WO2021231437A1 - Rna-guided nucleic acid binding proteins and active fragments and variants thereof and methods of use - Google Patents

Abstract

Compositions and methods for binding to a target sequence of interest are provided. The compositions find use in cleaving or modifying a target sequence of interest, visualization of a target sequence of interest, and modifying the expression of a sequence of interest. Compositions comprise RNA-guided nucleic acid binding protein (RGNABP) polypeptides, fusion polypeptides comprising a RGNABP, CRISPR RNAs, trans-activating CRISPR RNAs, guide RNAs, and nucleic acid molecules encoding the same. Vectors and host cells comprising the nucleic acid molecules are also provided. Further provided are RGNABP systems for binding a target sequence of interest, wherein the RGNABP system comprises an RGNABP polypeptide and one or more guide RNAs.

Description

RNA-GUIDED NUCLEIC ACID BINDING PROTEINS AND ACTIVE FRAGMENTS AND VARIANTS

THEREOF AND METHODS OF USE

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application No. 63/023,009, filed May 11, 2020, which is incorporated by reference herein in its entirety.

STATEMENT REGARDING THE SEQUENCE LISTING The Sequence Listing associated with this application is provided in ASCII format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The ASCII copy named L103438_1210WO_0086_7_SL is 335,010 bytes in size, was created on May 11, 2021, and is being submitted electronically via EFS-Web.

FIELD OF THE INVENTION

The present invention relates to the field of molecular biology and gene editing.

BACKGROUND OF THE INVENTION

Targeted genome editing or modification is rapidly becoming an important tool for basic and applied research. Initial methods involved engineering nucleases such as meganucleases, zinc finger fusion proteins or TALENs, requiring the generation of chimeric nucleases with engineered, programmable, sequence- specific DNA-binding domains specific for each particular target sequence. RNA-guided nucleic acid binding proteins, such as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)- associated (Cas) proteins of the CRISPR-Cas bacterial system, allow for the targeting of specific sequences by complexing the protein with guide RNA that specifically hybridizes with a particular target sequence. Producing target-specific guide RNAs is less costly and more efficient than generating chimeric nucleases for each target sequence. Such RNA-guided nucleic acid binding proteins can be used to edit genomes optionally through the introduction of a sequence-specific, double-stranded break that in some embodiments may require fusion with a nuclease domain, that is repaired via error-prone non-homologous end-joining (NHEJ) to introduce a mutation at a specific genomic location. Alternatively, heterologous DNA may be introduced into the genomic site via homology-directed repair. Alternative genome edits or expression modulation may be obtained through sequence-specific binding when fusion proteins are introduced, including base editors, transcription activation domains, and transcriptional repressors.

BRIEF SUMMARY OF THE INVENTION

Compositions and methods for binding a target sequence of interest are provided. The compositions find use in binding, cleaving or modifying a target sequence of interest, detection of a target sequence of interest, and modifying the expression of a sequence of interest. Compositions comprise RNA-guided, nucleic acid binding protein (RGNABP) polypeptides, CRISPR RNAs (crRNAs), trans-activating CRISPR RNAs (tracrRNAs), guide RNAs (gRNAs), nucleic acid molecules encoding the same, and vectors and host cells comprising the nucleic acid molecules. Also provided are RGNABP systems for binding a target sequence of interest, wherein the RGNABP system comprises an RNA-guided nucleic acid binding protein polypeptide and one or more guide RNAs. Thus, methods disclosed herein are drawn to binding a target sequence of interest, and in some embodiments, cleaving or modifying the target sequence of interest. The target sequence of interest can be modified, for example, as a result of non-homologous end joining or homology-directed repair with an introduced donor sequence, or base editing.

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 shows RNA expression at the bacterial genomic loci of representative RGNABPs of the invention.

DETAILED DESCRIPTION

Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended embodiments. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

I. Overview

RNA-guided nucleic acid-binding proteins (RGNABPs) allow for the targeted manipulation of specific site(s) within a genome and are useful in the context of gene targeting for therapeutic and research applications. In a variety of organisms, including mammals, RNA-guided nucleic acid-binding proteins have been used for genome engineering by stimulating non-homologous end joining and homologous recombination, for example. The compositions and methods described herein are useful for creating single- or double-stranded breaks in polynucleotides, modifying polynucleotides, detecting a particular site within a polynucleotide, or modifying the expression of a particular gene.

The RNA-guided nucleic acid-binding proteins disclosed herein can alter gene expression by modifying a target sequence or binding at a site of interest. In specific embodiments, the RNA-guided nucleic acid-binding proteins are directed to the target sequence by a guide RNA (gRNA) as part of a

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) RNA-guided nucleic acid binding protein system. The RGNABPs are considered “RNA-guided” because guide RNAs form a complex with the RNA-guided nucleic acid-binding protein to direct the RNA-guided nucleic acid-binding protein to bind to a target sequence which is hybridized and bound by the guide RNA and in some embodiments, introduce a single-stranded or double-stranded break at the target. Through introduction of a protein fusion, any number of genome modifications can be made in a sequence-specific manner. Thus, provided herein are methods for using the RNA-guided nucleic acid-binding proteins to target and/or modify a target sequence in the DNA or RNA of host cells. For example, RNA-guided nucleic acid-binding proteins can be used to modify a target sequence at a genomic locus of eukaryotic cells or prokaryotic cells.

II. RNA-guided nucleic acid binding proteins

Provided herein are RNA-guided nucleic acid-binding proteins. The term RNA-guided nucleic acid binding proteins (RGNABPs) refers to a polypeptide that binds to a particular target nucleotide sequence in a sequence-specific manner and is directed to the target nucleotide sequence by a guide RNA molecule that is complexed with the polypeptide and hybridizes with the target sequence. RGNABPs can be capable of cleaving the target sequence upon binding, particularly when operably fused with a nuclease domain. Cleavage of a target sequence by an RGNABP fused to a nuclease domain can result in a single- or double- stranded break. RGNABPs only capable of cleaving a single strand of a double-stranded nucleic acid molecule are referred to herein as nickases.

The RGNABPs of the invention are CRISPR-associated but do not necessarily contain any of the protein domains previously described in canonical CRISPR-Cas effector proteins (Makarova et al 2011, Nat Rev Microbiol, doi: 10.1038/nrmicro3569; Koonin et al 2017, Curr Opin Microbiol, doi: 10.1016/j.mib.2017.05.008; Makarova et al 2020, Nat Rev Microbiol, doi: 10.1038/s41579-019-0299-x; Zetsche et al 2015, Cell doi: 10.1016/j .cell.2015.09.038; Shmakov et al 2017, Nat Rev Microbiol doi:10.1038/nrmicro.2016.184; Yan et al 2018, Science doi:10.1126/science.aav7271; Harrington et al 2018, Science doi: 10.1126/science. aav4294). The main effector proteins for each type of Class II CRISPR systems are known to contain a nuclease domain; for Type II systems, the effector protein Cas9 contains an HNH domain and a split RuvC domain; for Type V systems, the effector protein Casl2 contains a split RuvC domain. For Class 1 systems, the effector proteins, Cas3 and CaslO, have an N-terminal histidine- aspartate (HD) domain. The RGNABPs of the invention lack all of these domains and also lack bridge-helix domains as found in Cas9 or Casl2, and helicase domains, as found in Cas3 and CaslO.

The RGNABPs described here contain an NHC signal peptide at the N-terminus. NHC signal peptides are tripartite signal sequences characterized by an N-terminal N-domain that is positively charged, a hydrophobic H-domain, and a polar C-domain. The signal peptide has also been removed for some variants tested herein. The RGNABP polypeptides also contain a coiled coil region, similar to a SipB Type III secretion system protein, in the middle of the coding sequence. Overall, the isoelectric point on these proteins is predicted to be neutral, unlike most effector Cas proteins which are typically greater than 10. These factors make the RGNABPs of the invention exceptionally different from any currently known CRISPR-associated proteins. The RGNABPs disclosed herein include the APG07446, APG07641, APG01250, and APG02261 RNA-guided, nucleic acid-binding proteins, the amino acid sequences of which are set forth, respectively, as SEQ ID NOs: 1, 2, 3, and 4, and active fragments or variants thereof that retain the ability to bind to a target nucleotide sequence in an RNA-guided sequence -specific manner. In some embodiments, an active variant of the APG07446, APG07641, APG01250, or APG02261 RGNABP comprises an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of the amino acid sequences set forth as SEQ ID NOs: 1, 2, 3, and 4. In certain embodiments, an active fragment of the APG07446, APG07641, APG01250, or APG02261 RGNABP comprises at least 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750 or more contiguous amino acid residues up to the full length of any one of the amino acid sequences set forth as SEQ ID NOs: 1, 2, 3, and 4. RNA-guided, nucleic acid-binding proteins provided herein can comprise at least one RNA recognition and/or RNA binding domain to interact with guide RNAs. Further domains that can be found in RGNABPs provided herein include, but are not limited to: nucleic acid binding domains, protein-protein interaction domains, and dimerization domains. In specific embodiments, the RGNABPs provided herein can comprise at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to one or more of a nucleic acid binding domain, protein-protein interaction domain, and dimerization domain.

A target nucleotide sequence is bound by an RNA-guided, nucleic acid-binding protein provided herein and hybridizes with the guide RNA associated with the RNA-guided, nucleic acid-binding protein. The target sequence can then be subsequently cleaved by the RNA-guided, nucleic acid-binding protein if the polypeptide possesses nuclease activity, for example as a RGNABP-nuclease fusion polypeptide. The terms “cleave” or “cleavage” refer to the hydrolysis of at least one phosphodiester bond within the backbone of a target nucleotide sequence that can result in either single-stranded or double-stranded breaks within the target sequence. Endonucleases are capable of cleaving nucleotides within a polynucleotide and an exonuclease removes successive nucleotides from the end (the 5' end and/or the 3' end) of a polynucleotide. Cleavage by nucleases can result in staggered breaks or blunt ends.

The presently disclosed RGNABPs can be wild-type sequences derived from bacterial or archaeal species. In some embodiments, the RGNABPs can be variants or fragments of wild-type polypeptides. The wild-type RGNABP can be modified to alter nucleic acid-binding activity or alter PAM specificity, for example. In some embodiments, the RNA-guided, nucleic acid-binding protein is not naturally -occurring.

In certain embodiments, the RNA-guided, nucleic acid-binding protein or fusion polypeptide comprising the same functions as a nickase, only cleaving a single strand of the target nucleotide sequence. Such RGNABPs or fusion polypeptides comprising the same have a single functioning nuclease domain. In some of these embodiments, additional nuclease domains have been mutated such that the nuclease activity is reduced or eliminated. RGNABPs that lack nuclease activity can be used to deliver a fused polypeptide, polynucleotide, or small molecule payload to a particular genomic location. In some of these embodiments, the RGNABP polypeptide or guide RNA can be fused to a detectable label to allow for detection of a particular sequence. As a non-limiting example, a RGNABP can be fused to a detectable label (e.g., fluorescent protein) and targeted to a particular sequence associated with a disease to allow for detection of the disease-associated sequence.

In some embodiments, RGNABPs can be targeted to particular genomic locations to alter the expression of a desired sequence. In some embodiments, the binding of a RNA-guided, nucleic acid-binding protein to a target sequence results in the reduction of expression of the target sequence or a gene under transcriptional control by the target sequence by interfering with the binding of RNA polymerase or transcription factors within the targeted genomic region. In some embodiments, the RGNABP or its complexed guide RNA further comprises an expression modulator that, upon binding to a target sequence, serves to either repress or activate the expression of the target sequence or a gene under transcriptional control by the target sequence. In some of these embodiments, the expression modulator modulates the expression of the target sequence or regulated gene through epigenetic mechanisms.

In some embodiments, an RGNABP can be targeted to particular genomic locations to modify the sequence of a target polynucleotide through fusion to a base-editing polypeptide, for example a deaminase polypeptide or active variant or fragment thereof that directly chemically modifies (e.g., deaminates) a nucleobase, resulting in conversion from one nucleobase to another. The base-editing polypeptide can be fused to the RGNABP at its N-terminal or C-terminal end. Additionally, the base-editing polypeptide may be fused to the RGNABP via a peptide linker. A non-limiting example of a deaminase polypeptide that is useful for such compositions and methods includes a cytidine deaminase or an adenine deaminase (such as the adenine base editor described in Gaudelli etal. (2017) Nature 551:464-471, U.S. Publ. Nos. 2017/0121693 and 2018/0073012, and International Publ. No. WO/2018/027078, or any of the deaminases disclosed in International Publ. No. WO 2020/139873, and U.S. Provisional Appl. Nos. 63/077,089 fried September 11, 2020, 63/146,840 fried February 8, 2021, and 63/164,273 fried March 22, 2021, each of which is herein incorporated by reference in its entirety). Further, it is known in the art that certain fusion proteins between an RGNABP and a base-editing enzyme may also comprise at least one uracil stabilizing polypeptide that increases the mutation rate of a cytidine, deoxycytidine, or cytosine to a thymidine, deoxythymidine, or thymine in a nucleic acid molecule by a deaminase. Non-limiting examples of uracil stabilizing polypeptides include those disclosed in U.S. Provisional Appl. No. 63/052,175, fried July 15, 2020, including USP2 (SEQ ID NO: 89), and a uracil glycosylase inhibitor (UGI) domain (SEQ ID NO: 90), which may increase base editing efficiency. Therefore, a fusion protein may comprise an RGNABP described herein or variant thereof, a deaminase, and optionally at least one uracil stabilizing polypeptide, such as UGI or USP2. In certain embodiments, the RGNABP that is fused to the base-editing polypeptide is a nickase that cleaves the DNA strand that is not acted upon by the base-editing polypeptide (e.g., deaminase).

RGNABPs that are fused to a polypeptide or domain can be separated or joined by a linker. The term "linker," as used herein, refers to a chemical group or a molecule linking two molecules or moieties, e.g., an RGNABP and a nuclease domain. In some embodiments, a linker joins a gRNA binding domain of an RGNABP and a base-editing polypeptide, such as a deaminase. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50

50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated.

The presently disclosed RGNABPs can comprise at least one nuclear localization signal (NLS) to enhance transport of the RGNABP to the nucleus of a cell. Nuclear localization signals are known in the art and generally comprise a stretch of basic amino acids (see, e.g., Lange etal., J. Biol. Chem. (2007) 282:5101-5105). In particular embodiments, the RGNABP comprises 2, 3, 4, 5, 6 or more nuclear localization signals. The nuclear localization signal(s) can be a heterologous NLS. Non-limiting examples of nuclear localization signals useful for the presently disclosed RGNABPs are the nuclear localization signals of SV40 Large T-antigen, nucleoplasmin, and c-Myc (see. e.g., Ray et al. (2015) Bioconjug Chem 26(6): 1004-7). In particular embodiments, the RGNABP comprises the NLS sequence set forth as SEQ ID NO: 47 or 48. The RGNABP can comprise one or more NLS sequences at its N-terminus, C- terminus, or both the N-terminus and C-terminus. For example, the RGNABP can comprise two NLS sequences at the N-terminal region and four NLS sequences at the C-terminal region.

Other localization signal sequences known in the art that localize polypeptides to particular subcellular location(s) can also be used to target the RGNABPs, including, but not limited to, plastid localization sequences, mitochondrial localization sequences, and dual-targeting signal sequences that target to both the plastid and mitochondria (see, e.g., Nassoury and Morse (2005) Biochim Biophys Acta 1743:5- 19; Kunze and Berger (2015) Front Physiol dx.doi.org/10.3389/fphys.2015.00259; Herrmann and Neupert (2003) IUBMB Life 55:219-225; Soil (2002) Curr Opin Plant Biol 5:529-535; Carrie and Small (2013) Biochim Biophys Acta 1833:253-259; Carrie etal. (2009) FEBSJ 276: 1187-1195; Silva-Filho (2003) Curr Opin Plant Biol 6:589-595; Peeters and Small (2001) Biochim Biophys Acta 1541:54-63; Murcha et al. (2014) J Exp Bot 65:6301-6335; Mackenzie (2005) Trends Cell Biol 15:548-554; Glaser etal. (1998) Plant Mol Biol 38:311-338).

In certain embodiments, the presently disclosed RGNABPs comprise at least one cell-penetrating domain that facilitates cellular uptake of the RGNABP. Cell-penetrating domains are known in the art and generally comprise stretches of positively charged amino acid residues (/. e. , polycationic cell-penetrating domains), alternating polar amino acid residues and non-polar amino acid residues (i.e., amphipathic cell- penetrating domains), or hydrophobic amino acid residues (i.e., hydrophobic cell-penetrating domains) (see, e.g., Milletti F. (2012) Drug Discov Today 17:850-860). A non-limiting example of a cell-penetrating domain is the trans-activating transcriptional activator (TAT) from the human immunodeficiency virus 1.

The nuclear localization signal, plastid localization signal, mitochondrial localization signal, dual targeting localization signal, and/or cell-penetrating domain can be located at the amino-terminus (N- terminus), the carboxyl-terminus (C-terminus), or in an internal location of the RNA-guided, nucleic acid binding protein.

The presently disclosed RGNABPs can be fused to an effector domain, such as a nuclease domain, a deaminase domain, or an expression modulator domain, either directly or indirectly via a linker peptide.

Such a domain can be located at the N-terminus, the C-terminus, or an internal location of the RNA-guided, nucleic acid-binding protein.

In some embodiments, the RGNABP fusion protein comprises a nuclease domain, which is any domain that is capable of cleaving a single or double strands of a polynucleotide (i.e., RNA, DNA, or RNA/DNA hybrid) and includes, but is not limited to, restriction endonucleases and homing endonucleases, such as Type IIS endonucleases (e.g., Fokl ) (see, e.g., Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Linn et al. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). In some embodiments, the nuclease domain can function as a nickase, only cleaving a single strand of a double-stranded nucleic acid molecule. In some embodiments, a non-specific nuclease domain, for example the nuclease domain from Fokl, is preferred. In some embodiments, the Fokl nuclease domain has been engineered to improve activity and/or specificity (for example, Guo et al. (2010) JMol Biol 400(1): 96-107; Miller et al. (2007) Nature Biotechnology 25(7):778-785). In some embodiments, two Fokl nuclease domains may be linked by an amino acid polypeptide linker (Sun and Zhao (2014) Mol BioSyst 10: 446), so that the active dimer is operably fused to an RGNABP. In some embodiments, the small, sequence-tolerant monomeric nuclease domain from the homing endonuclease l-Tevl (Kleinstiver etal, (2014) (13: Genes, Genomes, Genetics 4(6): 1155-1165) may be operably fused to an RGNABP. Additional enzymes which cleave DNA are known (e.g., SI Nuclease; mung bean nuclease; pancreatic DNase I; micrococcal nuclease; yeast HO endonuclease; see also Linn, et al. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). One or more of these enzymes (or functional fragments thereof) can be used as a source of nuclease domains and nuclease half domains which may be operably fused to an RGNABP of the invention.

In some embodiments, the RGNABP fusion protein comprises a deaminase domain that deaminates a nucleobase, resulting in conversion from one nucleobase to another, and includes, but is not limited to, a cytidine deaminase or an adenine deaminase base editor (see, e.g., Gaudelli etal. (2017) Nature 551:464- 471, U.S. Publ. Nos. 2017/0121693 and 2018/0073012, U.S. Patent No. 9,840,699, and International Publ. No. WO/2018/027078). In some embodiments, the effector domain of the RGNABP fusion protein can be an expression modulator domain, which is a domain that either serves to upregulate or downregulate transcription. The expression modulator domain can be an epigenetic modification domain, a transcriptional repressor domain or a transcriptional activation domain.

In some of these embodiments, the expression modulator of the RGNABP fusion protein comprises an epigenetic modification domain that covalently modifies DNA or histone proteins to alter histone structure and/or chromosomal structure without altering the DNA sequence, leading to changes in gene expression (i.e., upregulation or downregulation). Non-limiting examples of epigenetic modifications include acetylation or methylation of lysine residues, arginine methylation, serine and threonine phosphorylation, lysine ubiquitination and sumoylation of histone proteins, and methylation and hydroxymethylation of cytosine residues in DNA. Non-limiting examples of epigenetic modification domains include histone acetyltransferase domains, histone deacetylase domains, histone methyltransferase domains, histone demethylase domains, DNA methyltransferase domains, and DNA demethylase domains. Epigenome editing is known in the art and includes operably fusing a DNA-binding protein, such as a nuclease deficient Cas9 (dCas9) or an RGNABP of the invention, to an effector polypeptide or protein domain. Such effectors include the histone methyltransferase G9a-SET domain; TET1, which induces demethylation of cytosine at CpG sites; LSD1, which induces the demethylation of H3K4mel/2; the DNMT3a catalytic domain, which has achieved targeted DNA methylation of a targeted region when fused to a dCas9 (McDonald et al., (2016) Biology Open, 2016, 5(6):866-74); and the catalytic core of the human acetyltransferase p300, which successfully catalyzes targeted acetylation of histone H3 lysine 27 as a dCas9- p300 fusion polypeptide (Hilton et al., (2015) Nature Biotechnology 33(5):510-517).

In some embodiments, the expression modulator of the fusion protein comprises a transcriptional repressor domain, which interacts with transcriptional control elements and/or transcriptional regulatory proteins, such as RNA polymerases and transcription factors, to reduce or terminate transcription of at least one gene. Transcriptional repressor domains are known in the art and include, but are not limited to, Spl- like repressors, the Mad mSIN3 interaction domain (SID), the ERF repressor domain (ERD), the CS (chromo shadow) domain of HPla (Hathaway et al., (2012) Cell 149: 1447-1460), the WRPW domain of Hesl (Fisher et al., (1996) Mol Cell Biol 16: 2670-2677), IKB, and Kriippel associated box (KRAB) domains (Margolin et al., (1994) PNAS 91(10):4509-4513). Other repressors include the TetR repressor, the Lacl repressor, or repressor protein Cl or an active fragment thereof.

In some embodiments, the expression modulator of the fusion protein comprises a transcriptional activation domain, which interacts with transcriptional control elements and/or transcriptional regulatory proteins, such as RNA polymerases and transcription factors, to increase or activate transcription of at least one gene. Transcriptional activation domains are known in the art and include, but are not limited to, a GAL4 activation domain, a herpes simplex virus VP 16 or VP64 activation domain, and a NFAT activation domain. In some embodiments, the transcriptional activator may incorporate multiple transcriptional factors, such as the tripartite activator VP64-p65-Rta, also referred to as VPR (Chavez et al., (2015) Nature Methods 12(4):326-328), or artificial transcription factors, also referred to as ATFs (Blancafort et al, (2004) Mol Pharmacol 66:1361-1371; Sera, (2009) Adv Drug Deliv Rev 61: 513-526).

Other examples include recruitment of multiplex transcriptional activators through guide RNA modification and/or RGNABP fusion polypeptides. In some embodiments, engineering of the guide RNA can create an RGNABP-SAM system, similar to dCas9-SAM (synergistic activation mediator) systems (Konermann et al., (2015) Nature 517(7536):583-588; Zhang et al., (2015) Scientific Reports 5:16277).

In some embodiments, the RGNABP fusion protein comprises a reverse transcriptase. In some embodiments, the RGNABP fusion protein comprises a polypeptide that recruits members of a functional nucleic acid repair complex, such as a member of the nucleotide excision repair (NER) or transcription coupled-nucleotide excision repair (TC-NER) pathway (Wei et al., 2015, PNAS USA 112(27):E3495-504 ; Troelstra et al., 1992, Cell 71:939-953; Mamef et al., 2017, JMol Biol 429(9): 1277-1288), as described in U.S. Provisional Application No. 62/966,203, which was filed on January 27, 2020, and is incorporated by reference in its entirety. In some embodiments, the RGNABP fusion protein comprises CSB (van den Boom et al., 2004, J Cell Biol 166(l):27-36; van Gool et al., 1997, EMBO J 16(19):5955-65; an example of which is set forth as SEQ ID NO: 88), which is a member of the TC-NER (nucleotide excision repair) pathway and functions in the recruitment of other members. In further embodiments, the RGNABP fusion protein comprises an active domain of CSB, such as the acidic domain of CSB which comprises amino acid residues 356-394 of SEQ ID NO: 88 (Teng et al., 2018, Nat Commun 9(1):4115).

The presently disclosed RGNABP polypeptides can comprise a detectable label or a purification tag. The detectable label or purification tag can be located at the N-terminus, the C-terminus, or an internal location of the RNA-guided, nucleic acid-binding protein, either directly or indirectly via a linker peptide.

In some of these embodiments, the RGNABP component of the fusion protein is a RGNABP which lacks nuclease activity. In some embodiments, the RGNABP component of the fusion protein is a RGNABP with nickase activity. In some embodiments, the RGNABP component of the fusion protein is an RGNABP capable of double -stranded DNA cleavage.

