNA editing by AD ARI marks dsRNA as “self’. Cell Res. 25, 1283-1284, which is incorporated by reference in its entirety.

VECTORS

The present invention provides a vector for expressing a nuclease described herein or nucleic acids encoding a nuclease described herein may be incorporated into a vector. In some embodiments, a vector of the invention includes a nucleotide sequence encoding a nuclease described herein. In some embodiments, a vector of the invention includes a nucleotide sequence encoding a nuclease described herein.

The present invention also provides a vector that may be used for preparation of a nuclease described herein or compositions comprising a nuclease described herein. In some embodiments, the invention includes the composition or vector described herein in a cell. In some embodiments, the invention includes a method of expressing the composition comprising a nuclease of the present invention, or vector or nucleic acid encoding the nuclease, in a cell. The method may comprise the steps of providing the composition, e.g., vector or nucleic acid, and delivering the composition to the cell.

Expression of natural or synthetic polynucleotides is typically achieved by operably linking a polynucleotide encoding the gene of interest, e.g., nucleotide sequence encoding a nuclease of the present invention, to a promoter and incorporating the construct into an expression vector. The expression vector is not particularly limited as long as it includes a polynucleotide encoding a nuclease of the present invention and can be suitable for replication and integration in eukaryotic cells.

Typical expression vectors include transcription and translation terminators, initiation sequences, and promoters useful for expression of the desired polynucleotide. For example, plasmid vectors carrying a recognition sequence for RNA polymerase (pSP64, pBluescript, etc.), may be used. Vectors including those derived from retroviruses such as lentivirus are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells. Examples of vectors include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. The expression vector may be provided to a cell in the form of a viral vector.

Viral vector technology is well known in the art and described in a variety of virology and molecular biology manuals. Viruses which are useful as vectors include, but are not limited to phage viruses, retroviruses, adenoviruses, adeno-associated viruses, herpes viruses, and lentiviruses. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers.

The kind of the vector is not particularly limited, and a vector that can be expressed in host cells can be appropriately selected. To be more specific, depending on the kind of the host cell, a promoter sequence to ensure the expression of a nuclease of the present invention from a polynucleotide is appropriately selected, and this promoter sequence and the polynucleotide are inserted into any of various plasmids etc. for preparation of the expression vector.

Additional promoter elements, e.g., enhancing sequences, regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. Depending on the promoter, it appears that individual elements can function either cooperatively or independently to activate transcription.

Further, the disclosure should not be limited to the use of constitutive promoters. Inducible promoters are also contemplated as part of the disclosure. The use of an inducible promoter provides a molecular switch capable of turning on expression of the polynucleotide sequence which it is operatively linked when such expression is desired or turning off the expression when expression is not desired. Examples of inducible promoters include, but are not limited to a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter.

The expression vector to be introduced can also contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or infected through viral vectors. In other aspects, the selectable marker may be carried on a separate piece of DNA and used in a co-transfection procedure. Both selectable markers and reporter genes may be flanked with appropriate transcriptional control sequences to enable expression in the host cells. Examples of such a marker include a dihydrofolate reductase gene and a neomycin resistance gene for eukaryotic cell culture; and a tetracycline resistance gene and an ampicillin resistance gene for culture of E. coli and other bacteria. By use of such a selection marker, it can be confirmed whether the polynucleotide encoding a nuclease of the present invention has been transferred into the host cells and then expressed without fail.

The preparation method for recombinant expression vectors is not particularly limited, and examples thereof include methods using a plasmid, a phage or a cosmid.

CELLS

The nucleases described herein can be introduced into a variety of cells. In some embodiments, the cell is an isolated cell. In some embodiments the cell is in cell culture. In some embodiments, the cell is ex vivo. In some embodiments, the cell is obtained from a living organism, and maintained in a cell culture. In some embodiments, the cell is a single-cellular organism.

In some embodiments, the cell is a prokaryotic cell. In some embodiments, the cell is a bacterial cell or derived from a bacterial cell. In some embodiments, the cell is an archaeal cell or derived from an archaeal cell.

