VARIANT TYPE V CRISPR/CAS EFFECTOR POLYPEPTIDES AND METHODS OF USE THEREOF

INTRODUCTION

Bacterial adaptive immune systems employ CRISPRs (clustered regularly interspaced short palindromic repeats) and CRISPR-associated (Cas) proteins for RNA-guided nucleic acid cleavage. The CRISPR-Cas systems thereby confer adaptive immunity in bacteria and archaea via RNA-guided nucleic acid interference. To provide anti-viral immunity, processed CRISPR array transcripts (crRNAs) assemble with Cas protein-containing surveillance complexes that recognize nucleic acids bearing sequence complementarity to the virus derived segment of the crRNAs, known as the spacer. Class 2 CRISPR-Cas are streamlined versions in which a single Cas protein bound to RNA is responsible for binding to and cleavage of a targeted sequence. The programmable nature of these minimal systems has facilitated their use as a versatile technology for genome editing.

SUMMARY

The present disclosure provides variant type V CRISPR/Cas effector polypeptides, nucleic acids encoding the variant polypeptides, and systems comprising the variant polypeptides or nucleic acids encoding same. The present disclosure provides methods for modifying a target nucleic acid, using a variant polypeptide of the present disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1F provide amino acid sequences of wild-type Lachnospiraceae bacterium Cas12a (Lb Cas12a) (FIG. 1A) and examples of variants (FIG. 1B-1F).

FIG. 2A-2F provide amino acid sequences of wild-type Acidaminococcus sp.BV3L6 Cas12a (FIG. 2A) and examples of variants (FIG. 2B-2F).

FIG. 3A-3F provide amino acid sequences of wild-type Francisella novicida U112 Cas12a (Fn Cas12a) (FIG. 3A) and examples of variants (FIG. 3B-3F).

FIG. 4A-4B provide amino acid sequences of wild-type Porphyromonas macacae Cas12a (FIG. 4A) and an example of a variant (FIG. 4B).

FIG. 5A-5B provide amino acid sequences of wild-type Moraxella bovoculi 237 Cas12a (FIG. 5A) and an example of a variant (FIG. 5B).

FIG. 6A-6B provide amino acid sequences of wild-type Moraxella bovoculi AAX08_00205 Cas12a (FIG. 6A) and an example of a variant (FIG. 6B).

FIG. 7A-7B provide amino acid sequences of wild-type Moraxella bovoculi AAX11_00205 Cas12a (FIG. 7A) and an example of a variant (FIG. 7B).

FIG. 8A-8B provide amino acid sequences of wild-type Thiomicrospira sp.XS5 Cas12a (FIG. 8A) and an example of a variant (FIG. 8B).

FIG. 9A-9B provide amino acid sequences of wild-type Butyrivibrio sp. NC3005 Cas12a (FIG. 9A) and an example of a variant (FIG. 9B).

FIG. 10A-10B provide amino acid sequences of wild-type Brumimicrobium aurantiacum Cas12a (FIG. 10A) and an example of a variant (FIG. 10B).

FIG. 11A-11B provide amino acid sequences of wild-type Porphyromonas crevioricanis Cas12a (FIG. 11A) and an example of a variant (FIG. 11B).

FIG. 12A-12B provide amino acid sequences of wild-type Francisella tularensis Cas12a (Ft Cas12a) (FIG. 12A) and an example of a variant (FIG. 12B).

FIG. 13A-13B provide amino acid sequences of wild-type Eubacterium ventriosum Cas12a (FIG. 13A) and an example of a variant (FIG. 13B).

FIG. 14A-14C provide amino acid sequences of wild-type Alicyclobacillus acidoterrestris Cas12b (FIG. 14A) and examples of variants (FIG. 14B-14C).

FIG. 15A-15C provide amino acid sequences of wild-type Alicyclobacillus kakegawensis Cas12b (FIG. 15A) and examples of variants (FIG. 15B-15C).

FIG. 16A-16C provide amino acid sequences of wild-type Alicyclobacillus macrosporangiidus Cas12b (FIG. 16A) and examples of variants (FIG. 16B-16C).

FIG. 17A-17C provide amino acid sequences of wild-type Alicyclobacillus hesperidum Cas12b (FIG. 17A) and examples of variants (FIG. 17B-17C).

FIG. 18A-18C provide amino acid sequences of wild-type Sulfobacillus thermotolerans Cas12b (FIG. 18A) and examples of variants (FIG. 18B-18C).

FIG. 19A-19C provide amino acid sequences of wild-type Deltaproteobacteria bacterium GWA2_43_19 Cas X (FIG. 19A) and examples of variants (FIG. 19B-19C).

FIG. 20A-20C provide amino acid sequences of wild-type Plantomycetes bacterium (FIG. 20A) and examples of variants (FIG. 20B-20C).

FIGS. 21A and 21B provide examples of crRNAs and a sgRNA (FIG. 21A) and examples of PAM sequences (FIG. 21B).

FIG. 22 depicts structures of examples of type V CRISPR/Cas effector polypeptides and the helix-loop element of examples of type V CRISPR/Cas effector polypeptides.

FIG. 23 depicts schematically the domain organization of Cas12a polypeptides.

FIG. 24 provides examples of mutations in the loop of the helix-loop element of Lb Cas12a (Lb Cpf1) that eliminate trans nuclease (cleavage) activity.

FIG. 25 depicts the effect of mutations in the loop of the helix-loop element of Lb Cas12a (Lb Cpf1) on trans cleavage activity.

DEFINITIONS

The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, terms “polynucleotide” and “nucleic acid” encompass single-stranded DNA; double-stranded DNA; multi-stranded DNA; single-stranded RNA; double-stranded RNA; multi-stranded RNA; genomic DNA; cDNA; DNA-RNA hybrids; and a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.

By “hybridizable” or “complementary” or “substantially complementary” it is meant that a nucleic acid (e.g. RNA, DNA) comprises a sequence of nucleotides that enables it to non-covalently bind, i.e. form Watson-Crick base pairs and/or G/U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence-specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. Standard Watson-Crick base-pairing includes: adenine/adenosine) (A) pairing with thymidine/thymidine (T), A pairing with uracil/uridine (U), and guanine/guanosine) (G) pairing with cytosine/cytidine (C). In addition, for hybridization between two RNA molecules (e.g., dsRNA), and for hybridization of a DNA molecule with an RNA molecule (e.g., when a DNA target nucleic acid base pairs with a guide RNA, etc.): G can also base pair with U. For example, G/U base-pairing is partially responsible for the degeneracy (i.e., redundancy) of the genetic code in the context of tRNA anti-codon base-pairing with codons in mRNA. Thus, in the context of this disclosure, a G (e.g., of a protein-binding segment (e.g., dsRNA duplex) of a guide RNA molecule; of a target nucleic acid (e.g., target DNA) base pairing with a guide RNA) is considered complementary to both a U and to C. For example, when a G/U base-pair can be made at a given nucleotide position of a protein-binding segment (e.g., dsRNA duplex) of a guide RNA molecule, the position is not considered to be non-complementary, but is instead considered to be complementary.

Hybridization requires that the two nucleic acids contain complementary sequences, although mismatches between bases are possible. The conditions appropriate for hybridization between two nucleic acids depend on the length of the nucleic acids and the degree of complementarity, variables well known in the art. The greater the degree of complementarity between two nucleotide sequences, the greater the value of the melting temperature (Tm) for hybrids of nucleic acids having those sequences. Typically, the length for a hybridizable nucleic acid is 8 nucleotides or more (e.g., 10 nucleotides or more, 12 nucleotides or more, 15 nucleotides or more, 20 nucleotides or more, 22 nucleotides or more, 25 nucleotides or more, or 30 nucleotides or more).

It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure or hairpin structure, a ‘bulge’, and the like). A polynucleotide can comprise 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 98% or more, 99% or more, 99.5% or more, or 100% sequence complementarity to a target region within the target nucleic acid sequence to which it will hybridize. For example, an antisense nucleic acid in which 18 of 20 nucleotides of the antisense compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. The remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides. Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined using any convenient method. Example methods include BLAST programs (basic local alignment search tools) and PowerBLAST programs (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656) or by using the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), e.g., using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489).

The terms “peptide,” “polypeptide,” and “protein” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.

“Binding” as used herein (e.g. with reference to an RNA-binding domain of a polypeptide, binding to a target nucleic acid, and the like) refers to a non-covalent interaction between macromolecules (e.g., between a protein and a nucleic acid; between a guide RNA and a target nucleic acid; and the like). While in a state of non-covalent interaction, the macromolecules are said to be “associated” or “interacting” or “binding” (e.g., when a molecule X is said to interact with a molecule Y, it is meant the molecule X binds to molecule Y in a non-covalent manner). Not all components of a binding interaction need be sequence-specific (e.g., contacts with phosphate residues in a DNA backbone), but some portions of a binding interaction may be sequence-specific. Binding interactions are generally characterized by a dissociation constant (K_d) of less than 10⁻⁶M, less than 10⁻⁷M, less than 10⁻⁸M, less than 10⁻⁹M, less than 10⁻¹⁰M, less than 10⁻¹¹M, less than 10⁻¹²M, less than 10⁻¹³M, less than 10⁻¹⁴M, or less than 10⁻¹⁵M. “Affinity” refers to the strength of binding, increased binding affinity being correlated with a lower K_d.

By “binding domain” it is meant a protein domain that is able to bind non-covalently to another molecule. A binding domain can bind to, for example, an RNA molecule (an RNA-binding domain) and/or a protein molecule (a protein-binding domain) In the case of a protein having a protein-binding domain, it can in some cases bind to itself (to form homodimers, homotrimers, etc.) and/or it can bind to one or more regions of a different protein or proteins.

The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide containing side chains consisting of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; a group of amino acids having acidic side chains consists of glutamate and aspartate; and a group of amino acids having sulfur containing side chains consists of cysteine and methionine. Exemplary conservative amino acid substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine-glycine, and asparagine-glutamine

A polynucleotide or polypeptide has a certain percent “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence identity can be determined in a number of different ways. To determine sequence identity, sequences can be aligned using various methods and computer programs (e.g., BLAST, T-COFFEE, MUSCLE, MAFFT, Phyre2, etc.), available over the world wide web at sites including ncbi.nlm.nili.gov/BLAST, ebi.ac.uk/Tools/msa/tcoffee/, ebi.ac.uk/Tools/msa/muscle/, mafft.cbrc.jp/alignment/software/, http://www.sbg.bio.ic.ac.uk/˜phyre2/. See, e.g., Altschul et al. (1990), J. Mol. Bioi. 215:403-10.

The terms “DNA regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate transcription of a non-coding sequence (e.g., guide RNA) or a coding sequence (e.g., protein coding) and/or regulate translation of an encoded polypeptide.

As used herein, a “promoter sequence” is a DNA regulatory region capable of binding RNA polymerase and initiating transcription of a downstream (3′ direction) coding or non-coding sequence. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Various promoters, including inducible promoters, may be used to drive the various nucleic acids (e.g., vectors) of the present disclosure.

The term “naturally-occurring” or “unmodified” or “wild type” as used herein as applied to a nucleic acid, a polypeptide, a cell, or an organism, refers to a nucleic acid, polypeptide, cell, or organism that is found in nature.

“Recombinant,” as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, polymerase chain reaction (PCR) and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. DNA sequences encoding polypeptides can be assembled from cDNA fragments or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5′ or 3′ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “DNA regulatory sequences”, above). Alternatively, DNA sequences encoding RNA (e.g., guide RNA) that is not translated may also be considered recombinant. Thus, e.g., the term “recombinant” nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such is usually done to replace a codon with a codon encoding the same amino acid, a conservative amino acid, or a non-conservative amino acid. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. When a recombinant polynucleotide encodes a polypeptide, the sequence of the encoded polypeptide can be naturally occurring (“wild type”) or can be a variant (e.g., a mutant) of the naturally occurring sequence. Thus, the term “recombinant” polypeptide does not necessarily refer to a polypeptide whose sequence does not naturally occur. Instead, a “recombinant” polypeptide is encoded by a recombinant DNA sequence, but the sequence of the polypeptide can be naturally occurring (“wild type”) or non-naturally occurring (e.g., a variant, a mutant, etc.). Thus, a “recombinant” polypeptide is the result of human intervention, but may have a naturally occurring amino acid sequence.

A “vector” or “expression vector” is a replicon, such as plasmid, phage, virus, or cosmid, to which another DNA segment, i.e. an “insert”, may be attached so as to bring about the replication of the attached segment in a cell.

An “expression cassette” comprises a DNA coding sequence operably linked to a promoter. “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression.

The terms “recombinant expression vector,” or “DNA construct” are used interchangeably herein to refer to a DNA molecule comprising a vector and one insert. Recombinant expression vectors are usually generated for the purpose of expressing and/or propagating the insert(s), or for the construction of other recombinant nucleotide sequences. The insert(s) may or may not be operably linked to a promoter sequence and may or may not be operably linked to DNA regulatory sequences.

“Heterologous,” as used herein, refers to a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively. For example, relative to a variant type V CRISPR/Cas effector polypeptide of the present disclosure, a heterologous polypeptide comprises an amino acid sequence from a protein other than the variant type V CRISPR/Cas effector polypeptide. As another example, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be fused to an active domain from a non-CRISPR/Cas effector protein (e.g., a histone deacetylase), and the sequence of the active domain could be considered a heterologous polypeptide (it is heterologous to the variant type V CRISPR/Cas effector polypeptide).

General methods in molecular and cellular biochemistry can be found in such standard textbooks as Molecular Cloning: A Laboratory Manual, 3rd Ed. (Sambrook et al., HaRBor Laboratory Press 2001); Short Protocols in Molecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons 1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); Nonviral Vectors for Gene Therapy (Wagner et al. eds., Academic Press 1999); Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); Immunology Methods Manual (I. Lefkovits ed., Academic Press 1997); and Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, John Wiley & Sons 1998), the disclosures of which are incorporated herein by reference.

Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.

It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a variant type V CRISPR/Cas effector polypeptide” includes a plurality of such polypeptides and reference to “the guide” includes reference to one or more guide RNAs and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to the invention are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present invention and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.

The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.

DETAILED DESCRIPTION

Variant Type V Crispr/Cas Effector Polypeptides

The present disclosure provides variant type V CRISPR/Cas effector polypeptides. The present disclosure also provides fusion polypeptides comprising: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a heterologous polypeptide (i.e., one or more heterologous polypeptides, where a heterologous polypeptide is also referred to herein as a “fusion partner”).

A wild-type type V CRISPR/Cas protein, e.g., Cas12 proteins such as Cpf1 (Cas12a) and C2c1 (Cas12b), can promiscuously cleave non-targeted single-stranded DNA (ssDNA) once activated by binding of a target DNA (double or single stranded). For example, a wild-type type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12f, Cas12g, Cas12h, or Cas12i) is activated by a guide RNA, which occurs when the guide RNA hybridizes to a target sequence of a target DNA, the protein becomes a nuclease that promiscuously cleaves ssDNAs (i.e., the nuclease cleaves non-target ssDNAs, i.e., ssDNAs to which the guide sequence of the guide RNA does not hybridize). When a type V CRISPR/Cas effector protein is activated by a guide RNA and exhibits on-target cleavage of the target ssDNA, such on-target cleavage is referred to as “cis” cleavage (Li et al (2018) Cell Research 28:491-493).

A variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, binds a target nucleic acid, where the guide RNA comprises a segment that hybridizes to a complementary segment in the target nucleic acid. A variant type V CRISPR/Cas effector polypeptide of the present disclosure exhibits reduced or no cleavage of a non-target single-stranded DNA. For example, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, binds a target nucleic acid, but exhibits less than 50% (e.g., less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2%, or less than 1%) of the cleavage of a non-target ssDNA exhibited by a wild-type type V CRISPR/Cas effector polypeptide. Cleavage of a non-target ssDNA is referred to herein as “trans cleavage.”

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, exhibits less than 50% (e.g., less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2%, or less than 1%) of the trans cleavage exhibited by a type V CRISPR/Cas effector polypeptide that does not include the one or more mutations in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, does not exhibit any detectable trans cleavage, as assayed using a method as described in Example 1.

FIG. 22 provides the structures of Cas12a, Cas12b, and a CasX protein. Beneath the structures are amino acid sequences of the loop of the helix-loop element of each protein. FIG. 23 presents a schematic diagram of the domain organization of Cas12a proteins. The amino acid numbering is based on the Francisella novicida Cas12a amino acid sequence depicted in FIG. 3A. The helix-loop is within the RuvC domain FIG. 24 shows amino acid changes made to the loop of the helix-loop element in Lachnospiraceae bacterium Cas12a (LbCas12a; also referred to as “LbCpf1”; amino acid sequence depicted in FIG. 1A). The wild-type (w t) amino acid sequence SGFKNSRVK (SEQ ID NO: 60) (corresponding to amino acids 929-937 of LbCas12a) of the loop of the helix-loop element of Lachnospiraceae bacterium Cas12a is shown; below the wild-type amino acid sequence are sequences of the loop of the helix-loop element of 3 variants: IL9, IL3, and ILO. The effect of the changes to the amino acid sequence of the loop in variants IL9 (“Cpf1d-IL9”), IL3 (“Cpf1-IL3”), and ILO (“Cpf1-IL0”) is depicted in FIG. 25. As shown in FIG. 25, variant IL9, IL3, and ILO do not exhibit trans cleavage activity (trans DNA nuclease activity), as determined by the assay described in Example 1.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, exhibits less than 50% (e.g., less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2%, or less than 1%) of the trans cleavage exhibited by a type V CRISPR/Cas effector polypeptide comprising one of the amino acid sequences depicted in FIG. 1A, FIG. 2A, FIG. 3A, FIG. 4A, FIG. 5A, FIG. 6A, FIG. 7A, FIG. 8A, FIG. 9A, FIG. 10A, FIG. 11A, FIG. 12A, FIG. 13A, FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, FIG. 18A, FIG. 19A, or FIG. 20A.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, exhibits less than 50% (e.g., less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2%, or less than 1%) of the trans cleavage exhibited by a type V CRISPR/Cas effector polypeptide comprising the following Lachnospiraceae bacterium Cas12a amino acid sequence (where the loop of the helix-loop element is indicated in bold underline):

(SEQ ID NO: 1)

MSKLEKFTNCYSLSKTLRFKAIPVGKTQENIDNKRLLVEDEKRAEDYKGV

KKLLDRYYLSFINDVLHSIKLKNLNNYISLFRKKTRTEKENKELENLEIN

LRKEIAKAFKGNEGYKSLFKKDIIETILPEFLDDKDEIALVNSFNGFTTA

FTGFFDNRENMFSEEAKSTSIAFRCINENLTRYISNMDIFEKVDAIFDKH

EVQEIKEKILNSDYDVEDFFEGEFFNFVLTQEGIDVYNAIIGGFVTESGE

KIKGLNEYINLYNQKTKQKLPKFKPLYKQVLSDRESLSFYGEGYTSDEEV

LEVFRNTLNKNSEIFSSIKKLEKLFKNFDEYSSAGIFVKNGPAISTISKD

IFGEWNVIRDKWNAEYDDIHLKKKAVVTEKYEDDRRKSFKKIGSFSLEQL

QEYADADLSVVEKLKEIIIQKVDEIYKVYGSSEKLFDADFVLEKSLKKND

AVVAIMKDLLDSVKSFENYIKAFFGEGKETNRDESFYGDFVLAYDILLKV

DHIYDAIRNYVTQKPYSKDKFKLYFQNPQFMGGWDKDKETDYRATILRYG

SKYYLAIMDKKYAKCLQKIDKDDVNGNYEKINYKLLPGPNKMLPKVFFSK

KWMAYYNPSEDIQKIYKNGTFKKGDMFNLNDCHKLIDFFKDSISRYPKWS

NAYDFNFSETEKYKDIAGFYREVEEQGYKVSFESASKKEVDKLVEEGKLY

MFQIYNKDFSDKSHGTPNLHTMYFKLLFDENNHGQIRLSGGAELFMRRAS

LKKEELVVHPANSPIANKNPDNPKKTTTLSYDVYKDKRFSEDQYELHIPI

AINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGERNLLYIVVVDGKGNI

VEQYSLNEIINNFNGIRIKTDYHSLLDKKEKERFEARQNWTSIENIKELK

AGYISQVVHKICELVEKYDAVIALEDLNSGFKNSRVKVEKQVYQKFEKML

IDKLNYMVDKKSNPCATGGALKGYQITNKFESFKSMSTQNGFIFYIPAWL

TSKIDPSTGFVNLLKTKYTSIADSKKFISSFDRIMYVPEEDLFEFALDYK

NFSRTDADYIKKWKLYSYGNRIRIFRNPKKNNVFDWEEVCLTSAYKELFN

KYGINYQQGDIRALLCEQSDKAFYSSFMALMSLMLQMRNSITGRTDVDFL

ISPVKNSDGIFYDSRNYEAQENAILPKNADANGAYNIARKVLWAIGQFKK

AEDEKLDKVKIAISNKEWLEYAQTSVKH.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, when complexed with a guide RNA, exhibits less than 50% (e.g., less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2%, or less than 1%) of the trans cleavage exhibited by a type V CRISPR/Cas effector polypeptide comprising the following Francisella novicida U112 Cas12a amino acid sequence (where the loop of the helix-loop element is indicated in bold underline):