A detectable label is a molecule that can be visualized or otherwise observed. The detectable label may be fused to the RGNABP as a fusion protein (e.g., fluorescent protein) or may be a small molecule conjugated to the RGNABP polypeptide that can be detected visually or by other means. Detectable labels that can be fused to the presently disclosed RGNABPs as a fusion protein include any detectable protein domain, including but not limited to, a fluorescent protein or a protein domain that can be detected with a specific antibody. Non-limiting examples of fluorescent proteins include green fluorescent proteins (e.g., GFP, EGFP, ZsGreenl) and yellow fluorescent proteins (e.g., YFP, EYFP, ZsYellowl). Non-limiting examples of small molecule detectable labels include radioactive labels, such as ³H and ³⁵S.

RGNABP polypeptides can also comprise a purification tag, which is any molecule that can be utilized to isolate a protein or fused protein from a mixture (e.g., biological sample, culture medium). Non- limiting examples of purification tags include biotin, myc, maltose binding protein (MBP), and glutathione- S-transferase (GST), and 3X FLAG tag.

Ill Guide RNA

The present disclosure provides guide RNAs and polynucleotides encoding the same. The term “guide RNA” refers to a nucleotide sequence having sufficient complementarity with a target nucleotide sequence to hybridize with the target sequence and direct sequence -specific binding of an associated RNA- guided, nucleic acid-binding protein to the target nucleotide sequence. Thus, an RGNABP’s respective guide RNA is one or more RNA molecules (generally, one or two), that can bind to the RGNABP and guide the RGNABP to bind to a particular target nucleotide sequence, and in those embodiments wherein the RGNABP has nickase or double-stranded nuclease activity, also cleave the target nucleotide sequence. In general, a guide RNA comprises a CRISPR RNA (crRNA) and in some embodiments, a trans-activating CRISPR RNA (tracrRNA). Native guide RNAs that comprise both a crRNA and a tracrRNA generally comprise two separate RNA molecules that hybridize to each other through the repeat sequence of the crRNA and the anti-repeat sequence of the tracrRNA.

Native direct repeat sequences within a CRISPR array generally range in length from 28 to 37 base pairs, although the length can vary between about 23 bp to about 55 bp. Spacer sequences within a CRISPR array generally range from about 32 to about 38 bp in length, although the length can be between about 21 bp to about 72 bp. Each CRISPR array generally comprises less than 50 units of the CRISPR repeat-spacer sequence. The CRISPRs are transcribed as part of a long transcript termed the primary CRISPR transcript, which comprises much of the CRISPR array. The primary CRISPR transcript is cleaved by Cas proteins to produce crRNAs or in some cases, to produce pre-crRNAs that are further processed by additional Cas proteins into mature crRNAs. Mature crRNAs comprise a spacer sequence and a CRISPR repeat sequence. In some embodiments in which pre-crRNAs are processed into mature (or processed) crRNAs, maturation involves the removal of about one to about six or more 5', 3', or 5' and 3' nucleotides. For the purposes of genome editing or targeting a particular target nucleotide sequence of interest, these nucleotides that are removed during maturation of the pre-crRNA molecule are not necessary for generating or designing a guide RNA.

A CRISPR RNA (crRNA) comprises a spacer sequence and a CRISPR repeat sequence. The “spacer sequence” is the nucleotide sequence that directly hybridizes with the target nucleotide sequence of interest. The spacer sequence is engineered to be fully or partially complementary with the target sequence of interest. In various embodiments, the spacer sequence can comprise from about 8 nucleotides to about 30 nucleotides, or more. For example, the spacer sequence can be about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, or more nucleotides in length. In some embodiments, the spacer sequence is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, the spacer sequence is about 10 to about 26 nucleotides in length, or about 12 to about 30 nucleotides in length. In particular embodiments, the spacer sequence is about 30 nucleotides in length. In some embodiments, the spacer sequence is 30 nucleotides in length. In some embodiments, the degree of complementarity between a spacer sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is between 50% and 99% or more, including but not limited to about or more than about 50%, about 60%, about 70%, about 75%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more. In particular embodiments, the degree of complementarity between a spacer sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more. In particular embodiments, the spacer sequence is free of secondary structure, which can be predicted using any suitable polynucleotide folding algorithm known in the art, including but not limited to mFold (see, e.g., Zuker and Stiegler (1981) Nucleic Acids Res. 9: 133-148) and RNAfold (see, e.g., Gruber et al. (2008) Cell 106(l):23-24).

The CRISPR RNA repeat sequence comprises a nucleotide sequence that forms a structure, either on its own or in concert with a hybridized tracrRNA, that is recognized by a RGNABP molecule. In various embodiments, the CRISPR RNA repeat sequence can comprise from about 8 nucleotides to about 30 nucleotides, or more. For example, the CRISPR repeat sequence can be about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, or more nucleotides in length. In particular embodiments, the CRISPR repeat sequence is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,

19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, the degree of complementarity between a CRISPR repeat sequence and its corresponding tracrRNA sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, about 60%, about 70%, about 75%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more. In particular embodiments, the degree of complementarity between a CRISPR repeat sequence and its corresponding tracrRNA sequence, when optimally aligned using a suitable alignment algorithm, is 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more.

In particular embodiments, the CRISPR repeat sequence comprises the nucleotide sequence of SEQ ID NO: 5 or 6, or an active variant or fragment thereof that when comprised within a guide RNA, is capable of directing the sequence-specific binding of an associated RNA-guided, nucleic acid-binding protein provided herein to a target sequence of interest. In certain embodiments, an active CRISPR repeat sequence variant of a wild-type sequence comprises a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the nucleotide sequence set forth as SEQ ID NO: 5 or 6. In certain embodiments, an active CRISPR repeat sequence fragment of a wild-type sequence comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 contiguous nucleotides of the nucleotide sequence set forth as SEQ ID NO: 5 or 6.

In certain embodiments, the crRNA is not naturally-occurring. In some of these embodiments, the specific CRISPR repeat sequence is not linked to the engineered spacer sequence in nature and the CRISPR repeat sequence is considered heterologous to the spacer sequence. In certain embodiments, the spacer sequence is an engineered sequence that is not naturally occurring.

In certain embodiments, guideRNAs further comprise a tracrRNA. A trans-activating CRISPR RNA or tracrRNA molecule comprises a nucleotide sequence comprising a region that has sufficient complementarity to hybridize to a CRISPR repeat sequence of a crRNA, which is referred to herein as the anti-repeat region. In some embodiments, the tracrRNA molecule further comprises a region with secondary structure (e.g., stem-loop) or forms secondary structure upon hybridizing with its corresponding crRNA. In particular embodiments, the region of the tracrRNA that is fully or partially complementary to a CRISPR repeat sequence is at the 5' end of the molecule and the 3' end of the tracrRNA comprises secondary structure.

In various embodiments, the anti-repeat region of the tracrRNA that is fully or partially complementary to the CRISPR repeat sequence comprises from about 8 nucleotides to about 30 nucleotides, or more. For example, the region of base pairing between the tracrRNA anti-repeat sequence and the CRISPR repeat sequence can be about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, or more nucleotides in length. In particular embodiments, the region of base pairing between the tracrRNA anti-repeat sequence and the CRISPR repeat sequence is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, the degree of complementarity between a CRISPR repeat sequence and its corresponding tracrRNA anti-repeat sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, about 60%, about 70%, about 75%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more. In particular embodiments, the degree of complementarity between a CRISPR repeat sequence and its corresponding tracrRNA anti-repeat sequence, when optimally aligned using a suitable alignment algorithm, is 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more.

In various embodiments, the entire tracrRNA can comprise from about 60 nucleotides to more than about 140 nucleotides. For example, the tracrRNA can be about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 95, about 100, about 105, about 110, about 115, about 120, about 125, about 130, about 135, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, or more nucleotides in length. In particular embodiments, the tracrRNA is 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 150, 160, 170, 180, 190, 200, 210 or more nucleotides in length. In particular embodiments, the tracrRNA is about 75 to about 100 nucleotides in length, including about 75, about 76, about 77, about 78, about 79, about 80, about 81, about 82, about 83, about 84, about 85, about 86, about 87, about 88, about 89, about 90, about 91, about 92, about 93, about 94, about 95, about 96, about 97, about 98, about 99, and about 100 nucleotides in length. In particular embodiments, the tracrRNA is 75 to 100 nucleotides in length, including 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, and 100 nucleotides in length.

In particular embodiments, the tracrRNA comprises the nucleotide sequence of SEQ ID NO: 7 or 8, or an active variant or fragment thereof that when comprised within a guide RNA is capable of directing the sequence-specific binding of an associated RNA-guided, nucleic acid-binding protein provided herein to a target sequence of interest. In certain embodiments, an active tracrRNA sequence variant of a wild-type sequence comprises a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the nucleotide sequence set forth as SEQ ID NO: 7 or 8. In certain embodiments, an active tracrRNA sequence fragment of a wild-type sequence comprises at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or more contiguous nucleotides of the nucleotide sequence set forth as SEQ ID NO: 7 or 8.

Two polynucleotide sequences can be considered to be substantially complementary when the two sequences hybridize to each other under stringent conditions. Likewise, an RGNABP is considered to bind to a particular target sequence within a sequence-specific manner if the guide RNA bound to the RGNABP binds to the target sequence under stringent conditions. By "stringent conditions" or "stringent hybridization conditions" is intended conditions under which the two polynucleotide sequences will hybridize to each other to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence -dependent and will be different in different circumstances. Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is at least about 30°C for short sequences (e.g., 10 to 50 nucleotides) and at least about 60°C for long sequences (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulfate) at 37°C, and a wash in IX to 2X SSC (20X SSC = 3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55°C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.

The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched sequence. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm = 81.5°C + 16.6 (log M) + 0.41 (%GC) - 0.61 (% form) - 500/L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4°C lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10°C lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20°C lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology — Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et ah, eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New York).

The term “sequence specific” can also refer to the binding of a target sequence at a greater frequency than binding to a randomized background sequence.

The guide RNA can be a single guide RNA or a dual -guide RNA system. A single guide RNA comprises the crRNA (and in some embodiments, tracrRNA) on a single molecule of RNA, whereas a dual guide RNA system comprises a crRNA and a tracrRNA present on two distinct RNA molecules, hybridized to one another through at least a portion of the CRISPR repeat sequence of the crRNA and at least a portion of the tracrRNA, which may be fully or partially complementary to the CRISPR repeat sequence of the crRNA. In some of those embodiments wherein the guide RNA is a single guide RNA, the crRNA and tracrRNA are separated by a linker nucleotide sequence. In general, the linker nucleotide sequence is one that does not include complementary bases in order to avoid the formation of secondary structure within or comprising nucleotides of the linker nucleotide sequence. In some embodiments, the linker nucleotide sequence between the crRNA and tracrRNA is at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, or more nucleotides in length. In particular embodiments, the linker nucleotide sequence of a single guide RNA is at least 4 nucleotides in length. In certain embodiments, the linker nucleotide sequence is the nucleotide sequence set forth as SEQ ID NO: 249. The single guide RNA or dual-guide RNA can be synthesized chemically or via in vitro transcription. Assays for determining sequence-specific binding between an RGNABP and a guide RNA are known in the art and include, but are not limited to, in vitro binding assays between an expressed RGNABP and the guide RNA, which can be tagged with a detectable label (e.g., biotin) and used in a pull-down detection assay in which the guide RNA:RGNABP complex is captured via the detectable label (e.g., with streptavidin beads). A control guide RNA with an unrelated sequence or structure to the guide RNA can be used as a negative control for non-specific binding of the RGNABP to RNA. In certain embodiments, the guide RNA is SEQ ID NO: 9 or 10, wherein the spacer sequence can be any sequence and is indicated as a poly-N sequence.

In certain embodiments, the guide RNA can be introduced into a target cell, organelle, or embryo as an RNA molecule. The guide RNA can be transcribed in vitro or chemically synthesized. In some embodiments, a nucleotide sequence encoding the guide RNA is introduced into the cell, organelle, or embryo. In some of these embodiments, the nucleotide sequence encoding the guide RNA is operably linked to a promoter (e.g. , an RNA polymerase III promoter). The promoter can be a native promoter or heterologous to the guide RNA-encoding nucleotide sequence.

In various embodiments, the guide RNA can be introduced into a target cell, organelle, or embryo as a ribonucleoprotein complex, as described herein, wherein the guide RNA is bound to an RNA-guided, nucleic acid-binding protein polypeptide.

The guide RNA directs an associated RNA-guided, nucleic acid-binding protein to a particular target nucleotide sequence of interest through hybridization of the guide RNA to the target nucleotide sequence. A target nucleotide sequence can comprise DNA, RNA, or a combination of both and can be single-stranded or double -stranded. A target nucleotide sequence can be genomic DNA (i.e., chromosomal DNA), plasmid DNA, or an RNA molecule (e.g., messenger RNA, ribosomal RNA, transfer RNA, micro RNA, small interfering RNA). The target nucleotide sequence can be bound (and in some embodiments, cleaved) by an RNA-guided, nucleic acid-binding protein in vitro or in a cell. The chromosomal sequence targeted by the RGNABP can be a nuclear, plastid or mitochondrial chromosomal sequence. In some embodiments, the target nucleotide sequence is unique in the target genome.

The target nucleotide sequence is adjacent to a protospacer adjacent motif (PAM). A protospacer adjacent motif is generally within about 1 to about 10 nucleotides from the target nucleotide sequence, including about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, or about 10 nucleotides from the target nucleotide sequence. In particular embodiments, a PAM is within 1 to 10 nucleotides from the target nucleotide sequence, including 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from the target nucleotide sequence. The PAM can be 5' or 3' of the target sequence. Generally, the PAM is a consensus sequence of about 3-4 nucleotides, but in particular embodiments, it can be 2, 3, 4, 5, 6, 7, 8, 9, or more nucleotides in length. In various embodiments, the PAM sequence recognized by the presently disclosed RGNABPs comprises the consensus sequence set forth as SEQ ID NO: 35 or 36. In particular embodiments, an RNA-guided, nucleic acid-binding protein having SEQ ID NO: 1, 2,

3, or 4 or an active variant or fragment thereof binds a target nucleotide sequence adjacent to a PAM sequence. In some of these embodiments, the RGNABP binds to a guide sequence comprising a CRISPR repeat sequence set forth in SEQ ID NO: 5 or 6, respectively, or an active variant or fragment thereof, and a tracrRNA sequence set forth in SEQ ID NO: 7 or 8, respectively, or an active variant or fragment thereof. The RGNABP systems are described further in the Examples of the present specification.

It is well-known in the art that PAM sequence specificity for a given RGNABP is affected by the concentration (see, e.g., Karvelis etal. (2015) Genome Biol 16:253), which may be modified by altering the promoter used to express the RGNABP, or the amount of ribonucleoprotein complex delivered to the cell, organelle, or embryo.

Upon recognizing its corresponding PAM sequence, the RGNABP or a fusion polypeptide comprising the same may cleave the target nucleotide sequence at a specific cleavage site. As used herein, a cleavage site is made up of the two particular nucleotides within a target nucleotide sequence between which the nucleotide sequence is cleaved by an RGNABP or a fusion polypeptide comprising the same. The cleavage site can comprise the 1^st and 2^nd, 2^nd and 3^ri, 3 ^rd and 4^th, 4^th and 5^th, 5^th and 6^th, 7^th and 8^th, or 8^th and 9^th nucleotides from the PAM in either the 5' or 3' direction. In some embodiments, the cleavage site may be over 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides from the PAM in either the 5 ’ or 3’ direction.

As RGNABPs or fusion polypeptides comprising the same may cleave a target nucleotide sequence resulting in staggered ends, in some embodiments, the cleavage site is defined based on the distance of the two nucleotides from the PAM on the positive (+) strand of the polynucleotide and the distance of the two nucleotides from the PAM on the negative (-) strand of the polynucleotide.

IV. Nucleotides Encoding RNA-guided, nucleic acid-binding proteins, CRISPR RNA, and/or tracrRNA

The present disclosure provides polynucleotides comprising the presently disclosed CRISPR RNAs, tracrRNAs, and/or sgRNAs and polynucleotides comprising a nucleotide sequence encoding the presently disclosed RGNABPs, CRISPR RNAs, tracrRNAs, and/or sgRNAs. Presently disclosed polynucleotides include those comprising or encoding a CRISPR repeat sequence comprising the nucleotide sequence of SEQ ID NO: 5 or 6, or an active variant or fragment thereof that when comprised within a guide RNA is capable of directing the sequence -specific binding of an associated RNA-guided, nucleic acid-binding protein to a target sequence of interest. Also disclosed are polynucleotides comprising or encoding a tracrRNA comprising the nucleotide sequence of SEQ ID NO: 7 or 8, or an active variant or fragment thereof that when comprised within a guide RNA is capable of directing the sequence-specific binding of an associated RNA-guided, nucleic acid-binding protein to a target sequence of interest. Polynucleotides are also provided that encode an RNA-guided, nucleic acid-binding protein comprising the amino acid sequence set forth as SEQ ID NO: 1, 2, 3, or 4, and active fragments or variants thereof that retain the ability to bind to a target nucleotide sequence in an RNA-guided sequence-specific manner. The use of the term "polynucleotide" or “nucleic acid molecule” is not intended to limit the present disclosure to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides can comprise ribonucleotides (RNA) and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. These include peptide nucleic acids (PNAs), PNA-DNA chimers, locked nucleic acids (LNAs), and phosphothiorate linked sequences. The polynucleotides disclosed herein also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, DNA-RNA hybrids, triplex structures, stem-and-loop structures, and the like.

The nucleic acid molecules encoding RGNABPs can be codon optimized for expression in an organism of interest. A "codon-optimized” coding sequence is a polynucleotide coding sequence having its frequency of codon usage designed to mimic the frequency of preferred codon usage or transcription conditions of a particular host cell. Expression in the particular host cell or organism is enhanced as a result of the alteration of one or more codons at the nucleic acid level such that the translated amino acid sequence is not changed. Nucleic acid molecules can be codon optimized, either wholly or in part. Codon tables and other references providing preference information for a wide range of organisms are available in the art (see. e.g.. Campbell and Gowri (1990) Plant Physiol. 92: 1-11 for a discussion of plant-preferred codon usage). Methods are available in the art for synthesizing plant-preferred genes or mammalian (for example human) codon-optimized coding sequences. See, for example, U.S. Patent Nos. 5,380,831, and 5,436,391, and Murray etal. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.

Polynucleotides encoding the RGNABPs, crRNAs, tracrRNAs, and/or sgRNAs provided herein can be provided in expression cassettes for in vitro expression or expression in a cell, organelle, embryo, or organism of interest. The cassette will include 5' and 3' regulatory sequences operably linked to a polynucleotide encoding an RGNABP, crRNA, tracrRNAs, and/or sgRNAs provided herein that allows for expression of the polynucleotide. The cassette may additionally contain at least one additional gene or genetic element to be cotransformed into the organism. Where additional genes or elements are included, the components are operably linked. The term “operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a promoter and a coding region of interest (e.g., region coding for an RGNABP, crRNA, tracrRNAs, and/or sgRNAs) is a functional link that allows for expression of the coding region of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame. In some embodiments, the additional gene(s) or element(s) can be provided on multiple expression cassettes. For example, the nucleotide sequence encoding a presently disclosed RGNABP can be present on one expression cassette, whereas the nucleotide sequence encoding a crRNA, tracrRNA, or complete guide RNA can be on a separate expression cassette. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotides to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain a selectable marker gene.

The expression cassette will include in the 5'-3' direction of transcription, a transcriptional (and, in some embodiments, translational) initiation region (i.e., a promoter), an RGNABP-, crRNA-, tracrRNA- and/or sgRNA- encoding polynucleotide of the invention, and a transcriptional (and in some embodiments, translational) termination region (i.e., termination region) functional in the organism of interest. The promoters of the invention are capable of directing or driving expression of a coding sequence in a host cell. The regulatory regions (e.g., promoters, transcriptional regulatory regions, and translational termination regions) may be endogenous or heterologous to the host cell or to each other. As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.

Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau etal. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon etal. (1991 ) Genes Dev. 5:141-149; Mogen etal. (1990) Plant Cell 2: 1261-1272; Munroe etal. (1990) Gene 91:151-158; Balias et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. ( 1987) Nucleic Acids Res. 15:9627-9639.

Additional regulatory signals include, but are not limited to, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Pat. Nos. 5,039,523 and 4,853,331; EPO 0480762A2; Sambrook et al. (1992) Molecular Cloning: A Laboratory Manual, ed. Maniatis et al. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), hereinafter "Sambrook 11"; Davis et al., eds. (1980) Advanced Bacterial Genetics (Cold Spring Harbor Laboratory Press), Cold Spring Harbor, N.Y., and the references cited therein.

In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. Lor this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.

A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. The nucleic acids can be combined with constitutive, inducible, growth stage-specific, cell type-specific, tissue-preferred, tissue-specific, or other promoters for expression in the organism of interest. See, for example, promoters set forth in WO 99/43838 and in US Patent Nos: 8,575,425; 7,790,846; 8,147,856; 8,586832; 7,772,369; 7,534,939; 6,072,050; 5,659,026; 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611; herein incorporated by reference.

For expression in plants, constitutive promoters also include CaMV 35S promoter (Odell etal. (1985) Nature 313:810-812); rice actin (McElroy etal. (1990) Plant Cell 2:163-171); ubiquitin (Christensen etal. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last etal. (1991) Theor. Appl. Genet. 81:581-588); and MAS (Velten etal. (1984) EMBOJ. 3:2723-2730).

Examples of inducible promoters are the Adhl promoter which is inducible by hypoxia or cold stress, the Hsp70 promoter which is inducible by heat stress, the PPDK promoter and the pepcarboxylase promoter which are both inducible by light. Also useful are promoters which are chemically inducible, such as the In2-2 promoter which is safener induced (U.S. Pat. No. 5,364,780), the Axigl promoter which is auxin induced and tapetum specific but also active in callus (PCT US01/22169), the steroid-responsive promoters (see, for example, the ERE promoter which is estrogen induced, and the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88: 10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991 )Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.

Tissue-specific or tissue-preferred promoters can be utilized to target expression of an expression construct within a particular tissue. In certain embodiments, the tissue-specific or tissue-preferred promoters are active in plant tissue. Examples of promoters under developmental control in plants include promoters that initiate transcription preferentially in certain tissues, such as leaves, roots, fruit, seeds, or flowers. A "tissue specific" promoter is a promoter that initiates transcription only in certain tissues. Unlike constitutive expression of genes, tissue-specific expression is the result of several interacting levels of gene regulation.

As such, promoters from homologous or closely related plant species can be preferable to use to achieve efficient and reliable expression of transgenes in particular tissues. In some embodiments, the expression comprises a tissue-preferred promoter. A "tissue preferred" promoter is a promoter that initiates transcription preferentially, but not necessarily entirely or solely in certain tissues.

In some embodiments, the nucleic acid molecules encoding an RGNABP, crRNA, and/or tracrRNA comprise a cell type-specific promoter. A "cell type specific" promoter is a promoter that primarily drives expression in certain cell types in one or more organs. Some examples of plant cells in which cell type specific promoters functional in plants may be primarily active include, for example, BETL cells, vascular cells in roots, leaves, stalk cells, and stem cells. The nucleic acid molecules can also include cell type preferred promoters. A "cell type preferred" promoter is a promoter that primarily drives expression mostly, but not necessarily entirely or solely in certain cell types in one or more organs. Some examples of plant cells in which cell type preferred promoters functional in plants may be preferentially active include, for example, BETL cells, vascular cells in roots, leaves, stalk cells, and stem cells. The nucleic acid sequences encoding the RGNABPs, crRNAs, tracrRNAs, and/or sgRNAs can be operably linked to a promoter sequence that is recognized by a phage RNA polymerase for example, for in vitro mRNA synthesis. In such embodiments, the in w/ro-transcribed RNA can be purified for use in the methods described herein. For example, the promoter sequence can be a T7, T3, or SP6 promoter sequence or a variation of a T7, T3, or SP6 promoter sequence. In such embodiments, the expressed protein and/or RNAs can be purified for use in the methods of genome modification described herein.

In certain embodiments, the polynucleotide encoding the RGNABP, crRNA, tracrRNA, and/or sgRNA also can be linked to a polyadenylation signal (e.g., SV40 polyA signal and other signals functional in plants) and/or at least one transcriptional termination sequence. Additionally, the sequence encoding the RGNABP also can be linked to sequence(s) encoding at least one nuclear localization signal, at least one cell-penetrating domain, and/or at least one signal peptide capable of trafficking proteins to particular subcellular locations, as described elsewhere herein.