In some embodiments, the cell is a eukaryotic cell. In some embodiments, the cell is a plant cell or derived from a plant cell. In some embodiments, the cell is a fungal cell or derived from a fungal cell. In some embodiments, the cell is an animal cell or derived from an animal cell. In some embodiments, the cell is an invertebrate cell or derived from an invertebrate cell. In some embodiments, the cell is a vertebrate cell or derived from a vertebrate cell. In some embodiments, the cell is a mammalian cell or derived from a mammalian cell. In some embodiments, the cell is a human cell. In some embodiments, the cell is a zebra fish cell. In some embodiments, the cell is a rodent cell. In some embodiments, the cell is synthetically made, sometimes termed an artificial cell.

In some embodiments, the cell is derived from a cell line. A wide variety of cell lines for tissue culture are known in the art. Examples of cell lines include, but are not limited to, 293T, MF7, K562, HeLa, and transgenic varieties thereof. Cell lines are available from a variety of sources known to those with skill in the art (see, e.g., the American Type Culture Collection (ATCC) (Manassas, Va.)). In some embodiments, a cell transfected with one or more nucleic acids (such as nuclease polypeptide encoding vector and RNA guide) is used to establish a new cell line comprising one or more vector-derived sequences to establish a new cell line comprising modification to the target nucleic acid or target locus. In some embodiments, the cell is an immortal or immortalized cell.

In some embodiments, the method comprises introducing into a host cell one or more nucleic acids comprising nucleotide sequences encoding a DNA-targeting RNA (e.g., RNA guide) and/or the nuclease. In one embodiment, a cell comprising a target DNA is in vitro, in vivo, or ex vivo. In other embodiments, nucleic acids comprising nucleotide sequences encoding a DNA-targeting RNA (e.g., RNA guide) and/or the nuclease include recombinant expression vectors e.g., including but not limited to adeno-associated virus constructs, recombinant adenoviral constructs, recombinant lentiviral constructs, recombinant retroviral constructs, and the like.

In some embodiments, the cell is a primary cell. In some embodiments, the cell is a stem cell such as a totipotent stem cell (e.g., omnipotent), a pluripotent stem cell, a multipotent stem cell, an oligopotent stem cell, or an unipotent stem cell. In some embodiments, the cell is an induced pluripotent stem cell (iPSC) or derived from an iPSC. In some embodiments, the cell is a differentiated cell. For example, in some embodiments, the differentiated cell is a muscle cell (e.g., a myocyte), a fat cell (e.g., an adipocyte), a bone cell (e.g., an osteoblast, osteocyte, osteoclast), a blood cell (e.g., a monocyte, a lymphocyte, a neutrophil, an eosinophil, a basophil, a macrophage, a erythrocyte, or a platelet), a nerve cell (e.g., a neuron), an epithelial cell, an immune cell (e.g., a lymphocyte, a neutrophil, a monocyte, or a macrophage), a liver cell (e.g., a hepatocyte), a fibroblast, or a sex cell. In some embodiments, the cell is a terminally differentiated cell. For example, in some embodiments, the terminally differentiated cell is a neuronal cell, an adipocyte, a cardiomyocyte, a skeletal muscle cell, an epidermal cell, or a gut cell. In some embodiments, the cell is a mammalian cell, e.g., a human cell or a murine cell. In some embodiments, the murine cell is derived from a wild-type mouse, an immunosuppressed mouse, or a disease-specific mouse model.

In some embodiments, a method for modifying a target DNA molecule in a cell is provided. The method comprises contacting the target DNA molecule inside of a cell with a nuclease described herein; and a single molecule DNA-targeting RNA comprising, in 5' to 3' order, a first nucleotide segment that hybridizes with a target sequence of the target DNA molecule; a nucleotide linker; and a second nucleotide segment that hybridizes with the first nucleotide segment to form a double-stranded RNA duplex. The variant polypeptide forms a complex with the single molecule DNA-targeting RNA inside the cell and the target DNA molecule is modified.