(SEQ ID NO: 3)

IMSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKK

AKQIIDKYHQFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFK

SAKDTIKKQISEYIKDSEKFKNLFNQNLIDAKKGQESDLILWLKQSKDNG

IELFKANSDITDIDEALEIIKSFKGWTTYFKGFHENRKNVYSSNDIPTSI

IYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAEELTFDIDYK

TSEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKG

INEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVV

TTMQSFYEQIAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSL

TDLSQQVFDDYSVIGTAVLEYITQQIAPKNLDNPSKKEQELIAKKTEKAK

YLSLETIKLALEEFNKHRDIDKQCRFEEILANFAAIPMIFDEIAQNKDNL

AQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNNLLHKLKIFHISQSE

DKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKLN

FENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKEN

KGEGYKKIVYKLLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTK

NGSPQKGYEKFEFNIEDCRKFIDFYKQSISKHPEWKDFGFRFSDTQRYNS

IDEFYREVENQGYKLTFENISESYIDSVVNQGKLYLFQIYNKDFSAYSKG

RPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIPKKITHPAKEAI

ANKNKDNPKKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANKFNDE

INLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRM

KTNYHDKLAAIEKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEY

NAIVVFEDLNFGFKRGREKVEKQVYQKLEKMLIEKLNYLVFKDNEFDKTG

GVLRAYQLTAPFETFKKMGKQTGIIYYVPAGFTSKICPVTGFVNQLYPKY

ESVSKSQEFFSKFDKICYNLDKGYFEFSFDYKNFGDKAAKGKWTIASFGS

RLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGES

DKKFFAKLTSVLNTILQMRNSKTGTELDYLISPVADVNGNFFDSRQAPKN

MPQDADANGAYHIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRN

N.

A variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises one or more mutations in the loop of the helix-loop element of the RuvC domain, compared with a wild-type type V CRISPR/Cas effector polypeptide. The one or more mutations can include: one or more amino acid substitutions; deletion of one or more amino acids; insertion of one or more amino acids; or a combination of deletion of one or more amino acids and a substitution of one or more amino acids. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a deletion of one or more amino acids in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of one or more charged amino acids with an amino acid other than Lys, Arg, His, Asp, or Glu in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of one or more charged amino acids with an amino acid having a polar uncharged side chain (e.g., Ser, Thr, Asn, or Gln) in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of one or more charged amino acids with an amino acid having a hydrophobic side chain (e.g., Ala, Val, Ile, Leu, Met, Phe, Tyr, or Trp) in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of one or more charged amino acids with a Gly or an Ala in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of a Lys with an amino acid other than Lys, Arg, His, Asp, or Glu in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of an Arg with an amino acid other than Lys, Arg, His, Asp, or Glu in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of a Lys and an Arg with amino acids other than Lys, Arg, His, Asp, or Glu in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of an Asp with an amino acid other than Lys, Arg, His, Asp, or Glu in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises a substitution of a Glu with an amino acid other than Lys, Arg, His, Asp, or Glu in the loop of the helix-loop element of the RuvC domain. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises two or more of any of the above disclosed substitutions in the loop of the helix loop element of Cas12a in any order; and exhibits decreased trans cleavage activity as compared with the wild type protein, as measured by methods known in the art (see e.g. Example 1).

For example, the loop of the helix-loop element of a Cas12a polypeptide that exhibits trans cleavage can comprise an amino acid sequence such as SGFKNSRVK (SEQ ID NO: 60), FGFKSKRTG (SEQ ID NO: 62), LSFMKGRKK (SEQ ID NO: 86), FGFKRGRFK (SEQ ID NO: 61), FGFKRGRQK (SEQ ID NO: 73), MGFKRGRFK (SEQ ID NO: 74), MGFKRGRQK (SEQ ID NO: 63), or QGFKRGRFK (SEQ ID NO: 75); and a variant Cas12a polypeptide of the present disclosure can comprise: i) a deletion of the entire loop; or ii) a deletion of 8 amino acids of the loop; or iii) a deletion of 7 amino acids of the loop element; or iv) a deletion of 6 amino acids of the loop; or v) a deletion of 5 amino acids of the loop; or vi) a deletion of 4 amino acids of the loop; or vii) a deletion of 3 amino acids of the loop; or viii) a substitution of one Lys of the loop with an amino acid other than Lys, Arg, or His; or ix) a substitution of both Lys of the loop with an amino acid other than Lys, Arg, or His; or x) a substitution of the Arg of the loop with an amino acid other than Lys, Arg, or His; or xi) an insertion of one or more amino acids into the loop; or xii) a replacement of the loop with 1, 2, 3, 4, 5, 6, 7, 8, or 9 amino acids, where the replacement comprises one or more Gly and/or one or more Ala. In some cases, where a Lys and/or an Arg is substituted with an amino acid other than Lys, Arg, or His, the Lys and/or the Arg is/are substituted with Ala, Val, Ile, Leu, Met, Phe, Tyr, Trp, Gly, Cys, Pro, Ser, Thr, Asn, Gln, Asp, or Glu. In some cases, where a Lys and/or an Arg is substituted with an amino acid other than Lys, Arg, or His, the Lys and/or the Arg is/are substituted with Ala, Val, Ile, Leu, Gly, Ser, or Thr. In some cases, where a Lys and/or an Arg is substituted with an amino acid other than Lys, Arg, or His, the Lys and/or the Arg is/are substituted with Ala or Gly. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises two or more of any of the above disclosed substitutions in the loop of the helix loop element of Cas12a in any order; and exhibits decreased trans cleavage activity as compared with the wild type protein, as measured by methods known in the art (see e.g. Example 1).

The loop of the helix-loop element of a Cas12a polypeptide can be, e.g., amino acids 929-937, based on the amino acid numbering of LbCas12a, or the corresponding amino acids of another Cas12a polypeptide. The loop of the helix-loop element of a Cas12b polypeptide can be, e.g., amino acids 852-865 of Aa Cas12b, or the corresponding amino acids of another Cas12b polypeptide. The loop of the helix-loop element of a CasX (Cas12e) polypeptide can be, e.g., amino acids 776-788 of Dpb CasX, or the corresponding amino acids of another CasX polypeptide. See, e.g., FIG. 22.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 1C, where the loop sequence SGFKNSRVK (SEQ ID NO: 60) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 1A has been mutated to GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 2C, where the loop having the sequence FGFKSKRTG (SEQ ID NO: 62) as depicted in FIG. 2A is mutated to GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 3C, where the loop having the sequence FGFKRGRFK (SEQ ID NO: 61) as depicted in FIG. 3A is mutated to GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 4A, but where the loop having the sequence LSFMKGRKK (SEQ ID NO: 86) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, LSFMAGRKK (SEQ ID NO: 86), LSFMKGRAA (SEQ ID NO: 87), LSFMAGRAA (SEQ ID NO: 88), or LSFMAGAKK (SEQ ID NO: 39).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 5A, but where the loop having the sequence FGFKRGRFK (SEQ ID NO: 61) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, FGFARGRFA (SEQ ID NO: 84), FGFKAGAFK (SEQ ID NO: 85), or FGFAAGAFA (SEQ ID NO: 90).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 6A, but where the loop having the sequence FGFKRGRFK (SEQ ID NO: 61) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, FGFARGRFA (SEQ ID NO: 84), FGFKAGAFK (SEQ ID NO: 85), FGFARGAFK (SEQ ID NO: 91), or FGFKAGRFA (SEQ ID NO: 92).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 7A, but where the loop having the sequence FGFKRGRFK (SEQ ID NO: 61) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, FGFARGRFA (SEQ ID NO: 84), FGFKAGAFK (SEQ ID NO: 85), FGFARGAFK (SEQ ID NO: 91), or FGFKAGRFA (SEQ ID NO: 92).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 8A, but where the loop having the sequence FGFKRGRFK (SEQ ID NO: 61) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, FGFARGRFA (SEQ ID NO: 84), FGFKAGAFK (SEQ ID NO: 85), FGFARGAFK (SEQ ID NO: 91), or FGFKAGRFA (SEQ ID NO: 92).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 9A, but where the loop having the sequence FGFKRGRQK (SEQ ID NO: 73) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, FGFARGRQA (SEQ ID NO: 93), FGFKAGAQK (SEQ ID NO: 94), FGFARGAQK (SEQ ID NO: 95), or FGFKAGRQA (SEQ ID NO: 96).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 10A, but where the loop having the sequence MGFKRGRFK (SEQ ID NO: 74) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, MGFARGRFA (SEQ ID NO: 97), MGFKAGAFK (SEQ ID NO: 98), MGFAAGRFK (SEQ ID NO: 99), or MGFKRGAFA (SEQ ID NO: 100).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 11A, but where the loop having the sequence MGFKRGRQK (SEQ ID NO: 63) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, MGFARGRQA (SEQ ID NO: 101), MGFKAGAQK (SEQ ID NO: 102), MGFARGAQK (SEQ ID NO: 103), or MGFKAGRQA (SEQ ID NO: 104).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 12A, but where the loop having the sequence FGFKRGRFK (SEQ ID NO: 61) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, FGFARGRFA (SEQ ID NO: 84), FGFKAGAFK (SEQ ID NO: 85), FGFARGAFK (SEQ ID NO: 91), or FGFKAGRFA (SEQ ID NO: 92).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 13A, but where the loop having the sequence QGFKRGRFK (SEQ ID NO: 75) is mutated to: GGAAGGAAG (SEQ ID NO: 77), GGAAGGAAP (SEQ ID NO: 76), GGAAGGGAG (SEQ ID NO: 81), GGAAGGAAA (SEQ ID NO: 78), GAA, GGA, AGG, AAG, GAP, QGFARGRFA (SEQ ID NO: 105), QGFKAGAFK (SEQ ID NO: 106), QGFARGAFK (SEQ ID NO: 107), or QGFKAGRFA (SEQ ID NO: 108).

As another example, the loop of the helix-loop element of a Cas12b polypeptide that exhibits trans cleavage can comprise an amino acid sequence such as EYQFNNDRPPSENN (SEQ ID NO: 64), EYRFSNDRPPSENS (SEQ ID NO: 65), RYRFQSDRPPSENS (SEQ ID NO: 66), AYRFSDDRPPSENS (SEQ ID NO: 67), or RYRFRTDRPRSENR (SEQ ID NO: 109); and a variant Cas12b polypeptide of the present disclosure can comprise: i) a deletion of the entire loop; or ii) a deletion of from 1 amino acid to 14 amino acids of the loop (e.g., a deletion of from 1 amino acid (aa) to 5 aa, from 5 aa to 10 aa, or from 10 aa to 14 aa of the loop) (e.g., a deletion of 1 aa, 2 aa, 3 aa, 4 aa, 5 aa, 6 aa, 7 aa, 8 aa, 9 aa, 10 aa, 11 aa, 12 aa, 13 aa, or 14 aa, of the loop); or iii) a substitution of an Asp of the loop with an amino acid other than Arg, His, Lys, Asp, or Glu; or ix) a substitution of an Arg of the loop with an amino acid other than Arg, His, Lys, Asp, or Glu; or x) a substitution of a Glu of the loop with an amino acid other than Arg, His, Lys, Asp, or Glu; or xi) an insertion of one or more amino acids into the loop; or xii) a replacement of the loop with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 amino acids, where the replacement comprises one or more Gly and/or one or more Ala. In some cases, where an Asp, and/or an Arg, and/or a Glu is substituted with an amino acid other than Arg, His, Lys, Asp, or Glu, the Asp and/or the Arg and/or the Glu is/are substituted with Ala, Val, Ile, Leu, Met, Phe, Tyr, Trp, Gly, Cys, Pro, Ser, Thr, Asn, or Gln. In some cases, the Asp and/or the Arg and/or the Glu is/are individually substituted with Gly or Ala. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises two or more of any of the above disclosed substitutions in the loop of the helix loop element of Cas12a in any order; and exhibits decreased trans cleavage activity as compared with the wild type protein, as measured by methods known in the art (see e.g. Example 1).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 14C, where the loop sequence EYQFNNDRPPSEN (SEQ ID NO: 110) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 14A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 15C, where the loop sequence AYRFSDDRPPSENS (SEQ ID NO: 67) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 15A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 16C, where the loop sequence EYRFSNDRPPSENS (SEQ ID NO: 65) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 16A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 17C, where the loop sequence RYRFQSDRPPSENS (SEQ ID NO: 66) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 17A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 18C, where the loop sequence RYRFRTDRPRSENR (SEQ ID NO: 109) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 18A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

As another example, the loop of the helix-loop element of a CasX polypeptide that exhibits trans cleavage can comprise an amino acid sequence such as GRQGKRTFMTERQ (SEQ ID NO: 68), or GRQGKRTFMAERQ (SEQ ID NO: 112); and a variant CasX polypeptide of the present disclosure can comprise: i) a deletion of the entire loop; or ii) a deletion of from 1 amino acid to 13 amino acids of the loop (e.g., a deletion of from 1 amino acid (aa) to 4 aa, from 4 aa to 9 aa, or from 9 aa to 13 aa of the loop) (e.g., a deletion of 1 aa, 2 aa, 3 aa, 4 aa, 5 aa, 6 aa, 7 aa, 8 aa, 9 aa, 10 aa, 11 aa, 12 aa, or 13 aa of the loop); or iii) a substitution of an Arg of the loop with an amino acid other than Arg, His, Lys, Asp, or Glu; or ix) a substitution of a Lys of the loop with an amino acid other than Arg, His, Lys, Asp, or Glu; or x) a substitution of a Glu of the loop with an amino acid other than Arg, His, Lys, Asp, or Glu; or xi) an insertion of one or more amino acids into the loop; or xii) a replacement of the loop with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 amino acids, where the replacement comprises one or more Gly and/or one or more Ala. In some cases, where an Arg, and/or a Lys, and/or a Glu is substituted with an amino acid other than Arg, His, Lys, Asp, or Glu, the Arg and/or the Lys and/or the Glu is/are substituted with Ala, Val, Ile, Leu, Met, Phe, Tyr, Trp, Gly, Cys, Pro, Ser, Thr, Asn, or Gln. In some cases, the Arg and/or the Lys and/or the Glu is/are individually substituted with Gly or Ala. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises two or more of any of the above disclosed substitutions in the loop of the helix loop element of Cas12a in any order; and exhibits decreased trans cleavage activity as compared with the wild type protein, as measured by methods known in the art (see e.g. Example 1).

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 19C, where the loop sequence GRQGKRTFMTERQ (SEQ ID NO: 68) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 19A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 20C, where the loop sequence GRQGKRTFMAERQ (SEQ ID NO: 112) present in the variant type V CRISPR/Cas effector polypeptide depicted in FIG. 20A has been mutated to GAAGAAGAAGAAGG (SEQ ID NO: 111), GGAAGGAAP (SEQ ID NO: 76), GGAAGGAAG (SEQ ID NO: 77), or GGAAGGAAA (SEQ ID NO: 78), or some other combination of Gly and Ala (e.g., a combination of Gly and Ala having a length of from 4 amino acids to 14 amino acids, e.g., from 4 amino acids to 10 amino acids, or from 10 amino acids to 14 amino acids.

Reference type V CRISPR/Cas Effector Proteins

As noted above, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises one or more mutations relative to a reference (e.g., wild-type) type V CRISPR/Cas effector polypeptide, and exhibits reduced trans cleavage, compared to the reference (e.g., a wild-type) type V CRISPR/Cas effector polypeptide. In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure comprises one or more mutations (e.g., one or more of: one or more substitution; one or more deletions; one or more insertions), in the loop of the helix-loop element, relative to a reference (e.g., wild-type) type V CRISPR/Cas effector polypeptide; and exhibits reduced trans cleavage, compared to the reference (e.g., a wild-type) type V CRISPR/Cas effector polypeptide, as assayed by methods known in the art, e.g., a method as described in Example 1.

Type V CRISPR/Cas effector proteins are a subtype of Class 2 CRISPR/Cas effector proteins. For examples of type V CRISPR/Cas systems and their effector proteins (e.g., Cas12 family proteins such as Cas12a), see, e.g., Shmakov et al., Nat Rev Microbiol. 2017 March; 15(3):169-182: “Diversity and evolution of class 2 CRISPR-Cas systems.” Examples include, but are not limited to, Cas12 family (Cas12a, Cas12b, Cas12c), C2c4, C2c8, C2c5, C2c10, and C2c9; as well as CasX (Cas12e) and CasY (Cas12d). Also see, e.g., Koonin et al., Curr Opin Microbiol. 2017 June; 37:67-78: “Diversity, classification and evolution of CRISPR-Cas systems.”

In some cases, a reference type V CRISPR/Cas effector protein is a Cas12 protein (e.g., Cas12a, Cas12b, Cas12c). In some cases, a reference type V CRISPR/Cas effector protein is a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12f, Cas12g, Cas12h, or Cas12i. In some cases, a reference type V CRISPR/Cas effector protein is a Cas12a protein. In some cases, a reference type V CRISPR/Cas effector protein is a Cas12b protein. In some cases, a reference type V CRISPR/Cas effector protein is a Cas12c protein. In some cases, a reference type V CRISPR/Cas effector protein is a Cas12d protein. In some cases, a reference type V CRISPR/Cas effector protein is a CasX (Cas12e) protein.

In some cases, the reference type V CRISPR/Cas effector protein is a naturally-occurring protein (e.g., naturally occurs in prokaryotic cells). In other cases, the reference type V CRISPR/Cas effector protein is not a naturally-occurring polypeptide. Examples of naturally occurring (“wild-type”) type V CRISPR/Cas effector proteins include, but are not limited to, those depicted in FIGS. 1A, 2A, 3A, 4A, 5A, 6A, 7A, 8A, 9A, 10A, 11A, 12A, 13A, 14A, 15A, 16A, 17A, 18A, 19A, and 20A. Any type V CRISPR/Cas effector protein can be suitable for modification, to generate a variant type V CRISPR/Cas effector polypeptide. A suitable reference type V CRISPR/Cas effector protein forms a complex with a guide RNA and exhibits ssDNA cleavage activity of non-target ssDNAs (trans cleavage) once it is activated (by hybridization of and associated guide RNA to its target DNA).