The polynucleotide encoding the RGNABP, crRNA, tracrRNA, and/or sgRNA can be present in a vector or multiple vectors. A “vector” refers to a polynucleotide composition for transferring, delivering, or introducing a nucleic acid into a host cell. Suitable vectors include plasmid vectors, phagemids, cosmids, artificial/mini-chromosomes, transposons, and viral vectors (e.g., lentiviral vectors, adeno-associated viral vectors, baculoviral vector). The vector can comprise additional expression control sequences (e.g., enhancer sequences, Kozak sequences, polyadenylation sequences, transcriptional termination sequences), selectable marker sequences (e.g., antibiotic resistance genes), origins of replication, and the like. Additional information can be found in "Current Protocols in Molecular Biology" Ausubel et al. , John Wiley & Sons, New York, 2003 or "Molecular Cloning: A Laboratory Manual" Sambrook & Russell, Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 3rd edition, 2001.

The vector can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D).

In some embodiments, the expression cassette or vector comprising the sequence encoding the RGNABP polypeptide can further comprise a sequence encoding a crRNA and/or a tracrRNA, or the crRNA and tracrRNA combined to create a guide RNA. The sequence(s) encoding the crRNA and/or tracrRNA can be operably linked to at least one transcriptional control sequence for expression of the crRNA and/or tracrRNA in the organism or host cell of interest. For example, the polynucleotide encoding the crRNA and/or tracrRNA can be operably linked to a promoter sequence that is recognized by RNA polymerase III (Pol III). Examples of suitable Pol III promoters include, but are not limited to, mammalian U6, U3, HI, and 7SL RNA promoters and rice U6 and U3 promoters.

As indicated, expression constructs comprising nucleotide sequences encoding the RGNABPs, crRNA, tracrRNA, and/or sgRNA can be used to transform organisms of interest. Methods for transformation involve introducing a nucleotide construct into an organism of interest. By "introducing" is intended to introduce the nucleotide construct to the host cell in such a manner that the construct gains access to the interior of the host cell. The methods of the invention do not require a particular method for introducing a nucleotide construct to a host organism, only that the nucleotide construct gains access to the interior of at least one cell of the host organism. The host cell can be a eukaryotic or prokaryotic cell. In particular embodiments, the eukaryotic host cell is a plant cell, a mammalian cell, an avian cell, or an insect cell. In some embodiments, the eukaryotic cell that comprises or expresses a presently disclosed RGNABP or that has been modified by a presently disclosed RGNABP is a human cell. In some embodiments, the eukaryotic cell that comprises or expresses a presently disclosed RGNABP or that has been modified by a presently disclosed RGNABP is a cell of hematopoietic origin, such as an immune cell (i.e., a cell of the innate or adaptive immune system) including but not limited to a B cell, a T cell, a natural killer (NK) cell, a pluripotent stem cell, an induced pluripotent stem cell, a chimeric antigen receptor T (CAR-T) cell, a monocyte, a macrophage, and a dendritic cell.

Methods for introducing nucleotide constructs into plants and other host cells are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus- mediated methods.

The methods result in a transformed organism, such as a plant, including whole plants, as well as plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, propagules, embryos and progeny of the same. Plant cells can be differentiated or undifferentiated (e.g. callus, suspension culture cells, protoplasts, leaf cells, root cells, phloem cells, pollen).

"Transgenic organisms" or "transformed organisms" or "stably transformed" organisms or cells or tissues refers to organisms that have incorporated or integrated a polynucleotide encoding an RGNABP, crRNA, and/or tracrRNA of the invention. It is recognized that other exogenous or endogenous nucleic acid sequences or DNA fragments may also be incorporated into the host cell. Agrobacterium- and biolistic- mediated transformation remain the two predominantly employed approaches for transformation of plant cells. However, transformation of a host cell may be performed by infection, transfection, microinjection, electroporation, microprojection, biolistics or particle bombardment, electroporation, silica/carbon fibers, ultrasound mediated, PEG mediated, calcium phosphate co-precipitation, polycation DMSO technique, DEAE dextran procedure, and viral mediated, liposome mediated and the like. Viral -mediated introduction of a polynucleotide encoding an RGNABP, crRNA, and/or tracrRNA includes retroviral, lentiviral, adenoviral, and adeno-associated viral mediated introduction and expression, as well as the use of Caulimo viruses, Geminiviruses, and RNA plant viruses.

Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of host cell (e.g., monocot or dicot plant cell) targeted for transformation. Methods for transformation are known in the art and include those set forth in US Patent Nos: 8,575,425; 7,692,068; 8,802,934; 7,541,517; each of which is herein incorporated by reference. See, also, Rakoczy-Trojanowska, M. (2002) Cell Mol Biol Lett. 7:849-858; Jones etal. (2005) Plant Methods 1:5; Rivera etal. (2012) Physics of Life Reviews 9:308-345; Bartlett etal. (2008) Plant Methods 4:1-12; Bates, G.W. (1999) Methods in Molecular Biology 111:359-366; Binns and Thomashow (1988) Annual Reviews in Microbiology 42:575-606; Christou, P. (1992) The Plant Journal 2:275-281; Christou, P. (1995) Euphytica 85:13-27; Tzfira et al. (2004) TRENDS in Genetics 20:375-383; Yao et al. (2006) Journal of Experimental Botany 57:3737-3746; Zupan and Zambryski (1995) Plant Physiology 107: 1041-1047;

Jones etal. (2005) Plant Methods 1:5;

Transformation may result in stable or transient incorporation of the nucleic acid into the cell.

"Stable transformation" is intended to mean that the nucleotide construct introduced into a host cell integrates into the genome of the host cell and is capable of being inherited by the progeny thereof. "Transient transformation" is intended to mean that a polynucleotide is introduced into the host cell and does not integrate into the genome of the host cell.

Methods for transformation of chloroplasts are known in the art. See, for example, Svab et al. (1990) Proc. Nail. Acad. Sci. USA 87:8526-8530; Svab and Maliga (1993) Proc. Natl. Acad. Sci. USA 90:913-917; Svab and Maliga (1993) EMBO J. 12:601-606. The method relies on particle gun delivery of DNA containing a selectable marker and targeting of the DNA to the plastid genome through homologous recombination. Additionally, plastid transformation can be accomplished by transactivation of a silent plastid-bome transgene by tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase. Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91:7301- 7305.

The cells that have been transformed may be grown into a transgenic organism, such as a plant, in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as "transgenic seed") having a nucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.

In some embodiments, cells that have been transformed may be introduced into an organism. These cells could have originated from the organism, wherein the cells are transformed in an ex vivo approach.

The sequences provided herein may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, com (maize), sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers.

Vegetables include, but are not limited to, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum. Preferably, plants of the present invention are crop plants (for example, maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.).

As used herein, the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides. Further provided is a processed plant product or byproduct that retains the sequences disclosed herein, including for example, soymeal.

The polynucleotides encoding the RGNABPs, crRNAs, and/or tracrRNAs can also be used to transform any prokaryotic species, including but not limited to, archaea and bacteria (e.g., Bacillus sp., Klebsiella sp. Streptomyces sp., Rhizobium sp., Escherichia sp., Pseudomonas sp., Salmonella sp., Shigella sp., Vibrio sp., Yersinia sp., Mycoplasma sp., Agrobacterium, Lactobacillus sp.).

The polynucleotides encoding the RGNABPs, crRNAs, and/or tracrRNAs can be used to transform any eukaryotic species, including but not limited to animals (e.g., mammals, insects, fish, birds, and reptiles), fungi, amoeba, algae, and yeast.

Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids in mammalian, insect, or avian cells or target tissues. Such methods can be used to administer nucleic acids encoding components of an RGNABP system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, RNA (e.g. a transcript of a vector described herein), naked nucleic acid, and nucleic acid complexed with a delivery vehicle, such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. For a review of gene therapy procedures, see Anderson, Science 256: 808- 813 (1992); Nabel & Feigner, TIBTECH 11:211-217 (1993); Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167- 175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10): 1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin 51(1):31-44 (1995); Haddada et ah, in Current Topics in Microbiology and Immunology, Doerfler and Bohm (eds) (1995); and Yu et ak, Gene Therapy 1:13-26 (1994). Methods of non-viral delivery of nucleic acids include lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid: nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat.

Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g.,

Transfectam ™ and Lipofectin™). Cationic and neutral lipids that are suitable for efficient receptor- recognition lipofection of polynucleotides include those of Feigner, WO 91/17424; WO 91/16024. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues (e.g. in vivo administration). The preparation of lipid: nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291- 297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

The use of RNA or DNA viral based systems for the delivery of nucleic acids takes advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro, and the modified cells may optionally be administered to patients (ex vivo). Conventional viral based systems could include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues.

The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV),

Simian Immuno deficiency virus (SIV), human immuno deficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Viral. 66:2731-2739 (1992); Johann et al., J. Viral. 66:1635-1640 (1992); Sommnerfelt et al., Viral. 176:58-59 (1990); Wilson et al., J. Viral. 63:2374-2378 (1989); Miller et al., 1 Viral. 65:2220-2224 (1991); PCT US94/05700).

In applications where transient expression is preferred, adenoviral based systems may be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus ("AAV") vectors may also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Katin, Human Gene Therapy 5:793-801 (1994); Muzyczka, 1. Clin. Invest. 94: 1351 (1994). Construction of recombinant AAV vectors are described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466- 6470 (1984); and Samulski et al., 1. Viral. 63:03822-3828 (1989). Packaging cells are typically used to form virus particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and y12 cells or PA317 cells, which package retrovirus.

Viral vectors used in gene therapy are usually generated by producing a cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide (s) to be expressed. The missing viral functions are typically supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences.

The cell line may also be infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV. Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art. See, for example, US20030087817, incorporated herein by reference.

In some embodiments, a host cell is transiently or non-transiently transfected with one or more vectors described herein. In some embodiments, a cell is transfected as it naturally occurs in a subject. In some embodiments, a cell that is transfected is taken from a subject. In some embodiments, the cell is derived from cells taken from a subject, such as a cell line. In some embodiments, the cell line may be mammalian, insect, or avian cells. A wide variety of cell lines for tissue culture are known in the art. Examples of cell lines include, but are not limited to, C8161, CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLaS3, Huhl, Huh4, Huh7, HUVEC, HASMC, HEKn, HEKa, MiaPaCell, Panel, PC-3, TF1, CTLL-2, CIR, Rat6, CVI, RPTE, AIO, T24, 182, A375, ARH-77, Calul, SW480, SW620, SKOV3, SK-UT, CaCo2, P388D1, SEM-K2, WEHI- 231, HB56, TIB55, Jurkat, 145.01, LRMB, Bcl-1, BC-3, IC21, DLD2,

Raw264.7, NRK, NRK-52E, MRC5, MEF, Hep G2, HeLa B, HeLa T4. COS, COS-1, COS-6, COS-M6A, BS-C-1 monkey kidney epithelial, BALB/3T3 mouse embryo fibroblast, 3T3 Swiss, 3T3-L1, 132-d5 human fetal fibroblasts; 10.1 mouse fibroblasts, 293-T, 3T3, 721, 9L, A2780, A2780ADR, A2780cis, A172, A20, A253, A431, A-549, ALC, B16, B35, BCP-I cells, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3, C3H- 10T1/2, C6/36, Cal-27, CHO, CHO-7, CHO-IR, CHO-K1, CHO-K2, CHO-T, CHO Dhfr-/-, COR-L23, COR- L23/CPR, COR-L235010, CORL23/ R23, COS-7, COV-434, CML Tl, CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa, Hepalclc7, HL-60, HMEC, HT-29, Jurkat, IY cells, K562 cells, Ku812, KCL22, KG1, KYOl, LNCap, Ma-Mel 1-48, MC-38, MCF-7, MCF-IOA, MDA-MB-231, MDA-MB-468, MDA-MB-435, MDCKII, MDCKII, MOR/ 0.2R, MONO-MAC 6, MTD-1A, MyEnd, NCI-H69/CPR, NCI-H69/LX10, NCI- H69/LX20, NCI-H69/LX4, NIH-3T3, NALM-1, NW-145, OPCN/OPCT cell lines, Peer, PNT-1A/ PNT 2, RenCa, RIN-5F, RMA/RMAS, Saos-2 cells, Sf-9, SkBr3, T2, T-47D, T84, THP1 cell line, U373, U87,

U937, VCaP, Vero cells, WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof. Cell lines are available from a variety of sources known to those with skill in the art (see, e.g., the American Type Culture Collection (ATCC) (Manassas, Va.)).

In some embodiments, a cell transfected with one or more vectors described herein is used to establish a new cell line comprising one or more vector-derived sequences. In some embodiments, a cell transiently transfected with the components of an RGNABP system as described herein (such as by transient transfection of one or more vectors, or transfection with RNA), and modified through the activity of an RGNABP system, is used to establish a new cell line comprising cells containing the modification but lacking any other exogenous sequence. In some embodiments, cells transiently or non-transiently transfected with one or more vectors described herein, or cell lines derived from such cells are used in assessing one or more test compounds.

In some embodiments, one or more vectors described herein are used to produce a non-human transgenic animal or transgenic plant. In some embodiments, the transgenic animal is a mammal, such as a mouse, rat, hamster, rabbit, cow, or pig. In some embodiments, the transgenic animal is a bird, such as a chicken or a duck. In some embodiments, the transgenic animal is an insect, such as a mosquito or a tick.

V Variants and Fragments of Polypeptides and Polynucleotides

The present disclosure provides active variants and fragments of a naturally-occurring (i.e.. wild- type) RNA-guided, nucleic acid-binding protein, the amino acid sequence of which is set forth as SEQ ID NO: 1, 2, 3, or 4, as well as active variants and fragments of naturally-occurring CRISPR repeats, such as the sequence set forth as SEQ ID NO: 5 or 6, and active variant and fragments of naturally-occurring tracrRNAs, such as the sequence set forth as SEQ ID NO: 7 or 8, and polynucleotides encoding the same.

While the activity of a variant or fragment may be altered compared to the polynucleotide or polypeptide of interest, the variant and fragment should retain the functionality of the polynucleotide or polypeptide of interest. For example, a variant or fragment may have increased activity, decreased activity, different spectrum of activity or any other alteration in activity when compared to the polynucleotide or polypeptide of interest.

Fragments and variants of naturally-occurring RGNABP polypeptides, such as those disclosed herein, will retain sequence-specific, RNA-guided DNA-binding activity. In particular embodiments, fragments and variants of naturally-occurring RGNABP polypeptides, such as those disclosed herein, may have nuclease activity (single -stranded or double-stranded).

Fragments and variants of naturally-occurring CRISPR repeats, such as those disclosed herein, will retain the ability, when part of a guide RNA (comprising a tracrRNA), to bind to and guide an RNA-guided, nucleic acid-binding protein (complexed with the guide RNA) to a target nucleotide sequence in a sequence- specific manner.

Fragments and variants of naturally -occurring tracrRNAs, such as those disclosed herein, will retain the ability, when part of a guide RNA (comprising a CRISPR RNA), to guide an RNA-guided, nucleic acid binding protein (complexed with the guide RNA) to a target nucleotide sequence in a sequence-specific manner.

The term “fragment” refers to a portion of a polynucleotide or polypeptide sequence of the invention. "Fragments" or "biologically active portions" include polynucleotides comprising a sufficient number of contiguous nucleotides to retain the biological activity (i.e.. binding to and directing an RGNABP in a sequence -specific manner to a target nucleotide sequence when comprised within a guideRNA). "Fragments" or "biologically active portions" include polypeptides comprising a sufficient number of contiguous amino acid residues to retain the biological activity (i.e., binding to a target nucleotide sequence in a sequence -specific manner when complexed with a guide RNA). Fragments of the RGNABP proteins include those that are shorter than the full-length sequences due to the use of an alternate downstream start site. A biologically active portion of an RGNABP protein can be a polypeptide that comprises, for example, 10, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750 or more contiguous amino acid residues of SEQ ID NO: 1, 2, 3, or 4. Such biologically active portions can be prepared by recombinant techniques and evaluated for sequence-specific, RNA-guided DNA-binding activity. A biologically active fragment of a CRISPR repeat sequence can comprise at least 8 contiguous amino acids of SEQ ID NO: 5 or 6. A biologically active portion of a CRISPR repeat sequence can be a polynucleotide that comprises, for example, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 contiguous nucleotides of SEQ ID NO: 5 or 6. A biologically active portion of a tracrRNA can be a polynucleotide that comprises, for example, 8, 9, 10, 11, 12, 13, 14,

15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, or 96 contiguous nucleotides of SEQ ID NO: 7 or 8.

In general, "variants" is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a deletion and/or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a "native" or “wild type” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the native amino acid sequence of the gene of interest. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant polynucleotides also include synthetically derived polynucleotides, such as those generated, for example, by using site-directed mutagenesis but which still encode the polypeptide or the polynucleotide of interest. Generally, variants of a particular polynucleotide disclosed herein will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein.

Variants of a particular polynucleotide disclosed herein (i.e.. the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides disclosed herein is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.

In particular embodiments, the presently disclosed polynucleotides encode an RNA-guided, nucleic acid-binding protein polypeptide comprising an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,

94%, 95%, 96%, 97%, 98%, 99%, or greater identity to an amino acid sequence of SEQ ID NO: 1, 2, 3, or 4.

A biologically active variant of an RGNABP polypeptide of the invention may differ by as few as about 1-15 amino acid residues, as few as about 1-10, such as about 6-10, as few as 5, as few as 4, as few as 3, as few as 2, or as few as 1 amino acid residue. In specific embodiments, the polypeptides can comprise an N-terminal or a C-terminal truncation, which can comprise at least a deletion of 10, 15, 20, 25, 30, 35, 40,

45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700,

750 amino acids or more from either the N or C terminus of the polypeptide.

In certain embodiments, the presently disclosed polynucleotides comprise or encode a CRISPR repeat comprising a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,

99%, or greater identity to the nucleotide sequence set forth as SEQ ID NO: 5 or 6.

The presently disclosed polynucleotides can comprise or encode a tracrRNA comprising a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to the nucleotide sequence set forth as SEQ ID NO: 7 or 8.

Biologically active variants of a CRISPR repeat or tracrRNA of the invention may differ by as few as about 1-15 nucleotides, as few as about 1-10, such as about 6-10, as few as 5, as few as 4, as few as 3, as few as 2, or as few as 1 nucleotide. In specific embodiments, the polynucleotides can comprise a 5' or 3' truncation, which can comprise at least a deletion of 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 95 nucleotides or more from either the 5' or 3' end of the polynucleotide.

It is recognized that modifications may be made to the RGNABP polypeptides, CRISPR repeats, and tracrRNAs provided herein creating variant proteins and polynucleotides. Changes designed by man may be introduced through the application of site-directed mutagenesis techniques. In some embodiments, native, as yet-unknown or as yet unidentified polynucleotides and/or polypeptides structurally and/or functionally- related to the sequences disclosed herein may also be identified that fall within the scope of the present invention. Conservative amino acid substitutions may be made in nonconserved regions that do not alter the function of the RGNABP proteins. In some embodiments, modifications may be made that improve the activity of the RGNABP.

Variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different RGNABP proteins disclosed herein (e.g., SEQ ID NO: 1, 2, 3, or 4) is manipulated to create a new RGNABP protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between the RGNABP sequences provided herein and other known RGNABP genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased K_m in the case of an enzyme. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore etal. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504- 4509; Crameri et al. (1998 ) Nature 391:288-291; and U.S. Patent Nos. 5,605,793 and 5,837,458. A "shuffled" nucleic acid is a nucleic acid produced by a shuffling procedure such as any shuffling procedure set forth herein. Shuffled nucleic acids are produced by recombining (physically or virtually) two or more nucleic acids (or character strings), for example in an artificial, and optionally recursive, fashion. Generally, one or more screening steps are used in shuffling processes to identify nucleic acids of interest; this screening step can be performed before or after any recombination step. In some (but not all) shuffling embodiments, it is desirable to perform multiple rounds of recombination prior to selection to increase the diversity of the pool to be screened. The overall process of recombination and selection are optionally repeated recursively. Depending on context, shuffling can refer to an overall process of recombination and selection, or, alternatively, can simply refer to the recombinational portions of the overall process.

As used herein, "sequence identity" or "identity" in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity". Means for making this adjustment are well known to those of skill in the art. Typically, this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California).

As used herein, "percentage of sequence identity" means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.

Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By "equivalent program" is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.

Two sequences are "optimally aligned" when they are aligned for similarity scoring using a defined amino acid substitution matrix (e.g., BLOSUM62), gap existence penalty and gap extension penalty so as to arrive at the highest score possible for that pair of sequences. Amino acid substitution matrices and their use in quantifying the similarity between two sequences are well-known in the art and described, e.g., in Dayhoff et al. (1978) "A model of evolutionary change in proteins." In "Atlas of Protein Sequence and Structure," Vol. 5, Suppl. 3 (ed. M. O. Dayhoff), pp. 345-352. Natl. Biomed. Res. Found., Washington, D.C. and Henikoff et al. (1992) Proc. Natl. Acad. Sci. USA 89:10915-10919. The BLOSUM62 matrix is often used as a default scoring substitution matrix in sequence alignment protocols. The gap existence penalty is imposed for the introduction of a single amino acid gap in one of the aligned sequences, and the gap extension penalty is imposed for each additional empty amino acid position inserted into an already opened gap. The alignment is defined by the amino acids positions of each sequence at which the alignment begins and ends, and optionally by the insertion of a gap or multiple gaps in one or both sequences, so as to arrive at the highest possible score. While optimal alignment and scoring can be accomplished manually, the process is facilitated by the use of a computer-implemented alignment algorithm, e.g., gapped BLAST 2.0, described in Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402, and made available to the public at the National Center for Biotechnology Information Website (www.ncbi.nlm.nih.gov). Optimal alignments, including multiple alignments, can be prepared using, e.g., PSI-BLAST, available through www.ncbi.nlm.nih.gov and described by Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402.

With respect to an amino acid sequence that is optimally aligned with a reference sequence, an amino acid residue "corresponds to" the position in the reference sequence with which the residue is paired in the alignment. The "position" is denoted by a number that sequentially identifies each amino acid in the reference sequence based on its position relative to the N-terminus. Owing to deletions, insertion, truncations, fusions, etc., that must be taken into account when determining an optimal alignment, in general the amino acid residue number in a test sequence as determined by simply counting from the N-terminal will not necessarily be the same as the number of its corresponding position in the reference sequence. For example, in a case where there is a deletion in an aligned test sequence, there will be no amino acid that corresponds to a position in the reference sequence at the site of deletion. Where there is an insertion in an aligned reference sequence, that insertion will not correspond to any amino acid position in the reference sequence. In the case of truncations or fusions there can be stretches of amino acids in either the reference or aligned sequence that do not correspond to any amino acid in the corresponding sequence.

VI. Antibodies

Antibodies to the RGNABP polypeptides or ribonucleoproteins comprising the RGNABP polypeptides of the present invention, including those having the amino acid sequence set forth as SEQ ID NO: 1, 2, 3, or 4 or active variants or fragments thereof, are also encompassed. Methods for producing antibodies are well known in the art (see, for example, Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; and U.S. Pat. No. 4,196,265). These antibodies can be used in kits for the detection and isolation of RGNABP polypeptides or ribonucleoproteins. Thus, this disclosure provides kits comprising antibodies that specifically bind to the polypeptides or ribonucleoproteins described herein, including, for example, polypeptides having the sequence of SEQ ID NO: 1, 2, 3, or 4.

VII. Systems and Ribonucleoprotein Complexes for Binding a Target Sequence of Interest and Methods of Making the Same

The present disclosure provides a system for binding a target sequence of interest, wherein the system comprises at least one guide RNA or a nucleotide sequence encoding the same, and at least one RNA-guided, nucleic acid-binding protein or a nucleotide sequence encoding the same. The guide RNA hybridizes to the target sequence of interest and also forms a complex with the RGNABP polypeptide, thereby directing the RGNABP polypeptide to bind to the target sequence. In some of these embodiments, the RGNABP comprises an amino acid sequence of SEQ ID NO: 1, 2, 3, or 4, or an active variant or fragment thereof. In various embodiments, the guide RNA comprises a CRISPR repeat sequence comprising the nucleotide sequence of SEQ ID NO: 5 or 6, or an active variant or fragment thereof. In particular embodiments, the guide RNA comprises a tracrRNA comprising a nucleotide sequence of SEQ ID NO: 7 or 8, or an active variant or fragment thereof. The guide RNA of the system can be a single guide RNA or a dual-guide RNA. In particular embodiments, the system comprises a RNA-guided, nucleic acid binding protein that is heterologous to the guide RNA, wherein the RGNABP and guide RNA are not found complexed to one another (i.e., bound to one another) in nature.