PREPARATION

In some embodiments, a nuclease of the present invention can be prepared by (I) culturing bacteria which produce a nuclease of the present invention, isolating the nuclease, and optionally, purifying the nuclease. The nuclease can be also prepared by (II) a known genetic engineering technique, specifically, by isolating a gene encoding a nuclease of the present invention from bacteria, constructing a recombinant expression vector, and then transferring the vector into an appropriate host cell for expression of a recombinant protein. Alternatively, a nuclease can be prepared by (III) an in vitro coupled transcriptiontranslation system. Bacteria that can be used for preparation of a nuclease of the present invention are not particularly limited as long as they can produce a nuclease of the present invention. Some non-limiting examples of the bacteria include E. coli cells described herein.

Methods of Expression

The present invention includes a method for protein expression, comprising translating a nuclease described herein.

In some embodiments, a host cell described herein is used to express a nuclease. The host cell is not particularly limited, and various known cells can be preferably used. Specific examples of the host cell include bacteria such as E. coli, yeasts (budding yeast, Saccharomyces cerevisiae, and fission yeast, Schizosaccharomyces pomhe). nematodes (('aenorhabdiiis elegants)'. Xenopus laevis oocytes, and animal cells (for example, CHO cells, COS cells and HEK293 cells). The method for transferring the expression vector described above into host cells, i.e., the transformation method, is not particularly limited, and known methods such as electroporation, the calcium phosphate method, the liposome method and the DEAE dextran method can be used.

After a host is transformed with the expression vector, the host cells may be cultured, cultivated or bred, for production of a nuclease. After expression of the nuclease, the host cells can be collected and nuclease purified from the cultures etc. according to conventional methods (for example, filtration, centrifugation, cell disruption, gel filtration chromatography, ion exchange chromatography, etc.).

In some embodiments, the methods for nuclease expression comprises translation of at least 5 amino acids, at least 10 amino acids, at least 15 amino acids, at least 20 amino acids, at least 50 amino acids, at least 100 amino acids, at least 150 amino acids, at least 200 amino acids, at least 250 amino acids, at least 300 amino acids, at least 400 amino acids, at least 500 amino acids, at least 600 amino acids, at least 700 amino acids, at least 800 amino acids, at least 900 amino acids, or at least 1000 amino acids of a nuclease. In some embodiments, the methods for protein expression comprises translation of about 5 amino acids, about 10 amino acids, about 15 amino acids, about 20 amino acids, about 50 amino acids, about 100 amino acids, about 150 amino acids, about 200 amino acids, about 250 amino acids, about 300 amino acids, about 400 amino acids, about 500 amino acids, about 600 amino acids, about 700 amino acids, about 800 amino acids, about 900 amino acids, about 1000 amino acids or more of a nuclease.

A variety of methods can be used to determine the level of production of a mature nuclease in a host cell. Such methods include, but are not limited to, for example, methods that utilize either polyclonal or monoclonal antibodies specific for a nuclease. Exemplary methods include, but are not limited to, enzyme-linked immunosorbent assays (ELISA), radioimmunoassays (MA), fluorescent immunoassays (FIA), and fluorescent activated cell sorting (FACS). These and other assays are well known in the art (See, e.g., Maddox et al., J. Exp. Med. 158: 1211 [1983]). The present disclosure provides methods of in vivo expression of a nuclease in a cell, comprising providing a polyribonucleotide encoding the nuclease to a host cell wherein the polyribonucleotide encodes the nuclease, expressing the nuclease in the cell, and obtaining the nuclease from the cell.

DELIVERY

Nucleases, RNA guides, tracrRNA sequences, sgRNA sequences, and/or compositions described herein may be formulated, for example, including a carrier, such as a carrier and/or a polymeric carrier, e.g., a liposome, and delivered by known methods to a cell (e.g., a prokaryotic, eukaryotic, plant, mammalian, etc.). Such methods include, but not limited to, transfection (e.g., lipid-mediated, cationic polymers, calcium phosphate, dendrimers); electroporation or other methods of membrane disruption (e.g., nucleofection), viral delivery (e.g., lentivirus, retrovirus, adenovirus, AAV), microinjection, microprojectile bombardment (“gene gun”), fugene, direct sonic loading, cell squeezing, optical transfection, protoplast fusion, impalefection, magnetofection, exosome-mediated transfer, lipid nanoparticle-mediated transfer, and any combination thereof.