In some cases, a reference type V CRISPR/Cas effector protein comprises an amino acid sequence having 20% or more sequence identity (e.g., 30% or more, 40% or more, 50% or more, 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100% sequence identity) with a Cas12 protein (e.g., a Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12f, Cas12g, Cas12h, or Cas12i, protein). For example, in some cases a reference type V CRISPR/Cas effector protein comprises an amino acid sequence having 50% or more sequence identity (e.g., 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100% sequence identity) with a Cas12a protein depicted in any one of FIGS. 1A, 2A, 3A, 4A, 5A, 6A, 7A, 8A, 9A, 10A, 11A, 12A, and 13A. As another example, in some cases a reference type V CRISPR/Cas effector protein comprises an amino acid sequence having 50% or more sequence identity (e.g., 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100% sequence identity) with a Cas12b protein depicted in any one of FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, or FIG. 18A. As another example, in some cases a reference type V CRISPR/Cas effector protein comprises an amino acid sequence having 50% or more sequence identity (e.g., 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100% sequence identity) with a CasX (Cas12e) protein depicted in FIG. 19A or FIG. 20A.

Fusion Polypeptides

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure is a fusion protein, e.g., the variant type V CRISPR/Cas effector polypeptide comprises a heterologous polypeptide (i.e., one or more heterologous polypeptides). A heterologous polypeptide is also referred to herein as a “fusion partner.”

In some cases, a heterologous polypeptide provides for subcellular localization, e.g., the heterologous polypeptide contains a subcellular localization sequence (e.g., a nuclear localization signal (NLS) for targeting to the nucleus; a sequence to keep the fusion protein out of the nucleus, e.g., a nuclear export sequence (NES); a sequence to keep the fusion protein retained in the cytoplasm; a mitochondrial localization signal for targeting to the mitochondria; a chloroplast localization signal for targeting to a chloroplast, an ER retention signal; and the like. In some cases, the heterologous polypeptide can provide a tag (i.e., the heterologous polypeptide is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), cyan fluorescent protein (CFP), mCherry, tdTomato, and the like; a histidine tag, e.g., a 6×His tag; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like.

In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure is a fusion protein comprising an NLS as the heterologous polypeptide. In some cases, a fusion protein of the present disclosure comprises: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs). In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus of the variant type V CRISPR/Cas effector polypeptide. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus of the variant type V CRISPR/Cas effector polypeptide. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus of the variant type V CRISPR/Cas effector polypeptide. In some cases, one or more NLSs (3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C-terminus of the variant type V CRISPR/Cas effector polypeptide. In some cases, an NLS is positioned at the N-terminus and an NLS is positioned at the C-terminus of the variant type V CRISPR/Cas effector polypeptide.

Non-limiting examples of NLSs include an NLS sequence derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO: 113); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO: 114)); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO: 115) or RQRRNELKRSP (SEQ ID NO: 116); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 117); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 118) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO: 119) and PPKKARED (SEQ ID NO: 120) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO: 121) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO: 122) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO: 123) and PKQKKRK (SEQ ID NO: 124) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 125) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO: 126) of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 127) of the human poly(ADP-ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 128) of the steroid hormone receptors (human) glucocorticoid. In general, NLS (or multiple NLSs) are of sufficient strength to drive accumulation of the protein in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique.

In some cases the fusion partner can modulate transcription (e.g., inhibit transcription, increase transcription) of a target DNA. For example, in some cases the fusion partner is a protein (or a domain from a protein) that inhibits transcription (e.g., a transcriptional repressor, a protein that functions via recruitment of transcription inhibitor proteins, modification of target DNA such as methylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like). In some cases the fusion partner is a protein (or a domain from a protein) that increases transcription (e.g., a transcription activator, a protein that acts via recruitment of transcription activator proteins, modification of target DNA such as demethylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like).

In some cases, a fusion protein of the present disclosure comprises: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a heterologous polypeptide that has enzymatic activity that modifies a target nucleic acid (e.g., nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity or glycosylase activity).

In some cases, a fusion protein of the present disclosure comprises: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a heterologous polypeptide that has enzymatic activity that modifies a polypeptide (e.g., a histone) associated with a target nucleic acid (e.g., methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity).

Examples of proteins (or fragments thereof) that can be used in increase transcription include but are not limited to: transcriptional activators such as VP16, VP64, VP48, VP160, p65 subdomain (e.g., from NFkB), and activation domain of EDLL and/or TAL acitvation domain (e.g., for activity in plants); histone lysine methyltransferases such as SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, and the like; histone lysine demethylases such as JHDM2a/b, UTX, JMJD3, and the like; histone acetyltransferases such as GCN5, PCAF, CBP, p300, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, SRC1, ACTR, P160, CLOCK, and the like; and DNA demethylases such as Ten-Eleven Translocation (TET) dioxygenase 1 (TET1CD), TET1, DME, DML1, DML2, ROS1, and the like.

Examples of proteins (or fragments thereof) that can be used in decrease transcription include but are not limited to: transcriptional repressors such as the Krüppel associated box (KRAB or SKD); KOX1 repression domain; the Mad mSIN3 interaction domain (SID); the ERF repressor domain (ERD), the SRDX repression domain (e.g., for repression in plants), and the like; histone lysine methyltransferases such as Pr-SET7/8, SUV4-20H1, RIZ1, and the like; histone lysine demethylases such as JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, JARID1D/SMCY, and the like; histone lysine deacetylases such as HDAC1, HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, SIRT1, SIRT2, HDAC11, and the like; DNA methylases such as HhaI DNA m5c-methyltransferase (M.HhaI), DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), METI, DRM3 (plants), ZMET2, CMT1, CMT2 (plants), and the like; and periphery recruitment elements such as Lamin A, Lamin B, and the like.

In some cases the fusion partner has enzymatic activity that modifies the target nucleic acid (e.g., ssRNA, dsRNA, ssDNA, dsDNA). Examples of enzymatic activity that can be provided by the fusion partner include but are not limited to: nuclease activity such as that provided by a restriction enzyme (e.g., FokI nuclease), methyltransferase activity such as that provided by a methyltransferase (e.g., HhaI DNA m5c-methyltransferase (M.HhaI), DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), METI, DRM3 (plants), ZMET2, CMT1, CMT2 (plants), and the like); demethylase activity such as that provided by a demethylase (e.g., Ten-Eleven Translocation (TET) dioxygenase 1 (TET1CD), TET1, DME, DML1, DML2, ROS1, and the like), DNA repair activity, DNA damage activity, deamination activity such as that provided by a deaminase (e.g., a cytosine deaminase enzyme such as rat APOBEC1; or an adenine deaminase activity such as E. coli TadA or ABE7.8, ABE7.9 and ABE7.10), dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity such as that provided by an integrase and/or resolvase (e.g., Gin invertase such as the hyperactive mutant of the Gin invertase, GinH106Y; human immunodeficiency virus type 1 integrase (IN); Tn3 resolvase; and the like), transposase activity, recombinase activity such as that provided by a recombinase (e.g., catalytic domain of Gin recombinase), polymerase activity, ligase activity, helicase activity, photolyase activity, and glycosylase activity).

In some cases, the fusion partner has enzymatic activity that modifies a protein associated with the target nucleic acid (e.g., ssRNA, dsRNA, ssDNA, dsDNA) (e.g., a histone, an RNA binding protein, a DNA binding protein, and the like). Examples of enzymatic activity (that modifies a protein associated with a target nucleic acid) that can be provided by the fusion partner include but are not limited to: methyltransferase activity such as that provided by a histone methyltransferase (HMT) (e.g., suppressor of variegation 3-9 homolog 1 (SUV39H1, also known as KMT1A), euchromatic histone lysine methyltransferase 2 (G9A, also known as KMT1C and EHMT2), SUV39H2, ESET/SETDB1, and the like, SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, DOT1L, Pr-SET7/8, SUV4-20H1, EZH2, RIZ1), demethylase activity such as that provided by a histone demethylase (e.g., Lysine Demethylase 1A (KDM1A also known as LSD1), JHDM2a/b, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, JARID1D/SMCY, UTX, JMJD3, and the like), acetyltransferase activity such as that provided by a histone acetylase transferase (e.g., catalytic core/fragement of the human acetyltransferase p300, GCN5, PCAF, CBP, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, HBO1/MYST2, HMOF/MYST1, SRC1, ACTR, P160, CLOCK, and the like), deacetylase activity such as that provided by a histone deacetylase (e.g., HDAC1, HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, SIRT1, SIRT2, HDAC11, and the like), kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity, and demyristoylation activity.

In some cases, fusion polypeptide of the present disclosure can comprise: a) variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) an endosomal escape peptide. In some cases, an endosomal escape polypeptide comprises the amino acid sequence GLFXALLXLLXSLWXLLLXA (SEQ ID NO: 129), wherein each X is independently selected from lysine, histidine, and arginine. In some cases, an endosomal escape polypeptide comprises the amino acid sequence GLFHALLHLLHSLWHLLLHA (SEQ ID NO: 130).

Additional suitable heterologous polypeptide include, but are not limited to, a polypeptide that directly and/or indirectly provides for increased transcription and/or translation of a target nucleic acid (e.g., a transcription activator or a fragment thereof, a protein or fragment thereof that recruits a transcription activator, a small molecule/drug-responsive transcription and/or translation regulator, a translation-regulating protein, etc.). Non-limiting examples of heterologous polypeptides to accomplish increased or decreased transcription include transcription activator and transcription repressor domains. In some such cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure is targeted by the guide nucleic acid (guide RNA) to a specific location (i.e., sequence) in the target nucleic acid and exerts locus-specific regulation such as blocking RNA polymerase binding to a promoter (which selectively inhibits transcription activator function), and/or modifying the local chromatin status (e.g., when a fusion sequence is used that modifies the target nucleic acid or modifies a polypeptide associated with the target nucleic acid). In some cases, the changes are transient (e.g., transcription repression or activation). In some cases, the changes are inheritable (e.g., when epigenetic modifications are made to the target nucleic acid or to proteins associated with the target nucleic acid, e.g., nucleosomal histones).

Non-limiting examples of heterologous polypeptides for use when targeting ssRNA target nucleic acids include (but are not limited to): splicing factors (e.g., RS domains); protein translation components (e.g., translation initiation, elongation, and/or release factors; e.g., eIF4G); RNA methylases; RNA editing enzymes (e.g., RNA deaminases, e.g., adenosine deaminase acting on RNA (ADAR), including A to I and/or C to U editing enzymes); helicases; RNA-binding proteins; and the like. It is understood that a heterologous polypeptide can include the entire protein or in some cases can include a fragment of the protein (e.g., a functional domain)

A fusion protein of the present disclosure can comprise: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a polypeptide capable of interacting with ssRNA (which, for the purposes of this disclosure, includes intramolecular and/or intermolecular secondary structures, e.g., double-stranded RNA duplexes such as hairpins, stem-loops, etc.), whether transiently or irreversibly, directly or indirectly, including but not limited to an effector domain selected from the group comprising; Endonucleases (for example RNase III, the CRR22 DYW domain, Dicer, and PIN (PilT N-terminus) domains from proteins such as SMG5 and SMG6); proteins and protein domains responsible for stimulating RNA cleavage (for example CPSF, CstF, CFIm and CFIIm); Exonucleases (for example XRN-1 or Exonuclease T); Deadenylases (for example HNT3); proteins and protein domains responsible for nonsense mediated RNA decay (for example UPF1, UPF2, UPF3, UPF3b, RNP S1, Y14, DEK, REF2, and SRm160); proteins and protein domains responsible for stabilizing RNA (for example PABP); proteins and protein domains responsible for repressing translation (for example Ago2 and Ago4); proteins and protein domains responsible for stimulating translation (for example Staufen); proteins and protein domains responsible for (e.g., capable of) modulating translation (e.g., translation factors such as initiation factors, elongation factors, release factors, etc., e.g., eIF4G); proteins and protein domains responsible for polyadenylation of RNA (for example PAP1, GLD-2, and Star-PAP); proteins and protein domains responsible for polyuridinylation of RNA (for example CI D1 and terminal uridylate transferase); proteins and protein domains responsible for RNA localization (for example from IMP1, ZBP1, She2p, She3p, and Bicaudal-D); proteins and protein domains responsible for nuclear retention of RNA (for example Rrp6); proteins and protein domains responsible for nuclear export of RNA (for example TAP, NXF1, THO, TREX, REF, and Aly); proteins and protein domains responsible for repression of RNA splicing (for example PTB, Sam68, and hnRNP A1); proteins and protein domains responsible for stimulation of RNA splicing (for example Serine/Arginine-rich (SR) domains); proteins and protein domains responsible for reducing the efficiency of transcription (for example FUS (TLS)); and proteins and protein domains responsible for stimulating transcription (for example CDK7 and HIV Tat). Alternatively, the effector domain may be selected from the group comprising Endonucleases; proteins and protein domains capable of stimulating RNA cleavage; Exonucleases; Deadenylases; proteins and protein domains having nonsense mediated RNA decay activity; proteins and protein domains capable of stabilizing RNA; proteins and protein domains capable of repressing translation; proteins and protein domains capable of stimulating translation; proteins and protein domains capable of modulating translation (e.g., translation factors such as initiation factors, elongation factors, release factors, etc., e.g., eIF4G); proteins and protein domains capable of polyadenylation of RNA; proteins and protein domains capable of polyuridinylation of RNA; proteins and protein domains having RNA localization activity; proteins and protein domains capable of nuclear retention of RNA; proteins and protein domains having RNA nuclear export activity; proteins and protein domains capable of repression of RNA splicing; proteins and protein domains capable of stimulation of RNA splicing; proteins and protein domains capable of reducing the efficiency of transcription; and proteins and protein domains capable of stimulating transcription. Another suitable heterologous polypeptide is a PUF RNA-binding domain, which is described in more detail in WO2012068627, which is hereby incorporated by reference in its entirety.

Some RNA splicing factors that can be used (in whole or as fragments thereof) as heterologous polypeptides for a fusion protein of the present disclosure have modular organization, with separate sequence-specific RNA binding modules and splicing effector domains. For example, members of the Serine/Arginine-rich (SR) protein family contain N-terminal RNA recognition motifs (RRMs) that bind to exonic splicing enhancers (ESEs) in pre-mRNAs and C-terminal RS domains that promote exon inclusion. As another example, the hnRNP protein hnRNP Al binds to exonic splicing silencers (ESSs) through its RRM domains and inhibits exon inclusion through a C-terminal Glycine-rich domain Some splicing factors can regulate alternative use of splice site (ss) by binding to regulatory sequences between the two alternative sites. For example, ASF/SF2 can recognize ESEs and promote the use of intron proximal sites, whereas hnRNP Al can bind to ESSs and shift splicing towards the use of intron distal sites. One application for such factors is to generate ESFs that modulate alternative splicing of endogenous genes, particularly disease associated genes. For example, Bcl-x pre-mRNA produces two splicing isoforms with two alternative 5′ splice sites to encode proteins of opposite functions. The long splicing isoform Bcl-xL is a potent apoptosis inhibitor expressed in long-lived postmitotic cells and is up-regulated in many cancer cells, protecting cells against apoptotic signals. The short isoform Bcl-xS is a pro-apoptotic isoform and expressed at high levels in cells with a high turnover rate (e.g., developing lymphocytes). The ratio of the two Bch x splicing isoforms is regulated by multiple c{dot over (ω)}-elements that are located in either the core exon region or the exon extension region (i.e., between the two alternative 5′ splice sites). For more examples, see WO2010075303, which is hereby incorporated by reference in its entirety.

Further suitable fusion partners include, but are not limited to proteins (or fragments thereof) that are boundary elements (e.g., CTCF), proteins and fragments thereof that provide periphery recruitment (e.g., Lamin A, Lamin B, etc.), protein docking elements (e.g., FKBP/FRB, Pil1/Aby1, etc.).

In some cases, fusion protein of the present disclosure comprises: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a “Protein Transduction Domain” or PTD (also known as a CPP—cell penetrating peptide). In some cases, a PTD is covalently linked to the amino terminus of a variant type V CRISPR/Cas effector polypeptide of the present disclosure. In some cases, a PTD is covalently linked to the carboxyl terminus of a variant type V CRISPR/Cas effector polypeptide of the present disclosure. In some cases, the PTD is inserted internally in a variant type V CRISPR/Cas effector polypeptide of the present disclosure at a suitable insertion site. In some cases, a subject fusion polypeptide includes one or more PTDs (e.g., two or more, three or more, four or more PTDs). Examples of PTDs include but are not limited to a minimal undecapeptide protein transduction domain (corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR; SEQ ID NO: 131); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8, 9, 10, or 10-50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther. 9(6):489-96); an Drosophila Antennapedia protein transduction domain (Noguchi et al. (2003) Diabetes 52(7):1732-1737); a truncated human calcitonin peptide (Trehin et al. (2004) Pharm. Research 21:1248-1256); polylysine (Wender et al. (2000) Proc. Natl. Acad. Sci. USA 97:13003-13008); RRQRRTSKLMKR (SEQ ID NO: 132); Transportan GWTLNSAGYLLGKINLKALAALAKKIL (SEQ ID NO: 133); KALAWEAKLAKALAKALAKHLAKALAKALKCEA (SEQ ID NO: 134); and RQIKIWFQNRRMKWKK (SEQ ID NO: 135). Exemplary PTDs include but are not limited to, YGRKKRRQRRR (SEQ ID NO: 131), RKKRRQRRR (SEQ ID NO: 136); an arginine homopolymer of from 3 arginine residues to 50 arginine residues; Exemplary PTD domain amino acid sequences include, but are not limited to, any of the following: YGRKKRRQRRR (SEQ ID NO: 131); RKKRRQRR (SEQ ID NO: 137); YARAAARQARA (SEQ ID NO: 138); THRLPRRRRRR (SEQ ID NO: 139); and GGRRARRRRRR (SEQ ID NO: 140). In some embodiments, the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol (Camb) June; 1(5-6): 371-381). ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or “E9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells. Upon cleavage of the linker, the polyanion is released, locally unmasking the polyarginine and its inherent adhesiveness, thus “activating” the ACPP to traverse the membrane.

Systems

The present disclosure provides a system comprising a variant type V CRISPR/Cas effector polypeptide of the present disclosure. A system of the present disclosure can comprise: a) a variant type V CRISPR/Cas polypeptide of the present disclosure and a type V CRISPR/Cas guide RNA; b) a variant type V CRISPR/Cas polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; c) a fusion polypeptide of the present disclosure and a type V CRISPR/Cas guide RNA; d) a fusion polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; e) an mRNA encoding a variant type V CRISPR/Cas polypeptide of the present disclosure; and a type V CRISPR/Cas guide RNA; f) an mRNA encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; g) an mRNA encoding a fusion polypeptide of the present disclosure; and a type V CRISPR/Cas guide RNA; h) an mRNA encoding a fusion polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; i) a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure and a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; j) a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a donor template nucleic acid; k) a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; 1) a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a donor template nucleic acid; m) a first recombinant expression vector comprising a nucleotide sequence encoding aa variant type V CRISPR/Cas polypeptide of the present disclosure and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; n) a first recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; and a donor template nucleic acid; o) a first recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; p) a first recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; and a donor template nucleic acid; q) a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, a nucleotide sequence encoding a first type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a second type V CRISPR/Cas guide RNA; or r) a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, a nucleotide sequence encoding a first type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a second type V CRISPR/Cas guide RNA; or some variation of one of (a) through (r).

Protospacer Adjacent Motif (PAM)

A type V CRISPR/Cas effector protein binds to target DNA at a target sequence defined by the region of complementarity between the DNA-targeting RNA and the target DNA. As is the case for many CRISPR/Cas endonucleases, site-specific binding (and/or cleavage) of a double stranded target DNA occurs at locations determined by both (i) base-pairing complementarity between the guide RNA and the target DNA; and (ii) a short motif (referred to as the protospacer adjacent motif (PAM)) in the target DNA. A variant type V CRISPR/Cas effector polypeptide of the present disclosure generally recognizes the same PAM as a reference (e.g., wild-type) type V CRISPR/Cas effector polypeptide. Non-limiting examples of PAM sequences are depicted in FIG. 21B.