The system for binding a target sequence of interest provided herein can be a ribonucleoprotein complex, which is at least one molecule of an RNA bound to at least one protein. The ribonucleoprotein complexes provided herein comprise at least one guide RNA as the RNA component and an RNA-guided, nucleic acid-binding protein as the protein component. Such ribonucleoprotein complexes can be purified from a cell or organism that naturally expresses an RGNABP polypeptide and has been engineered to express a particular guide RNA that is specific for a target sequence of interest. In some embodiments, the ribonucleoprotein complex can be purified from a cell or organism that has been transformed with polynucleotides that encode an RGNABP polypeptide and a guide RNA and cultured under conditions to allow for the expression of the RGNABP polypeptide and guide RNA. Thus, methods are provided for making an RGNABP polypeptide or an RGNABP ribonucleoprotein complex. Such methods comprise culturing a cell comprising a nucleotide sequence encoding an RGNABP polypeptide, and in some embodiments a nucleotide sequence encoding a guide RNA, under conditions in which the RGNABP polypeptide (and in some embodiments, the guide RNA) is expressed. The RGNABP polypeptide or RGNABP ribonucleoprotein can then be purified from a lysate of the cultured cells.

Methods for purifying an RGNABP polypeptide or RGNABP ribonucleoprotein complex from a lysate of a biological sample are known in the art (e.g., size exclusion and/or affinity chromatography, 20- PAGE, HPLC, reversed-phase chromatography, immunoprecipitation). In particular methods, the RGNABP polypeptide is recombinantly produced and comprises a purification tag to aid in its purification, including but not limited to, glutathione-S-transferase (GST), chitin binding protein (CBP), maltose binding protein, thioredoxin (TRX), poly(NANP), tandem affinity purification (TAP) tag, myc, AcV5, AU1, AU5, E, ECS, E2, FLAG, HA, nus, Softag 1, Softag 3, Strep, SBP, Glu-Glu, HSV, KT3, S, SI, T7, V5, VSV-G, 6xHis, lOxHis, biotin carboxyl carrier protein (BCCP), and calmodulin. Generally, the tagged RGNABP polypeptide or RGNABP ribonucleoprotein complex is purified using immobilized metal affinity chromatography. It will be appreciated that other similar methods known in the art may be used, including other forms of chromatography or for example immunoprecipitation, either alone or in combination.

An "isolated" or "purified" polypeptide, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polypeptide as found in its naturally occurring environment. Thus, an isolated or purified polypeptide is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. A protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein. When the protein of the invention or biologically active portion thereof is recombinantly produced, optimally culture medium represents less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non-protein-of-interest chemicals.

Particular methods provided herein for binding and/or cleaving a target sequence of interest involve the use of an in vitro assembled RGNABP ribonucleoprotein complex. In vitro assembly of an RGNABP ribonucleoprotein complex can be performed using any method known in the art in which an RGNABP polypeptide is contacted with a guide RNA under conditions to allow for binding of the RGNABP polypeptide to the guide RNA. As used herein, "contact", contacting", "contacted," refer to placing the components of a desired reaction together under conditions suitable for carrying out the desired reaction.

The RGNABP polypeptide can be purified from a biological sample, cell lysate, or culture medium, produced via in vitro translation, or chemically synthesized. The guide RNA can be purified from a biological sample, cell lysate, or culture medium, transcribed in vitro, or chemically synthesized. The RGNABP polypeptide and guide RNA can be brought into contact in solution (e.g., buffered saline solution) to allow for in vitro assembly of the RGNABP ribonucleoprotein complex.

VIII. Methods of Binding, Cleaving, or Modifying a Target Sequence

The present disclosure provides methods for binding, cleaving, and/or modifying a target nucleotide sequence of interest. The methods include delivering a system comprising at least one guide RNA or a polynucleotide encoding the same, and at least one RGNABP polypeptide or RGNABP fusion polypeptide or a polynucleotide encoding the same to the target sequence or a cell, organelle, or embryo comprising the target sequence. In some of these embodiments, the RGNABP comprises the amino acid sequence of SEQ ID NO: 1, 2, 3, or 4, or an active variant or fragment thereof. In various embodiments, the guide RNA comprises a CRISPR repeat sequence comprising the nucleotide sequence of SEQ ID NO: 5 or 6, or an active variant or fragment thereof. In particular embodiments, the guide RNA comprises a tracrRNA comprising the nucleotide sequence of SEQ ID NO: 7 or 8, or an active variant or fragment thereof. The guide RNA of the system can be a single guide RNA or a dual-guide RNA. The RGNABP of the system may be a fusion polypeptide. In some embodiments, the fusion polypeptide comprises a base-editing polypeptide, for example a cytidine deaminase or an adenosine deaminase. In some embodiments, the fusion polypeptide comprises an expression modulator, such as an epigenetic modification domain, a transcriptional activator domain, or a transcriptional repressor domain. In some embodiments, the fusion polypeptide comprises a nuclease domain. In particular embodiments, the RGNABP and/or guide RNA is heterologous to the cell, organelle, or embryo to which the RGNABP and/or guide RNA (or polynucleotide(s) encoding at least one of the RGNABP and guide RNA) are introduced.

In those embodiments wherein the method comprises delivering a polynucleotide encoding a guide RNA and/or an RGNABP polypeptide, the cell or embryo can then be cultured under conditions in which the guide RNA and/or RGNABP polypeptide are expressed. In various embodiments, the method comprises contacting a target sequence with an RGNABP ribonucleoprotein complex. The RGNABP ribonucleoprotein complex may comprise an RGNABP that is a fusion polypeptide. In some embodiments, the RGNABP of the ribonucleoprotein complex is a fusion polypeptide comprising a base-editing polypeptide, a nuclease domain, and/or an expression modulator. In certain embodiments, the method comprises introducing into a cell, organelle, or embryo comprising a target sequence an RGNABP ribonucleoprotein complex. The RGNABP ribonucleoprotein complex can be one that has been purified from a biological sample, recombinantly produced and subsequently purified, or in vvVra-asscmblcd as described herein. In those embodiments wherein the RGNABP ribonucleoprotein complex that is contacted with the target sequence or a cell organelle, or embryo has been assembled in vitro, the method can further comprise the in vitro assembly of the complex prior to contact with the target sequence, cell, organelle, or embryo.

A purified or in vitro assembled RGNABP ribonucleoprotein complex can be introduced into a cell, organelle, or embryo using any method known in the art, including, but not limited to electroporation. In some embodiments, a polynucleotide encoding an RGNABP polypeptide and/or polynucleotide encoding or comprising the guide RNA can be introduced into a cell, organelle, or embryo using any method known in the art (e.g., electroporation).

Upon delivery to or contact with the target sequence or cell, organelle, or embryo comprising the target sequence, the guide RNA directs the RGNABP to bind to the target sequence in a sequence-specific manner. In those embodiments wherein the RGNABP or a fusion polypeptide comprising the same has nuclease activity, the RGNABP polypeptide cleaves the target sequence of interest upon binding. The target sequence can subsequently be modified via endogenous repair mechanisms, such as non-homologous end joining, or homology-directed repair with a provided donor polynucleotide. Methods to measure binding of an RGNABP polypeptide to a target sequence are known in the art and include chromatin immunoprecipitation assays, gel mobility shift assays, DNA pull-down assays, reporter assays, microplate capture and detection assays. Likewise, methods to measure cleavage or modification of a target sequence are known in the art and include in vitro or in vivo cleavage assays wherein cleavage is confirmed using PCR, sequencing, or gel electrophoresis, with or without the attachment of an appropriate label (e.g., radioisotope, fluorescent substance) to the target sequence to facilitate detection of degradation products. In some embodiments, the nicking triggered exponential amplification reaction (NTEXPAR) assay can be used (see, e.g., Zhang et al. (2016) Chem. Sci. 7:4951- 4957). In vivo cleavage can be evaluated using the Surveyor assay (Guschin et al. (2010) Methods Mol Biol 649:247-256).

In some embodiments, the methods involve the use of a single type of RGNABP complexed with more than one guide RNA. The more than one guide RNA can target different regions of a single gene or can target multiple genes.

In those embodiments wherein a donor polynucleotide is not provided, a double-stranded break introduced by an RGNABP or RGNABP fusion polypeptide can be repaired by a non-homologous end joining (NHEJ) repair process. Due to the error-prone nature of NHEJ, repair of the double-stranded break can result in a modification to the target sequence. As used herein, a “modification” in reference to a nucleic acid molecule refers to a change in the nucleotide sequence of the nucleic acid molecule, which can be a deletion, insertion, or substitution of one or more nucleotides, or a combination thereof. Modification of the target sequence can result in the expression of an altered protein product or inactivation of a coding sequence.

In those embodiments wherein a donor polynucleotide is present, the donor sequence in the donor polynucleotide can be integrated into or exchanged with the target nucleotide sequence during the course of repair of the introduced double -stranded break, resulting in the introduction of the exogenous donor sequence. A donor polynucleotide thus comprises a donor sequence that is desired to be introduced into a target sequence of interest. In some embodiments, the donor sequence alters the original target nucleotide sequence such that the newly integrated donor sequence will not be recognized and cleaved by the RGNABP or RGNABP fusion polypeptide. Integration of the donor sequence can be enhanced by the inclusion within the donor polynucleotide of flanking sequences, referred to herein as “homology arms” that have substantial sequence identity with the sequences flanking the target nucleotide sequence, allowing for a homology- directed repair process. In some embodiments, homology arms have a length of at least 50 base pairs, at least 100 base pairs, and up to 2000 base pairs or more, and have at least 90%, at least 95%, or more, sequence homology to their corresponding sequence within the target nucleotide sequence.

In those embodiments wherein the RGNABP or fusion polypeptide introduces double-stranded staggered breaks, the donor polynucleotide can comprise a donor sequence flanked by compatible overhangs, allowing for direct ligation of the donor sequence to the cleaved target nucleotide sequence comprising overhangs by a non-homologous repair process during repair of the double-stranded break.

In those embodiments wherein the method involves the use of an RGNABP or RGNABP fusion polypeptide that is a nickase (i.e., is only able to cleave a single strand of a double -stranded polynucleotide), the method can comprise introducing two RGNABP nickases that target identical or overlapping target sequences and cleave different strands of the polynucleotide. For example, an RGNABP nickase that only cleaves the positive (+) strand of a double -stranded polynucleotide can be introduced along with a second RGNABP nickase that only cleaves the negative (-) strand of a double-stranded polynucleotide.

In various embodiments, a method is provided for binding a target nucleotide sequence and detecting the target sequence, wherein the method comprises introducing into a cell, organelle, or embryo at least one guide RNA or a polynucleotide encoding the same, and at least one RGNABP polypeptide or a polynucleotide encoding the same, expressing the guide RNA and/or RGNABP polypeptide (if coding sequences are introduced), wherein the RGNABP polypeptide may be a fusion polypeptide and further comprises a detectable label, and the method further comprises detecting the detectable label. The detectable label may be fused to the RGNABP as a fusion protein (e.g., fluorescent protein) or may be a small molecule conjugated to or incorporated within the RGNABP polypeptide that can be detected visually or by other means.

Also provided herein are methods for modulating the expression of a target sequence or a gene of interest under the regulation of a target sequence. The methods comprise introducing into a cell, organelle, or embryo at least one guide RNA or a polynucleotide encoding the same, and at least one RGNABP polypeptide or a polynucleotide encoding the same, expressing the guide RNA and/or RGNABP polypeptide (if coding sequences are introduced), wherein the RGNABP polypeptide may be a fusion polypeptide. In some of these embodiments, the RGNABP is a fusion protein comprising an expression modulator domain (i.e.. epigenetic modification domain, transcriptional activation domain or a transcriptional repressor domain) as described herein.

The present disclosure also provides methods for binding and/or modifying a target nucleotide sequence of interest. The methods include delivering a system comprising at least one guide RNA or a polynucleotide encoding the same, and at least one fusion polypeptide comprises an RGNABP of the invention and a base-editing polypeptide, for example a cytidine deaminase or an adenosine deaminase, or a polynucleotide encoding the fusion polypeptide, to the target sequence or a cell, organelle, or embryo comprising the target sequence.

One of ordinary skill in the art will appreciate that any of the presently disclosed methods can be used to target a single target sequence or multiple target sequences. Thus, methods comprise the use of a single RGNABP polypeptide in combination with multiple, distinct guide RNAs, which can target multiple, distinct sequences within a single gene and/or multiple genes. Also encompassed herein are methods wherein multiple, distinct guide RNAs are introduced in combination with multiple, distinct RGNABP polypeptides. These guide RNAs and guide RNA/RGNABP polypeptide systems can target multiple, distinct sequences within a single gene and/or multiple genes.

In one aspect, the invention provides kits containing any one or more of the elements disclosed in the above methods and compositions. In some embodiments, the kit comprises a vector system and instructions for using the kit. In some embodiments, the vector system comprises (a) a first regulatory element operably linked to a DNA sequence encoding the crRNA sequence and one or more insertion sites for inserting a guide sequence upstream of the encoded crRNA sequence, wherein when expressed, the guide sequence directs sequence -specific binding of an RGNABP complex to a target sequence in a eukaryotic cell, wherein the RGNABP complex comprises an RGNABP complexed with the guide RNA polynucleotide; and/or (b) a second regulatory element operably linked to a coding sequence encoding said RGNABP comprising a nuclear localization sequence. In some embodiments, the RGNABP is a fusion polypeptide. Elements may be provided individually or in combinations, and may be provided in any suitable container, such as a vial, a bottle, or a tube.

In some embodiments, the kit includes instructions in one or more languages. In some embodiments, a kit comprises one or more reagents for use in a process utilizing one or more of the elements described herein. Reagents may be provided in any suitable container. For example, a kit may provide one or more reaction or storage buffers. Reagents may be provided in a form that is usable in a particular assay, or in a form that requires addition of one or more other components before use (e.g. in concentrate or lyophilized form). A buffer can be any buffer, including but not limited to a sodium carbonate buffer, a sodium bicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and combinations thereof. In some embodiments, the buffer is alkaline. In some embodiments, the buffer has a pH from about 7 to about 10.

In some embodiments, the kit comprises one or more oligonucleotides corresponding to a guide sequence for insertion into a vector so as to operably link the guide sequence and a regulatory element. In some embodiments, the kit comprises a homologous recombination template polynucleotide. In one aspect, the invention provides methods for using one or more elements of an RGNABP system. The RGNABP system of the invention provides an effective means for binding a target polynucleotide. The RGNABP system of the invention has a wide variety of utility including modifying (e.g., deleting, inserting, translocating, inactivating, activating, base editing) a target polynucleotide in a multiplicity of cell types. As such the RGNABP system of the invention has a broad spectrum of applications in, e.g., gene therapy, drug screening, disease diagnosis, and prognosis. An exemplary RGNABP system, or RGNABP complex, comprises an RGNABP or an RGNABP fusion polypeptide complexed with a guide sequence hybridized to a target sequence within the target polynucleotide.

IX. Target Polynucleotides In one aspect, the invention provides for methods of modifying a target polynucleotide in a eukaryotic cell, which may be in vivo, ex vivo or in vitro. In some embodiments, the method comprises sampling a cell or population of cells from a human or non-human animal or plant (including microalgae) and modifying the cell or cells. Culturing may occur at any stage ex vivo. The cell or cells may even be re introduced into the non-human animal or plant (including micro-algae).

Using natural variability, plant breeders combine most useful genes for desirable qualities, such as yield, quality, uniformity, hardiness, and resistance against pests. These desirable qualities also include growth, day length preferences, temperature requirements, initiation date of floral or reproductive development, fatty acid content, insect resistance, disease resistance, nematode resistance, fungal resistance, herbicide resistance, tolerance to various environmental factors including drought, heat, wet, cold, wind, and adverse soil conditions including high salinity The sources of these useful genes include native or foreign varieties, heirloom varieties, wild plant relatives, and induced mutations, e.g., treating plant material with mutagenic agents. Using the present invention, plant breeders are provided with a new tool to induce mutations. Accordingly, one skilled in the art can analyze the genome for sources of useful genes, and in varieties having desired characteristics or traits employ the present invention to induce the rise of useful genes, with more precision than previous mutagenic agents and hence accelerate and improve plant breeding programs.

The target polynucleotide of an RGNABP system can be any polynucleotide endogenous or exogenous to the eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cell. The target polynucleotide can be a sequence coding a gene product (e.g., a protein) or a non-coding sequence (e.g., a regulatory polynucleotide or a junk DNA). Without wishing to be bound by theory, the target sequence should be associated with a PAM (protospacer adjacent motif); that is, a short sequence recognized by the RGNABP system. The precise sequence and length requirements for the PAM differ depending on the RGNABP used, but PAMs are typically 2-5 base pair sequences adjacent the protospacer (that is, the target sequence).

The target polynucleotide of an RGNABP system may include a number of disease-associated genes and polynucleotides as well as signaling biochemical pathway-associated genes and polynucleotides. Examples of target polynucleotides include a sequence associated with a signaling biochemical pathway, e.g., a signaling biochemical pathway-associated gene or polynucleotide. Examples of target polynucleotides include a disease associated gene or polynucleotide. A "disease-associated" gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in an abnormal form in cells derived from a disease-affected tissues compared with tissues or cells of a non-disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a gene that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and/or progression of the disease. A disease-associated gene also refers to a gene possessing mutation(s) or genetic variation that is directly responsible or is in linkage disequilibrium with a gene(s) that is responsible for the etiology of a disease (e.g., a causal mutation). The transcribed or translated products may be known or unknown, and further may be at a normal or abnormal level. In some embodiments, the disease may be an animal disease. In some embodiments, the disease may be an avian disease. In some embodiments, the disease may be a mammalian disease. In some embodiments, the disease may be a human disease. Examples of disease-associated genes and polynucleotides in humans are available from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore,

Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web.

Although RGNABP systems are particularly useful for their relative ease in targeting to genomic sequences of interest, there still remains an issue of what the RGNABP can do to address a causal mutation. One approach is to produce a fusion protein between an RGNABP (preferably an inactive or nickase variant of the RGNABP) and a base-editing enzyme or the active domain of a base editing enzyme, such as a cytidine deaminase or an adenosine deaminase base editor (U.S. Patent No. 9,840,699, herein incorporated by reference). In some embodiments, the methods comprise contacting a DNA molecule with (a) a fusion protein comprising an RGNABP of the invention and a base-editing polypeptide such as a deaminase; and (b) a gRNA targeting the fusion protein of (a) to a target nucleotide sequence of the DNA strand; wherein the DNA molecule is contacted with the fusion protein and the gRNA in an amount effective and under conditions suitable for the deamination of a nucleobase. In some embodiments, the target DNA sequence comprises a sequence associated with a disease or disorder, and wherein the deamination of the nucleobase results in a sequence that is not associated with a disease or disorder. In some embodiments, the target DNA sequence resides in an allele of a crop plant, wherein the particular allele of the trait of interest results in a plant of lesser agronomic value. The deamination of the nucleobase results in an allele that improves the trait and increases the agronomic value of the plant.

In some embodiments, the DNA sequence comprises a T- C or A- G point mutation associated with a disease or disorder, and wherein the deamination of the mutant C or G base results in a sequence that is not associated with a disease or disorder. In some embodiments, the deamination corrects a point mutation in the sequence associated with the disease or disorder.

In some embodiments, the sequence associated with the disease or disorder encodes a protein, and wherein the deamination introduces a stop codon into the sequence associated with the disease or disorder, resulting in a truncation of the encoded protein. In some embodiments, the contacting is performed in vivo in a subject susceptible to having, having, or diagnosed with the disease or disorder. In some embodiments, the disease or disorder is a disease associated with a point mutation, or a single-base mutation, in the genome. In some embodiments, the disease is a genetic disease, a cancer, a metabolic disease, or a lysosomal storage disease.

X. Pharmaceutical Compositions and Methods of Treatment Pharmaceutical compositions comprising the presently disclosed RGNABP polypeptides and active variants and fragments thereof, as well as polynucleotides encoding the same, the presently disclosed gRNAs or polynucleotides encoding the same, the presently disclosed systems, or cells comprising any of the RGNABP polypeptides or RGNABP-encoding polynucleotides, gRNA or gRNA-encoding polynucleotides, or the RGNABP systems, and a pharmaceutically acceptable carrier are provided.

A pharmaceutical composition is a composition that is employed to prevent, reduce in intensity, cure or otherwise treat a target condition or disease that comprises an active ingredient (i.e., RGNABP polypeptides, RGNABP-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGNABP systems, or cells comprising any one of these) and a pharmaceutically acceptable carrier.

As used herein, a “pharmaceutically acceptable carrier” refers to a material that does not cause significant irritation to an organism and does not abrogate the activity and properties of the active ingredient (i.e., RGNABP polypeptides, RGNABP-encoding polynucleotides, gRNA, gRNA-encoding polynucleotides, RGNABP systems, or cells comprising any one of these). Carriers must be of sufficiently high purity and of sufficiently low toxicity to render them suitable for administration to a subject being treated. The carrier can be inert, or it can possess pharmaceutical benefits. In some embodiments, a pharmaceutically acceptable carrier comprises one or more compatible solid or liquid filler, diluents or encapsulating substances which are suitable for administration to a human or other vertebrate animal. In some embodiments, the pharmaceutically acceptable carrier is not naturally-occurring. In some embodiments, the pharmaceutically acceptable carrier and the active ingredient are not found together in nature.

Pharmaceutical compositions used in the presently disclosed methods can be formulated with suitable carriers, excipients, and other agents that provide suitable transfer, delivery, tolerance, and the like. A multitude of appropriate formulations are known to those skilled in the art. See, e.g., Remington, The Science and Practice of Pharmacy (21st ed. 2005). Suitable formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LIPOFECTIN vesicles), lipid nanoparticles, DNA conjugates, anhydrous absorption pastes, oil-in-water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax. Pharmaceutical compositions for oral or parenteral use may be prepared into dosage forms in a unit dose suited to fit a dose of the active ingredients. Such dosage forms in a unit dose include, for example, tablets, pills, capsules, injections (ampoules), suppositories, etc.

In some embodiments wherein cells comprising or modified with the presently disclosed RGNABPs, gRNAs, RGNABP systems or polynucleotides encoding the same are administered to a subject, the cells are administered as a suspension with a pharmaceutically acceptable carrier. One of skill in the art will recognize that a pharmaceutically acceptable carrier to be used in a cell composition will not include buffers, compounds, cryopreservation agents, preservatives, or other agents in amounts that substantially interfere with the viability of the cells to be delivered to the subject. A formulation comprising cells can include e.g., osmotic buffers that permit cell membrane integrity to be maintained, and optionally, nutrients to maintain cell viability or enhance engraftment upon administration. Such formulations and suspensions are known to those of skill in the art and/or can be adapted for use with the cells described herein using routine experimentation.

A cell composition can also be emulsified or presented as a liposome composition, provided that the emulsification procedure does not adversely affect cell viability. The cells and any other active ingredient can be mixed with excipients that are pharmaceutically acceptable and compatible with the active ingredient, and in amounts suitable for use in the therapeutic methods described herein.

Additional agents included in a cell composition can include pharmaceutically acceptable salts of the components therein. Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the polypeptide) that are formed with inorganic acids, such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, tartaric, mandelic and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases, such as, for example, sodium, potassium, ammonium, calcium or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine and the like.

Physiologically tolerable and pharmaceutically acceptable carriers are well known in the art. Exemplary liquid carriers are sterile aqueous solutions that contain no materials in addition to the active ingredients and water, or contain a buffer such as sodium phosphate at physiological pH value, physiological saline or both, such as phosphate-buffered saline. Still further, aqueous carriers can contain more than one buffer salt, as well as salts such as sodium and potassium chlorides, dextrose, polyethylene glycol and other solutes. Liquid compositions can also contain liquid phases in addition to and to the exclusion of water. Exemplary of such additional liquid phases are glycerin, vegetable oils such as cottonseed oil, and water-oil emulsions. The amount of an active compound used in the cell compositions that is effective in the treatment of a particular disorder or condition can depend on the nature of the disorder or condition, and can be determined by standard clinical techniques.

The presently disclosed RGNABP polypeptides, guide RNAs, RGNABP systems or polynucleotides encoding the same can be formulated with pharmaceutically acceptable excipients such as carriers, solvents, stabilizers, adjuvants, diluents, etc., depending upon the particular mode of administration and dosage form. In some embodiments, these pharmaceutical compositions are formulated to achieve a physiologically compatible pH, and range from a pH of about 3 to a pH of about 11, about pH 3 to about pH 7, depending on the formulation and route of administration. In some embodiments, the pH can be adjusted to a range from about pH 5.0 to about pH 8. In some embodiments, the compositions can comprise a therapeutically effective amount of at least one compound as described herein, together with one or more pharmaceutically acceptable excipients. In some embodiments, the compositions comprise a combination of the compounds described herein, or include a second active ingredient useful in the treatment or prevention of bacterial growth (for example and without limitation, anti-bacterial or anti-microbial agents), or include a combination of reagents of the present disclosure.