In some embodiments, the method comprises delivering one or more nucleic acids (e.g., nucleic acids encoding a nuclease, RNA guide, donor DNA, etc.), one or more transcripts thereof, and/or a preformed nuclease/RNA guide complex to a cell. Exemplary intracellular delivery methods, include, but are not limited to: viruses or virus-like agents; chemical-based transfection methods, such as those using calcium phosphate, dendrimers, liposomes, or cationic polymers (e.g., DEAE-dextran or polyethylenimine); non-chemical methods, such as microinjection, electroporation, cell squeezing, sonoporation, optical transfection, impalefection, protoplast fusion, bacterial conjugation, delivery of plasmids or transposons; particle -based methods, such as using a gene gun, magnectofection or magnet assisted transfection, particle bombardment; and hybrid methods, such as nucleofection. In some embodiments, the present application further provides cells produced by such methods, and organisms (such as animals, plants, or fungi) comprising or produced from such cells.

KITS

The invention also provides kits that can be used, for example, to carry out a method described herein. In some embodiments, the kits include a nuclease of the present invention. In some embodiments, the kits include a polynucleotide that encodes such a nuclease, and optionally the polynucleotide is comprised within a vector, e.g., as described herein. The kits also can optionally include an RNA guide, e.g., as described herein. The RNA guide of the kits of the invention can be designed to target a sequence of interest, as is known in the art. The nuclease and the RNA guide can be packaged within the same vial or other vessel within a kit or can be packaged in separate vials or other vessels, the contents of which can be mixed prior to use. The kits can additionally include, optionally, a buffer and/or instructions for use of the nuclease and/or RNA guide.

All references and publications cited herein are hereby incorporated by reference.

EXAMPLES

The following examples are provided to further illustrate some embodiments of the present invention but are not intended to limit the scope of the invention; it will be understood by their exemplary nature that other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.

Example 1 - Expression of Effectors in E. coli

In this Example, a system individually comprising an effector of any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 is engineered and introduced into E. coli.

For each effector, a polynucleotide encoding the effector is E. coli codon-optimized, synthesized (Genscript), and individually cloned into a custom expression system derived from pET-28a(+) (EMD- Millipore). The vector includes a polynucleotide encoding each effector under the control of a lac promoter and an E. coli ribosome binding sequence. The vector also includes sites for atracrRNA and an RNA guide or a sgRNA as described herein following the open reading frame for the effector. Plasmid configurations are shown in Table 2. The spacers are designed to target sequences of a pACYC184 plasmid and E. coli essential genes.

Table 2. Bacterial Plasmids.

The plasmids described in Table 2 are electroporated into E. Cloni electrocompetent E. col (Lucigen). The plasmids are either co-transformed with purified pACYC184 plasmid or directly transformed into pACYC184-containing E. Cloni electrocompetent E. coli (Lucigen), plated onto agar containing the proper antibiotics, and incubated for 10-12 hours at 37 °C.

A proxy for activity of the engineered effector systems in E. coli is investigated, wherein bacterial cell death is used as the proxy for system activity. An active effector associated with an RNA guide and tracrRNA or with an sgRNA can disrupt expression of a spacer sequence target, e.g., a pACY C 184 plasmid sequence or an E. coli essential gene, resulting in cell death. Using this proxy, the ability of the effectors disclosed herein can be determined in E. coli.

Example 2 - Expression of Effectors in Mammalian Cells

This Example describes an indel assessment on mammalian targets by the effector of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 introduced into mammalian cells by transient transfection.