In some cases, the PAM for a variant type V CRISPR/Cas effector polypeptide of the present disclosure is immediately 5′ of the target sequence (e.g., of the non-complementary strand of the target DNA—the complementary strand hybridizes to the guide sequence of the guide RNA while the non-complementary strand does not directly hybridize with the guide RNA and is the reverse complement of the non-complementary strand). In some cases, the PAM sequence is 5′-TTN-3′. In some cases, the PAM sequence is 5′-TTTN-3.′

Guide RNA

A nucleic acid molecule (e.g., a natural crRNA) that binds to a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12f, Cas12g, Cas12h, or Cas12i), forming a ribonucleoprotein complex (RNP), and that targets the complex to a specific target sequence within a target DNA is referred to herein as a “guide RNA.” It is to be understood that in some cases, a hybrid DNA/RNA can be made such that a guide RNA includes DNA bases in addition to RNA bases—but the term “guide RNA” is still used herein to encompass such hybrid molecules. A subject guide RNA includes a guide sequence (also referred to as a “spacer”)(that hybridizes to target sequence of a target DNA) and a constant region (e.g., a region that is adjacent to the guide sequence and binds to the type V CRISPR/Cas effector protein). A “constant region” can also be referred to herein as a “protein-binding segment.” In some cases, e.g., for Cas12a, the constant region is 5′ of the guide sequence. A variant type V CRISPR/Cas effector polypeptide of the present disclosure will bind guide RNAs in substantially the same manner as a reference (e.g., a wild-type) type V CRISPR/Cas effector polypeptide. Thus, the discussion of guide RNAs, below, pertains to guide RNAs suitable for use with a variant type V CRISPR/Cas effector polypeptide of the present disclosure. A guide RNA that comprises: a) a guide sequence that hybridizes to a target nucleotide sequence of a target nucleic acid; and b) a constant region that binds to a variant type V CRISPR/Cas effector polypeptide is referred to herein as a “type V CRISPR/Cas guide RNA,” or a “subject guide RNA.”

Guide Sequence

The guide sequence has complementarity with (hybridizes to) a target sequence of the target DNA. In some cases, the guide sequence is 15-28 nucleotides (nt) in length (e.g., 15-26, 15-24, 15-22, 15-20, 15-18, 16-28, 16-26, 16-24, 16-22, 16-20, 16-18, 17-26, 17-24, 17-22, 17-20, 17-18, 18-26, 18-24, or 18-22 nt in length). In some cases, the guide sequence is 18-24 nucleotides (nt) in length. In some cases, the guide sequence is at least 15 nt long (e.g., at least 16, 18, 20, or 22 nt long). In some cases, the guide sequence is at least 17 nt long. In some cases, the guide sequence is at least 18 nt long. In some cases, the guide sequence is at least 20 nt long.

In some cases, the guide sequence has 80% or more (e.g., 85% or more, 90% or more, 95% or more, or 100% complementarity) with the target sequence of the target DNA. In some cases, the guide sequence is 100% complementary to the target sequence of the target DNA. In some cases, the target DNA includes at least 15 nucleotides (nt) of complementarity with the guide sequence of the guide RNA.

Constant Region

Examples of constant regions for guide RNAs that can be used with a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e, Cas12f, Cas12g, Cas12h, or Cas12i) are presented in FIG. 21A.

In some embodiments a “guide RNA” includes two separate molecules (e.g., a tracrRNA and a crRNA) that hybridize to one another—and such a guide RNA can be referred to as a “dual-molecule” or “dual guide” RNA. The constant region of such a guide RNA would include a duplex formed from hybridization of the two separate molecules (e.g., a crRNA hybridized to a tracrRNA). For example, some naturally-occurring type V CRISPR-Cas systems (e.g., Cas12b) include and require a tracrRNA as part of the guide RNA; see, Shmakov et al. (2017) Nature 15:169.

In some cases, a “guide RNA” includes two separate molecules (e.g., a crRNA and a tracrRNA) that are covalently linked to one another via a non-nucleic acid linkage (e.g., a non-phosphodiester linkage) (see, e.g., US20180142236, WO2018126176, and He et al., Chembiochem. 2016 Oct. 4; 17(19):1809-1812, “Conjugation and Evaluation of Triazole-Linked Single Guide RNA for CRISPR-Cas9 Gene Editing”). For example, a guide RNA can include: i) a first RNA that comprises a nucleotide sequence that is complementary to a nucleotide sequence in a target nucleic acid (e.g., a target DNA); and ii) a second RNA comprising a nucleotide sequence that interacts with a type V CRISPR/Cas effector polypeptide, where the first RNA and the second RNA are joined via a non-phosphodiester covalent linkage. For example, the non-phosphodiester covalent linkage can comprise a moiety selected from a carbamate, an ether, an ester, an amide, an imine, an amidine, an aminotrizine, a hydrozone, a disulfide, a thioether, a thioester, a phosphorothioate, a phosphorodithioate, a sulfonamide, a sulfonate, a fulfone, a sulfoxide, a urea, a thiourea, a hydrazide, an oxime, a triazole, a photolabile linkage, a C—C bond forming group such as Diels-Alder cyclo-addition pair or ring-closing metathesis pair, and a Michael reaction pair.

In some cases, a “guide RNA” is a single molecule. For example, in some cases, a single-molecule guide RNA includes a crRNA but not a tracrRNA (e.g., some naturally-occurring type V CRISPR-Cas systems (e.g., Cas12a) do not include or require a tracrRNA). In some cases, a single-molecule guide RNA includes a crRNA conjugated to (e.g., via intervening nucleotides) a tracrRNA. For example, some naturally-occurring type V CRISPR-Cas systems include a guide RNA in which the tracrRNA and crRNA are separate molecules hybridized to one another—but those separate molecules can be conjugated (covalently linked) to one another, thus forming a single molecule.

In some embodiments a “guide RNA” is a single molecule. For example, in some cases a single-molecule guide RNA includes a crRNA but not a tracrRNA (e.g., some natural type V CRISPR-Cas systems do not include or require a tracrRNA). In some cases, a single-molecule guide RNA includes a crRNA conjugated to (e.g., via intervening nucleotides) a tracrRNA. For example, some natural type V CRISPR-Cas systems include a guide RNA in which the tracrRNA and crRNA are separate molecules hybridized to one another—but those separate molecules can be conjugated (covalently linked) to one another, thus forming a single molecule

In some cases, a subject guide RNA includes a nucleotide sequence having 70% or more identity (e.g., 80% or more, 85% or more, 90% or more, 95% or more, 98% or more, 99% or more, or 100% identity) with any one of the crRNA repeat sequences set forth in FIG. 21A. In some cases, a subject guide RNA includes a nucleotide sequence having 90% or more identity (e.g., 95% or more, 98% or more, 99% or more, or 100% identity) with any one of the crRNA repeat sequences set forth in FIG. 21A. In some cases, a subject guide RNA includes a crRNA nucleotide sequence set forth in FIG. 21A.

In some cases, the guide RNA includes a double stranded RNA duplex (dsRNA duplex). In some cases, a guide RNA includes a dsRNA duplex with a length of from 2 to 12 bp (e.g., from 2 to 10 bp, 2 to 8 bp, 2 to 6 bp, 2 to 5 bp, 2 to 4 bp, 3 to 12 bp, 3 to 10 bp, 3 to 8 bp, 3 to 6 bp, 3 to 5 bp, 3 to 4 bp, 4 to 12 bp, 4 to 10 bp, 4 to 8 bp, 4 to 6 bp, or 4 to 5 bp). In some cases, a guide RNA includes a dsRNA duplex that is 2 or more bp in length (e.g., 3 or more, 4 or more, 5 or more, 6 or more, or 7 or more bp in length). In some cases, a guide RNA includes a dsRNA duplex that is longer than the dsRNA duplex of a corresponding wild type guide RNA. In some cases, a guide RNA includes a dsRNA duplex that is shorter than the dsRNA duplex of a corresponding wild type guide RNA.

In some cases, the constant region of a guide RNA is 15 or more nucleotides (nt) in length (e.g., 18 or more, 20 or more, 21 or more, 22 or more, 23 or more, 24 or more, 25 or more, 26 or more, 27 or more, 28 or more, 29 or more, 30 or more, 31 or more nt, 32 or more, 33 or more, 34 or more, or 35 or more nt in length). In some cases, the constant region of a guide RNA is 18 or more nt in length.

In some cases, the constant region of a guide RNA has a length in a range of from 12 to 100 nt (e.g., from 12 to 90, 12 to 80, 12 to 70, 12 to 60, 12 to 50, 12 to 40, 15 to 100, 15 to 90, 15 to 80, 15 to 70, 15 to 60, 15 to 50, 15 to 40, 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 25 to 100, 25 to 90, 25 to 80, 25 to 70, 25 to 60, 25 to 50, 25 to 40, 28 to 100, 28 to 90, 28 to 80, 28 to 70, 28 to 60, 28 to 50, 28 to 40, 29 to 100, 29 to 90, 29 to 80, 29 to 70, 29 to 60, 29 to 50, or 29 to 40 nt). In some cases, the constant region of a guide RNA has a length in a range of from 28 to 100 nt. In some cases, the region of a guide RNA that is 5′ of the guide sequence has a length in a range of from 28 to 40 nt.

In some cases, the constant region of a guide RNA is truncated relative to (shorter than) the corresponding region of a corresponding wild type guide RNA. In some cases, the constant region of a guide RNA is extended relative to (longer than) the corresponding region of a corresponding wild type guide RNA. In some cases, a subject guide RNA is 30 or more nucleotides (nt) in length (e.g., 34 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 65 or more, 70 or more, or 80 or more nt in length). In some cases, the guide RNA is 35 or more nt in length.

Precursor Guide RNA Array

A Type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e) can cleave a precursor guide RNA into a mature guide RNA, e.g., by endoribonucleolytic cleavage of the precursor. A Type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e) can cleave a precursor guide RNA array (that includes more than one guide RNA arrayed in tandem) into two or more individual guide RNAs. Similarly, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can cleave a precursor guide RNA into a mature guide RNA. Thus, in some cases, a precursor guide RNA array comprises two or more (e.g., 3 or more, 4 or more, 5 or more, 2, 3, 4, or 5) guide RNAs (e.g., arrayed in tandem as precursor molecules). In other words, in some cases, two or more guide RNAs can be present on an array (a precursor guide RNA array). A Type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e) can cleave the precursor guide RNA array into individual guide RNAs. Similarly, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can cleave the precursor guide RNA array into individual guide RNAs.

In some cases, a subject guide RNA array includes 2 or more guide RNAs (e.g., 3 or more, 4 or more, 5 or more, 6 or more, or 7 or more, guide RNAs). The guide RNAs of a given array can target (i.e., can include guide sequences that hybridize to) different target sites of the same target DNA and/or can target different target DNA molecules (e.g., single nucleotide polymorphisms (SNPs), different strains of a particular virus, etc.). In some cases, each guide RNA of a precursor guide RNA array has a different guide sequence. In some cases, two or more guide RNAs of a precursor guide RNA array have the same guide sequence.

In some cases, the precursor guide RNA array comprises two or more guide RNAs that target different target sites within the same target DNA molecule. As such, in some cases as subject composition (e.g., kit) or method includes two or more guide RNAs (in the context of a precursor guide RNA array, or not in the context of a precursor guide RNA array, e.g., the guide RNAs can be mature guide RNAs).

In some cases, the precursor guide RNA array comprises two or more guide RNAs that target different target DNA molecules. As such, in some cases as subject composition (e.g., kit) or method includes two or more guide RNAs (in the context of a precursor guide RNA array, or not in the context of a precursor guide RNA array, e.g., the guide RNAs can be mature guide RNAs).

Nucleic Acid Modifications

In some cases, a guide RNA comprises one or more modifications, e.g., a base modification, a backbone modification, a sugar modification, etc., to provide the nucleic acid with a new or enhanced feature (e.g., improved stability). As is known in the art, a nucleoside is a base-sugar combination. The base portion of the nucleoside is normally a heterocyclic base. The two most common classes of such heterocyclic bases are the purines and the pyrimidines. Nucleotides are nucleosides that further include a phosphate group covalently linked to the sugar portion of the nucleoside. For those nucleosides that include a pentofuranosyl sugar, the phosphate group can be linked to the 2′, the 3′, or the 5′ hydroxyl moiety of the sugar. In forming oligonucleotides, the phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound. In turn, the respective ends of this linear polymeric compound can be further joined to form a circular compound, however, linear compounds are generally suitable. In addition, linear compounds may have internal nucleotide base complementarity and may therefore fold in a manner as to produce a fully or partially double-stranded compound. Within oligonucleotides, the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide. The normal linkage or backbone of RNA and DNA is a 3′ to 5′ phosphodiester linkage.

Modified Backbones and Modified Internucleoside Linkages

Examples of suitable guide RNA modifications include modified nucleic acid backbones and non-natural internucleoside linkages. Nucleic acids having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone.

Suitable modified oligonucleotide backbones containing a phosphorus atom therein include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates, 5′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, phosphorodiamidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, selenophosphates and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein one or more internucleotide linkages is a 3′ to 3′, 5′ to 5′ or 2′ to 2′ linkage. Suitable oligonucleotides having inverted polarity comprise a single 3′ to 3′ linkage at the 3′-most internucleotide linkage i.e. a single inverted nucleoside residue which may be a basic (the nucleobase is missing or has a hydroxyl group in place thereof). Various salts (such as, for example, potassium or sodium), mixed salts and free acid forms are also included.

In some cases, a guide RNA comprises one or more phosphorothioate and/or heteroatom internucleoside linkages, in particular —CH₂—NH—O—CH₂—, —CH₂—N(CH₃)—O—CH₂— (known as a methylene (methylimino) or MMI backbone), —CH₂—O—N(CH₃)—CH₂—, —CH₂—N(CH₃)—N(CH₃)—CH₂— and —O—N(CH₃)—CH₂—CH₂— (wherein the native phosphodiester internucleotide linkage is represented as —O—P(═O)(OH)—O—CH₂—). MMI type internucleoside linkages are disclosed in the above referenced U.S. Pat. No. 5,489,677. Suitable amide internucleoside linkages are disclosed in t U.S. Pat. No. 5,602,240.

Also suitable are nucleic acids having morpholino backbone structures as described in, e.g., U.S. Pat. No. 5,034,506. For example, in some cases, a guide RNA comprises a 6-membered morpholino ring in place of a ribose ring. In some cases, a phosphorodiamidate or other non-phosphodiester internucleoside linkage replaces a phosphodiester linkage.

Suitable modified polynucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; riboacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂component parts.

Mimetics

A guide RNA can be a nucleic acid mimetic. The term “mimetic” as it is applied to polynucleotides is intended to include polynucleotides wherein only the furanose ring or both the furanose ring and the internucleotide linkage are replaced with non-furanose groups, replacement of only the furanose ring is also referred to in the art as being a sugar surrogate. The heterocyclic base moiety or a modified heterocyclic base moiety is maintained for hybridization with an appropriate target nucleic acid. One such nucleic acid, a polynucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA, the sugar-backbone of a polynucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleotides are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.

One polynucleotide mimetic that has been reported to have excellent hybridization properties is a peptide nucleic acid (PNA). The backbone in PNA compounds is two or more linked aminoethylglycine units which gives PNA an amide containing backbone. The heterocyclic base moieties are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative U.S. patents that describe the preparation of PNA compounds include, but are not limited to: U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262.

Another class of polynucleotide mimetic that has been studied is based on linked morpholino units (morpholino nucleic acid) having heterocyclic bases attached to the morpholino ring. A number of linking groups have been reported that link the morpholino monomeric units in a morpholino nucleic acid. One class of linking groups has been selected to give a non-ionic oligomeric compound. The non-ionic morpholino-based oligomeric compounds are less likely to have undesired interactions with cellular proteins. Morpholino-based polynucleotides are non-ionic mimics of oligonucleotides which are less likely to form undesired interactions with cellular proteins (Dwaine A. Braasch and David R. Corey, Biochemistry, 2002, 41(14), 4503-4510). Morpholino-based polynucleotides are disclosed in U.S. Pat. No. 5,034,506. A variety of compounds within the morpholino class of polynucleotides have been prepared, having a variety of different linking groups joining the monomeric subunits.

A further class of polynucleotide mimetic is referred to as cyclohexenyl nucleic acids (CeNA). The furanose ring normally present in a DNA/RNA molecule is replaced with a cyclohexenyl ring. CeNA DMT protected phosphoramidite monomers have been prepared and used for oligomeric compound synthesis following classical phosphoramidite chemistry. Fully modified CeNA oligomeric compounds and oligonucleotides having specific positions modified with CeNA have been prepared and studied (see Wang et al., J. Am. Chem. Soc., 2000, 122, 8595-8602). In general, the incorporation of CeNA monomers into a DNA chain increases its stability of a DNA/RNA hybrid. CeNA oligoadenylates formed complexes with RNA and DNA complements with similar stability to the native complexes. The study of incorporating CeNA structures into natural nucleic acid structures was shown by NMR and circular dichroism to proceed with easy conformational adaptation.

A further modification includes Locked Nucleic Acids (LNAs) in which the 2′-hydroxyl group is linked to the 4′ carbon atom of the sugar ring thereby forming a 2′-C,4′-C-oxymethylene linkage thereby forming a bicyclic sugar moiety. The linkage can be a methylene (—CH₂—), group bridging the 2′ oxygen atom and the 4′ carbon atom wherein n is 1 or 2 (Singh et al., Chem. Commun., 1998, 4, 455-456). LNA and LNA analogs display very high duplex thermal stabilities with complementary DNA and RNA (Tm=+3 to +10° C.), stability towards 3′-exonucleolytic degradation and good solubility properties. Potent and nontoxic antisense oligonucleotides containing LNAs have been described (Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 5633-5638).

The synthesis and preparation of the LNA monomers adenine, cytosine, guanine, 5-methyl-cytosine, thymine and uracil, along with their oligomerization, and nucleic acid recognition properties have been described (Koshkin et al., Tetrahedron, 1998, 54, 3607-3630). LNAs and preparation thereof are also described in WO 98/39352 and WO 99/14226.

Modified Sugar Moieties

A guide RNA can also include one or more substituted sugar moieties. Suitable polynucleotides comprise a sugar substituent group selected from: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C.sub.1 to C₁₀alkyl or C₂to C₁₀alkenyl and alkynyl. Particularly suitable are O((CH₂)_nO)_mCH₃, O(CH₂)_nOCH₃, O(CH₂)_nNH₂, O(CH₂)_nCH₃, O(CH₂)_nONH₂, and O(CH₂)_nON((CH₂)_nCH₃)₂, where n and m are from 1 to about 10. Other suitable polynucleotides comprise a sugar substituent group selected from: C₁to C₁₀lower alkyl, substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. A suitable modification includes 2′-methoxyethoxy (2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-504) i.e., an alkoxyalkoxy group. A further suitable modification includes 2′-dimethylaminooxyethoxy, i.e., a O(CH₂)₂ON(CH₃)₂group, also known as 2′-DMAOE, as described in examples hereinbelow, and 2′-dimethylaminoethoxyethoxy (also known in the art as 2′-O-dimethyl-amino-ethoxy-ethyl or 2′-DMAEOE), i.e., 2′-O—CH₂—O—CH₂—N(CH₃)₂.

Other suitable sugar substituent groups include methoxy (—O—CH₃), aminopropoxy CH₂CH₂CH₂NH₂), allyl (—CH₂—CH═CH₂), —O-allyl CH₂—CH═CH₂) and fluoro (F). 2′-sugar substituent groups may be in the arabino (up) position or ribo (down) position. A suitable 2′-arabino modification is 2′-F Similar modifications may also be made at other positions on the oligomeric compound, particularly the 3′ position of the sugar on the 3′ terminal nucleoside or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide. Oligomeric compounds may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.