Suitable excipients include, for example, carrier molecules that include large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive virus particles. Other exemplary excipients can include antioxidants (for example and without limitation, ascorbic acid), chelating agents (for example and without limitation, EDTA), carbohydrates (for example and without limitation, dextrin, hydroxyalkylcellulose, and hydroxyalkylmethylcellulose), stearic acid, liquids (for example and without limitation, oils, water, saline, glycerol and ethanol), wetting or emulsifying agents, pH buffering substances, and the like.

In some embodiments, the formulations are provided in unit-dose or multi-dose containers, for example sealed ampules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring the addition of the sterile liquid carrier, for example, saline, water-for-injection, a semi-liquid foam, or gel, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described. In some embodiments, the active ingredient is dissolved in a buffered liquid solution that is frozen in a unit-dose or multi -dose container and later thawed for injection or kept/stabilized under refrigeration until use.

The therapeutic agent(s) may be contained in controlled release systems. In order to prolong the effect of a drug, it often is desirable to slow the absorption of the drug from subcutaneous, intrathecal, or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. In some embodiments, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle. In some embodiments, the use of a long-term sustained release implant may be particularly suitable for treatment of chronic conditions. Long-term sustained release implants are well- known to those of ordinary skill in the art.

Methods of treating a disease in a subject in need thereof are provided herein. The methods comprise administering to a subject in need thereof an effective amount of a presently disclosed RGNABP polypeptide or active variant or fragment thereof or a polynucleotide encoding the same, a presently disclosed gRNA or a polynucleotide encoding the same, a presently disclosed RGNABP system, or a cell modified by or comprising any one of these compositions.

In some embodiments, the treatment comprises in vivo gene editing by administering a presently disclosed RGNABP polypeptide, gRNA, or RGNABP system or polynucleotide(s) encoding the same. In some embodiments, the treatment comprises ex vivo gene editing wherein cells are genetically modified ex vivo with a presently disclosed RGNABP polypeptide, gRNA, or RGNABP system or polynucleotide(s) encoding the same and then the modified cells are administered to a subject. In some embodiments, the genetically modified cells originate from the subject that is then administered the modified cells, and the transplanted cells are referred to herein as autologous. In some embodiments, the genetically modified cells originate from a different subject (i.e., donor) within the same species as the subject that is administered the modified cells (i.e., recipient), and the transplanted cells are referred to herein as allogeneic. In some examples described herein, the cells can be expanded in culture prior to administration to a subject in need thereof.

In some embodiments, the disease to be treated with the presently disclosed compositions is one that can be treated with immunotherapy, such as with a chimeric antigen receptor (CAR) T cell. Such diseases include but are not limited to cancer. In some embodiments, the disease to be treated with the presently disclosed compositions is associated with a causal mutation. As used herein, a “causal mutation” refers to a particular nucleotide, nucleotides, or nucleotide sequence in the genome that contributes to the severity or presence of a disease or disorder in a subject. The correction of the causal mutation leads to the improvement of at least one symptom resulting from a disease or disorder. In some embodiments, the causal mutation is adjacent to a PAM site recognized by an RGNABP disclosed herein. The causal mutation can be corrected with a presently disclosed RGNABP or a fusion polypeptide comprising a presently disclosed RGNABP and a base-editing polypeptide (i.e., a base editor). Non-limiting examples of diseases associated with a causal mutation include cystic fibrosis, Hurler syndrome, Friedreich’s Ataxia, Huntington’s Disease, and sickle cell disease. Additional non-limiting examples of disease-associated genes and mutations are available from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore,

Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web.

As used herein, "treatment" or "treating," or "palliating" or "ameliorating" are used interchangeably. These terms refer to an approach for obtaining beneficial or desired results including but not limited to a therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant any therapeutically relevant improvement in or effect on one or more diseases, conditions, or symptoms under treatment. For prophylactic benefit, the compositions may be administered to a subject at risk of developing a particular disease, condition, or symptom, or to a subject reporting one or more of the physiological symptoms of a disease, even though the disease, condition, or symptom may not have yet been manifested.

The term "effective amount" or "therapeutically effective amount" refers to the amount of an agent that is sufficient to effect beneficial or desired results. The therapeutically effective amount may vary depending upon one or more of: the subject and disease condition being treated, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The specific dose may vary depending on one or more of: the particular agent chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, and the delivery system in which it is carried.

The term "administering" refers to the placement of an active ingredient into a subject, by a method or route that results in at least partial localization of the introduced active ingredient at a desired site, such as a site of injury or repair, such that a desired effect(s) is produced. In those embodiments wherein cells are administered, the cells can be administered by any appropriate route that results in delivery to a desired location in the subject where at least a portion of the implanted cells or components of the cells remain viable. The period of viability of the cells after administration to a subject can be as short as a few hours, e.g., twenty-four hours, to a few days, to as long as several years, or even the life time of the patient, i.e., long-term engraftment. For example, in some aspects described herein, an effective amount of photoreceptor cells or retinal progenitor cells is administered via a systemic route of administration, such as an intraperitoneal or intravenous route.

In some embodiments, the administering comprises administering by viral delivery. In some embodiments, the administering comprises administering by electroporation. In some embodiments, the administering comprises administering by nanoparticle delivery. In some embodiments, the administering comprises administering by liposome delivery. Any effective route of administration can be used to administer an effective amount of a pharmaceutical composition described herein. In some embodiments, the administering comprises administering by a method selected from the group consisting of: intravenously, subcutaneously, intramuscularly, orally, rectally, by aerosol, parenterally, ophthalmicly, pulmonarily, transdermally, vaginally, otically, nasally, and by topical administration, or any combination thereof. In some embodiments, for the delivery of cells, administration by injection or infusion is used.

As used herein, the term "subject" refers to any individual for whom diagnosis, treatment or therapy is desired. In some embodiments, the subject is an animal. In some embodiments, the subject is a mammal. In some embodiments, the subject is a human being.

The efficacy of a treatment can be determined by the skilled clinician. However, a treatment is considered an "effective treatment," if any one or all of the signs or symptoms of a disease or disorder are altered in a beneficial manner (e.g., decreased by at least 10%), or other clinically accepted symptoms or markers of disease are improved or ameliorated. Efficacy can also be measured by failure of an individual to worsen as assessed by hospitalization or need for medical interventions (e.g., progression of the disease is halted or at least slowed). Methods of measuring these indicators are known to those of skill in the art. Treatment includes: (1) inhibiting the disease, e.g., arresting, or slowing the progression of symptoms; or (2) relieving the disease, e.g., causing regression of symptoms; and (3) preventing or reducing the likelihood of the development of symptoms.

A. Modifying causal mutations using base-editing

An example of a genetically inherited disease which could be corrected using an approach that relies on an RGNABP-base editor fusion protein of the invention is Hurler Syndrome. Hurler Syndrome, also known as MPS-1, is the result of a deficiency of a-L-iduronidase (IDUA) resulting in a lysosomal storage disease characterized at the molecular level by the accumulation of dermatan sulfate and heparan sulfate in lysosomes. This disease is generally an inherited genetic disorder caused by mutations in the IDUA gene encoding a-L-iduronidase. Common IDUA mutations are W402X and Q70X, both nonsense mutations resulting in premature termination of translation. Such mutations are well addressed by precise genome editing (PGE) approaches, since reversion of a single nucleotide, for example by a base-editing approach, would restore the wild-type coding sequence and result in protein expression controlled by the endogenous regulatory mechanisms of the genetic locus. Additionally, since heterozygotes are known to be asymptomatic, a PGE therapy that targets one of these mutations would be useful to a large proportion of patients with this disease, as only one of the mutated alleles needs to be corrected (Bunge et al. (1994) Hum. Mol. Genet. 3(6): 861-866, herein incorporated by reference).

Current treatments for Hurler Syndrome include enzyme replacement therapy and bone marrow transplants (Vellodi et al. (1997) Arch. Dis. Child. 76(2): 92-99; Peters et al. (1998) Blood 91(7): 2601- 2608, herein incorporated by reference). While enzyme replacement therapy has had a dramatic effect on the survival and quality of life of Hurler Syndrome patients, this approach requires costly and time- consuming weekly infusions. Additional approaches include the delivery of the IDUA gene on an expression vector or the insertion of the gene into a highly expressed locus such as that of serum albumin (U.S. Patent No. 9,956,247, herein incorporated by reference). However, these approaches do not restore the original IDUA locus to the correct coding sequence. A genome -editing strategy would have a number of advantages, most notably that regulation of gene expression would be controlled by the natural mechanisms present in healthy individuals. Additionally, using base editing does not necessitate causing a double stranded DNA breaks, which could lead to large chromosomal rearrangements, cell death, or oncogenecity by the disruption of tumor suppression mechanisms. A general strategy may be directed toward using RGNABP-base editor fusion proteins of the invention to target and correct certain disease-causing mutations in the human genome. It will be appreciated that similar approaches to target diseases that can be corrected by base-editing may also be pursued. It will be further appreciated that similar approaches to target disease- causing mutations in other species, particularly common household pets or livestock, can also be deployed using the RGNABPs of the invention. Common household pets and livestock include dogs, cats, horses, pigs, cows, sheep, chickens, donkeys, snakes, ferrets, and fish including salmon and shrimp.

B. Modifying causal mutations by targeted deletion

RGNABPs of the invention could also be useful in human therapeutic approaches where the causal mutation is more complicated. For example, some diseases such as Friedreich’s Ataxia and Huntington’s Disease are the result of a significant increase in repeats of a three nucleotide motif at a particular region of a gene, which affects the ability of the expressed protein to function or to be expressed. Friedreich’s Ataxia (FRDA) is an autosomal recessive disease resulting in progressive degeneration of nervous tissue in the spinal cord. Reduced levels of the frataxin (FXN) protein in the mitochondria cause oxidative damages and iron deficiencies at the cellular level. The reduced FXN expression has been linked to a GAA triplet expansion within the intron 1 of the somatic and germline FXN gene. In FRDA patients, the GAA repeat frequently consists of more than 70, sometimes even more than 1000 (most commonly 600-900) triplets, whereas unaffected individuals have about 40 repeats or less (Pandolfo et al. (2012) Handbook of Clinical Neurology 103: 275-294; Campuzano et al. (1996) Science 271: 1423-1427; Pandolfo (2002) Adv. Exp. Med. Biol. 516: 99-118; all herein incorporated by reference).

The expansion of the trinucleotide repeat sequence causing Friedreich’s Ataxia (FRDA) occurs in a defined genetic locus within the FXN gene, referred to as the FRDA instability region. RGNABPs alone or RGNABP-nuclease domain fusion polypeptides may be used for excising the instability region in FRDA patient cells. This approach requires 1) an RGNABP and guide RNA sequence that can be programmed to target the allele in the human genome; and 2) a delivery approach for the RGNABP and guide sequence. Many nucleases used for genome editing, such as the commonly used Cas9 nuclease from S. pyogenes (SpCas9), are too large to be packaged into adeno-associated viral (AAV) vectors, especially when considering the length of the SpCas9 gene and the guide RNA in addition to other genetic elements required for functional expression cassettes. This makes an approach using SpCas9 more difficult.

Certain RGNABPs or RGNABP-nuclease domain fusion polypeptides of the invention are well suited for packaging into an AAV vector along with a guide RNA. Packing two guide RNAs would likely require a second vector, but this approach still compares favorably to what would be required of a larger nuclease such as SpCas9, which may require splitting the protein sequence between two vectors. The present invention encompasses a strategy using RGNABPs of the invention in which a region of genomic instability is removed. Such a strategy is applicable to other diseases and disorders which have a similar genetic basis, such as Huntington’s Disease. Similar strategies using RGNABPs of the invention may also be applicable to similar diseases and disorders in non-human animals of agronomic or economic importance, including dogs, cats, horses, pigs, cows, sheep, chickens, donkeys, snakes, ferrets, and fish including salmon and shrimp.

C. Modifying causal mutations by targeted mutagenesis

RGNABPs of the invention could also be used to introduce disruptive mutations that may result in a beneficial effect. Genetic defects in the genes encoding hemoglobin, particularly the beta globin chain (the HBB gene), can be responsible for a number of diseases known as hemoglobinopathies, including sickle cell anemia and thalassemias.

In adult humans, hemoglobin is a heterotetramer comprising two alpha (a)-like globin chains and two beta (b)-1 ike globin chains and 4 heme groups. In adults the a2b2 tetramer is referred to as Hemoglobin A (HbA) or adult hemoglobin. Typically, the alpha and beta globin chains are synthesized in an approximate 1:1 ratio and this ratio seems to be critical in terms of hemoglobin and red blood cell (RBC) stabilization. In a developing fetus, a different form of hemoglobin, fetal hemoglobin (HbF), is produced which has a higher binding affinity for oxygen than Hemoglobin A such that oxygen can be delivered to the baby's system via the mother's blood stream. Fetal hemoglobin also contains two a globin chains, but in place of the adult b- globin chains, it has two fetal gamma (y)-globin chains (i.e., fetal hemoglobin is a2g2). The regulation of the switch from production of gamma- to beta-globin is quite complex, and primarily involves a down- regulation of gamma globin transcription with a simultaneous up-regulation of beta globin transcription. At approximately 30 weeks of gestation, the synthesis of gamma globin in the fetus starts to drop while the production of beta globin increases. By approximately 10 months of age, the newborn's hemoglobin is nearly all a2b2 although some HbF persists into adulthood (approximately 1-3% of total hemoglobin). In the majority of patients with hemoglobinopathies, the genes encoding gamma globin remain present, but expression is relatively low due to normal gene repression occurring around parturition as described above.

Sickle cell disease is caused by a V6E mutation in the b globin gene (HBB) (a GAG to GTG at the DNA level), where the resultant hemoglobin is referred to as “hemoglobins” or “HbS.” Under lower oxygen conditions, HbS molecules aggregate and form fibrous precipitates. These aggregates cause the abnormality or ‘sickling’ of the RBCs, resulting in a loss of flexibility of the cells. The sickling RBCs are no longer able to squeeze into the capillary beds and can result in vaso-occlusive crisis in sickle cell patients. In addition, sickled RBCs are more fragile than normal RBCs, and tend towards hemolysis, eventually leading to anemia in the patient.

Treatment and management of sickle cell patients is a life-long proposition involving antibiotic treatment, pain management and transfusions during acute episodes. One approach is the use of hydroxyurea, which exerts its effects in part by increasing the production of gamma globin. Long term side effects of chronic hydroxyurea therapy are still unknown, however, and treatment gives unwanted side effects and can have variable efficacy from patient to patient. Despite an increase in the efficacy of sickle cell treatments, the life expectancy of patients is still only in the mid to late 50's and the associated morbidities of the disease have a profound impact on a patient's quality of life.

Thalassemias (alpha thalassemias and beta thalassemia) are also diseases relating to hemoglobin and typically involve a reduced expression of globin chains. This can occur through mutations in the regulatory regions of the genes or from a mutation in a globin coding sequence that results in reduced expression or reduced levels or functional globin protein. Treatment of thalassemias usually involves blood transfusions and iron chelation therapy. Bone marrow transplants are also being used for treatment of people with severe thalassemias if an appropriate donor can be identified, but this procedure can have significant risks.

One approach that has been proposed for the treatment of both sickle cell disease (SCD) and beta thalassemias is to increase the expression of gamma globin so that HbF functionally replaces the aberrant adult hemoglobin. As mentioned above, treatment of SCD patients with hydroxyurea is thought to be successful in part due to its effect on increasing gamma globin expression (DeSimone (1982) Proc Nat'l Acad Sci USA 79(14):4428-31; Ley, et ak, (1982) N. Engl. J. Medicine, 307: 1469-1475; Ley, et ah, (1983) Blood 62: 370-380; Constantoulakis et ak, (1988) Blood 72(6): 1961-1967, all herein incorporated by reference). Increasing the expression of HbF involves identification of genes whose products play a role in the regulation of gamma globin expression. One such gene is BCL11A. BCL11A encodes a zinc finger protein that expressed in adult erythroid precursor cells, and down-regulation of its expression leads to an increase in gamma globin expression (Sankaran et at (2008) Science 322: 1839, herein incorporated by reference). Use of an inhibitory RNA targeted to the BCL11A gene has been proposed (e.g., U.S. Patent Publication 2011/0182867, herein incorporated by reference) but this technology has several potential drawbacks, including that complete knock down may not be achieved, delivery of such RNAs may be problematic, and the RNAs must be present continuously, requiring multiple treatments for life.

RGNABPs and/or RGNABP-nuclease domain fusion proteins of the invention may be used to target the BCL11A enhancer region to disrupt expression of BCL11A, thereby increasing gamma globin expression. This targeted disruption can be achieved by non-homologous end joining (NHEJ), whereby an RGNABP of the invention or a fusion polypeptide comprising the same targets to a particular sequence within the BCL11A enhancer region, makes a double-stranded DNA cleavage, and the cell’s machinery repairs the break, typically simultaneously introducing deleterious mutations. Similar to what is described for other disease targets, RGNABPs of the invention may have advantages over other known targeting nucleases due to their relatively small size, which enables packaging expression cassettes for the RGNABP and its guide RNA into a single AAV vector for in vivo delivery. Similar strategies using RGNABPs of the invention may also be applicable to similar diseases and disorders in both humans and in non-human animals of agronomic or economic importance.

XI. Cells Comprising a Polynucleotide Genetic Modification

Provided herein are cells and organisms comprising a target sequence of interest that has been modified using a process mediated by an RGNABP, crRNA, and/or tracrRNA as described herein. In some of these embodiments, the RGNABP comprises the amino acid sequence of SEQ ID NO: 1, 2, 3, or 4, or an active variant or fragment thereof. In various embodiments, the guide RNA comprises a CRISPR repeat sequence comprising the nucleotide sequence of SEQ ID NO: 5 or 6, or an active variant or fragment thereof. In particular embodiments, the guide RNA comprises a tracrRNA comprising the nucleotide sequence of SEQ ID NO: 7 or 8, or an active variant or fragment thereof. The guide RNA of the system can be a single guide RNA or a dual-guide RNA. In some embodiments, the RGNABP is a fusion polypeptide. In some embodiments, the fusion polypeptide comprises a base-editing polypeptide, for example a cytidine deaminase or an adenosine deaminase. In some embodiments, the fusion polypeptide comprises an expression modulator, such as an epigenetic modification domain, a transcriptional activator domain, or a transcriptional repressor domain. In some embodiments, the fusion polypeptide comprises a nuclease domain.

The modified cells can be eukaryotic (e.g., mammalian, plant, insect cell) or prokaryotic. Also provided are organelles and embryos comprising at least one nucleotide sequence that has been modified by a process utilizing an RGNABP, crRNA, and/or tracrRNA as described herein. The genetically modified cells, organisms, organelles, and embryos can be heterozygous or homozygous for the modified nucleotide sequence.

The chromosomal modification of the cell, organism, organelle, or embryo can result in altered expression (up-regulation or down-regulation), inactivation, or the expression of an altered protein product or an integrated sequence. In those embodiments wherein the chromosomal modification results in either the inactivation of a gene or the expression of a non-functional protein product, the genetically modified cell, organism, organelle, or embryo is referred to as a “knock out”. The knock out phenotype can be the result of a deletion mutation (i.e., deletion of at least one nucleotide), an insertion mutation (i.e.. insertion of at least one nucleotide), or a nonsense mutation (i.e.. substitution of at least one nucleotide such that a stop codon is introduced).

In some embodiments, the chromosomal modification of a cell, organism, organelle, or embryo can produce a “knock in”, which results from the chromosomal integration of a nucleotide sequence that encodes a protein. In some of these embodiments, the coding sequence is integrated into the chromosome such that the chromosomal sequence encoding the wild-type protein is inactivated, but the exogenously introduced protein is expressed.

In some embodiments, the chromosomal modification results in the production of a variant protein product. The expressed variant protein product can have at least one amino acid substitution and/or the addition or deletion of at least one amino acid. The variant protein product encoded by the altered chromosomal sequence can exhibit modified characteristics or activities when compared to the wild-type protein, including but not limited to altered enzymatic activity or substrate specificity.

In some embodiments, the chromosomal modification can result in an altered expression pattern of a protein. As a non-limiting example, chromosomal alterations in the regulatory regions controlling the expression of a protein product can result in the overexpression or downregulation of the protein product or an altered tissue or temporal expression pattern.

The cells that have been modified can be grown into an organism, such as a plant, in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same modified strain or different strains, and the resulting hybrid having the genetic modification. The present invention provides genetically modified seed. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the genetic modification. Further provided is a processed plant product or byproduct that retains the genetic modification, including for example, soymeal.

The methods provided herein may be used for modification of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, com (maize), sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp., alfalfa, rye, millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana, avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers.

Vegetables include, but are not limited to, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Curcumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum. Preferably, plants of the present invention are crop plants (for example, maize, sorghum, wheat, sunflower, tomato, crucifers, peppers, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, oilseed rape, etc.).

The methods provided herein can also be used to genetically modify any prokaryotic species, including but not limited to, archaea and bacteria (e.g., Bacillus sp., Klebsiella sp. Streptomyces sp., Rhizobium sp., Escherichia sp., Pseudomonas sp., Salmonella sp., Shigella sp., Vibrio sp., Yersinia sp., Mycoplasma sp., Agrobacterium, Lactobacillus sp.).

The methods provided herein can be used to genetically modify any eukaryotic species or cells therefrom, including but not limited to animals (e.g., mammals, insects, fish, birds, and reptiles), fungi, amoeba, algae, and yeast. In some embodiments, the cell that is modified by the presently disclosed methods include cells of hematopoietic origin, such as cells of the immune system including but not limited to B cells, T cells, natural killer (NK) cells, pluripotent stem cells, induced pluripotent stem cells, chimeric antigen receptor T (CAR-T) cells, monocytes, macrophages, and dendritic cells.

Cells that have been modified may be introduced into an organism. These cells could have originated from the same organism (e.g., person) in the case of autologous cellular transplants, wherein the cells are modified in an ex vivo approach. In some embodiments, the cells originated from another organism within the same species (e.g., another person) in the case of allogeneic cellular transplants.

The article “a” and “an” are used herein to refer to one or more than one (/. e. , to at least one) of the grammatical object of the article. By way of example, “a polypeptide” means one or more polypeptides.

All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this disclosure pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended embodiments.

Non-limiting embodiments include:

1. A nucleic acid molecule comprising a polynucleotide encoding an RNA-guided nucleic acid binding protein (RGNABP) polypeptide, wherein said polynucleotide comprises a nucleotide sequence encoding an RGNABP polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; wherein said RGNABP polypeptide is capable of binding a target sequence of a nucleic acid molecule in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA) capable of hybridizing to said target sequence, and wherein said polynucleotide encoding an RGNABP polypeptide is operably linked to a promoter heterologous to said polynucleotide.

2. The nucleic acid molecule of embodiment 1, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

3. The nucleic acid molecule of embodiment 1, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

4. The nucleic acid molecule of embodiment 1, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

5. The nucleic acid molecule of embodiment 1, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

6. The nucleic acid molecule of any one of embodiments 1-5, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

7. The nucleic acid molecule of any one of embodiments 1-5, wherein said RGNABP polypeptide is a fusion polypeptide.

8. The RGNABP polypeptide of embodiment 7, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

9. The nucleic acid molecule of embodiment 6 or 8, wherein said RGNABP polypeptide is capable of generating a double -stranded break.

10. The nucleic acid molecule of embodiment 6 or 8, wherein said RGNABP polypeptide is capable of generating a single-stranded break.

11. The nucleic acid molecule of embodiment 7, wherein said fusion polypeptide is an RGNABP operably fused to a base-editing polypeptide.

12. The nucleic acid molecule of embodiment 11, wherein the base-editing polypeptide is a deaminase.

13. The nucleic acid molecule of embodiment 12, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

14. The nucleic acid molecule of embodiment 7, wherein said fusion polypeptide is an RGNABP operably fused to an expression modulator polypeptide.

15. The nucleic acid molecule of any one of embodiments 1-14, wherein the RGNABP polypeptide comprises one or more nuclear localization signals. 16. The nucleic acid molecule of any one of embodiments 1-15, wherein the RGNABP polypeptide is codon optimized for expression in a eukaryotic cell.

17. The nucleic acid molecule of any one of embodiments 1-16, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

18. A vector comprising the nucleic acid molecule of any one of embodiments 1-17.

19. The vector of embodiment 18, further comprising at least one nucleotide sequence encoding said gRNA capable of hybridizing to said target sequence.