The effectors of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 are individually cloned into a pcda3.1 backbone (Invitrogen). The plasmids are then maxi -prepped and diluted to 1 pg/pL. The sgRNA sequences are further individually cloned into a plasmid, purified, and diluted. Targets are selected to be adjacent to PAM sequences for effectors for which a PAM sequence is required.

Approximately 16 hours prior to transfection, 100 pl of 25,000 HEK293T cells in DMEM/10%FBS+Pen/Strep are plated into each well of a 96-well plate. On the day of transfection, the cells are 70-90% confluent. For each well to be transfected, a mixture of 0.5 pl of Lipofectamine 2000 and 9.5 pl of Opti-MEM is prepared and then incubated at room temperature for 5-20 minutes (Solution 1). After incubation, the lipofectamine :OptiMEM mixture is added to a separate mixture containing 182 ng of effector plasmid and 14 ng of sgRNA and water up to 10 pL (Solution 2). In the case of negative controls, the sgRNA is not included in Solution 2. The solution 1 and solution 2 mixtures are mixed by pipetting up and down and then incubated at room temperature for 25 minutes. Following incubation, 20 pL of the Solution 1 and Solution 2 mixture are added dropwise to each well of a 96 well plate containing the cells. 72 hours post transfection, cells are trypsinized by adding 10 pL of TrypLE to the center of each well and incubated for approximately 5 minutes. 100 pL of D10 media is then added to each well and mixed to resuspend cells. The cells are then spun down at 500g for 10 minutes, and the supernatant is discarded. QuickExtract buffer is added to 1/5 the amount of the original cell suspension volume. Cells are incubated at 65°C for 15 minutes, 68°C for 15 minutes, and 98°C for 10 minutes.

Samples for Next Generation Sequencing are prepared by two rounds of PCR. The first round (PCR1) is used to amplify specific genomic regions depending on the target. PCR1 products are purified by column purification. Round 2 PCR (PCR2) is done to add Illumina adapters and indexes. Reactions are then pooled and purified by column purification. Sequencing runs are done with a 150 cycle NextSeq v2.5 mid or high output kit.

Presence of indels at the analyzed targets, as determined by NGS, are indicative of mammalian activity of the effectors of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1.

Enumerated Embodiments The following enumerated embodiments are provided, the numbering of which is not to be construed as designating levels of importance.

Enumerated embodiment 1 provides a composition comprising:

(a) a nuclease or a nucleic acid encoding the nuclease, wherein the nuclease comprises an amino acid sequence with at least 80% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 ; and

(b) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid.

Enumerated embodiment 2 provides the composition of enumerated embodiment 1, wherein the nuclease comprises a RuvC domain or a split RuvC domain.

Enumerated embodiment 3 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises a catalytic residue.

Enumerated embodiment 4 provides the composition of enumerated embodiment 3, wherein the catalytic residue is aspartic acid or glutamic acid.

Enumerated embodiment 5 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1. Enumerated embodiment 6 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 and the direct repeat sequence comprises a nucleotide sequence with at least 90% or at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat in Column 2 of Table 1, or to a portion of any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat in Column 2 of Table 1 .

Enumerated embodiment 7 provides the composition of any previous enumerated embodiment, wherein the RNA guide further comprises a trans-activating crRNA (tracrRNA) sequence.

Enumerated embodiment 8 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 and the tracrRNA sequence comprises a nucleotide sequence, or an RNA transcript thereof, with at least 90% or at least 95% identity to a portion of any one of SEQ ID NOs: 1-3875 which is referred to as a non-coding sequence in Column 2 of Table 1, to the reverse complement thereof, or to a portion of the reverse complement thereof.

Enumerated embodiment 9 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 and the tracrRNA sequence comprises a nucleotide sequence, or an RNA transcript thereof, with at least 90% or at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat homology-containing sequence in Column 2 of Table 1, to a portion thereof, to the reverse complement thereof, or to a portion of the reverse complement thereof.

Enumerated embodiment 10 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 and the tracrRNA sequence comprises a nucleotide sequence set forth in any one or more of SEQ ID NOs: 1-3875 which is referred to as a direct repeat homology sequence in Column 2 of Table 1.