Base Modifications and Substitutions

A guide RNA may also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl (—C═C—CH₃) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine(1H-pyrimido(5,4-b)(1,4)benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido(5,4-b)(1,4)benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9-(2-aminoethoxy)-H-pyrimido(5,4-(b) (1,4)benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido(4,5-b)indol-2-one), pyridoindole cytidine (H-pyrido(3′,2′:4,5)pyrrolo(2,3-d)pyrimidin-2-one).

Heterocyclic base moieties may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC Press, 1993. Certain of these nucleobases are useful for increasing the binding affinity of an oligomeric compound. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi et al., eds., Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are suitable base substitutions, e.g., when combined with 2′-O-methoxyethyl sugar modifications.

Donor Nucleic Acid

In some cases, a system of the present disclosure comprises a donor nucleic acid. By a “donor nucleic acid” or “donor sequence” or “donor polynucleotide” or “donor template” it is meant a nucleic acid sequence to be inserted at the site cleaved by a CRISPR/Cas effector protein (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA, and the like). The donor polynucleotide can contain sufficient homology to a genomic sequence at the target site, e.g. 70%, 80%, 85%, 90%, 95%, or 100% homology with the nucleotide sequences flanking the target site, e.g. within about 50 bases or less of the target site, e.g. within about 30 bases, within about 15 bases, within about 10 bases, within about 5 bases, or immediately flanking the target site, to support homology-directed repair between it and the genomic sequence to which it bears homology. Approximately 25, 50, 100, or 200 nucleotides, or more than 200 nucleotides, of sequence homology between a donor and a genomic sequence (or any integral value between 10 and 200 nucleotides, or more) can support homology-directed repair. Donor polynucleotides can be of any length, e.g. 10 nucleotides or more, 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 500 nucleotides or more, 1000 nucleotides or more, 5000 nucleotides or more, etc.

The donor sequence is typically not identical to the genomic sequence that it replaces. Rather, the donor sequence may contain at least one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the genomic sequence, so long as sufficient homology is present to support homology-directed repair (e.g., for gene correction, e.g., to convert a disease-causing base pair or a non disease-causing base pair). In some embodiments, the donor sequence comprises a non-homologous sequence flanked by two regions of homology, such that homology-directed repair between the target DNA region and the two flanking sequences results in insertion of the non-homologous sequence at the target region. Donor sequences may also comprise a vector backbone containing sequences that are not homologous to the DNA region of interest and that are not intended for insertion into the DNA region of interest. Generally, the homologous region(s) of a donor sequence will have at least 50% sequence identity to a genomic sequence with which recombination is desired. In certain embodiments, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.9% sequence identity is present. Any value between 1% and 100% sequence identity can be present, depending upon the length of the donor polynucleotide.

The donor sequence may comprise certain sequence differences as compared to the genomic sequence, e.g. restriction sites, nucleotide polymorphisms, selectable markers (e.g., drug resistance genes, fluorescent proteins, enzymes etc.), etc., which may be used to assess for successful insertion of the donor sequence at the cleavage site or in some cases may be used for other purposes (e.g., to signify expression at the targeted genomic locus). In some cases, if located in a coding region, such nucleotide sequence differences will not change the amino acid sequence, or will make silent amino acid changes (i.e., changes which do not affect the structure or function of the protein). Alternatively, these sequences differences may include flanking recombination sequences such as FLPs, loxP sequences, or the like, that can be activated at a later time for removal of the marker sequence.

In some cases, the donor sequence is provided to the cell as single-stranded DNA. In some cases, the donor sequence is provided to the cell as double-stranded DNA. It may be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the donor sequence may be protected (e.g., from exonucleolytic degradation) by any convenient method and such methods are known to those of skill in the art. For example, one or more dideoxynucleotide residues can be added to the 3′ terminus of a linear molecule and/or self-complementary oligonucleotides can be ligated to one or both ends. See, for example, Chang et al. (1987) Proc. Natl. Acad Sci USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889. Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues. As an alternative to protecting the termini of a linear donor sequence, additional lengths of sequence may be included outside of the regions of homology that can be degraded without impacting recombination. A donor sequence can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance.

Nucleic Acids

The present disclosure provides one or more nucleic acids comprising one or more of: a donor nucleic acid, a nucleotide sequence encoding variant type V CRISPR/Cas effector polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a type V CRISPR/Cas guide RNA. The present disclosure provides a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide comprising: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a heterologous polypeptide (a fusion partner). The present disclosure provides a recombinant expression vector that comprises a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure. The present disclosure provides a recombinant expression vector that comprises a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a recombinant expression vector that comprises: a) a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a nucleotide sequence encoding a type V CRISPR/Cas guide RNA(s). The present disclosure provides a recombinant expression vector that comprises: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and b) a nucleotide sequence encoding a type V CRISPR/Cas guide RNA(s). In some cases, the nucleotide sequence encoding the variant type V CRISPR/Cas effector polypeptide of the present disclosure and/or the nucleotide sequence encoding the type V CRISPR/Cas guide RNA and/or the nucleotide sequence encoding the fusion polypeptide is operably linked to a promoter that is operable in a cell type of choice (e.g., a prokaryotic cell, a eukaryotic cell, a plant cell, an animal cell, a mammalian cell, a primate cell, a rodent cell, a human cell, etc.). Various nucleic acid and expression vectors are described below in the context of a variant type V CRISPR/Cas effector polypeptide of the present disclosure; these descriptions apply equally to a fusion polypeptide of the present disclosure.

In some cases, a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure, or a fusion polypeptide of the present disclosure, is codon optimized. This type of optimization can entail a mutation of a variant type V CRISPR/Cas effector polypeptide-encoding nucleotide sequence to mimic the codon preferences of the intended host organism or cell while encoding the same protein. Thus, the codons can be changed, but the encoded protein remains unchanged. For example, if the intended target cell was a human cell, a human codon-optimized variant type V CRISPR/Cas effector polypeptide-encoding nucleotide sequence could be used. As another non-limiting example, if the intended host cell were a mouse cell, then a mouse codon-optimized variant type V CRISPR/Cas effector polypeptide-encoding nucleotide sequence could be generated. As another non-limiting example, if the intended host cell were a plant cell, then a plant codon-optimized variant type V CRISPR/Cas effector polypeptide-encoding nucleotide sequence could be generated. As another non-limiting example, if the intended host cell were an insect cell, then an insect codon-optimized variant type V CRISPR/Cas effector polypeptide-encoding nucleotide sequence could be generated.

The present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence of a donor template nucleic acid (where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)); (ii) a nucleotide sequence that encodes a type V CRISPR/Cas guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (iii) a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell). The present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence of a donor template nucleic acid (where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)); and (ii) a nucleotide sequence that encodes a type V CRISPR/Cas guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell). The present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence that encodes a type V CRISPR/Cas guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (ii) a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell).

Suitable expression vectors include viral expression vectors (e.g. viral vectors based on vaccinia virus; poliovirus; adenovirus (see, e.g., Li et al., Invest Opthalmol Vis Sci 35:2543 2549, 1994; Borras et al., Gene Ther 6:515 524, 1999; Li and Davidson, PNAS 92:7700 7704, 1995; Sakamoto et al., H Gene Ther 5:1088 1097, 1999; WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938; WO 95/11984 and WO 95/00655); adeno-associated virus (AAV) (see, e.g., Ali et al., Hum Gene Ther 9:81 86, 1998, Flannery et al., PNAS 94:6916 6921, 1997; Bennett et al., Invest Opthalmol Vis Sci 38:2857 2863, 1997; Jomary et al., Gene Ther 4:683 690, 1997, Rolling et al., Hum Gene Ther 10:641 648, 1999; Ali et al., Hum Mol Genet 5:591 594, 1996; Srivastava in WO 93/09239, Samulski et al., J. Vir. (1989) 63:3822-3828; Mendelson et al., Virol. (1988) 166:154-165; and Flotte et al., PNAS (1993) 90:10613-10617); SV40; herpes simplex virus; human immunodeficiency virus (see, e.g., Miyoshi et al., PNAS 94:10319 23, 1997; Takahashi et al., J Virol 73:7812 7816, 1999); a retroviral vector (e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus, human immunodeficiency virus, myeloproliferative sarcoma virus, and mammary tumor virus); and the like. In some cases, a recombinant expression vector of the present disclosure is a recombinant adeno-associated virus (AAV) vector. In some cases, a recombinant expression vector of the present disclosure is a recombinant lentivirus vector. In some cases, a recombinant expression vector of the present disclosure is a recombinant retroviral vector.

Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector.

In some embodiments, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA is operably linked to a control element, e.g., a transcriptional control element, such as a promoter. In some embodiments, a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure or a fusion polypeptide of the present disclosure is operably linked to a control element, e.g., a transcriptional control element, such as a promoter.

The transcriptional control element can be a promoter. In some cases, the promoter is a constitutively active promoter. In some cases, the promoter is a regulatable promoter. In some cases, the promoter is an inducible promoter. In some cases, the promoter is a tissue-specific promoter. In some cases, the promoter is a cell type-specific promoter. In some cases, the transcriptional control element (e.g., the promoter) is functional in a targeted cell type or targeted cell population. For example, in some cases, the transcriptional control element can be functional in eukaryotic cells, e.g., hematopoietic stem cells (e.g., mobilized peripheral blood (mPB) CD34(+) cell, bone marrow (BM) CD34(+) cell, etc.).

Non-limiting examples of eukaryotic promoters (promoters functional in a eukaryotic cell) include EF1α, those from cytomegalovirus (CMV) immediate early, herpes simplex virus (HSV) thymidine kinase, early and late SV40, long terminal repeats (LTRs) from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression. The expression vector may also include nucleotide sequences encoding protein tags (e.g., 6×His tag, hemagglutinin tag, fluorescent protein, etc.) that can be fused to variant type V CRISPR/Cas effector polypeptide of the present disclosure, thus resulting in a fusion polypeptide.

In some cases, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA and/or a variant type V CRISPR/Cas effector polypeptide of the present disclosure, or a fusion polypeptide of the present disclosure, is operably linked to an inducible promoter. In some cases, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA and/or a variant type V CRISPR/Cas effector polypeptide of the present disclosure is operably linked to a constitutive promoter.

A promoter can be a constitutively active promoter (i.e., a promoter that is constitutively in an active/“ON” state), it may be an inducible promoter (i.e., a promoter whose state, active/“ON” or inactive/“OFF”, is controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein.), it may be a spatially restricted promoter (i.e., transcriptional control element, enhancer, etc.)(e.g., tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, e.g., hair follicle cycle in mice).

Suitable promoters can be derived from viruses and can therefore be referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol II, pol III). Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (Miyagishi et al., Nature Biotechnology 20, 497-500 (2002)), an enhanced U6 promoter (e.g., Xia et al., Nucleic Acids Res. 2003 Sep. 1; 31(17)), a human H1 promoter (H1), and the like.

In some cases, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA is operably linked to (under the control of) a promoter operable in a eukaryotic cell (e.g., a U6 promoter, an enhanced U6 promoter, an H1 promoter, and the like). As would be understood by one of ordinary skill in the art, when expressing an RNA (e.g., a guide RNA) from a nucleic acid (e.g., an expression vector) using a U6 promoter (e.g., in a eukaryotic cell), or another PolIII promoter, the RNA may need to be mutated if there are several Ts in a row (coding for Us in the RNA). This is because a string of Ts (e.g., 5 Ts) in DNA can act as a terminator for polymerase III (Pol III). Thus, in order to ensure transcription of a guide RNA in a eukaryotic cell it may sometimes be necessary to modify the sequence encoding the guide RNA to eliminate runs of Ts. In some cases, a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure is operably linked to a promoter operable in a eukaryotic cell (e.g., a CMV promoter, an EF1α promoter, an estrogen receptor-regulated promoter, and the like).

Examples of inducible promoters include, but are not limited to T7 RNA polymerase promoter, T3 RNA polymerase promoter, Isopropyl-beta-D-thiogalactopyranoside (IPTG)-regulated promoter, lactose induced promoter, heat shock promoter, Tetracycline-regulated promoter, Steroid-regulated promoter, Metal-regulated promoter, estrogen receptor-regulated promoter, etc. Inducible promoters can therefore be regulated by molecules including, but not limited to, doxycycline; estrogen and/or an estrogen analog; IPTG; etc.

Inducible promoters suitable for use include any inducible promoter described herein or known to one of ordinary skill in the art. Examples of inducible promoters include, without limitation, chemically/biochemically-regulated and physically-regulated promoters such as alcohol-regulated promoters, tetracycline-regulated promoters (e.g., anhydrotetracycline (aTc)-responsive promoters and other tetracycline-responsive promoter systems, which include a tetracycline repressor protein (tetR), a tetracycline operator sequence (tetO) and a tetracycline transactivator fusion protein (tTA)), steroid-regulated promoters (e.g., promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid receptor superfamily), metal-regulated promoters (e.g., promoters derived from metallothionein (proteins that bind and sequester metal ions) genes from yeast, mouse and human), pathogenesis-regulated promoters (e.g., induced by salicylic acid, ethylene or benzothiadiazole (BTH)), temperature/heat-inducible promoters (e.g., heat shock promoters), and light-regulated promoters (e.g., light responsive promoters from plant cells).

In some cases, the promoter is a spatially restricted promoter (i.e., cell type specific promoter, tissue specific promoter, etc.) such that in a multi-cellular organism, the promoter is active (i.e., “ON”) in a subset of specific cells. Spatially restricted promoters may also be referred to as enhancers, transcriptional control elements, control sequences, etc. Any convenient spatially restricted promoter may be used as long as the promoter is functional in the targeted host cell (e.g., eukaryotic cell; prokaryotic cell).

In some cases, the promoter is a reversible promoter. Suitable reversible promoters, including reversible inducible promoters are known in the art. Such reversible promoters may be isolated and derived from many organisms, e.g., eukaryotes and prokaryotes. Modification of reversible promoters derived from a first organism for use in a second organism, e.g., a first prokaryote and a second a eukaryote, a first eukaryote and a second a prokaryote, etc., is well known in the art. Such reversible promoters, and systems based on such reversible promoters but also comprising additional control proteins, include, but are not limited to, alcohol regulated promoters (e.g., alcohol dehydrogenase I (alcA) gene promoter, promoters responsive to alcohol transactivator proteins (AlcR), etc.), tetracycline regulated promoters, (e.g., promoter systems including TetActivators, TetON, TetOFF, etc.), steroid regulated promoters (e.g., rat glucocorticoid receptor promoter systems, human estrogen receptor promoter systems, retinoid promoter systems, thyroid promoter systems, ecdysone promoter systems, mifepristone promoter systems, etc.), metal regulated promoters (e.g., metallothionein promoter systems, etc.), pathogenesis-related regulated promoters (e.g., salicylic acid regulated promoters, ethylene regulated promoters, benzothiadiazole regulated promoters, etc.), temperature regulated promoters (e.g., heat shock inducible promoters (e.g., HSP-70, HSP-90, soybean heat shock promoter, etc.), light regulated promoters, synthetic inducible promoters, and the like.

Methods of introducing a nucleic acid (e.g., a nucleic acid comprising a donor polynucleotide sequence, one or more nucleic acids encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure (or a fusion polypeptide of the present disclosure) and/or a type V CRISPR/Cas guide RNA, and the like) into a host cell are known in the art, and any convenient method can be used to introduce a nucleic acid (e.g., an expression construct) into a cell. Suitable methods include e.g., viral infection, transfection, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct microinjection, nanoparticle-mediated nucleic acid delivery, and the like.

Introducing the recombinant expression vector into cells can occur in any culture media and under any culture conditions that promote the survival of the cells. Introducing the recombinant expression vector into a target cell can be carried out in vivo or ex vivo. Introducing the recombinant expression vector into a target cell can be carried out in vitro.

In some embodiments, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be provided as RNA. The RNA can be provided by direct chemical synthesis or may be transcribed in vitro from a DNA (e.g., encoding the variant type V CRISPR/Cas effector polypeptide). Once synthesized, the RNA may be introduced into a cell by any of the well-known techniques for introducing nucleic acids into cells (e.g., microinjection, electroporation, transfection, etc.).

Nucleic acids may be provided to the cells using well-developed transfection techniques; see, e.g. Angel and Yanik (2010) PLoS ONE 5(7): e11756, and the commercially available TransMessenger® reagents from Qiagen, Stemfect™ RNA Transfection Kit from Stemgent, and TransIT®-mRNA Transfection Kit from Minis Bio LLC. See also Beumer et al. (2008) PNAS 105(50):19821-19826.

Vectors may be provided directly to a target host cell. In other words, the cells are contacted with vectors comprising the subject nucleic acids (e.g., recombinant expression vectors having the donor template sequence and encoding a type V CRISPR/Cas guide RNA; recombinant expression vectors encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure (or a fusion polypeptide of the present disclosure); etc.) such that the vectors are taken up by the cells. Methods for contacting cells with nucleic acid vectors that are plasmids, include electroporation, calcium chloride transfection, microinjection, and lipofection are well known in the art. For viral vector delivery, cells can be contacted with viral particles comprising the subject viral expression vectors.

Retroviruses, for example, lentiviruses, are suitable for use in methods of the present disclosure. Commonly used retroviral vectors are “defective”, i.e. unable to produce viral proteins required for productive infection. Rather, replication of the vector requires growth in a packaging cell line. To generate viral particles comprising nucleic acids of interest, the retroviral nucleic acids comprising the nucleic acid are packaged into viral capsids by a packaging cell line. Different packaging cell lines provide a different envelope protein (ecotropic, amphotropic or xenotropic) to be incorporated into the capsid, this envelope protein determining the specificity of the viral particle for the cells (ecotropic for murine and rat; amphotropic for most mammalian cell types including human, dog and mouse; and xenotropic for most mammalian cell types except murine cells). The appropriate packaging cell line may be used to ensure that the cells are targeted by the packaged viral particles. Methods of introducing subject vector expression vectors into packaging cell lines and of collecting the viral particles that are generated by the packaging lines are well known in the art. Nucleic acids can also introduced by direct micro-injection (e.g., injection of RNA).

Vectors used for providing the nucleic acids encoding type V CRISPR/Cas guide RNA and/or a variant type V CRISPR/Cas effector polypeptide of the present disclosure (or a fusion polypeptide of the present disclosure) to a target host cell can include suitable promoters for driving the expression, that is, transcriptional activation, of the nucleic acid of interest. In other words, in some cases, the nucleic acid of interest will be operably linked to a promoter. This may include ubiquitously acting promoters, for example, the CMV-β-actin promoter, or inducible promoters, such as promoters that are active in particular cell populations or that respond to the presence of drugs such as tetracycline. By transcriptional activation, it is intended that transcription will be increased above basal levels in the target cell by 10 fold, by 100 fold, more usually by 1000 fold. In addition, vectors used for providing a nucleic acid encoding a type V CRISPR/Cas guide RNA and/or a variant type V CRISPR/Cas effector polypeptide of the present disclosure to a cell may include nucleic acid sequences that encode for selectable markers in the target cells, so as to identify cells that have taken up the type V CRISPR/Cas guide RNA and/or variant type V CRISPR/Cas effector polypeptide.

A nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure, or a fusion polypeptide of the present disclosure (a fusion polypeptide comprising: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; and b) a heterologous polypeptide), is in some cases an RNA. Thus, a fusion protein of the present disclosure can be introduced into cells as RNA. Methods of introducing RNA into cells are known in the art and may include, for example, direct injection, transfection, or any other method used for the introduction of DNA. A variant type V CRISPR/Cas effector polypeptide of the present disclosure may instead be provided to cells as a polypeptide. Such a polypeptide may optionally be fused to a polypeptide domain that increases solubility of the product. The domain may be linked to the polypeptide through a defined protease cleavage site, e.g. a TEV sequence, which is cleaved by TEV protease. The linker may also include one or more flexible sequences, e.g. from 1 to 10 glycine residues. In some embodiments, the cleavage of the fusion protein is performed in a buffer that maintains solubility of the product, e.g. in the presence of from 0.5 to 2 M urea, in the presence of polypeptides and/or polynucleotides that increase solubility, and the like. Domains of interest include endosomolytic domains, e.g. influenza HA domain; and other polypeptides that aid in production, e.g. IF2 domain, GST domain, GRPE domain, and the like. The polypeptide may be formulated for improved stability. For example, the peptides may be PEGylated, where the polyethyleneoxy group provides for enhanced lifetime in the blood stream.