20. The vector of embodiment 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

21. The vector of embodiment 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

22. The vector of embodiment 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

23. The vector of embodiment 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

24. The vector of embodiment 19, wherein the guide RNA comprises a CRISPR RNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

25. The vector of embodiment 19, wherein said gRNA comprises a crRNA and a tracrRNA.

26. The vector of embodiment 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

27. The vector of embodiment 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

28. The vector of embodiment 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to

SEQ ID NO: 5 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

29. The vector of embodiment 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

30. The vector of embodiment 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

31. The vector of any one of embodiments 25-30, where said gRNA is a single guide RNA.

32. The vector of any one of embodiments 25-30, wherein said gRNA is a dual-guide RNA.

33. A cell comprising the nucleic acid molecule of any one of embodiments 1-17 or the vector of any one of embodiments 18-32.

34. A method for making an RGNABP polypeptide comprising culturing the cell of embodiment 33 under conditions in which the RGNABP polypeptide is expressed.

35. A method for making an RGNABP polypeptide comprising introducing into a cell a heterologous nucleic acid molecule comprising a nucleotide sequence encoding an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; wherein said RGNABP polypeptide is capable of binding a target sequence of a nucleic acid molecule in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA) capable of hybridizing to said target sequence; and culturing said cell under conditions in which the RGNABP polypeptide is expressed.

36. The method of embodiment 35, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4. 37. The method of embodiment 35, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

38. The method of embodiment 35, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

39. The method of embodiment 35, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

40. The method of any one of embodiments 34-39, further comprising purifying said RGNABP polypeptide.

41. The method of any one of embodiments 34-39, wherein said cell further expresses one or more guide RNAs that binds to said RGNABP polypeptide to form an RGNABP ribonucleoprotein complex.

42. The method of embodiment 41, further comprising purifying said RGNABP ribonucleoprotein complex.

43. An isolated RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; and wherein said RGNABP polypeptide is capable of binding a target sequence of a nucleic acid molecule in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA) capable of hybridizing to said target sequence.

44. The isolated RGNABP polypeptide of embodiment 43, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

45. The isolated RGNABP polypeptide of embodiment 43, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

46. The isolated RGNABP polypeptide of embodiment 43, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

47. The isolated RGNABP polypeptide of embodiment 43, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

48. The isolated RGNABP polypeptide of any one of embodiments 43-47, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

49. The isolated RGNABP polypeptide of any one of embodiments 43-47, wherein said RGNABP polypeptide is a fusion polypeptide.

50. The isolated RGNABP polypeptide of embodiment 49, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

51. The isolated RGNABP polypeptide of embodiment 48 or 50, wherein said RGNABP polypeptide is capable of generating a double-stranded break.

52. The isolated RGNABP polypeptide of embodiment 48 or 50, wherein said RGNABP polypeptide is capable of generating a single-stranded break. 53. The isolated RGNABP polypeptide of embodiment 49, wherein the RGNABP polypeptide is operably fused to a base-editing polypeptide.

54. The isolated RGNABP polypeptide of embodiment 53, wherein the base-editing polypeptide is a deaminase.

55. The isolated RGNABP polypeptide of embodiment 54, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

56. The isolated RGNABP polypeptide of embodiment 49, wherein said fusion polypeptide is an RGNABP operably fused to an expression modulator polypeptide.

57. The isolated RGNABP polypeptide of any one of embodiments 43-56, wherein the RGNABP polypeptide comprises one or more nuclear localization signals.

58. The isolated RGNABP polypeptide of any one of embodiments 43-57, wherein the RGNABP polypeptide is codon optimized for expression in a eukaryotic cell.

59. The isolated RGNABP polypeptide of any one of embodiments 43-58, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

60. A nucleic acid molecule comprising a polynucleotide encoding a CRISPR RNA (crRNA), wherein said crRNA comprises a spacer sequence and a CRISPR repeat sequence, wherein said CRISPR repeat sequence comprises a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 5 or 6; wherein a guide RNA comprising said crRNA is capable of hybridizing to a target sequence of a nucleic acid molecule in a sequence specific manner through the spacer sequence of said crRNA when said guide RNA is bound to an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, and wherein said polynucleotide encoding a crRNA is operably linked to a promoter heterologous to said polynucleotide.

61. The nucleic acid molecule of embodiment 60, wherein said CRISPR repeat sequence comprises a nucleotide sequence having at least 80% sequence identity to SEQ ID NO: 5 or 6.

62. The nucleic acid molecule of embodiment 60, wherein said CRISPR repeat sequence comprises a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 5 or 6.

63. The nucleic acid molecule of embodiment 60, wherein said CRISPR repeat sequence comprises a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 5 or 6.

64. The nucleic acid molecule of embodiment 60, wherein said CRISPR repeat sequence comprises a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 5 or 6.

65. The nucleic acid molecule of embodiment 60, wherein said CRISPR repeat sequence comprises a nucleotide sequence having 100% sequence identity to SEQ ID NO: 5 or 6.

66. A vector comprising the nucleic acid molecule of any one of embodiments 60-65. 67. The vector of embodiment 66, wherein said vector further comprises a polynucleotide encoding a trans-activating CRISPR RNA (tracrRNA) capable of hybridizing to said CRISPR repeat sequence of said crRNA.

68. The vector of embodiment 67, wherein said tracrRNA is selected from the group consisting of: a) a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said CRISPR repeat sequence has at least 70% sequence identity to SEQ ID NO: 5; and b) a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said CRISPR repeat sequence has at least 70% sequence identity to SEQ ID NO: 6.

69. The vector of embodiment 67, wherein said tracrRNA is selected from the group consisting of: a) a tracrRNA having at least 80% sequence identity to SEQ ID NO: 7, wherein said CRISPR repeat sequence has at least 80% sequence identity to SEQ ID NO: 5; and b) a tracrRNA having at least 80% sequence identity to SEQ ID NO: 8, wherein said CRISPR repeat sequence has at least 80% sequence identity to SEQ ID NO: 6.

70. The vector of embodiment 67, wherein said tracrRNA is selected from the group consisting of: a) a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said CRISPR repeat sequence has at least 85% sequence identity to SEQ ID NO: 5; and b) a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said CRISPR repeat sequence has at least 85% sequence identity to SEQ ID NO: 6.

71. The vector of embodiment 67, wherein said tracrRNA is selected from the group consisting of: a) a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said CRISPR repeat sequence has at least 90% sequence identity to SEQ ID NO: 5; and b) a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said CRISPR repeat sequence has at least 90% sequence identity to SEQ ID NO: 6.

72. The vector of embodiment 67, wherein said tracrRNA is selected from the group consisting of: a) a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said CRISPR repeat sequence has at least 95% sequence identity to SEQ ID NO: 5; and b) a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said CRISPR repeat sequence has at least 95% sequence identity to SEQ ID NO: 6.

73. The vector of embodiment 67, wherein said tracrRNA is selected from the group consisting of: a) a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said CRISPR repeat sequence has 100% sequence identity to SEQ ID NO: 5; and b) a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said CRISPR repeat sequence has 100% sequence identity to SEQ ID NO: 6.

74. The vector of any one of embodiments 67-73, wherein said polynucleotide encoding said crRNA and said polynucleotide encoding said tracrRNA are operably linked to the same promoter and are encoded as a single guide RNA.

75. The vector of any one of embodiments 67-73, wherein said polynucleotide encoding said crRNA and said polynucleotide encoding said tracrRNA are operably linked to separate promoters.

76. The vector of any one of embodiments 67-75, wherein said vector further comprises a polynucleotide encoding said RGNABP polypeptide.

77. The vector of embodiment 76, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 80% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 70% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 70% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 80% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 70% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 70% sequence identity to SEQ ID NO: 8.

78. The vector of embodiment 76, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 85% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 85% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 85% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 85% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 85% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 85% sequence identity to SEQ ID NO: 8.

79. The vector of embodiment 76, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 90% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 90% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 90% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 90% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 90% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 90% sequence identity to SEQ ID NO: 8. 80. The vector of embodiment 76, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 95% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 95% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 95% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 95% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 95% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 95% sequence identity to SEQ ID NO: 8.

81. The vector of embodiment 76, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having 100% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has 100% sequence identity to SEQ ID NO: 5 and said tracrRNA has 100% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having 100% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has 100% sequence identity to SEQ ID NO: 6 and said tracrRNA has 100% sequence identity to SEQ ID NO: 8.

82. The vector of any one of embodiments 76-81, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

83. The vector of any one of embodiments 76-81, wherein said RGNABP polypeptide is a fusion polypeptide.

84. The vector of embodiment 83, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

85. The vector of embodiment 83, wherein said fusion polypeptide is an RGNABP operably fused to a base-editing polypeptide.

86. The vector of embodiment 83, wherein said fusion polypeptide is an RGNABP operably fused to an expression modulator polypeptide.

87. A nucleic acid molecule comprising a polynucleotide encoding a trans-activating CRISPR RNA (tracrRNA) comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 7 or 8; wherein a guide RNA comprising: a) said tracrRNA; and b) a crRNA comprising a spacer sequence and a CRISPR repeat sequence, wherein said tracrRNA hybridizes with said CRISPR repeat sequence of said crRNA; is capable of hybridizing to a target sequence of a nucleic acid molecule in a sequence specific manner through the spacer sequence of said crRNA when said guide RNA is bound to an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, and wherein said polynucleotide encoding a tracrRNA is operably linked to a promoter heterologous to said polynucleotide.

88. The nucleic acid molecule of embodiment 87, wherein said tracrRNA comprises a nucleotide sequence having at least 80% sequence identity to SEQ ID NO: 7 or 8.

89. The nucleic acid molecule of embodiment 87, wherein said tracrRNA comprises a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 7 or 8.

90. The nucleic acid molecule of embodiment 87, wherein said tracrRNA comprises a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 7 or 8.

91. The nucleic acid molecule of embodiment 87, wherein said tracrRNA comprises a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 7 or 8.

92. The nucleic acid molecule of embodiment 87, wherein said tracrRNA comprises a nucleotide sequence having 100% sequence identity to SEQ ID NO: 7 or 8.

93. A vector comprising the nucleic acid molecule of any one of embodiments 87-92.

94. The vector of embodiment 93, wherein said vector further comprises a polynucleotide encoding said crRNA.

95. The vector of embodiment 94, wherein said crRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5, wherein said tracrRNA has at least 70% sequence identity to SEQ ID NO: 7; and b) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6, wherein said tracrRNA has at least 70% sequence identity to SEQ ID NO: 8.

96. The vector of embodiment 94, wherein said crRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 80% sequence identity to SEQ ID NO: 5, wherein said tracrRNA has at least 80% sequence identity to SEQ ID NO: 7; and b) a CRISPR repeat sequence having at least 80% sequence identity to SEQ ID NO: 6, wherein said tracrRNA has at least 80% sequence identity to SEQ ID NO: 8.

97. The vector of embodiment 94, wherein said crRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5, wherein said tracrRNA has at least 85% sequence identity to SEQ ID NO: 7; and b) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6, wherein said tracrRNA has at least 85% sequence identity to SEQ ID NO: 8.

98. The vector of embodiment 94, wherein said crRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5, wherein said tracrRNA has at least 90% sequence identity to SEQ ID NO: 7; and b) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6, wherein said tracrRNA has at least 90% sequence identity to SEQ ID NO: 8.

99. The vector of embodiment 94, wherein said crRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5, wherein said tracrRNA has at least 95% sequence identity to SEQ ID NO: 7; and b) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6, wherein said tracrRNA has at least 95% sequence identity to SEQ ID NO: 8.

100. The vector of embodiment 94, wherein said crRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5, wherein said tracrRNA has 100% sequence identity to SEQ ID NO: 7; and b) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6, wherein said tracrRNA has 100% sequence identity to SEQ ID NO: 8.

101. The vector of any one of embodiments 94-100, wherein said polynucleotide encoding said crRNA and said polynucleotide encoding said tracrRNA are operably linked to the same promoter and are encoded as a single guide RNA.

102. The vector of any one of embodiments 94-100, wherein said polynucleotide encoding said crRNA and said polynucleotide encoding said tracrRNA are operably linked to separate promoters.

103. The vector of any one of embodiments 94-100, wherein said vector further comprises a polynucleotide encoding said RGNABP polypeptide.

104. The vector of embodiment 103, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 80% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 70% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 70% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 80% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 70% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 70% sequence identity to SEQ ID NO: 8.

105. The vector of embodiment 103, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 85% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 85% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 85% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 85% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 85% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 85% sequence identity to SEQ ID NO: 8.

106. The vector of embodiment 103, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 90% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 90% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 90% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 90% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 90% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 90% sequence identity to SEQ ID NO: 8.

107. The vector of embodiment 103, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having at least 95% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has at least 95% sequence identity to SEQ ID NO: 5 and said tracrRNA has at least 95% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having at least 95% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has at least 95% sequence identity to SEQ ID NO: 6 and said tracrRNA has at least 95% sequence identity to SEQ ID NO: 8.

108. The vector of embodiment 103, wherein said RGNABP polypeptide is selected from the group consisting of: a) an RGNABP polypeptide having 100% sequence identity to SEQ ID NO: 1 or 2, wherein said CRISPR repeat sequence has 100% sequence identity to SEQ ID NO: 5 and said tracrRNA has 100% sequence identity to SEQ ID NO: 7; and b) an RGNABP polypeptide having 100% sequence identity to SEQ ID NO: 3 or 4, wherein said CRISPR repeat sequence has 100% sequence identity to SEQ ID NO: 6 and said tracrRNA has 100% sequence identity to SEQ ID NO: 8.

109. The vector of any one of embodiments 103-108, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

110. The vector of any one of embodiments 103-108, wherein said RGNABP polypeptide is a fusion polypeptide.

111. The vector of embodiment 110, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

112. The vector of embodiment 110, wherein said fusion polypeptide is an RGNABP operably fused to a base-editing polypeptide. 113. The vector of embodiment 110, wherein said fusion polypeptide is an RGNABP operably fused to an expression modulator polypeptide.

114. A system for binding a target sequence of a nucleic acid molecule, said system comprising: a) one or more guide RNAs capable of hybridizing to said target sequence or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more guide RNAs (gRNAs); and b) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4 or a polynucleotide comprising a nucleotide sequence encoding the RGNABP polypeptide; wherein at least one of said nucleotide sequences encoding the one or more guide RNAs and said nucleotide sequence encoding the RGNABP polypeptide is operably linked to a promoter heterologous to said nucleotide sequence; wherein the one or more guide RNAs are capable of hybridizing to the target sequence; and wherein the one or more guide RNAs are capable of forming a complex with the RGNABP polypeptide, in order to direct said RGNABP polypeptide to bind to said target sequence of the nucleic acid molecule.

115. A system for binding a target sequence of a nucleic acid molecule, said system comprising: a) one or more guide RNAs capable of hybridizing to said target sequence or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more guide RNAs (gRNAs); and b) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; wherein the one or more guide RNAs are capable of hybridizing to the target sequence; and wherein the one or more guide RNAs are capable of forming a complex with the RGNABP polypeptide in order to direct said RGNABP polypeptide to bind to said target sequence of the nucleic acid molecule.

116. The system of embodiment 114 or 115, wherein at least one of said nucleotides sequences encoding the one or more guide RNAs is operably linked to a promoter heterologous to said nucleotide sequence.

117. The system of any one of embodiments 114-116, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

118. The system of any one of embodiments 114-116, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

119. The system of any one of embodiments 114-116, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4. 120. The system of any one of embodiments 114-116, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

121. The system of any one of embodiments 114-120, wherein said RGNABP polypeptide and said one or more guide RNAs are not found complexed to one another in nature.

122. The system of any one of embodiments 114-121, wherein said target DNA sequence is a eukaryotic target DNA sequence.

123. The system of any one of embodiments 114-122, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

124. The system of any one of embodiments 114-122, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

125. The system of any one of embodiments 114-122, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

126. The system of any one of embodiments 114-122, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

127. The system of any one of embodiments 114-122, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

128. The system of any one of embodiments 114-122, wherein said gRNA comprises a crRNA and atracrRNA.

129. The system of embodiment 128, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

130. The system of embodiment 128, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

131. The system of embodiment 128, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

132. The system of embodiment 128, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

133. The system of embodiment 128, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

134. The system of any one of embodiments 128-133, wherein said gRNA is a single guide RNA (sgRNA).

135. The system of any one of embodiments 128-133, wherein said gRNA is a dual-guide RNA.

136. The system of any one of embodiments 114-135, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

137. The system of any one of embodiments 114-136, wherein the target sequence is within a cell.

138. The system of embodiment 137, wherein the cell is a eukaryotic cell.

139. The system of embodiment 138, wherein the eukaryotic cell is a plant cell.

140. The system of embodiment 138, wherein the eukaryotic cell is a mammalian cell. 141. The system of embodiment 140, wherein said mammalian cell is a human cell.

142. The system of embodiment 141, wherein said human cell is an immune cell.

143. The system of embodiment 142, wherein said immune cell is a stem cell.

144. The system of embodiment 143, wherein said stem cell is an induced pluripotent stem cell.

145. The system of embodiment 138, wherein the eukaryotic cell is an insect cell.

146. The system of embodiment 137, wherein the cell is a prokaryotic cell.

147. The system of any of embodiments 114-146, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

148. The system of embodiment 147, wherein said RGNABP polypeptide is capable of generating a double -stranded break.

149. The system of embodiment 147, wherein said RGNABP polypeptide is capable of generating a single-strand break.

150. The system of any of embodiments 114-146, wherein said RGNABP polypeptide is a fusion polypeptide.

151. The system of embodiment 150, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

152. The system of embodiment 150, wherein the fusion polypeptide is an RGNABP polypeptide operably linked to a base-editing polypeptide.

153. The system of embodiment 152, wherein the base-editing polypeptide is a deaminase.

154. The system of embodiment 153, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

155. The system of embodiment 150, wherein the fusion polypeptide is an RGNABP polypeptide operably linked to an expression modulator polypeptide.

156. The system of any one of embodiments 114-155, wherein the RGNABP polypeptide comprises one or more nuclear localization signals.

157. The system of any one of embodiments 114-156, wherein the RGNABP polypeptide is codon optimized for expression in a eukaryotic cell.

158. The system of any one of embodiments 114-157, wherein polynucleotides comprising the nucleotide sequences encoding the one or more guide RNAs and the polynucleotide comprising the nucleotide sequence encoding an RGNABP polypeptide are located on one vector.

159. The system of any one of embodiments 114-158, wherein said system further comprises one or more donor polynucleotides or one or more nucleotide sequences encoding the one or more donor polynucleotides.

160. A pharmaceutical composition comprising the nucleic acid molecule of any one of embodiments 1-17, 60-65, and 87-92, the vector of any one of embodiments 18-32, 66-86, and 93-113, the cell of embodiment 33, the isolated RGNABP polypeptide of any one of embodiments 43-59, or the system of any one of embodiments 114-159, and a pharmaceutically acceptable carrier.

161. A method for binding a target sequence of a nucleic acid molecule comprising delivering a system according to any one of embodiments 114-159, to said target sequence or a cell comprising the target sequence.

162. The method of embodiment 161, wherein said RGNABP polypeptide or said guide RNA further comprises a detectable label, thereby allowing for detection of said target sequence.

163. The method of embodiment 161, wherein said guide RNA or said RGNABP polypeptide further comprises an expression modulator, thereby modulating expression of said target sequence or a gene under transcriptional control by said target sequence.

164. A method for cleaving or modifying a target sequence of a nucleic acid molecule comprising delivering a system according to any one of embodiments 114-159, to said target sequence or a cell comprising the nucleic acid molecule.

165. The method of embodiment 164, wherein said modified target sequence comprises insertion of heterologous DNA into the target sequence.

166. The method of embodiment 164, wherein said modified target sequence comprises deletion of at least one nucleotide from the target sequence.

167. The method of embodiment 164, wherein said modified target sequence comprises mutation of at least one nucleotide in the target sequence.

168. A method for binding a target sequence of a nucleic acid molecule, said method comprising: a) assembling an RNA-guided nucleic acid-binding protein (RGNABP) ribonucleotide complex in vitro by combining: i) one or more guide RNAs capable of hybridizing to the target sequence; and ii) an RGNABP polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; under conditions suitable for formation of the RGNABP ribonucleotide complex; and b) contacting said target sequence or a cell comprising said target sequence with the in vitro- assembled RGNABP ribonucleotide complex; wherein the one or more guide RNAs hybridize to the target sequence, thereby directing said RGNABP polypeptide to bind to said target sequence.

169. The method of embodiment 168, wherein said RGNABP polypeptide or said guide RNA further comprises a detectable label, thereby allowing for detection of said target sequence.

170. The method of embodiment 168, wherein said guide RNA or said RGNABP polypeptide further comprises an expression modulator, thereby allowing for the modulation of expression of said target sequence. 171. A method for cleaving and/or modifying a target sequence of a nucleic acid molecule, comprising contacting the nucleic acid molecule with: a) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein said RGNABP comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1, 2, 3, or 4; and b) one or more guide RNAs capable of targeting the RGNABP of (a) to the target sequence; wherein the one or more guide RNAs hybridize to the target sequence, thereby directing said

RGNABP polypeptide to bind to said target sequence and cleavage and/or modification of said target sequence occurs.

172. The method of embodiment 171, wherein said RGNABP polypeptide is a fusion polypeptide.

173. The method of embodiment 172, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

174. The method of any one of embodiments 171-173, wherein the cleavage by said RGNABP polypeptide generates a double-stranded break.

175. The method of any one of embodiments 171-173, wherein the cleavage by said RGNABP polypeptide generates a single -stranded break.

176. The method of embodiment 172, wherein said RGNABP polypeptide is operably fused to a base-editing polypeptide.

177. The method of embodiment 176, wherein the base-editing polypeptide is a deaminase.

178. The method of embodiment 177, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

179. The method of embodiment 171, wherein said modified target sequence comprises insertion of heterologous DNA into the target sequence.

180. The method of embodiment 171, wherein said modified target sequence comprises deletion of at least one nucleotide from the target sequence.

181. The method of embodiment 171, wherein said modified target sequence comprises mutation of at least one nucleotide in the target sequence.

182. The method of any one of embodiments 168-181, wherein said RGNABP comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

183. The method of any one of embodiments 168-181, wherein said RGNABP comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

184. The method of any one of embodiments 168-181, wherein said RGNABP comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

185. The method of any one of embodiments 168-181, wherein said RGNABP comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

186. The method of any one of embodiments 168-181, wherein: a) said RGNABP has at least 80% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 80% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 6.

187. The method of any one of embodiments 168-181, wherein: a) said RGNABP has at least 85% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 85% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 6.

188. The method of any one of embodiments 168-181, wherein: a) said RGNABP has at least 90% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 90% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 6.

189. The method of any one of embodiments 168-181, wherein: a) said RGNABP has at least 95% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 95% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 6.

190. The method of any one of embodiments 168-181, wherein: a) said RGNABP has 100% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 5; or b) said RGNABP has 100% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 6.

191. The method of any one of embodiments 168-181, wherein said gRNA comprises a crRNA and atracrRNA. 192. The method of embodiment 191, wherein: a) said RGNABP has at least 80% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 80% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 8.

193. The method of embodiment 191, wherein: a) said RGNABP has at least 85% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 85% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 8.

194. The method of embodiment 191, wherein: a) said RGNABP has at least 90% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 90% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 8.

195. The method of embodiment 191, wherein: a) said RGNABP has at least 95% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 95% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 8. 196. The method of embodiment 191, wherein: a) said RGNABP has 100% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 7; or b) said RGNABP has 100% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 8.

197. The method of any one of embodiments 191-196, wherein said gRNA is a single guide RNA (sgRNA).

198. The method of any one of embodiments 191-196, wherein said gRNA is a dual-guide RNA.

199. The method of any one of embodiments 168-198, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

200. The method of any one of embodiments 168-199, wherein the target sequence is within a cell.

201. The method of embodiment 200, wherein the cell is a eukaryotic cell.

202. The method of embodiment 201, wherein the eukaryotic cell is a plant cell.

203. The method of embodiment 201, wherein the eukaryotic cell is a mammalian cell.

204. The method of embodiment 201, wherein the mammalian cell is a human cell.

205. The method of embodiment 204, wherein the human cell is an immune cell.

206. The method of embodiment 205, wherein the immune cell is a stem cell.

207. The method of embodiment 206, wherein the stem cell is an induced pluripotent stem cell.

208. The method of embodiment 201, wherein the eukaryotic cell is an insect cell.

209. The method of embodiment 200, wherein the cell is a prokaryotic cell.

210. The method of any one of embodiments 200-209, further comprising culturing the cell under conditions in which the RGNABP polypeptide is expressed and produces a nucleic acid molecule comprising a modified target sequence; and selecting a cell comprising said modified target sequence.