Enumerated embodiment 11 provides the composition of any one of enumerated embodiments 8- 10, wherein the direct repeat sequence is fused to the tracrRNA sequence.

Enumerated embodiment 12 provides the composition of any previous enumerated embodiment, wherein the RNA guide is a single molecule RNA guide (sgRNA).

Enumerated embodiment 13 provides the composition of any previous enumerated embodiment, wherein the spacer sequence comprises between about 10 nucleotides and about 60 nucleotides in length. Enumerated embodiment 14 provides the composition of any previous enumerated embodiment, wherein the spacer sequence comprises between about 10 nucleotides and about 35 nucleotides in length.

Enumerated embodiment 15 provides the composition of any previous enumerated embodiment, wherein the spacer sequence comprises between about 20 nucleotides and about 25 nucleotides in length.

Enumerated embodiment 16 provides the composition of any previous enumerated embodiment, wherein the target nucleic acid comprises a sequence complementary to a nucleotide sequence in the spacer sequence.

Enumerated embodiment 17 provides the composition of any previous enumerated embodiment, wherein the target nucleic acid is adjacent to a protospacer adjacent motif (PAM) sequence.

Enumerated embodiment 18 provides the composition of any previous enumerated embodiment, wherein the composition further comprises a modulator RNA.

Enumerated embodiment 19 provides the composition of any previous enumerated embodiment, wherein the nuclease comprises the amino acid sequence set forth in any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 .

Enumerated embodiment 20 provides the composition of any previous enumerated embodiment, wherein the nuclease cleaves the target nucleic acid.

Enumerated embodiment 21 provides the composition of any previous enumerated embodiment, wherein the target nucleic acid is single -stranded DNA or double -stranded DNA.

Enumerated embodiment 22 provides the composition of any previous enumerated embodiment, wherein the target nucleic acid is double-stranded DNA and wherein the nuclease cleaves one strand of the target sequence or both strands of the target sequence.

Enumerated embodiment 23 provides the composition of any previous enumerated embodiment, wherein the composition comprises at least 10% greater enzymatic activity than that of a reference composition.

Enumerated embodiment 24 provides the composition of enumerated embodiment 23, wherein the enzymatic activity is nuclease activity or nickase activity.

Enumerated embodiment 25 provides the composition of any previous enumerated embodiment, wherein the nuclease further comprises a peptide tag, a fluorescent protein, a base-editing domain, a DNA methylation domain, a histone residue modification domain, a localization factor, a transcription modification factor, a light-gated control factor, a chemically inducible factor, or a chromatin visualization factor.

Enumerated embodiment 26 provides the composition of any previous enumerated embodiment, wherein the nucleic acid encoding the nuclease is codon-optimized for expression in a cell. Enumerated embodiment 27 provides the composition of any previous enumerated embodiment, wherein the nucleic acid encoding the nuclease is operably linked to a promoter.

Enumerated embodiment 28 provides the composition of any previous enumerated embodiment, wherein the nucleic acid encoding the nuclease is in a vector.

Enumerated embodiment 29 provides the composition of any previous enumerated embodiment, wherein the vector comprises a retroviral vector, a lentiviral vector, a phage vector, an adenoviral vector, an adeno-associated vector, or a herpes simplex vector.

Enumerated embodiment 30 provides the composition of any previous enumerated embodiment, wherein the composition is present in a delivery composition comprising a nanoparticle, a liposome, an exosome, a microvesicle, or a gene-gun.

Enumerated embodiment 31 provides a cell comprising the composition of any previous enumerated embodiment.

Enumerated embodiment 32 provides the cell of enumerated embodiment 31, wherein the cell is a eukaryotic cell or a prokaryotic cell.

Enumerated embodiment 33 provides the cell of any previous enumerated embodiment, wherein the cell is a mammalian cell or a plant cell.

Enumerated embodiment 34 provides the cell of any previous enumerated embodiment, wherein the cell is a human cell.