Additionally, or alternatively, a variant type V CRISPR/Cas effector polypeptide of the present disclosure may be fused to a polypeptide permeant domain to promote uptake by the cell. A number of permeant domains are known in the art and may be used in the non-integrating polypeptides of the present disclosure, including peptides, peptidomimetics, and non-peptide carriers. For example, a permeant peptide may be derived from the third alpha helix of Drosophila melanogaster transcription factor Antennapaedia, referred to as penetratin, which comprises the amino acid sequence RQIKIWFQNRRMKWKK (SEQ ID NO: 135). As another example, the permeant peptide comprises the HIV-1 tat basic region amino acid sequence, which may include, for example, amino acids 49-57 of naturally-occurring tat protein. Other permeant domains include poly-arginine motifs, for example, the region of amino acids 34-56 of HIV-1 rev protein, nona-arginine, octa-arginine, and the like. (See, for example, Futaki et al. (2003) Curr Protein Pept Sci. 2003 April; 4(2): 87-9 and 446; and Wender et al. (2000) Proc. Natl. Acad. Sci. U.S.A 2000 Nov. 21; 97(24):13003-8; published U.S. Patent applications 20030220334; 20030083256; 20030032593; and 20030022831, herein specifically incorporated by reference for the teachings of translocation peptides and peptoids). The nona-arginine (R9) sequence can be used. The site at which the fusion is made may be selected in order to optimize the biological activity, secretion or binding characteristics of the polypeptide. The optimal site will be determined by routine experimentation.

A variant type V CRISPR/Cas effector polypeptide of the present disclosure may be produced in vitro or by eukaryotic cells or by prokaryotic cells, and it may be further processed by unfolding, e.g. heat denaturation, dithiothreitol reduction, etc. and may be further refolded, using methods known in the art.

Modifications of interest that do not alter primary sequence include chemical derivatization of polypeptides, e.g., acylation, acetylation, carboxylation, amidation, etc. Also included are modifications of glycosylation, e.g. those made by modifying the glycosylation patterns of a polypeptide during its synthesis and processing or in further processing steps; e.g. by exposing the polypeptide to enzymes which affect glycosylation, such as mammalian glycosylating or deglycosylating enzymes. Also embraced are sequences that have phosphorylated amino acid residues, e.g. phosphotyrosine, phosphoserine, or phosphothreonine.

Also suitable for inclusion in embodiments of the present disclosure are nucleic acids (e.g., encoding a type V CRISPR/Cas guide RNA, encoding a fusion protein of the present disclosure, etc.) and proteins (e.g., a variant type V CRISPR/Cas effector polypeptide of the present disclosure; a fusion protein of the present disclosure) that have been modified using ordinary molecular biological techniques and synthetic chemistry so as to improve their resistance to proteolytic degradation, to change the target sequence specificity, to optimize solubility properties, to alter protein activity (e.g., transcription modulatory activity, enzymatic activity, etc.) or to render them more suitable. Analogs of such polypeptides include those containing residues other than naturally occurring L-amino acids, e.g. D-amino acids or non-naturally occurring synthetic amino acids. D-amino acids may be substituted for some or all of the amino acid residues.

A variant type V CRISPR/Cas effector polypeptide of the present disclosure may be prepared by in vitro synthesis, using conventional methods as known in the art. Various commercial synthetic apparatuses are available, for example, automated synthesizers by Applied Biosystems, Inc., Beckman, etc. By using synthesizers, naturally occurring amino acids may be substituted with unnatural amino acids. The particular sequence and the manner of preparation will be determined by convenience, economics, purity required, and the like.

If desired, various groups may be introduced into the peptide during synthesis or during expression, which allow for linking to other molecules or to a surface. Thus, cysteines can be used to make thioethers, histidines for linking to a metal ion complex, carboxyl groups for forming amides or esters, amino groups for forming amides, and the like.

A variant type V CRISPR/Cas effector polypeptide of the present disclosure may also be isolated and purified in accordance with conventional methods of recombinant synthesis. A lysate may be prepared of the expression host and the lysate purified using high performance liquid chromatography (HPLC), exclusion chromatography, gel electrophoresis, affinity chromatography, or other purification technique. For the most part, the compositions which are used will comprise 20% or more by weight of the desired product, more usually 75% or more by weight, preferably 95% or more by weight, and for therapeutic purposes, usually 99.5% or more by weight, in relation to contaminants related to the method of preparation of the product and its purification. Usually, the percentages will be based upon total protein. Thus, in some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, or a fusion polypeptide of the present disclosure, is at least 80% pure, at least 85% pure, at least 90% pure, at least 95% pure, at least 98% pure, or at least 99% pure (e.g., free of contaminants, non-variant type V CRISPR/Cas proteins or other macromolecules, etc.).

To induce cleavage or any desired modification to a target nucleic acid (e.g., genomic DNA), or any desired modification to a polypeptide associated with target nucleic acid, the type V CRISPR/Cas guide RNA and/or the variant type V CRISPR/Cas effector polypeptide of the present disclosure and/or the donor template sequence, whether they be introduced as nucleic acids or polypeptides, are provided to the cells for about 30 minutes to about 24 hours, e.g., 1 hour, 1.5 hours, 2 hours, 2.5 hours, 3 hours, 3.5 hours 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 12 hours, 16 hours, 18 hours, 20 hours, or any other period from about 30 minutes to about 24 hours, which may be repeated with a frequency of about every day to about every 4 days, e.g., every 1.5 days, every 2 days, every 3 days, or any other frequency from about every day to about every four days. The agent(s) may be provided to the subject cells one or more times, e.g. one time, twice, three times, or more than three times, and the cells allowed to incubate with the agent(s) for some amount of time following each contacting event e.g. 16-24 hours, after which time the media is replaced with fresh media and the cells are cultured further.

In cases in which two or more different targeting complexes are provided to the cell (e.g., two different type V CRISPR/Cas guide RNAs that are complementary to different sequences within the same or different target nucleic acid), the complexes may be provided simultaneously (e.g. as two polypeptides and/or nucleic acids), or delivered simultaneously. Alternatively, they may be provided consecutively, e.g. the targeting complex being provided first, followed by the second targeting complex, etc. or vice versa.

To improve the delivery of a DNA vector into a target cell, the DNA can be protected from damage and its entry into the cell facilitated, for example, by using lipoplexes and polyplexes. Thus, in some cases, a nucleic acid of the present disclosure (e.g., a recombinant expression vector of the present disclosure) can be covered with lipids in an organized structure like a micelle or a liposome. When the organized structure is complexed with DNA it is called a lipoplex. There are three types of lipids, anionic (negatively-charged), neutral, or cationic (positively-charged). Lipoplexes that utilize cationic lipids have proven utility for gene transfer. Cationic lipids, due to their positive charge, naturally complex with the negatively charged DNA. Also, as a result of their charge, they interact with the cell membrane. Endocytosis of the lipoplex then occurs, and the DNA is released into the cytoplasm. The cationic lipids also protect against degradation of the DNA by the cell.

Complexes of polymers with DNA are called polyplexes. Most polyplexes consist of cationic polymers and their production is regulated by ionic interactions. One large difference between the methods of action of polyplexes and lipoplexes is that polyplexes cannot release their DNA load into the cytoplasm, so to this end, co-transfection with endosome-lytic agents (to lyse the endosome that is made during endocytosis) such as inactivated adenovirus must occur. However, this is not always the case; polymers such as polyethylenimine have their own method of endosome disruption as does chitosan and trimethylchitosan.

Dendrimers, a highly branched macromolecule with a spherical shape, may be also be used to genetically modify stem cells. The surface of the dendrimer particle may be functionalized to alter its properties. In particular, it is possible to construct a cationic dendrimer (i.e., one with a positive surface charge). When in the presence of genetic material such as a DNA plasmid, charge complementarity leads to a temporary association of the nucleic acid with the cationic dendrimer. On reaching its destination, the dendrimer-nucleic acid complex can be taken up into a cell by endocytosis.

In some cases, a nucleic acid of the disclosure (e.g., an expression vector) includes an insertion site for a guide sequence of interest. For example, a nucleic acid can include an insertion site for a guide sequence of interest, where the insertion site is immediately adjacent to a nucleotide sequence encoding the portion of a type V CRISPR/Cas guide RNA that does not change when the guide sequence is changed to hybridized to a desired target sequence (e.g., sequences that contribute to the type V CRISRP/Cas polypeptide-binding aspect of the guide RNA, e.g., the sequences that contribute to the dsRNA duplex(es) of the type V CRISPR/Cas guide RNA—this portion of the guide RNA can also be referred to as the ‘scaffold’ or ‘constant region’ of the guide RNA). Thus, in some cases, a subject nucleic acid (e.g., an expression vector) includes a nucleotide sequence encoding a type V CRISPR/Cas guide RNA, except that the portion encoding the guide sequence portion of the guide RNA is an insertion sequence (an insertion site). An insertion site is any nucleotide sequence used for the insertion of a desired sequence. “Insertion sites” for use with various technologies are known to those of ordinary skill in the art and any convenient insertion site can be used. An insertion site can be for any method for manipulating nucleic acid sequences. For example, in some cases the insertion site is a multiple cloning site (MCS) (e.g., a site including one or more restriction enzyme recognition sequences), a site for ligation independent cloning, a site for recombination-based cloning (e.g., recombination based on att sites), a nucleotide sequence recognized by a CRISPR/Cas (e.g. Cas9) based technology, and the like.

An insertion site can be any desirable length, and can depend on the type of insertion site (e.g., can depend on whether (and how many) the site includes one or more restriction enzyme recognition sequences, whether the site includes a target site for a CRISPR/Cas protein, etc.). In some cases, an insertion site of a subject nucleic acid is 3 or more nucleotides (nt) in length (e.g., 5 or more, 8 or more, 10 or more, 15 or more, 17 or more, 18 or more, 19 or more, 20 or more or 25 or more, or 30 or more nt in length). In some cases, the length of an insertion site of a subject nucleic acid has a length in a range of from 2 to 50 nucleotides (nt) (e.g., from 2 to 40 nt, from 2 to 30 nt, from 2 to 25 nt, from 2 to 20 nt, from 5 to 50 nt, from 5 to 40 nt, from 5 to 30 nt, from 5 to 25 nt, from 5 to 20 nt, from 10 to 50 nt, from 10 to 40 nt, from 10 to 30 nt, from 10 to 25 nt, from 10 to 20 nt, from 17 to 50 nt, from 17 to 40 nt, from 17 to 30 nt, from 17 to 25 nt). In some cases, the length of an insertion site of a subject nucleic acid has a length in a range of from 5 to 40 nt.

Modified Host Cells

The present disclosure provides a modified cell comprising a variant type V CRISPR/Cas polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure. The description, below, of modified host cells that comprise a variant type V CRISPR/Cas polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure apply equally to a modified host cell comprising a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. Thus, for example, the present disclosure provides a modified host cell comprising a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a modified cell comprising a variant type V CRISPR/Cas polypeptide of the present disclosure, where the modified cell is a cell that does not normally comprise a variant type V CRISPR/Cas polypeptide of the present disclosure. The present disclosure provides a modified cell (e.g., a genetically modified cell) comprising nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with an mRNA comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure; and b) a nucleotide sequence encoding a type V CRISP/Cas guide RNA of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure e; b) a nucleotide sequence encoding a type V CRISPR/Cas guide RNA of the present disclosure; and c) a nucleotide sequence encoding a donor template.

A cell that serves as a recipient for a variant type V CRISPR/Cas polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure and/or a type V CRISPR/Cas guide RNA of the present disclosure, can be any of a variety of cells, including, e.g., in vitro cells; in vivo cells; ex vivo cells; primary cells; cancer cells; animal cells; plant cells; algal cells; fungal cells; etc. A cell that serves as a recipient for variant type V CRISPR/Cas polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure and/or a guide RNA of the present disclosure is referred to as a “host cell” or a “target cell.” A host cell or a target cell can be a recipient of a type V CRISPR/Cas system of the present disclosure. A host cell or a target cell can be a recipient of a RNP of the present disclosure. A host cell or a target cell can be a recipient of a single component of a system of the present disclosure.

Non-limiting examples of cells (target cells) include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant (e.g., cells from plant crops, fruits, vegetables, grains, soy bean, corn, maize, wheat, seeds, tomatoes, rice, cassava, sugarcane, pumpkin, hay, potatoes, cotton, Cannabis, tobacco, flowering plants, conifers, gymnosperms, angiosperms, ferns, clubmosses, hornworts, liverworts, mosses, dicotyledons, monocotyledons, etc.), an algal cell, (e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like), seaweeds (e.g. kelp) a fungal cell (e.g., a yeast cell, a cell from a mushroom), an animal cell, a cell from an invertebrate animal (e.g., fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal (e.g., an ungulate (e.g., a pig, a cow, a goat, a sheep); a rodent (e.g., a rat, a mouse); a non-human primate; a human; a feline (e.g., a cat); a canine (e.g., a dog); etc.), and the like. In some cases, the cell is a cell that does not originate from a natural organism (e.g., the cell can be a synthetically made cell; also referred to as an artificial cell).

A cell can be an in vitro cell (e.g., established cultured cell line). A cell can be an ex vivo cell (cultured cell from an individual). A cell can be and in vivo cell (e.g., a cell in an individual). A cell can be an isolated cell. A cell can be a cell inside of an organism. A cell can be an organism. A cell can be a cell in a cell culture (e.g., in vitro cell culture). A cell can be one of a collection of cells. A cell can be a prokaryotic cell or derived from a prokaryotic cell. A cell can be a bacterial cell or can be derived from a bacterial cell. A cell can be an archaeal cell or derived from an archaeal cell. A cell can be a eukaryotic cell or derived from a eukaryotic cell. A cell can be a plant cell or derived from a plant cell. A cell can be an animal cell or derived from an animal cell. A cell can be an invertebrate cell or derived from an invertebrate cell. A cell can be a vertebrate cell or derived from a vertebrate cell. A cell can be a mammalian cell or derived from a mammalian cell. A cell can be a rodent cell or derived from a rodent cell. A cell can be a human cell or derived from a human cell. A cell can be a microbe cell or derived from a microbe cell. A cell can be a fungi cell or derived from a fungi cell. A cell can be an insect cell. A cell can be an arthropod cell. A cell can be a protozoan cell. A cell can be a helminth cell.

Suitable cells include a stem cell (e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell; a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.); a somatic cell, e.g. a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, etc.

Suitable cells include human embryonic stem cells, fetal cardiomyocytes, myofibroblasts, mesenchymal stem cells, cardiomyocytes, adipocytes, totipotent cells, pluripotent cells, blood stem cells, myoblasts, adult stem cells, bone marrow cells, mesenchymal cells, embryonic stem cells, parenchymal cells, epithelial cells, endothelial cells, mesothelial cells, fibroblasts, osteoblasts, chondrocytes, exogenous cells, endogenous cells, stem cells, hematopoietic stem cells, bone-marrow derived progenitor cells, myocardial cells, skeletal cells, fetal cells, undifferentiated cells, multi-potent progenitor cells, unipotent progenitor cells, monocytes, cardiac myoblasts, skeletal myoblasts, macrophages, capillary endothelial cells, xenogenic cells, allogenic cells, and post-natal stem cells.

In some cases, the cell is an immune cell, a neuron, an epithelial cell, and endothelial cell, or a stem cell. In some cases, the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage. In some cases, the immune cell is a cytotoxic T cell. In some cases, the immune cell is a helper T cell. In some cases, the immune cell is a regulatory T cell (Treg).

In some cases, the cell is a stem cell. Stem cells include adult stem cells. Adult stem cells are also referred to as somatic stem cells.

Adult stem cells are resident in differentiated tissue, but retain the properties of self-renewal and ability to give rise to multiple cell types, usually cell types typical of the tissue in which the stem cells are found. Numerous examples of somatic stem cells are known to those of skill in the art, including muscle stem cells; hematopoietic stem cells; epithelial stem cells; neural stem cells; mesenchymal stem cells; mammary stem cells; intestinal stem cells; mesodermal stem cells; endothelial stem cells; olfactory stem cells; neural crest stem cells; and the like.

Stem cells of interest include mammalian stem cells, where the term “mammalian” refers to any animal classified as a mammal, including humans; non-human primates; domestic and farm animals; and zoo, laboratory, sports, or pet animals, such as dogs, horses, cats, cows, mice, rats, rabbits, etc. In some cases, the stem cell is a human stem cell. In some cases, the stem cell is a rodent (e.g., a mouse; a rat) stem cell. In some cases, the stem cell is a non-human primate stem cell.

Stem cells can express one or more stem cell markers, e.g., SOX9, KRT19, KRT7, LGR5, CA9, FXYD2, CDH6, CLDN18, TSPAN8, BPIFB1, OLFM4, CDH17, and PPARGC1A.

In some embodiments, the stem cell is a hematopoietic stem cell (HSC). HSCs are mesoderm-derived cells that can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac. HSCs are characterized as CD34+ and CD3−. HSCs can repopulate the erythroid, neutrophil-macrophage, megakaryocyte and lymphoid hematopoietic cell lineages in vivo. In vitro, HSCs can be induced to undergo at least some self-renewing cell divisions and can be induced to differentiate to the same lineages as is seen in vivo. As such, HSCs can be induced to differentiate into one or more of erythroid cells, megakaryocytes, neutrophils, macrophages, and lymphoid cells.

In other embodiments, the stem cell is a neural stem cell (NSC). Neural stem cells (NSCs) are capable of differentiating into neurons, and glia (including oligodendrocytes, and astrocytes). A neural stem cell is a multipotent stem cell which is capable of multiple divisions, and under specific conditions can produce daughter cells which are neural stem cells, or neural progenitor cells that can be neuroblasts or glioblasts, e.g., cells committed to become one or more types of neurons and glial cells respectively. Methods of obtaining NSCs are known in the art.

In other embodiments, the stem cell is a mesenchymal stem cell (MSC). MSCs originally derived from the embryonal mesoderm and isolated from adult bone marrow, can differentiate to form muscle, bone, cartilage, fat, marrow stroma, and tendon. Methods of isolating MSC are known in the art; and any known method can be used to obtain MSC. See, e.g., U.S. Pat. No. 5,736,396, which describes isolation of human MSC.

A cell is in some cases a plant cell. A plant cell can be a cell of a monocotyledon. A cell can be a cell of a dicotyledon.