211. A cell comprising a modified target sequence according to the method of embodiment 210.

212. The cell of embodiment 211, wherein the cell is a eukaryotic cell.

213. The cell of embodiment 212, wherein the eukaryotic cell is a plant cell.

214. A plant comprising the cell of embodiment 213.

215. A seed comprising the cell of embodiment 213.

216. The cell of embodiment 212, wherein the eukaryotic cell is a mammalian cell.

217. The cell of embodiment 216, wherein said mammalian cell is a human cell.

218. The cell of embodiment 217, wherein said human cell is an immune cell.

219. The cell of embodiment 218, wherein said immune cell is an induced pluripotent stem cell. 220. The cell of embodiment 212, wherein the eukaryotic cell is an insect cell.

221. The cell of embodiment 211, wherein the cell is a prokaryotic cell.

222. A pharmaceutical composition comprising the cell of any one of embodiments 212 and 216- 219 and a pharmaceutically acceptable carrier.

223. A method for producing a genetically modified cell with a correction in a causal mutation for a genetically inherited disease, the method comprising introducing into the cell: a) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein the RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4, or a polynucleotide encoding said RGNABP polypeptide, wherein said polynucleotide encoding the RGNABP polypeptide is operably linked to a promoter to enable expression of the RGNABP polypeptide in the cell; and b) a guide RNA (gRNA) or a polynucleotide encoding said gRNA, wherein said polynucleotide encoding the gRNA is operably linked to a promoter to enable expression of the gRNA in the cell; whereby the RGNABP and gRNA target to the genomic location of the causal mutation and modify the genomic sequence to remove the causal mutation.

224. The method of embodiment 223, wherein the RGNABP is fused to a nuclease domain.

225. The method of embodiment 223, wherein the RGNABP is fused to a polypeptide which has base-editing activity.

226. The method of embodiment 225, wherein the base-editing polypeptide is a deaminase.

227. The method of embodiment 226, wherein the polypeptide with base-editing activity is a cytidine deaminase or an adenine deaminase.

228. The method of any one of embodiments 223-227, wherein the genetically inherited disease is caused by a single nucleotide polymorphism.

229. The method of embodiment 228, wherein the gRNA comprises a spacer sequence that targets a region proximal to the causal single nucleotide polymorphism.

230. The method of any one of embodiments 223-229, wherein said genetically inherited disease is Hurler Syndrome.

231. A method for producing a genetically modified cell with a deletion in a disease-causing genomic region of instability, the method comprising introducing into the cell: a) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein the RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1, 2, 3, or 4, or a polynucleotide encoding said RGNABP polypeptide, wherein said polynucleotide encoding the RGNABP polypeptide is operably linked to a promoter to enable expression of the RGNABP polypeptide in the cell; and b) a first guide RNA (gRNA) or a polynucleotide encoding said first gRNA, wherein said polynucleotide encoding the first gRNA is operably linked to a promoter to enable expression of the first gRNA in the cell, and wherein the first gRNA comprises a spacer sequence that targets the 5' flank of the genomic region of instability; and c) a second guide RNA (gRNA) or a polynucleotide encoding said second gRNA, wherein said polynucleotide encoding the second gRNA is operably linked to a promoter to enable expression of the second gRNA in the cell, and wherein said second gRNA comprises a spacer sequence that targets the 3' flank of the genomic region of instability; whereby the RGNABP and the two gRNAs target to the genomic region of instability and at least a portion of the genomic region of instability is removed.

232. The method of embodiment 231, wherein the genetically inherited disease is Friedrich’s Ataxia or Huntington’s Disease.

233. The method of embodiment 231 or 232, wherein the first gRNA comprises a spacer sequence that targets a region within or proximal to the genomic region of instability.

234. The method of any one of embodiments 231-233, wherein the second gRNA comprises a spacer sequence that targets a region within or proximal to the genomic region of instability.

235. The method of any one of embodiments 223-234, wherein said RGNABP polypeptide has at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

236. The method of any one of embodiments 223-234, wherein said RGNABP polypeptide has at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

237. The method of any one of embodiments 223-234, wherein said RGNABP polypeptide has at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

238. The method of any one of embodiments 223-234, wherein said RGNABP polypeptide has 100% sequence identity to any one of SEQ ID NOs: 1-4.

239. The method of any one of embodiments 223-238, wherein said gRNA, said first gRNA, said second gRNA, or said first gRNA and said second gRNA is selected from a gRNA selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

240. The method of any one of embodiments 223-238, wherein said gRNA, said first gRNA, said second gRNA, or said first gRNA and said second gRNA is selected from a gRNA selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

241. The method of any one of embodiments 223-238, wherein said gRNA, said first gRNA, said second gRNA, or said first gRNA and said second gRNA is selected from a gRNA selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

242. The method of any one of embodiments 223-238, wherein said gRNA, said first gRNA, said second gRNA, or said first gRNA and said second gRNA is selected from a gRNA selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

243. The method of any one of embodiments 223-238, wherein said gRNA, said first gRNA, said second gRNA, or said first gRNA and said second gRNA is selected from a gRNA selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

244. The method of any one of embodiments 223-243, wherein the RGNABP is operably fused to a nuclease domain.

245. The method of any one of embodiments 223-244, wherein the cell is an animal cell. 246. The method of embodiment 245, wherein the animal cell is a mammalian cell.

247. The method of embodiment 245, wherein the cell is derived from a dog, cat, mouse, rat, rabbit, horse, cow, pig, or human.

248. A method for producing a genetically modified mammalian hematopoietic progenitor cell having decreased BCL11A mRNA and protein expression, the method comprising introducing into an isolated human hematopoietic progenitor cell: a) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein the RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4, or a polynucleotide encoding said RGNABP polypeptide, wherein said polynucleotide encoding the RGNABP polypeptide is operably linked to a promoter to enable expression of the RGNABP polypeptide in the cell; and b) a guide RNA (gRNA) or a polynucleotide encoding said gRNA, wherein said polynucleotide encoding the gRNA is operably linked to a promoter to enable expression of the gRNA in the cell, whereby the RGNABP and gRNA are expressed in the cell and cleave at the BCL11A enhancer region, resulting in genetic modification of the human hematopoietic progenitor cell and reducing the mRNA and/or protein expression of BCL11A.

249. The method of embodiment 248, wherein the RGNABP polypeptide is operably fused to a nuclease domain.

250. The method of embodiment 248 or 249, wherein the gRNA comprises a spacer sequence that targets a region within or proximal to the BCL11A enhancer region.

251. The method of any one of embodiments 248-250, wherein said RGNABP polypeptide has at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

252. The method of any one of embodiments 248-250, wherein said RGNABP polypeptide has at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

253. The method of any one of embodiments 248-250, wherein said RGNABP polypeptide has at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

254. The method of any one of embodiments 248-250, wherein said RGNABP polypeptide has 100% sequence identity to any one of SEQ ID NOs: 1-4.

255. The method of any one of embodiments 248-254, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4. 256. The method of any one of embodiments 248-254, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

257. The method of any one of embodiments 248-254, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

258. The method of any one of embodiments 248-254, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

259. The method of any one of embodiments 248-254, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide has an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; or b) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide has an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

260. A method of treating a disease, said method comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition of embodiment 160 or 222.

261. The method of embodiment 260, wherein said disease is associated with a causal mutation and said effective amount of said pharmaceutical composition corrects said causal mutation. 262. Use of the nucleic acid molecule of any one of embodiments 1-17, 60-65, and 87-92, the vector of any one of embodiments 18-32, 66-86, and 93-113, the cell of any one of embodiments 33, 212, and 216-219, the isolated RGNABP polypeptide of any one of embodiments 43-59, or the system of any one of embodiments 114-159 for the treatment of a disease in a subject.

263. The use of embodiment 262, wherein said disease is associated with a causal mutation and said treating comprises correcting said causal mutation.

264. Use of the nucleic acid molecule of any one of embodiments 1-17, 60-65, and 87-92, the vector of any one of embodiments 18-32, 66-86, and 93-113, the cell of any one of embodiments 32, 212, and 216-219, the isolated RGNABP polypeptide of any one of embodiments 43-59, or the system of any one of embodiments 114-159 for the manufacture of a medicament useful for treating a disease.

265. The use of embodiment 264, wherein said disease is associated with a causal mutation and an effective amount of said medicament corrects said causal mutation.

The following examples are offered by way of illustration and not by way of limitation.

EXAMPUES

Example 1. Identification of RNA-guided nucleic acid binding proteins

A propriety collection of microbes for which each genome was fully sequenced was used to mine for novel CRISPR-Cas systems. CRISPR repeats were identified using minCED (mining CRISPRs in Environmental Datasets; github.com/ctSkennerton/minced), which is derived from the CRISPR Recognition Tool (CRT; Bland et al., BMC Bioinformatics 2997, 8: 209, doi: 10.1186/1471-2105-8-209). The minimum number of repeats in array set to two, as well as CRISPR detect. Repetitive features outside of 27 to 47 nucleotides in length were determined not to be CRISPR-related and were removed. Only intergenic repeats were considered for further analysis.

The CRISPR arrays identified were then manually searched to identify putative single effector CRISPR-Cas systems. All putative protein-encoding sequences within a 20kb window of repeat-spacer arrays were extracted and clustered into gene neighborhoods. Systems classified as known Type II, V or VI systems were removed. Remaining systems were then further analyzed.

Cultures of bacteria comprising each of the remaining systems were grown to mid-log phase (OD600 of -0.600), pelleted, and flash frozen. RNA was isolated from the pellets using a mirVANA miRNA Isolation Kit (Life Technologies, Carlsbad, CA), and sequencing libraries were prepared from the isolated RNA using an NEBNext Small RNA Library Prep kit (NEB, Beverly, MA). The library prep was fractionated on a 6% polyacrylamide gel to capture the RNA species less than 200nt to detect crRNAs and tracrRNAs, respectively. Deep sequencing (75 bp paired-end) was performed on a Next Seq 500 (High Output kit) by a service provider (MoGene, St. Louis, MO). Reads were quality trimmed using Cutadapt and mapped to reference genomes using Bowtie2. A custom RNAseq pipeline was written in Python to detect the crRNA and tracrRNA transcripts. Processed crRNA boundaries were determined by sequence coverage of the native repeat spacer array. The anti-repeat portion of the tracrRNA was identified using permissive BLASTn parameters. RNA sequencing depth confirmed the boundaries of the processed tracrRNA by identifying the transcript containing the anti -repeat. Manual curation of RNAs was performed using secondary structure prediction by RNAfold, an RNA folding software. Single guide RNA (sgRNA) cassettes were prepared by DNA synthesis and were generally designed as follows (5'->3'): a 20-30 bp spacer sequence, operably linked at its 3' end to the processed repeat portion of the crRNA, operably linked at its 3' end to a 4 bp noncomplementary linker (AAAG; SEQ ID NO: 52), operably linked at its 3' end to the processed tracrRNA. Other 4 bp noncomplementary linkers may also be used.

The RGNABPs disclosed herein are encoded by 500 base pairs immediately upstream of the repeat spacer arrays in the bacterial genome, and the expressed tracrRNA is encoded by 16 base pairs from the RGNABP gene sequence. The tracrRNAs are transcribed co-directionally with the gene of interest (i.e., the RGNABP) and the crRNAs (Figure 1). An antirepeat was identified in the expressed tracrRNA using the methods established in Briner et al 2016 doi: 10.1101/pdb.prot086785. The orientation of the formed crRNA:tracrRNA complex is 5'-crRNA-tracrRNA-3'. The tracrRNA does not contain any structure or sequence similarities identified in Type II or Type V tracrRNAs (Briner et al 2014, Mol Cell doi: 10.1016/j.molcel.2014.09.019; Shmakov et al 2017, Nat Rev Microbiol doi: 10.1038/nrmicro.2016.184; Yan et al 2018, Science doi: 10.1126/science. aav7271; Harrington et al 2018, Science doi: 10.1126/science.aav4294).

Interestingly, a complete Type I system with related repeats is also present in the genome for two of the RGNABPs, APG07446 and APG01250. TracrRNAs have never been described as part of functional Type I systems (Makarova et al 2011, Nat Rev Microbiol, doi: 10.1038/nrmicro3569; Koonin et al 2017, Curr Opin Microbiol, doi: 10.1016/j.mib.2017.05.008; Makarova et al 2020, Nat Rev Microbiol, doi: 10.1038/s41579-019-0299-x). It is possible these proteins can interact with the Type I system as they share related repeats, but the proteins identified here are likely to be independent RNA-guided proteins.

The locus surrounding each putative RGNABP was searched for potential accessory genes that might be needed for CRISPR immunity. The RGNABPs disclosed herein were not in operonic structures, suggesting they do not have accessory genes (Figure 1).

Table 1: System Information

Example 2: Identification of protospacer hits and PAM determination

The spacer sequences from each system were BLASTed against the public database at NCBI to identify potential protospacer hits. Seven protospacers were identified, all matching sequences in Bacillus sp. plasmids or phage sequences. This is consistent with functional bacterial adaptive immunity (Horvath et al 2008, J Bac doi: 10.1128/JB.01415-07). These protospacers are shown in Table 2, with their description, accession number (Ace. No.), and sequence. The spacer number describes their position in the native repeat spacer array. The 5' flanking region from each of the protospacer hits (5' flank SEQ ID NO.) were aligned to identify a potential PAM sequence (Mojica et al, 2009, Microbiol Soc, doi: 10.1099/mic.0.023960-0). There is a conserved motif of 5'-TCA-3' (SEQ ID NO: 35) flanking the 5' side of the target sequence. If these targets are actually recognized in the opposite orientation, then the PAM sequence would be 5'-TGA-3'

(SEQ ID NO: 36) on the 3' side of the target sequence. Table 2: Identification of Protospacer

Example 3: Protein analysis

Nuclease domains were predicted by searching for domains in the interpro, ProDom, PRINTS, PIRSF, Pfam, SMART, TIGRFAM. PrositeProfdes, HAMAP, PrositePattems, SuperFamily, SignalP, TMHHMM, Panther, Gene3d and Phobius databases. Additionally, profdes of the Type II HNH domain, Type I HD domain, and split RuvC nuclease domains for Types II and V were generated based on known reference Cas sets from the CRISPRdisco software (Crawley et al 2018, doi: 10.1089/crispr.2017.0022). No nuclease domains were identified based on the HMM models or databases referenced. APG0776 and APG01250 contain an NHC signal peptide at the N-terminus followed by a non-cytoplasmic domain. These RGNABPs with the signal peptide are likely membrane bound or excreted. LocateP (Zhou et al 2008, doi: 10.1186/1471-2105-9-173) determined the subcellular localization was most likely to be N-terminally anchored, membrane-bound without a cleavage site. The signal peptide has been removed for some variants of APG0776 and APG01250 tested herein. The RGNABPs also contain a coiled coil region, similar to a SipB Type III section system protein, in the middle of the coding sequence. The isoelectric point on these proteins is predicted to be neutral, unlike most effector Cas proteins which have isoelectric points greater than 10. Overall, these features indicate the RGNABPs described herein are exceptionally different from any currently known CRISPR-associated protein.

Example 4: Guide RNA confirmation

For in vitro assays, sgRNAs and tracrRNAs are synthesized by in vitro transcription of the sgRNA cassettes using the TranscriptAid™ T7 High Yield Transcription Kit (ThermoFisher). crRNAs and some tracrRNAs are produced synthetically.

For protein expression and purification, plasmids containing the putative RGNABPs fused to a C terminal HislO tag are constructed and transformed into BL21 (DE3) strains of E. coli. Expression is performed using MagicMedia™ self-inducing media supplemented with kanamycin. After lysis and clarification, the proteins are purified by immobilized metal affinity chromatography. The tracrRNAs are produced by in vitro transcription (IVT) using a dsDNA template with T7 promoter upstream of the tracrRNA sequence. The template for IVT is amplified by PCR from a synthesized gBlock® template (Integrated DNA Technologies). Additional tracr and crRNAs are produced synthetically.

RNA binding is confirmed by differential scanning fluorimetry (Niesen, F.H., H. Berglund, and M. Vedadi. 2007. Nat. Protoc. 2:2212-2221). Dual RNA complexes are produced by mixing an excess of crRNA with tracrRNA in Annealing Buffer (Synthego, 60 mM KC16 mM HEPES pH 7). The candidate effector protein and guide RNA (either dual RNA complex or sgRNA) are incubated at final concentrations of 0.5 mM effector protein and 1 mM guide RNA in phosphate buffered saline (PBS, Thermo Fisher). These are incubated for 20 minutes at room temperature and then mixed 1 : 1 with Sypro® Orange dye solution that had been diluted in PBS. A melt curve is obtained measuring fluorescence intensity (FI) as a function of temperature and the first derivative of the melt curve (dFI/dT) is calculated. A shift in the peak of dFI/dT as a function of temperature of the putative RNP relative to the original protein indicates RNA binding and is used to evaluate putative guide RNA combinations.

Example 5: PAM determination dsDNA and RNA substrates for PAM determination

PAM requirements for each dsDNA binding RGNABP are determined using a PAM depletion assay essentially adapted from Kleinstiver et al. (2015, Nature 523:481-485), Zetsche et al. (2015, Cell 163:759- 771), and Abudayyeh et al. (2016, Science 353:6299). Briefly, two plasmid libraries (LI and L2) are generated in a pBR323 backbone (ampR), with each containing a distinct 30 bp protospacer (target) sequence flanked by 6 random nucleotides (i.e., the PAM region) in the 5' end of the b-lactamase gene. The target sequence and flanking PAM region for library 1 (LI) is SEQ ID NO: 37, and for library 2 (L2) is SEQ ID NO: 38.

The libraries are separately electroporated into E. coli BL21(DE3) cells harboring pRSF-lb expression vectors comprising an expression cassette comprising an E. coli codon-optimized coding sequence for an RGNABP of the invention, and further comprising an expression cassette comprising the coding sequence for a cognate sgRNA containing a spacer sequence corresponding to the protospacer in LI or L2. Sufficient library plasmid is used in the transformation reaction to obtain >10⁶ CFU. Both the RGNABP and sgRNA in the pRSF-lb backbone are under the control of T7 promoters. The transformation reaction is allowed to recover for 1 hr after which it is diluted into LB media containing carbenicillin and kanamycin and grown overnight. The following day, the mixture is diluted into self-inducing Overnight Express™ Instant TB Medium (Millipore Sigma) to allow expression of the RGNABP and sgRNA, and grown for an additional 4 h or 20 h after which the cells are spun down and plasmid DNA is isolated with a Mini -prep kit (Qiagen, Germantown, MD). In the presence of the appropriate sgRNA, plasmids containing a PAM that is recognizable by the RGNABP will be bound by the RGNABP and prevent the expression of the b-lactamase TEM gene, resulting in their removal from the population. Plasmids containing PAMs that are not recognizable by the RGNABP, or that are transformed into bacteria not containing an appropriate sgRNA, will survive and replicate. The PAM and protospacer regions of surviving plasmids are PCR- amplified and prepared for sequencing following published protocols (16s-metagenomic library prep guide 15044223B, Illumina, San Diego, CA). Deep sequencing (75bp single end reads) is performed on a MiSeq (Illumina) by a service provider (MoGene, St. Louis, MO). Typically, 1-4M reads are obtained per amplicon. PAM regions are extracted, counted, and normalized to total reads for each sample. PAMs that lead to plasmid binding are identified by being underrepresented when compared to controls (i.e., when the library is transformed into E. coli containing the RGNABP but lacking an appropriate sgRNA). To represent PAM requirements for a novel RGNABP, the depletion ratios (frequency in sample/frequency in control) for all sequences in the region in question are converted to enrichment values with a -log base 2 transformation. Sufficient PAMs are defined as those with enrichment values >2.3 (which corresponds to depletion ratios < -0.2). PAMs above this threshold in both libraries are collected and used to generate web logos, which for example can be generated using a web-based service on the internet known as “weblogo”. PAM sequences are identified and reported when there is a consistent pattern in the top enriched PAMs.

Confirmation of PAM determined via bioinformatic identification of protospacers

The PAM sequence identified via bioinformatic identification of the protospacers (SEQ ID NO: 35) may also be tested for plasmid depletion. A protospacer sequence identified in Table 2 which comprises SEQ ID NO: 35 was incorporated into the 5' end of the b-lacatamase gene in place of the library sequence to generate the targeting plasmid. Additionally, E. coli BL21(DE3) cells are produced which contain a pRSF- lb expression vector comprising an expression cassette comprising an E. coli codon-optimized coding sequence of an RGNABP of the invention and further comprising an expression cassette comprising the coding sequence for a cognate sgRNA containing a spacer sequence corresponding to the protospacer. Both the RGNABP and sgRNA in the pRSF-lb backbone are under the control of T7 promoters. The targeting plasmid is electroporated into the E. coli BL21 (DE3) cells to obtain >10⁶ CFU in the transformation reaction. The transformation reaction is allowed to recover for 1 hr after which it is diluted into LB media containing carbenicillin and kanamycin and grown overnight. In the presence of the appropriate sgRNA, plasmids containing a PAM that is recognizable by the RGNABP will be bound by the RGNABP and prevent the expression of the b-lactamase TEM gene, resulting in their removal from the population. Serial dilutions of the recovered cells are plated on ampicillin to test for a decrease in survival rates. Decreased surviving cell counts demonstrate that the PAM predicted is correct and the system is capable of sequence- specific nucleic acid binding.

Example 6: RGNABP-nuclease domain fusion proteins cleave DNA RGNABPs of the invention are operably linked to a nuclease domain to assay for nucleotide cleavage. Fusion proteins of RGNABP and single chain Fokl (scFokl) are described in Table 3. Each of these fusion proteins is further operably linked to N-terminal nucleoplasmin NLS (SEQ ID NO: 48), a C- terminal SV40 NLS (SEQ ID NO: 47), and C-terminal TEV and His tags. Controls where the RGNABP is not operably linked to a nuclease domain, but is operably linked to NLS’s and TEV and His tags, are also assayed.

Table 3: RGNABP-nuclease domain fusion proteins

A PCR-amplified target DNA comprising the protospacer target sequence from Table 2 and a defined PAM as determined in Example 5 is provided. A ribonucleoprotein (RNP) complex comprising a nuclease domain fusion protein of Table 3 and an sgRNA is formed by incubation of the nuclease domain fusion protein and the sgRNA in an appropriate buffered solution for 20 min at room temperature. The RNP complex and the PCR amplified target DNA are each introduced to a tube containing digestion buffer (such as NEBuffer 2 or Cutsmart, New England Biolabs), and the tube is incubated at 25 °C to 37°C for 30 min and then 95°C for 5 min. Residual guide RNA can be removed by RNase digestion. Digestion efficiency for the RNP complex is evaluated by performing gel electrophoresis on a Lonza FlashGel™, and then visualizing and quantifying the cleaved and intact target DNA bands.

Example 7: Programmable DNA cleavage including editing in eukaryotic cells

Oligonucleotides and PCR from mammalian cell genomic DNA preparations

All PCRs described below are performed using 10 mΐ of 2X Master Mix Phusion® High-Fidelity DNA polymerase (Thermo Scientific) in a 20 mΐ reaction including 0.5 mM of each primer. Large genomic regions encompassing each target gene are first amplified using PCR#1 primers, using a program of: 98°C.,

1 min; 30 cycles of [98°C., 10 sec; 62°C., 15 sec; 72°C., 5 min]; 72°C., 5 min; 12°C., forever. One microliter of this PCR reaction is then further amplified using primers specific for each guide (PCR#2 primers), using a program of: 98°C., 1 min; 35 cycles of [98°C., 10 sec; 67°C., 15 sec; 72°C., 30 sec]; 72°C., 5 min; 12°C., forever. Primers for PCR#2 include Nextera Read 1 and Read 2 Transposase Adapter overhang sequences for Illumina sequencing.

Construction of RGNABP -nuclease domain fusion proteins and gRNA mammalian expression plasmids

RGNABP-nuclease domain fusion constructs similar to those described in Example 6 are synthesized and cloned into mammalian expression vectors. Human codon-optimized RGNABP-scFokI fusion proteins (Genscript) with N-terminal SV40 and C-terminal nucleoplasmin NLS sequences (SEQ ID NOs: 47 and 48, respectively) and an N-terminal 3xFLAG tag (SEQ ID NO: 49) under control of a cytomegalovirus (CMV) promoter (SEQ ID NO: 50) is cloned into pTwist-CMV using the Noil and BamHI insertion sites. Guide RNA expression constructs encoding a single gRNA each under the control of a human RNA polymerase III U6 promoter (SEQ ID NO: 51) are synthesized and cloned into the pTwist High Copy Amp vector.