Enumerated embodiment 35 provides a method of binding the composition of any previous enumerated embodiment to the target nucleic acid in a cell, the method comprising:

(a) providing the composition; and

(b) delivering the composition to the cell, wherein the cell comprises the target nucleic acid, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to the target nucleic acid.

Enumerated embodiment 36 provides a method of introducing an indel into a target nucleic acid in a cell, the method comprising:

(a) providing the composition of any previous enumerated embodiment; and

(b) delivering the composition to the cell, wherein recognition of the target nucleic acid by the composition results in a modification of the target nucleic acid.

Enumerated embodiment 37 provides the method of enumerated embodiment 35 or enumerated embodiment 36, wherein delivering the composition to the cell is by transfection.

Enumerated embodiment 38 provides the method of any previous enumerated embodiment, wherein the cell is a eukaryotic cell. Enumerated embodiment 39 provides the method of any previous enumerated embodiment, wherein the cell is a prokaryotic cell.

Enumerated embodiment 40 provides the method of any previous enumerated embodiment, wherein the cell is a human cell.

Other Embodiments

The disclosures of each and every patent, patent application, and publication cited herein are hereby incorporated herein by reference in their entirety. While this invention has been disclosed with reference to specific embodiments, it is apparent that other embodiments and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such embodiments and equivalent variations.

Claims

What is claimed is:

1. A composition comprising:

(a) a nuclease or a nucleic acid encoding the nuclease, wherein the nuclease comprises an amino acid sequence with at least 80% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 ; and

(b) an RNA guide or a nucleic acid encoding the RNA guide, wherein the RNA guide comprises a direct repeat sequence and a spacer sequence, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to a target nucleic acid.

2. The composition of claim 1, wherein the nuclease comprises a RuvC domain or a split RuvC domain.

3. The composition of any previous claim, wherein the nuclease comprises a catalytic residue.

4. The composition of claim 3, wherein the catalytic residue is aspartic acid or glutamic acid.

5. The composition of any previous claim, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1.

6. The composition of any previous claim, wherein the nuclease comprises an amino acid sequence with at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1 and the direct repeat sequence comprises a nucleotide sequence with at least 90% or at least 95% identity to any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat in Column 2 of Table 1 , or to a portion of any one of SEQ ID NOs: 1-3875 which is referred to as a direct repeat in Column 2 of Table 1 .

7. The composition of any previous claim, wherein the RNA guide further comprises a transactivating crRNA (tracrRNA) sequence.

8. Thecompositionofanypreviousclaim,whereinthenucleasecomprisesanaminoacidsequence withatleast95%identitytoanyoneofSEQIDNOs: 1-3875whichisreferredtoasaneffector inColumn2ofTable 1 andthetracrRNAsequencecomprisesanucleotidesequence,oran RNAtranscriptthereof,withatleast90%oratleast95%identitytoaportionofanyoneofSEQ IDNOs: 1-3875whichisreferredtoasanon-codingsequenceinColumn2ofTable 1,tothe reversecomplementthereof, ortoaportionofthereversecomplementthereof. 9. Thecompositionofanypreviousclaim,whereinthenucleasecomprisesanaminoacidsequence withatleast95%identitytoanyoneofSEQIDNOs: 1-3875whichisreferredtoasaneffector inColumn2ofTable 1 andthetracrRNAsequencecomprisesanucleotidesequence,oran RNAtranscriptthereof,withatleast90%oratleast95%identityto anyoneofSEQIDNOs: 1- 3875whichisreferredtoasadirectrepeathomology-containingsequenceinColumn2of Table 1,toaportionthereof,tothereversecomplementthereof,ortoaportionofthereverse complementthereof. 10. Thecompositionofanypreviousclaim,whereinthenucleasecomprisesanaminoacidsequence withatleast95%identitytoanyoneofSEQIDNOs: 1-3875whichisreferredtoasaneffector inColumn2ofTable 1 andthetracrRNAsequencecomprisesanucleotidesequencesetforth inanyoneormoreofSEQIDNOs: 1-3875whichisreferredtoasadirectrepeathomology sequenceinColumn2ofTable 1. 1111. Thecompositionofanyoneofclaims8-10,whereinthedirectrepeatsequenceisfusedtothe tracrRNAsequence. 12. Thecompositionofanypreviousclaim,whereintheRNAguideisasinglemoleculeRNAguide (sgRNA). 13. Thecompositionofanypreviousclaim,whereinthespacersequencecomprisesbetweenabout 10 nucleotidesandabout60nucleotidesinlength. 14. Thecompositionofanypreviousclaim,whereinthespacersequencecomprisesbetweenabout 10 nucleotidesandabout35nucleotidesinlength.