In some cases, the cell is a plant cell. For example, the cell can be a cell of a major agricultural plant, e.g., Barley, Beans (Dry Edible), Canola, Corn, Cotton (Pima), Cotton (Upland), Flaxseed, Hay (Alfalfa), Hay (Non-Alfalfa), Oats, Peanuts, Rice, Sorghum, Soybeans, Sugarbeets, Sugarcane, Sunflowers (Oil), Sunflowers (Non-Oil), Sweet Potatoes, Tobacco (Burley), Tobacco (Flue-cured), Tomatoes, Wheat (Durum), Wheat (Spring), Wheat (Winter), and the like. As another example, the cell is a cell of a vegetable crops which include but are not limited to, e.g., alfalfa sprouts, aloe leaves, arrow root, arrowhead, artichokes, asparagus, bamboo shoots, banana flowers, bean sprouts, beans, beet tops, beets, bittermelon, bok choy, broccoli, broccoli rabe (rappini), brussels sprouts, cabbage, cabbage sprouts, cactus leaf (nopales), calabaza, cardoon, carrots, cauliflower, celery, chayote, chinese artichoke (crosnes), chinese cabbage, chinese celery, chinese chives, choy sum, chrysanthemum leaves (tung ho), collard greens, corn stalks, corn-sweet, cucumbers, daikon, dandelion greens, dasheen, dau mue (pea tips), donqua (winter melon), eggplant, endive, escarole, fiddle head ferns, field cress, frisee, gai choy (chinese mustard), gailon, galanga (siam, thai ginger), garlic, ginger root, gobo, greens, hanover salad greens, huauzontle, jerusalem artichokes, jicama, kale greens, kohlrabi, lamb's quarters (quilete), lettuce (bibb), lettuce (boston), lettuce (boston red), lettuce (green leaf), lettuce (iceberg), lettuce (lolla rossa), lettuce (oak leaf—green), lettuce (oak leaf—red), lettuce (processed), lettuce (red leaf), lettuce (romaine), lettuce (ruby romaine), lettuce (russian red mustard), linkok, lo bok, long beans, lotus root, mache, maguey (agave) leaves, malanga, mesculin mix, mizuna, moap (smooth luffa), moo, moqua (fuzzy squash), mushrooms, mustard, nagaimo, okra, ong choy, onions green, opo (long squash), ornamental corn, ornamental gourds, parsley, parsnips, peas, peppers (bell type), peppers, pumpkins, radicchio, radish sprouts, radishes, rape greens, rape greens, rhubarb, romaine (baby red), rutabagas, salicornia (sea bean), sinqua (angled/ridged luffa), spinach, squash, straw bales, sugarcane, sweet potatoes, swiss chard, tamarindo, taro, taro leaf, taro shoots, tatsoi, tepeguaje (guaje), tindora, tomatillos, tomatoes, tomatoes (cherry), tomatoes (grape type), tomatoes (plum type), tumeric, turnip tops greens, turnips, water chestnuts, yampi, yams (names), yu choy, yuca (cassava), and the like.

A cell is in some cases an arthropod cell. For example, the cell can be a cell of a sub-order, a family, a sub-family, a group, a sub-group, or a species of, e.g., Chelicerata, Myriapodia, Hexipodia, Arachnida, Insecta, Archaeognatha, Thysanura, Palaeoptera, Ephemeroptera, Odonata, Anisoptera, Zygoptera, Neoptera, Exopterygota, Plecoptera, Embioptera, Orthoptera, Zoraptera, Dermaptera, Dictyoptera, Notoptera, Grylloblattidae, Mantophasmatidae, Phasmatodea, Blattaria, Isoptera, Mantodea, Parapneuroptera, Psocoptera, Thysanoptera, Phthiraptera, Hemiptera, Endopterygota or Holometabola, Hymenoptera, Coleoptera, Strepsiptera, Raphidioptera, Megaloptera, Neuroptera, Mecoptera, Siphonaptera, Diptera, Trichoptera, or Lepidoptera.

A cell is in some cases an insect cell. For example, in some cases, the cell is a cell of a mosquito, a grasshopper, a true bug, a fly, a flea, a bee, a wasp, an ant, a louse, a moth, or a beetle.

Kits

The present disclosure provides a kit comprising a system of the present disclosure, or a component of a system of the present disclosure.

A kit of the present disclosure can comprise: a) a variant type V CRISPR/Cas polypeptide of the present disclosure and a type V CRISPR/Cas guide RNA; b) a variant type V CRISPR/Cas polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; c) a fusion polypeptide of the present disclosure and a type V CRISPR/Cas guide RNA; d) a fusion polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; e) an mRNA encoding a variant type V CRISPR/Cas polypeptide of the present disclosure; and a type V CRISPR/Cas guide RNA; f) an mRNA encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; g) an mRNA encoding a fusion polypeptide of the present disclosure; and a type V CRISPR/Cas guide RNA; h) an mRNA encoding a fusion polypeptide of the present disclosure, a type V CRISPR/Cas guide RNA, and a donor template nucleic acid; i) a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure and a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; j) a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a donor template nucleic acid; k) a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; 1) a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, a nucleotide sequence encoding a type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a donor template nucleic acid; m) a first recombinant expression vector comprising a nucleotide sequence encoding aa variant type V CRISPR/Cas polypeptide of the present disclosure and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; n) a first recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; and a donor template nucleic acid; o) a first recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; p) a first recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, and a second recombinant expression vector comprising a nucleotide sequence encoding a type V CRISPR/Cas guide RNA; and a donor template nucleic acid; q) a recombinant expression vector comprising a nucleotide sequence encoding a variant type V CRISPR/Cas polypeptide of the present disclosure, a nucleotide sequence encoding a first type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a second type V CRISPR/Cas guide RNA; or r) a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, a nucleotide sequence encoding a first type V CRISPR/Cas guide RNA, and a nucleotide sequence encoding a second type V CRISPR/Cas guide RNA; or some variation of one of (a) through (r).

A kit of the present disclosure can comprise: a) a component, as described above, of a system of the present disclosure, or can comprise a system of the present disclosure; and b) one or more additional reagents, e.g., i) a buffer; ii) a protease inhibitor; iii) a nuclease inhibitor; iv) a reagent required to develop or visualize a detectable label; v) a positive and/or negative control target DNA; vi) a positive and/or negative control type V CRISPR/Cas guide RNA; and the like. A kit of the present disclosure can comprise: a) a component, as described above, of a system of the present disclosure, or can comprise a system of the present disclosure; and b) a therapeutic agent.

A kit of the present disclosure can comprise a recombinant expression vector comprising: a) an insertion site for inserting a nucleic acid comprising a nucleotide sequence encoding a portion of a type V CRISPR/Cas guide RNA that hybridizes to a target nucleotide sequence in a target nucleic acid; and b) a nucleotide sequence encoding the variant type V CRISPR/Cas effector polypeptide-binding portion of a type V CRISPR/Cas guide RNA. A kit of the present disclosure can comprise a recombinant expression vector comprising: a) an insertion site for inserting a nucleic acid comprising a nucleotide sequence encoding a portion of a type V CRISPR/Cas guide RNA that hybridizes to a target nucleotide sequence in a target nucleic acid; b) a nucleotide sequence encoding the variant type V CRISPR/Cas effector polypeptide-binding portion of a type V CRISPR/Cas guide RNA; and c) a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure.

Utility

A variant type V CRISPR/Cas effector polypeptide of the present disclosure, or a fusion polypeptide of the present disclosure, finds use in a variety of methods (e.g., in combination with a type V CRISPR/Cas guide RNA and in some cases further in combination with a donor template). For example, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be used to (i) modify (e.g., cleave, e.g., nick; methylate; base edit; etc.) target nucleic acid (DNA or RNA; single stranded or double stranded); (ii) modulate transcription of a target nucleic acid; (iii) label a target nucleic acid; (iv) bind a target nucleic acid (e.g., for purposes of isolation, labeling, imaging, tracking, etc.); (v) modify a polypeptide (e.g., a histone) associated with a target nucleic acid; and the like. Thus, the present disclosure provides a method of modifying a target nucleic acid. In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting the target nucleic acid with: a) a variant type V CRISPR/Cas effector polypeptide (or fusion polypeptide) of the present disclosure; and b) one or more (e.g., two) type V CRISPR/Cas guide RNAs. In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting the target nucleic acid with: a) a variant type V CRISPR/Cas effector polypeptide of the present disclosure; b) a type V CRISPR/Cas guide RNA; and c) a donor nucleic acid (e.g., a donor template). In some cases, the contacting step is carried out in a cell in vitro. In some cases, the contacting step is carried out in a cell in vivo. In some cases, the contacting step is carried out in a cell ex vivo.

Because a method that uses a variant type V CRISPR/Cas effector polypeptide of the present disclosure includes binding of the variant type V CRISPR/Cas effector polypeptide to a particular region in a target nucleic acid (by virtue of being targeted there by an associated type V CRISPR/Cas guide RNA), the methods are generally referred to herein as methods of binding (e.g., a method of binding a target nucleic acid). However, it is to be understood that in some cases, while a method of binding may result in nothing more than binding of the target nucleic acid, in other cases, the method can have different final results (e.g., the method can result in modification of the target nucleic acid, e.g., cleavage/methylation/etc., modulation of transcription from the target nucleic acid; modulation of translation of the target nucleic acid; genome editing; modulation of a protein associated with the target nucleic acid; isolation of the target nucleic acid; etc.).

For examples of suitable methods, see, for example, Jinek et al., Science. 2012 Aug. 17; 337(6096):816-21; Chylinski et al., RNA Biol. 2013 May; 10(5):726-37; Ma et al., Biomed Res Int. 2013; 2013:270805; Hou et al., Proc Natl Acad Sci USA. 2013 Sep. 24; 110(39):15644-9; Jinek et al., Elife. 2013; 2:e00471; Pattanayak et al., Nat Biotechnol. 2013 September; 31(9):839-43; Qi et al, Cell. 2013 Feb. 28; 152(5):1173-83; Wang et al., Cell. 2013 May 9; 153(4):910-8; Auer et al., Genome Res. 2013 Oct. 31; Chen et al., Nucleic Acids Res. 2013 Nov. 1; 41(20):e19; Cheng et al., Cell Res. 2013 October; 23(10):1163-71; Cho et al., Genetics. 2013 November; 195(3):1177-80; DiCarlo et al., Nucleic Acids Res. 2013 April; 41(7):4336-43; Dickinson et al., Nat Methods. 2013 October; 10(10):1028-34; Ebina et al., Sci Rep. 2013; 3:2510; Fujii et al, Nucleic Acids Res. 2013 Nov. 1; 41(20):e187; Hu et al., Cell Res. 2013 November; 23(11):1322-5; Jiang et al., Nucleic Acids Res. 2013 Nov. 1; 41(20):e188; Larson et al., Nat Protoc. 2013 November; 8(11):2180-96; Mali et. at., Nat Methods. 2013 October; 10(10):957-63; Nakayama et al., Genesis. 2013 December; 51(12):835-43; Ran et al., Nat Protoc. 2013 November; 8(11):2281-308; Ran et al., Cell. 2013 Sep. 12; 154(6):1380-9; Upadhyay et al., G3 (Bethesda). 2013 Dec. 9; 3(12):2233-8; Walsh et al., Proc Natl Acad Sci USA. 2013 Sep. 24; 110(39):15514-5; Xie et al., Mol Plant. 2013 Oct. 9; Yang et al., Cell. 2013 Sep. 12; 154(6):1370-9; and U.S. patents and patent applications: U.S. Pat. Nos. 8,906,616; 8,895,308; 8,889,418; 8,889,356; 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231; 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557; 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063; 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405; 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; each of which is hereby incorporated by reference in its entirety.

For example, the present disclosure provides (but is not limited to) methods of cleaving a target nucleic acid; methods of editing a target nucleic acid; methods of modulating transcription from a target nucleic acid; methods of isolating a target nucleic acid, methods of binding a target nucleic acid, methods of imaging a target nucleic acid, methods of modifying a target nucleic acid, and the like.

As used herein, the terms/phrases “contact a target nucleic acid” and “contacting a target nucleic acid”, for example, with a variant type V CRISPR/Cas effector polypeptide of the present disclosure or with a fusion polypeptide of the present disclosure, etc., encompass all methods for contacting the target nucleic acid. For example, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be provided to a cell as protein, RNA (encoding the variant type V CRISPR/Cas effector polypeptide), or DNA (encoding the variant type V CRISPR/Cas effector polypeptide); while a type V CRISPR/Cas guide RNA can be provided as a guide RNA or as a nucleic acid encoding the guide RNA. As such, when, for example, performing a method in a cell (e.g., inside of a cell in vitro, inside of a cell in vivo, inside of a cell ex vivo), a method that includes contacting the target nucleic acid encompasses the introduction into the cell of any or all of the components in their active/final state (e.g., in the form of a protein(s) for variant type V CRISPR/Cas effector polypeptide; in the form of a protein for a fusion polypeptide; in the form of an RNA in some cases for the guide RNA), and also encompasses the introduction into the cell of one or more nucleic acids encoding one or more of the components (e.g., nucleic acid(s) comprising nucleotide sequence(s) encoding a variant type V CRISPR/Cas effector polypeptide or a fusion polypeptide comprising a variant type V CRISPR/Cas effector polypeptide, nucleic acid(s) comprising nucleotide sequence(s) encoding guide RNA(s), nucleic acid comprising a nucleotide sequence encoding a donor template, and the like). Because the methods can also be performed in vitro outside of a cell, a method that includes contacting a target nucleic acid, (unless otherwise specified) encompasses contacting outside of a cell in vitro, inside of a cell in vitro, inside of a cell in vivo, inside of a cell ex vivo, etc.

In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting a target nucleic acid with a variant type V CRISPR/Cas effector polypeptide of the present disclosure, or with a fusion polypeptide of the present disclosure. In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting a target nucleic acid with a variant type V CRISPR/Cas effector polypeptide of the present disclosure and a type V CRISPR/Cas guide RNA. In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting a target nucleic acid with a variant type V CRISPR/Cas effector polypeptide of the present disclosure, a first type V CRISPR/Cas guide RNA, and a second type V CRISPR/Cas guide RNA In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting a target nucleic acid with a variant type V CRISPR/Cas effector polypeptide of the present disclosure and a type V CRISPR/Cas guide RNA and a donor DNA template.

Introducing Components into a Target Cell

A guide RNA (or a nucleic acid comprising a nucleotide sequence encoding the guide RNA) and/or a variant type V CRISPR/Cas effector polypeptide of the present disclosure (or a nucleic acid comprising a nucleotide sequence encoding the variant type V CRISPR/Cas effector polypeptide), and optionally also a donor template nucleic acid, can be introduced into a host cell by any of a variety of well-known methods. As a non-limiting example, a guide RNA and/or a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be combined with a lipid. As a non-limiting example, a guide RNA, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, and a donor template nucleic acid, can be combined with a lipid. As another non-limiting example, a guide RNA and/or variant type V CRISPR/Cas effector polypeptide of the present disclosure can be combined with a particle, or formulated into a particle. As another non-limiting example, a guide RNA, a variant type V CRISPR/Cas effector polypeptide of the present disclosure, and a donor template nucleic acid, can be combined with a particle, or formulated into a particle.

Methods of introducing a nucleic acid and/or protein into a host cell are known in the art, and any convenient method can be used to introduce a subject nucleic acid (e.g., an expression construct/vector) into a target cell (e.g., prokaryotic cell, eukaryotic cell, plant cell, animal cell, mammalian cell, human cell, and the like). Suitable methods include, e.g., viral infection, transfection, conjugation, protoplast fusion, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct micro injection, nanoparticle-mediated nucleic acid delivery (see, e.g., Panyam et al. Adv Drug Deliv Rev. 2012 Sep. 13. pii: 50169-409X(12)00283-9. doi: 10.1016/j.addr.2012.09.023), and the like.

A guide RNA can be introduced, e.g., as a DNA molecule encoding the guide RNA, or can be provided directly as an RNA molecule (or a hybrid molecule when applicable). In some cases, a variant type V CRISPR/Cas effector polypeptide of the present disclosure is provided as a nucleic acid (e.g., an mRNA, a DNA, a plasmid, an expression vector, a viral vector, etc.) that encodes the protein. In some cases, the variant type V CRISPR/Cas effector protein is provided directly as a protein (e.g., without an associated guide RNA or with an associate guide RNA, i.e., as a ribonucleoprotein complex—RNP). Like a guide RNA, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be introduced into a cell (provided to the cell) by any convenient method; such methods are known to those of ordinary skill in the art. As an illustrative example, a variant type V CRISPR/Cas effector polypeptide of the present disclosure can be injected directly into a cell (e.g., with or without a guide RNA or nucleic acid encoding a guide RNA). As another example, a pre-formed complex of a variant type V CRISPR/Cas effector polypeptide of the present disclosure and a guide RNA (an RNP) can be introduced into a cell (e.g., eukaryotic cell) (e.g., via injection, via nucleofection; via a protein transduction domain (PTD) conjugated to one or more components, e.g., conjugated to the variant type V CRISPR/Cas effector protein, conjugated to a guide RNA; etc.).

In some cases, a nucleic acid (e.g., a guide RNA; a nucleic acid comprising a nucleotide sequence encoding a variant type V CRISPR/Cas effector polypeptide of the present disclosure; a nucleic acid comprising a nucleotide sequence encoding a guide RNA; a donor template nucleic acid; etc.) and/or a polypeptide (e.g., a variant type V CRISPR/Cas effector polypeptide of the present disclosure) is delivered to a cell (e.g., a target host cell) in a particle, or associated with a particle. The terms “particle” and “nanoparticle” can be used interchangeably, as appropriate.

This can be achieved, e.g., using particles or lipid envelopes, e.g., a ribonucleoprotein (RNP) complex can be delivered via a particle, e.g., a delivery particle comprising lipid or lipidoid and hydrophilic polymer, e.g., a cationic lipid and a hydrophilic polymer, for instance wherein the cationic lipid comprises 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or 1,2-ditetradecanoyl-sn-glycero-3-phosphocholine (DMPC) and/or wherein the hydrophilic polymer comprises ethylene glycol or polyethylene glycol (PEG); and/or wherein the particle further comprises cholesterol (e.g., particle from formulation 1=DOTAP 100, DMPC 0, PEG 0, Cholesterol 0; formulation number 2=DOTAP 90, DMPC 0, PEG 10, Cholesterol 0; formulation number 3=DOTAP 90, DMPC 0, PEG 5, Cholesterol 5).

A variant type V CRISPR/Cas effector polypeptide of the present disclosure (or an mRNA or a DNA comprising a nucleotide sequence encoding the protein) and/or a guide RNA (or a nucleic acid such as one or more expression vectors encoding the guide RNA) may be delivered simultaneously using particles or lipid envelopes. For example, a biodegradable core-shell structured nanoparticle with a poly (β-amino ester) (PBAE) core enveloped by a phospholipid bilayer shell can be used. In some cases, particles/nanoparticles based on self assembling bioadhesive polymers are used; such particles/nanoparticles may be applied to oral delivery of peptides, intravenous delivery of peptides and nasal delivery of peptides, e.g., to the brain. Other embodiments, such as oral absorption and ocular delivery of hydrophobic drugs are also contemplated. A molecular envelope technology, which involves an engineered polymer envelope which is protected and delivered to the site of the disease, can be used. Doses of about 5 mg/kg can be used, with single or multiple doses, depending on various factors, e.g., the target tissue.

Lipidoid compounds (e.g., as described in US patent publication 20110293703) are also useful in the administration of polynucleotides, and can be used. In one aspect, aminoalcohol lipidoid compounds are combined with an agent to be delivered to a cell or a subject to form microparticles, nanoparticles, liposomes, or micelles. The aminoalcohol lipidoid compounds may be combined with other aminoalcohol lipidoid compounds, polymers (synthetic or natural), surfactants, cholesterol, carbohydrates, proteins, lipids, etc. to form the particles. These particles may then optionally be combined with a pharmaceutical excipient to form a pharmaceutical composition.