15. The composition of any previous claim, wherein the spacer sequence comprises between about 20 nucleotides and about 25 nucleotides in length.

16. The composition of any previous claim, wherein the target nucleic acid comprises a sequence complementary to a nucleotide sequence in the spacer sequence.

17. The composition of any previous claim, wherein the target nucleic acid is adjacent to a protospacer adjacent motif (PAM) sequence.

18. The composition of any previous claim, wherein the composition further comprises a modulator RNA.

19. The composition of any previous claim, wherein the nuclease comprises the amino acid sequence set forth in any one of SEQ ID NOs: 1-3875 which is referred to as an effector in Column 2 of Table 1.

20. The composition of any previous claim, wherein the nuclease cleaves the target nucleic acid.

21. The composition of any previous claim, wherein the target nucleic acid is single -stranded DNA or double -stranded DNA.

22. The composition of any previous claim, wherein the target nucleic acid is double-stranded DNA and wherein the nuclease cleaves one strand of the target sequence or both strands of the target sequence.

23. The composition of any previous claim, wherein the composition comprises at least 10% greater enzymatic activity than that of a reference composition.

24. The composition of claim 23, wherein the enzymatic activity is nuclease activity or nickase activity.

25. The composition of any previous claim, wherein the nuclease further comprises a peptide tag, a fluorescent protein, a base-editing domain, a DNA methylation domain, a histone residue modification domain, a localization factor, a transcription modification factor, a light-gated control factor, a chemically inducible factor, or a chromatin visualization factor.

26. The composition of any previous claim, wherein the nucleic acid encoding the nuclease is codon- optimized for expression in a cell.

27. The composition of any previous claim, wherein the nucleic acid encoding the nuclease is operably linked to a promoter.

28. The composition of any previous claim, wherein the nucleic acid encoding the nuclease is in a vector.

29. The composition of any previous claim, wherein the vector comprises a retroviral vector, a lentiviral vector, a phage vector, an adenoviral vector, an adeno-associated vector, or a herpes simplex vector.

30. The composition of any previous claim, wherein the composition is present in a delivery composition comprising a nanoparticle, a liposome, an exosome, a microvesicle, or a gene-gun.

31. A cell comprising the composition of any previous claim.

32. The cell of claim 31, wherein the cell is a eukaryotic cell or a prokaryotic cell.

33. The cell of any previous claim, wherein the cell is a mammalian cell or a plant cell.

34. The cell of any previous claim, wherein the cell is a human cell.

35. A method of binding the composition of any previous claim to the target nucleic acid in a cell, the method comprising:

(a) providing the composition; and

(b) delivering the composition to the cell, wherein the cell comprises the target nucleic acid, wherein the nuclease binds to the RNA guide, and wherein the spacer sequence binds to the target nucleic acid.

36. A method of introducing an indel into a target nucleic acid in a cell, the method comprising:

(a) providing the composition of any previous claim; and

(b) delivering the composition to the cell, wherein recognition of the target nucleic acid by the composition results in a modification of the target nucleic acid.

37. The method of claim 35 or claim 36, wherein delivering the composition to the cell is by transfection.

38. The method of any previous claim, wherein the cell is a eukaryotic cell.

39. The method of any previous claim, wherein the cell is a prokaryotic cell.

40. The method of any previous claim, wherein the cell is a human cell.