A poly(beta-amino alcohol) (PBAA) can be used, sugar-based particles may be used, for example GalNAc, as described with reference to WO2014118272 (incorporated herein by reference) and Nair, J K et al., 2014, Journal of the American Chemical Society 136 (49), 16958-16961). In some cases, lipid nanoparticles (LNPs) are used. Spherical Nucleic Acid (SNA™) constructs and other nanoparticles (particularly gold nanoparticles) can be used to a target cell. See, e.g., Cutler et al., J. Am. Chem. Soc. 2011 133:9254-9257, Hao et al., Small 2011 7:3158-3162, Zhang et al., ACS Nano. 2011 5:6962-6970, Cutler et al., J. Am. Chem. Soc. 2012 134:1376-1391, Young et al., Nano Lett. 2012 12:3867-71, Zheng et al., Proc. Natl. Acad. Sci. USA. 2012 109:11975-80, Mirkin, Nanomedicine 2012 7:635-638 Zhang et al., J. Am. Chem. Soc. 2012 134:16488-1691, Weintraub, Nature 2013 495:S14-S16, Choi et al., Proc. Natl. Acad. Sci. USA. 2013 110(19): 7625-7630, Jensen et al., Sci. Transl. Med. 5, 209ra152 (2013) and Mirkin, et al., Small, 10:186-192. Semi-solid and soft nanoparticles are also suitable for delivery. An exosome can be used for delivery. Exosomes are endogenous nano-vesicles that transport RNAs and proteins, and which can deliver RNA to the brain and other target organs. Supercharged proteins can be used for delivery to a cell. Supercharged proteins are a class of engineered or naturally occurring proteins with unusually high positive or negative net theoretical charge. Both supernegatively and superpositively charged proteins exhibit the ability to withstand thermally or chemically induced aggregation. Superpositively charged proteins are also able to penetrate mammalian cells. Associating cargo with these proteins, such as plasmid DNA, RNA, or other proteins, can facilitate the functional delivery of these macromolecules into mammalian cells both in vitro and in vivo. Cell Penetrating Peptides (CPPs) can be used for delivery. CPPs typically have an amino acid composition that either contains a high relative abundance of positively charged amino acids such as lysine or arginine or has sequences that contain an alternating pattern of polar/charged amino acids and non-polar, hydrophobic amino acids.

Target Nucleic Acids and Target Cells of Interest

A variant type V CRISPR/Cas effector polypeptide of the present disclosure, or a fusion polypeptide of the present disclosure, when bound to a type V CRISPR/Cas guide RNA, can bind to a target nucleic acid, and in some cases, can bind to and modify a target nucleic acid. A target nucleic acid can be any nucleic acid (e.g., DNA, RNA), can be double stranded or single stranded, can be any type of nucleic acid (e.g., a chromosome (genomic DNA), derived from a chromosome, chromosomal DNA, plasmid, viral, extracellular, intracellular, mitochondrial, chloroplast, linear, circular, etc.) and can be from any organism (e.g., as long as the type V CRISPR/Cas guide RNA comprises a nucleotide sequence that hybridizes to a target sequence in a target nucleic acid, such that the target nucleic acid can be targeted).

A target nucleic acid can be DNA or RNA. A target nucleic acid can be double stranded (e.g., dsDNA, dsRNA) or single stranded (e.g., ssRNA, ssDNA). In some cases, a target nucleic acid is single stranded. In some cases, a target nucleic acid is a single stranded RNA (ssRNA). In some cases, a target ssRNA (e.g., a target cell ssRNA, a viral ssRNA, etc.) is selected from: mRNA, rRNA, tRNA, non-coding RNA (ncRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). In some cases, a target nucleic acid is a single stranded DNA (ssDNA) (e.g., a viral DNA). As noted above, in some cases, a target nucleic acid is single stranded.

A target nucleic acid can be located anywhere, for example, outside of a cell in vitro, inside of a cell in vitro; inside of a cell in vivo; inside of a cell ex vivo; or inside of an organelle (e.g., mitochondrion; nucleus; etc.) within a cell that is in vitro, in vivo, or ex vivo. Suitable target cells (which can comprise target nucleic acids such as genomic DNA) include, but are not limited to: a bacterial cell; an archaeal cell; a cell of a single-cell eukaryotic organism; a plant cell; an algal cell, e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like; a fungal cell (e.g., a yeast cell); an animal cell; a cell from an invertebrate animal (e.g. fruit fly, a cnidarian, an echinoderm, a nematode, etc.); a cell of an insect (e.g., a mosquito; a bee; an agricultural pest; etc.); a cell of an arachnid (e.g., a spider; a tick; etc.); a cell from a vertebrate animal (e.g., a fish, an amphibian, a reptile, a bird, a mammal); a cell from a mammal (e.g., a cell from a rodent; a cell from a human; a cell of a non-human mammal; a cell of a rodent (e.g., a mouse, a rat); a cell of a lagomorph (e.g., a rabbit); a cell of an ungulate (e.g., a cow, a horse, a camel, a llama, a vicuña, a sheep, a goat, etc.); a cell of a marine mammal (e.g., a whale, a seal, an elephant seal, a dolphin, a sea lion; etc.) and the like. Any type of cell may be of interest (e.g. a stem cell, e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell, a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.), an adult stem cell, a somatic cell, e.g. a fibroblast, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell; an in vitro or in vivo embryonic cell of an embryo at any stage, e.g., a 1-cell, 2-cell, 4-cell, 8-cell, etc. stage zebrafish embryo; etc.).

Cells may be from established cell lines or they may be primary cells, where “primary cells”, “primary cell lines”, and “primary cultures” are used interchangeably herein to refer to cells and cells cultures that have been derived from a subject and allowed to grow in vitro for a limited number of passages, i.e. splittings, of the culture. For example, primary cultures are cultures that may have been passaged 0 times, 1 time, 2 times, 4 times, 5 times, 10 times, or 15 times, but not enough times go through the crisis stage. Typically, the primary cell lines are maintained for fewer than 10 passages in vitro. Target cells can be unicellular organisms and/or can be grown in culture. If the cells are primary cells, they may be harvest from an individual by any convenient method. For example, leukocytes may be conveniently harvested by apheresis, leukocytopheresis, density gradient separation, etc., while cells from tissues such as skin, muscle, bone marrow, spleen, liver, pancreas, lung, intestine, stomach, etc. can be conveniently harvested by biopsy.

In some of the above applications, the subject methods may be employed to induce target nucleic acid cleavage, target nucleic acid modification, and/or to bind target nucleic acids (e.g., for visualization, for collecting and/or analyzing, etc.) in mitotic or post-mitotic cells in vivo and/or ex vivo and/or in vitro (e.g., to disrupt production of a protein encoded by a targeted mRNA, to cleave or otherwise modify target DNA, to genetically modify a target cell, and the like). Because the guide RNA provides specificity by hybridizing to target nucleic acid, a mitotic and/or post-mitotic cell of interest in the disclosed methods may include a cell from any organism (e.g. a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a plant cell, an algal cell, e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like, a fungal cell (e.g., a yeast cell), an animal cell, a cell from an invertebrate animal (e.g. fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal, a cell from a rodent, a cell from a human, etc.). In some cases, a variant type V CRISPR/Cas polypeptide of the present disclosure (and/or nucleic acid encoding the protein such as DNA and/or RNA), and/or type V CRISPR/Cas guide RNA (and/or a DNA encoding the guide RNA), and/or donor template, and/or RNP can be introduced into an individual (i.e., the target cell can be in vivo) (e.g., a mammal, a rat, a mouse, a pig, a primate, a non-human primate, a human, etc.). In some case, such an administration can be for the purpose of treating and/or preventing a disease, e.g., by editing the genome of targeted cells.

Plant cells include cells of a monocotyledon, and cells of a dicotyledon. The cells can be root cells, leaf cells, cells of the xylem, cells of the phloem, cells of the cambium, apical meristem cells, parenchyma cells, collenchyma cells, sclerenchyma cells, and the like. Plant cells include cells of agricultural crops such as wheat, corn, rice, sorghum, millet, soybean, etc. Plant cells include cells of agricultural fruit and nut plants, e.g., plant that produce apricots, oranges, lemons, apples, plums, pears, almonds, etc.

Additional examples of target cells are listed above in the section titled “Modified cells.” Non-limiting examples of cells (target cells) include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant (e.g., cells from plant crops, fruits, vegetables, grains, soy bean, corn, maize, wheat, seeds, tomatoes, rice, cassava, sugarcane, pumpkin, hay, potatoes, cotton, Cannabis, tobacco, flowering plants, conifers, gymnosperms, angiosperms, ferns, clubmosses, hornworts, liverworts, mosses, dicotyledons, monocotyledons, etc.), an algal cell, (e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like), seaweeds (e.g. kelp) a fungal cell (e.g., a yeast cell, a cell from a mushroom), an animal cell, a cell from an invertebrate animal (e.g., fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal (e.g., an ungulate (e.g., a pig, a cow, a goat, a sheep); a rodent (e.g., a rat, a mouse); a non-human primate; a human; a feline (e.g., a cat); a canine (e.g., a dog); etc.), and the like. In some cases, the cell is a cell that does not originate from a natural organism (e.g., the cell can be a synthetically made cell; also referred to as an artificial cell).

A cell can be an in vitro cell (e.g., established cultured cell line). A cell can be an ex vivo cell (cultured cell from an individual). A cell can be an in vivo cell (e.g., a cell in an individual). A cell can be an isolated cell. A cell can be a cell inside of an organism. A cell can be an organism. A cell can be a cell in a cell culture (e.g., in vitro cell culture). A cell can be one of a collection of cells. A cell can be a prokaryotic cell or derived from a prokaryotic cell. A cell can be a bacterial cell or can be derived from a bacterial cell. A cell can be an archaeal cell or derived from an archaeal cell. A cell can be a eukaryotic cell or derived from a eukaryotic cell. A cell can be a plant cell or derived from a plant cell. A cell can be an animal cell or derived from an animal cell. A cell can be an invertebrate cell or derived from an invertebrate cell. A cell can be a vertebrate cell or derived from a vertebrate cell. A cell can be a mammalian cell or derived from a mammalian cell. A cell can be a rodent cell or derived from a rodent cell. A cell can be a human cell or derived from a human cell. A cell can be a microbe cell or derived from a microbe cell. A cell can be a fungi cell or derived from a fungi cell. A cell can be an insect cell. A cell can be an arthropod cell. A cell can be a protozoan cell. A cell can be a helminth cell.

In some cases, the cell is a stem cell. Stem cells include adult stem cells. Adult stem cells are also referred to as somatic stem cells.

Stem cells can express one or more stem cell markers, e.g., SOX9, KRT19, KRT7, LGR5, CA9, FXYD2, CDH6, CLDN18, TSPAN8, BPIFB1, OLFM4, CDH17, and PPARGC1A.

In some cases, the stem cell is a hematopoietic stem cell (HSC). HSCs are mesoderm-derived cells that can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac. HSCs are characterized as CD34+ and CD3−. HSCs can repopulate the erythroid, neutrophil-macrophage, megakaryocyte and lymphoid hematopoietic cell lineages in vivo. In vitro, HSCs can be induced to undergo at least some self-renewing cell divisions and can be induced to differentiate to the same lineages as is seen in vivo. As such, HSCs can be induced to differentiate into one or more of erythroid cells, megakaryocytes, neutrophils, macrophages, and lymphoid cells.

In other cases, the stem cell is a neural stem cell (NSC). Neural stem cells (NSCs) are capable of differentiating into neurons, and glia (including oligodendrocytes, and astrocytes). A neural stem cell is a multipotent stem cell which is capable of multiple divisions, and under specific conditions can produce daughter cells which are neural stem cells, or neural progenitor cells that can be neuroblasts or glioblasts, e.g., cells committed to become one or more types of neurons and glial cells respectively. Methods of obtaining NSCs are known in the art.

In other cases, the stem cell is a mesenchymal stem cell (MSC). MSCs originally derived from the embryonal mesoderm and isolated from adult bone marrow, can differentiate to form muscle, bone, cartilage, fat, marrow stroma, and tendon. Methods of isolating MSC are known in the art; and any known method can be used to obtain MSC. See, e.g., U.S. Pat. No. 5,736,396, which describes isolation of human MSC.

A cell is in some cases a plant cell. A plant cell can be a cell of a monocotyledon. A cell can be a cell of a dicotyledon.

A cell is in some cases an insect cell. For example, in some cases, the cell is a cell of a mosquito, a grasshopper, a true bug, a fly, a flea, a bee, a wasp, an ant, a louse, a moth, or a beetle.

Examples of Non-Limiting Aspects of the Disclosure

Aspects, including embodiments, of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting aspects of the disclosure numbered 1-44 are provided below. As will be apparent to those of skill in the art upon reading this disclosure, each of the individually numbered aspects may be used or combined with any of the preceding or following individually numbered aspects. This is intended to provide support for all such combinations of aspects and is not limited to combinations of aspects explicitly provided below:

Aspect 1. A variant type V CRISPR/Cas effector polypeptide comprising at least one mutation in the loop of the helix-loop element of the RuvC domain compared to a wild-type type V CRISPR/Cas effector polypeptide, wherein the at least one mutation provides for a reduction of at least 50% in the trans cleavage activity exhibited by the wild-type type V CRISPR/Cas effector polypeptide.

Aspect 2. The variant type V CRISPR/Cas effector polypeptide of aspect 1, wherein the wild-type type V CRISPR/Cas effector polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to a Cas12a polypeptide.

Aspect 3. The variant type V CRISPR/Cas effector polypeptide of aspect 1, wherein the wild-type type V CRISPR/Cas effector polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to a Cas12b polypeptide.

Aspect 4. The variant type V CRISPR/Cas effector polypeptide of aspect 1, wherein the wild-type type V CRISPR/Cas effector polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to a Cas12e polypeptide.

Aspect 5. The variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-4, wherein the at least one mutation provides for a reduction of at least 95% in the trans cleavage activity exhibited by the wild-type type V CRISPR/Cas effector polypeptide.

Aspect 6. The variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-5, wherein the mutation comprises deletion of one or more amino acids of the loop.

Aspect 7. The variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-5, wherein the mutation comprises substitution of one or more Lys and Arg amino acids in the loop with an amino acid other than Lys or Arg.

Aspect 8. The variant type V CRISPR/Cas effector polypeptide of aspect 7, wherein a Lys residue is substituted with an amino acid other than Lys.

Aspect 9. The variant type V CRISPR/Cas effector polypeptide of aspect 7, wherein an Arg residue is substituted with an amino acid other than Arg.

Aspect 10. The variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-5, wherein the mutation comprises substitution of one or more amino acids in the loop with a Gly.

Aspect 11. The variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-5, wherein the mutation comprises substitution of one or more amino acids in the loop with an Ala.

Aspect 12. The variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-11, comprising at least one nuclear localization signal (NLS).

Aspect 13. A nucleic acid comprising a nucleotide sequence encoding the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12.

Aspect 14. A recombinant expression vector comprising the nucleic acid of aspect 13.

Aspect 15. The recombinant expression vector of aspect 14, wherein the nucleotide sequence is codon optimized for expression in a host cell.

Aspect 16. The recombinant expression vector of aspect 14 or 15, wherein the nucleotide sequence is operably linked to a promoter.

Aspect 17. The recombinant expression vector of aspect 16, wherein the promoter is a regulatable promoter.

Aspect 18. A composition comprising the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12.

Aspect 19. The composition of aspect 18, comprising one or more of: a) a lipid; b) a buffer; c) a nuclease inhibitor; and d) a protease inhibitor.

Aspect 20. A system comprising the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12.

Aspect 21. The system of aspect 20, further comprising a type V CRISPR/Cas guide RNA.

Aspect 22. The system of aspect 20, further comprising 2 type V CRISPR/Cas guide RNAs.

Aspect 23. The system of aspect 21 or aspect 22, wherein the guide RNA(s) comprises one or more of a base modification, a sugar modification, and a backbone modification.

Aspect 24. The system of any one of aspects 20-23, further comprising a donor DNA template.

Aspect 25. A fusion polypeptide comprising: a) the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12; and b) a heterologous polypeptide.

Aspect 26. The fusion polypeptide of aspect 25, wherein the heterologous polypeptide is a targeting polypeptide that provides for binding to a cell surface moiety on a target cell or target cell type.

Aspect 27. The fusion polypeptide of aspect 25, wherein the heterologous polypeptide exhibits an enzymatic activity that modifies target DNA.

Aspect 28. The fusion polypeptide of aspect 27, wherein the heterologous polypeptide exhibits one or more enzymatic activities selected from: nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity and glycosylase activity.

Aspect 29. The fusion polypeptide of aspect 25, wherein the heterologous polypeptide is an endosomal escape polypeptide.

Aspect 30. A nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of aspects 25-29.

Aspect 31. A host cell comprising: a) the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12; or b) a nucleic acid comprising a nucleotide sequence encoding the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12; or c) the fusion polypeptide of any one of aspects 25-29; or d) a nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of aspects 25-29.

Aspect 32. The host cell of aspect 31, further comprising a CRISPR/Cas guide RNA, or a nucleic acid comprising a nucleotide sequence encoding the CRISPR/Cas guide RNA.

Aspect 33. The host cell of aspect 31 or aspect 32, wherein the host cell is a eukaryotic cell.

Aspect 34. The host cell of aspect 33, wherein the eukaryotic cell is a plant cell, a mammalian cell, an insect cell, an arachnid cell, a fungal cell, a bird cell, a reptile cell, an amphibian cell, an invertebrate cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, or a human cell.

Aspect 35. The host cell of aspect 31 or aspect 32, wherein the host cell is a prokaryotic cell.

Aspect 36. A method of modifying a target nucleic acid, the method comprising contacting the target nucleic acid with: a) the variant type V CRISPR/Cas effector polypeptide of any one of aspects 1-12 or the fusion polypeptide of any one of aspects 25-29; and b) a CRISPR/Cas guide RNA that comprising a guide sequence that hybridizes to a target sequence of the target nucleic acid, wherein said contacting results in modification of the target nucleic acid by the variant type V CRISPR/Cas effector polypeptide or the fusion polypeptide.

Aspect 37. The method of aspect 36, wherein said modification is cleavage of the target nucleic acid.

Aspect 38. The method of aspect 36 or aspect 37, wherein the target nucleic acid is selected from: double stranded DNA, single stranded DNA, RNA, genomic DNA, and extrachromosomal DNA.

Aspect 39. The method of any one of aspects 36-38, wherein said contacting takes place in vitro outside of a cell.

Aspect 40. The method of any one of aspects 36-38, wherein said contacting takes place inside of a cell in vitro.

Aspect 41. The method of any one of aspects 36-38, wherein said contacting takes place inside of a cell in vivo.

Aspect 42. The method of aspect 40 or aspect 41, wherein the cell is selected from: a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.

Aspect 43. The method of any one of aspects 36-42, wherein said contacting results in genome editing.

Aspect 44. The method of any one of aspects 40-43, wherein said contacting further comprises: introducing a DNA donor template into the cell.

EXAMPLES

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like.

Example 1: Effect of Loop Mutations on Cis and Trans Cleavage
Cis- and Trans-DNA Cleavage Assays

Cas12a-mediated DNA cleavage assays were carried out in Cleavage Buffer consisting of 20 mM HEPES (pH 7.5), 150 mM KCl, 10 mM MgCl₂, 1% glycerol and 0.5 mM dithiothreitol (DTT), and the 5′-end-labeled DNA substrates used were generated with T4 PNK (NEB) in the presence of gamma ³²P-ATP.

For cis-targeting assays, 30 nM Cas12a was pre-assembled with 36 nM of crRNA for 15 minutes at room temperature. The reaction was initiated by adding 2-4 nM of labeled dsDNA (non-targeting strand labeled) and incubated at 37° C. for indicated time points.

For trans-targeting assays, Cas12a RNP was first formed from 30 nM Cas12a and 36 nM of crRNA by incubation of 15 minutes at room temperature. After addition of 45 nM of activator (target dsDNA pre-annealed from target and non-target 55 nt DNA oligos) to the Cas12a RNP, the mixture was incubated for 30 min at 37 C to form activated Cas12a complex. For cas12a-mediated trans-DNA cleavage assays, the activator-activated Cas12a complex was incubated with a labeled and non-related ssDNA for indicated time points at 37 C.

Reactions from either cis or trans cleavage assays were quenched with loading buffer (final concentration 45% formamide and 15 mM EDTA, with trace amount of xylene cyanol and bromophenol blue) for 3 min at 90° C. The substrates and products were resolved by 12% urea-denaturing polyacrylamide gel electrophoresis (PAGE) gel and quantified with Amersham Typhoon (GE Healthcare).

The data are shown in FIG. 25.

While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

	Number	Date	Country
	62881533	Aug 2019	US
	62871408	Jul 2019	US

VARIANT TYPE V CRISPR/CAS EFFECTOR POLYPEPTIDES AND METHODS OF USE THEREOF

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STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

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Provisional Applications (2)