Transfection and expression in mammalian cells

One day prior to transfection, lxlO⁵ HEK293T cells (Sigma) are plated in 24-well dishes in Dulbecco’s modified Eagle medium (DMEM) plus 10% (vol/vol) fetal bovine serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). When the cells are at 50-60% confluency, 500 ng of a RGNABP-scFokI expression plasmid plus 500ng of a single gRNA expression plasmid are co-transfected using 1.5 pL of Lipofectamine 3000 (Thermo Scientific) per well, following the manufacturer’s instructions. After 48 hours of growth, total genomic DNA is harvested using a genomic DNA isolation kit (Machery -Nagel) according to the manufacturer’s instructions.

T7 endonuclease I assay

Purified genomic DNA is subjected to PCR#1 and PCR#2 as above. Following the second PCR amplification DNA is cleaned using a PCR cleanup kit (Zymo) according to the manufacturer’s instructions and eluted in water. 200-500 ng of purified PCR#2 product is combined with 2 pL of 10X NEB Buffer 2 and water in a 20 pL reaction and annealed to form heteroduplex DNA using a program of: 95 °C, 5 min; 95- 85°C; cooled at a rate of 2°C / sec; 85-25°C. cooled at a rate of 0.1°C / sec.; 12°C, forever. Following annealing, 5 pL of DNA is removed as a no enzyme control, and 1 pL of T7 Endonuclease I (NEB) is added and the reaction incubated at 37°C for 1 hr. After incubation 5x FlashGel™ loading dye (Lonza) is added and 5 pL of each reaction and controls is loaded onto a 2.2% agarose FlashGel™ (Lonza). Gels are visualized on a BioRad ChemiDoc™ MP imager and the percentage of non-homologous end joining determined using the following equation: %NHEJ events = 100 x [1-(1 -fraction cleaved)^(½)], where (fraction cleaved) is defined as: (density of digested products)/(density of digested products + undigested parental band). Products from PCR#2 containing Illumina overhang sequences underwent library preparation following the Illumina 16S Metagenomic Sequencing Library protocol. Deep sequencing is performed on an Illumina Mi-Seq platform by a service provider (MOGene). Typically, 200,000250 bp paired-end reads (2 x 100,000 reads) are generated per amplicon. The reads are analyzed using CRISPResso (Pinello, et al. 2016 Nature Biotech, 34:695-697) to calculate the rates of editing. Output alignments are hand-curated to confirm insertion and deletion sites as well as identify microhomology sites at the recombination sites. Additional analyses for base editing rates are performed. Each position across the target is analyzed to determine the editing rate and specific nucleotide changes that occur at each position.

Example 8: Programmable DNA binding and gene activation

Construction of RGNABP gene activation and gRNA mammalian expression plasmids

RGNABPs may be fused to a transcriptional activator domain, such as the tripartite activator VPR (Chavez et al., Nature Methods 2015, 12(4):326-328), for transcriptional activation of atargeted coding sequence. RGNABP-VPR fusion constructs for mammalian expression described in Table 4 are synthesized. Each construct encodes for an activator fusion protein of Table 4 operably linked to N-terminal SV40 and C-terminal nucleoplasmin NLS sequences (SEQ ID NOs: 47 and 48, respectively), an N-terminal 3xFLAG tag (SEQ ID NO: 49), and a C- or N-terminal VPR activation domain (for example, encoded by SEQ ID NO: 53; Chavez, et al. 2015, Nature Methods, 12(4): 326-328). Each fusion protein coding sequence is under the control of a cytomegalovirus (CMV) promoter (SEQ ID NO: 50) and is introduced into a mammalian expression vector. Guide RNA expression constructs encoding a single gRNA each under the control of a human RNA polymerase III U6 promoter (SEQ ID NO: 51) are also produced.

Table 4: RGNABP-activator fusion proteins

Transfection and expression in mammalian cells

One day prior to transfection, lxl 0⁴ HEK293T cells (Sigma) are plated in 96-well plates in Dulbecco’s modified Eagle medium (DMEM) plus 10% (vol/vol) fetal bovine serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). The next day when the cells are at 50-60% confluency, 100 ng of an RGNABP-activator expression plasmid plus 100 ng of a single gRNA expression plasmid are co-transfected using 0.3 pL of Lipofectamine 3000 (Thermo Scientific) per well, following the manufacturer’s instructions. After 48 hours of growth, total RNA is harvested using the Cells-to-Ct™ One Step kit (ThermoFisher).

Taqman assay for target gene expression

Endogenous genes were chosen which normally have low expression in HEK cells, but which can be induced upon CRISPR activation. RHOXF2 and CD2 were chosen for this purpose. TaqMan® gene expression assays are performed using FAM labelled probes for RHOXF2 (Assay ID: Hs00261259_ml) and CD2 (Assay ID: Hs00233515_ml), and a VIC labelled probe for ACTS (Assay ID: Hs01060665_gl, all from ThermoFisher) as a normalization control. TaqMan assays are performed following the manufacturer’s instructions in the Cells-to-CT™ One Step kit (Thermofisher) m a BioRad CFX96 Real Time thermocycler. Background is measured in similar experiments where no gRNA is present. Fold changes in gene expression relative to background are calculated using the C^D& method (Livak et al. 2001, Methods, 25(4):402-8), normalizing expression to ACTB transcript levels.

Example 9: Programmable DNA binding and base editing

Construction of RGNABP base editing and gRNA mammalian expression plasmids

Deaminases which modify nucleotides are useful for targeted introduction of certain point mutations, also referred to as base editing. RGNABPs of the invention may be fused to deaminases for base editing. RGNABP-deaminase fusion constructs for mammalian expression described in Table 5 are synthesized. Each construct encodes for a deaminase fusion protein of Table 5 operably linked to N- terminal SV40 and C-terminal nucleoplasmin NLS sequences (SEQ ID NOs: 47 and 48, respectively), an N- terminal 3xFLAG tag (SEQ ID NO: 49), and a C-terminal deaminase (for example, hAPOBEC3A or AD AT; SEQ ID NO: 62 or 63, respectively). Each fusion protein coding sequence is under the control of a cytomegalovirus (CMV) promoter (SEQ ID NO: 50) and is introduced into a mammalian expression vector. Guide RNA expression constructs encoding a single gRNA each under the control of a human RNA polymerase III U6 promoter (SEQ ID NO: 51) are also produced.

Table 5: Deaminase-RGNABP fusion proteins

Base editing in mammalian cells

One day prior to transfection, lxl 0⁵ HEK293T cells (Sigma) are plated in 24-well dishes in Dulbecco’s modified Eagle medium (DMEM) plus 10% (vol/vol) fetal bovine serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). When the cells are at 50-60% confluency, 500 ng of a deaminase- RGNABP fusion protein expression plasmid plus 500 ng of a single gRNA expression plasmid are co transfected using 1.5 pL of Lipofectamine 3000 (Thermo Scientific) per well, following the manufacturer’s instructions. After 48 hours of growth, total genomic DNA is harvested using a genomic DNA isolation kit (Machery-Nagel) according to the manufacturer’s instructions. The targeted genomic DNA is sequenced and analyzed for the presence of the targeted base-editing mutations, similar to the sequence analysis described in Example 7.

Example 10: PAM-independent ssDNA target cleavage

Purified RGNABPs are each incubated with a single guide RNA (sgRNA) comprising the target sequence of SEQ ID NO: 72 in Cutsmart buffer (New England Biolabs B7204S) at a final concentration of 200 nM RGNABP and 400 nM sgRNA for 20 minutes. These are then added at a final concentration of 100 nM RGNABP to solutions of 5' Cy5 labeled ssDNA LEI 11 or LEI 13 (SEQ ID NO: 73 and 74, respectively) at 10 nM in Cutsmart buffer (New England Biolabs B7204S).

Samples are quenched by adding RNase A and EDTA at a final concentration of 0.1 mg/mL and 45 mM respectively and placed on ice for 0, 40, 80, or 120 minutes. After quenching, samples are incubated at 50°C for 30 min, then 95°C for 5 min. One-fifth volume of loading buffer (lx TBE, 12% Ficoll, 7 M urea) is added to each reaction and incubated at 95°C for 15 min, and 5 pi of each reaction is analyzed using a 15% TBE-urea acrylamide gel (Bio-Rad 3450092).

Quantitation of the cleaved product as a function of time, RGNABP, and guide RNA is determined. Sequence LEI 11 is used as a negative control, while sequence LEI 13 comprises a target sequence for the sgRNA that was loaded onto the RGNABP.

Example 11: Induction of trans ssDNA cleavage with ssDNA targets

Purified RGNABPs are each incubated with single guide RNA (sgRNA) comprising the target sequence of SEQ ID NO: 72 in Cutsmart buffer (New England Biolabs B7204S) at a final concentration of 200 nM RGNABP and 400 nM sgRNA for 20 minutes.

These RNP solutions are then added to solutions of ssDNA comprising either a target ssDNA or a negative control ssDNA at a final concentration of 10 nM and a fluorophore-quencher labeled reporter probe (for example, TB0125, which comprises SEQ ID NO: 75 with the following chemical modifications indicated: 5'-6-FAM-AGCGGTGGG-ZEN-AAAGGAATCCC-3'-IABkFQ, using the modification nomenclature of Integrated DNA Technologies) at a final concentration of 250 nM in Cutsmart buffer (New England Biolabs B7204S). These chemical modifications indicate a fluorescent dye at the 5' end, a quencher at the 3' end, and an internal quencher. Cleavage of the reporter probe results in dequenching of the fluorescent dye and thus an increase in fluorescence signal. To monitor fluorescence intensity, 10 pi of each reaction is incubated in a Coming low volume 384-well microplate at 37°C in a microplate reader (CLARIOstar Plus).

If incubation with target sequences results in a substantial increase in fluorescence intensity as a function of time relative to the negative control, this demonstrates target induced trans ssDNA cleavage. The rate of cleavage is summarized as the slope of the linear portion of the fluorescence vs. time data series.

Example 12: Induction of trans ssDNA cleavage with PCR products bearing randomized PAM sequences

Oligonucleotides containing degenerate nucleotides 5' of the PAM target were PCR amplified to produce target sequences, referred to herein as dsPCR2 (SEQ ID NO: 80) and dsPCR3 (SEQ ID NO: 81). Target dsPCR2 and dsPCR3 contain an 8 bp or a 5 bp degenerate region, respectively, operably linked to the 5' end of the target encoded by the guide RNA. The oligo pairs were annealed to provide a PCR template for the indicated intended product.

Table 6: Synthesis of target nucleotide molecules with randomized PAM sequences

These annealed oligonucleotides were PCR amplified by primers (SEQ ID NO: 82 and 83) that installed adapters for potential use in future next generation sequencing experiments. This product was then further PCR amplified using primers (SEQ ID NO: 84 and 85, operably linked to different fluorophores at their 5' ends; 6-FAM fluorophore on SEQ ID NO: 84 and Cy5 fluorophore on SEQ ID NO: 85) at a larger scale to produce enough material for in vitro cleavage reactions.

Purified RGNABPs are incubated with a single guide RNA (sgRNA) comprising a target sequence as indicated in Table 7 in Cutsmart buffer (New England Biolabs B7204S) at a final concentration of 200 nM RGNABP and 400 nM sgRNA for 20 minutes.

Table 7: Target sequence of sgRNAs

These RNP solutions are then added to solutions of ssDNA - a target (or control strand that does not match the guide) at a final concentration of 10 nM and a reporter probe (for example, TB0125, which comprises SEQ ID NO: 75 with the following chemical modifications indicated: 5'-6-FAM- AGCGGTGGG-ZEN-AAAGGAATCCC-3'-IABkFQ) at a final concentration of 250 nM in Cutsmart buffer (New England Biolabs B7204S). These chemical modifications indicate a fluorescent dye at the 5' end, a quencher at the 3' end, and an internal quencher. To monitor fluorescence intensity, 10 pi of each reaction is incubated in a Coming low volume 384-well microplate at 37°C in a microplate reader (CLARIOstar Plus). Cleavage of the reporter probe results in dequenching of the fluorescent dye and thus an increase in fluorescence signal. The rate of cleavage is summarized as the slope of the linear portion of the fluorescence vs. time data series.

Example 13: Use of induction of trans ssDNA cleavage to determine PAM sequences

Oligonucleotides SEQ ID NO: 79 and SEQ ID NO: 87 comprising a target sequence operably linked at the 5'end to a 5 bp degenerate sequence (NNNNN) are annealed and cloned into double digested pUC19 plasmid using NEBuilder HiFi DNA Assembly Master Mix (New England Biolabs). Each colony resulting from the transformation of this reaction corresponds to a clonal plasmid DNA sequence, so that preparations of plasmid DNA from cultures deriving from single colonies are unique plasmid preparations sampled from the original library. Plasmid preparations are obtained from a sampling of 96 colonies. These preparations are individually subjected to Sanger sequencing to verify their PAM sequence.

Purified RGNABPs are incubated with single guide RNA (sgRNA) comprising the target sequence of SEQ ID NO: 72 in Cutsmart buffer (New England Biolabs B7204S) at a final concentration of 200 nM RGNABP and 400 nM sgRNA for 20 minutes.

These RNP solutions are added at a final concentration of 100 nM to solutions of plasmid DNA targets at a final concentration of 20 nM and TB0125 reporter probe (which comprises SEQ ID NO: 75 with the following chemical modifications indicated: 5'-6-FAM-AGCGGTGGG-ZEN-AAAGGAATCCC-3'- IABkFQ) at a final concentration of 250 nM in Cutsmart buffer (New England Biolabs B7204S). These chemical modifications indicate a fluorescent dye at the 5' end, a quencher at the 3' end, and an internal quencher. To monitor fluorescence intensity, 10 mΐ of each reaction is incubated in a Coming low volume 384-well microplate at 37°C in a microplate reader (CLARIOstar Plus). Cleavage of the reporter probe results in dequenching of the fluorescent dye and thus an increase in fluorescence signal. The rate of cleavage is summarized as the slope of the linear portion of the fluorescence vs. time data series. Samples with a considerably higher rate of cleavage than others will indicate hits. Follow up experiments can be performed that use plasmid libraries in which certain positions are fixed, to further and more precisely establish the PAM sequence.

Example 14: PAM determination by binding to a DNA library Isolation of the ternary complex containing a DNA target (including a PAM library) with the RNP and sequencing of the DNA recovered from it can be used to identify the PAM sequence, if the given system requires a PAM for DNA binding, modification or cleavage. The complex can be captured by a number of methods well-known in the art, such as immuno-pulldown, capture with immobilized metal affinity resin (such as Ni-NTA agarose), or isolation by size exclusion chromatography.

Claims

THAT WHICH IS CLAIMED:

1. A nucleic acid molecule comprising a polynucleotide encoding an RNA-guided nucleic acid binding protein (RGNABP) polypeptide, wherein said polynucleotide comprises a nucleotide sequence encoding an RGNABP polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; wherein said RGNABP polypeptide is capable of binding a target sequence of a nucleic acid molecule in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA) capable of hybridizing to said target sequence, and wherein said polynucleotide encoding an RGNABP polypeptide is operably linked to a promoter heterologous to said polynucleotide.

2. The nucleic acid molecule of claim 1, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

3. The nucleic acid molecule of claim 1, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

4. The nucleic acid molecule of claim 1, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

5. The nucleic acid molecule of claim 1, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

6. The nucleic acid molecule of any one of claims 1-5, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

7. The nucleic acid molecule of any one of claims 1-5, wherein said RGNABP polypeptide is a fusion polypeptide.

8. The RGNABP polypeptide of claim 7, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

9. The nucleic acid molecule of claim 6 or 8, wherein said RGNABP polypeptide is capable of generating a double -stranded break.

10. The nucleic acid molecule of claim 6 or 8, wherein said RGNABP polypeptide is capable of generating a single-stranded break.

11. The nucleic acid molecule of claim 7, wherein said fusion polypeptide is an RGNABP operably fused to a base-editing polypeptide.

12. The nucleic acid molecule of claim 11, wherein the base-editing polypeptide is a deaminase.

13. The nucleic acid molecule of claim 12, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

14. The nucleic acid molecule of claim 7, wherein said fusion polypeptide is an RGNABP operably fused to an expression modulator polypeptide.

15. The nucleic acid molecule of any one of claims 1-14, wherein the RGNABP polypeptide comprises one or more nuclear localization signals.

16. The nucleic acid molecule of any one of claims 1-15, wherein the RGNABP polypeptide is codon optimized for expression in a eukaryotic cell.

17. The nucleic acid molecule of any one of claims 1-16, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

18. A vector comprising the nucleic acid molecule of any one of claims 1-17.

19. The vector of claim 18, further comprising at least one nucleotide sequence encoding said gRNA capable of hybridizing to said target sequence.

20. The vector of claim 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

21. The vector of claim 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

22. The vector of claim 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

23. The vector of claim 19, wherein the guide RNA comprises a CRISPR RNA comprising a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

24. The vector of claim 19, wherein the guide RNA comprises a CRISPR RNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5; wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6; wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

25. The vector of claim 19, wherein said gRNA comprises a crRNA and a tracrRNA.

26. The vector of claim 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

27. The vector of claim 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

28. The vector of claim 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

29. The vector of claim 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

30. The vector of claim 25, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

31. The vector of any one of claims 25-30, where said gRNA is a single guide RNA.

32. The vector of any one of claims 25-30, wherein said gRNA is a dual-guide RNA.

33. A cell comprising the nucleic acid molecule of any one of claims 1-17 or the vector of any one of claims 18-32.

34. A method for making an RGNABP polypeptide comprising culturing the cell of claim 33 under conditions in which the RGNABP polypeptide is expressed.

35. A method for making an RGNABP polypeptide comprising introducing into a cell a heterologous nucleic acid molecule comprising a nucleotide sequence encoding an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; wherein said RGNABP polypeptide is capable of binding a target sequence of a nucleic acid molecule in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA) capable of hybridizing to said target sequence; and culturing said cell under conditions in which the RGNABP polypeptide is expressed.

36. The method of claim 35, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

37. The method of claim 35, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

38. The method of claim 35, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

39. The method of claim 35, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

40. The method of any one of claims 34-39, further comprising purifying said RGNABP polypeptide.

41. The method of any one of claims 34-39, wherein said cell further expresses one or more guide RNAs that binds to said RGNABP polypeptide to form an RGNABP ribonucleoprotein complex.

42. The method of claim 41, further comprising purifying said RGNABP ribonucleoprotein complex.

43. An isolated RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; and wherein said RGNABP polypeptide is capable of binding a target sequence of a nucleic acid molecule in an RNA-guided sequence specific manner when bound to a guide RNA (gRNA) capable of hybridizing to said target sequence.

44. The isolated RGNABP polypeptide of claim 43, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

45. The isolated RGNABP polypeptide of claim 43, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

46. The isolated RGNABP polypeptide of claim 43, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

47. The isolated RGNABP polypeptide of claim 43, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

48. The isolated RGNABP polypeptide of any one of claims 43-47, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

49. The isolated RGNABP polypeptide of any one of claims 43-47, wherein said RGNABP polypeptide is a fusion polypeptide.

50. The isolated RGNABP polypeptide of claim 49, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

51. The isolated RGNABP polypeptide of claim 48 or 50, wherein said RGNABP polypeptide is capable of generating a double -stranded break.

52. The isolated RGNABP polypeptide of claim 48 or 50, wherein said RGNABP polypeptide is capable of generating a single-stranded break.

53. The isolated RGNABP polypeptide of claim 49, wherein the RGNABP polypeptide is operably fused to a base-editing polypeptide.

54. The isolated RGNABP polypeptide of claim 53, wherein the base-editing polypeptide is a deaminase.

55. The isolated RGNABP polypeptide of claim 54, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

56. The isolated RGNABP polypeptide of claim 49, wherein said fusion polypeptide is an RGNABP operably fused to an expression modulator polypeptide.

57. The isolated RGNABP polypeptide of any one of claims 43-56, wherein the RGNABP polypeptide comprises one or more nuclear localization signals.

58. The isolated RGNABP polypeptide of any one of claims 43-57, wherein the RGNABP polypeptide is codon optimized for expression in a eukaryotic cell.

59. The isolated RGNABP polypeptide of any one of claims 43-58, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

60. A system for binding a target sequence of a nucleic acid molecule, said system comprising: a) one or more guide RNAs capable of hybridizing to said target sequence or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more guide RNAs (gRNAs); and b) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4 or a polynucleotide comprising a nucleotide sequence encoding the RGNABP polypeptide; wherein at least one of said nucleotide sequences encoding the one or more guide RNAs and said nucleotide sequence encoding the RGNABP polypeptide is operably linked to a promoter heterologous to said nucleotide sequence; wherein the one or more guide RNAs are capable of hybridizing to the target sequence; and wherein the one or more guide RNAs are capable of forming a complex with the RGNABP polypeptide, in order to direct said RGNABP polypeptide to bind to said target sequence of the nucleic acid molecule.

61. A system for binding a target sequence of a nucleic acid molecule, said system comprising: a) one or more guide RNAs capable of hybridizing to said target sequence or one or more polynucleotides comprising one or more nucleotide sequences encoding the one or more guide RNAs (gRNAs); and b) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; wherein the one or more guide RNAs are capable of hybridizing to the target sequence; and wherein the one or more guide RNAs are capable of forming a complex with the RGNABP polypeptide in order to direct said RGNABP polypeptide to bind to said target sequence of the nucleic acid molecule.

62. The system of claim 60 or 61, wherein at least one of said nucleotides sequences encoding the one or more guide RNAs is operably linked to a promoter heterologous to said nucleotide sequence.

63. The system of any one of claims 60-62, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

64. The system of any one of claims 60-62, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

65. The system of any one of claims 60-62, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

66. The system of any one of claims 60-62, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

67. The system of any one of claims 60-66, wherein said RGNABP polypeptide and said one or more guide RNAs are not found complexed to one another in nature.

68. The system of any one of claims 60-67, wherein said target DNA sequence is a eukaryotic target DNA sequence.

69. The system of any one of claims 60-68, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

70. The system of any one of claims 60-68, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

71. The system of any one of claims 60-68, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

72. The system of any one of claims 60-68, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

73. The system of any one of claims 60-68, wherein said gRNA comprises a CRISPR repeat sequence selected from the group consisting of: a) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

74. The system of any one of claims 60-68, wherein said gRNA comprises a crRNA and a tracrRNA.

75. The system of claim 74, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 70% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 3 or 4.

76. The system of claim 74, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 85% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 3 or 4.

77. The system of claim 74, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 90% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 3 or 4.

78. The system of claim 74, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA having at least 95% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 3 or 4.

79. The system of claim 74, wherein said gRNA is selected from the group consisting of: a) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA having 100% sequence identity to SEQ ID NO: 7, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 or 2; and b) a gRNA comprising a CRISPR repeat sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA having 100% sequence identity to SEQ ID NO: 8, wherein said RGNABP polypeptide comprises an amino acid sequence having 100% sequence identity to SEQ ID NO: 3 or 4.

80. The system of any one of claims 74-79, wherein said gRNA is a single guide RNA (sgRNA).

81. The system of any one of claims 74-79, wherein said gRNA is a dual-guide RNA.

82. The system of any one of claims 74-81, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

83. The system of any one of claims 74-82, wherein the target sequence is within a cell.

84. The system of claim 83, wherein the cell is a eukaryotic cell.

85. The system of claim 84, wherein the eukaryotic cell is a plant cell.

86. The system of claim 84, wherein the eukaryotic cell is a mammalian cell.

87. The system of claim 86, wherein said mammalian cell is a human cell.

88. The system of claim 84, wherein the eukaryotic cell is an insect cell.

89. The system of claim 83, wherein the cell is a prokaryotic cell.

90. The system of any of claims 74-89, wherein said RGNABP polypeptide is capable of cleaving said target sequence upon binding.

91. The system of claim 90, wherein said RGNABP polypeptide is capable of generating a double -stranded break.

92. The system of claim 90, wherein said RGNABP polypeptide is capable of generating a single-strand break.

93. The system of any of claims 74-89, wherein said RGNABP polypeptide is a fusion polypeptide.

94. The system of claim 93, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

95. The system of claim 93, wherein the fusion polypeptide is an RGNABP polypeptide operably linked to a base-editing polypeptide.

96. The system of claim 95, wherein the base-editing polypeptide is a deaminase.

97. The system of claim 96, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

98. The system of claim 93, wherein the fusion polypeptide is an RGNABP polypeptide operably linked to an expression modulator polypeptide.

99. The system of any one of claims 74-98, wherein the RGNABP polypeptide comprises one or more nuclear localization signals.

100. The system of any one of claims 74-99, wherein the RGNABP polypeptide is codon optimized for expression in a eukaryotic cell.

101. The system of any one of claims 74-100, wherein polynucleotides comprising the nucleotide sequences encoding the one or more guide RNAs and the polynucleotide comprising the nucleotide sequence encoding an RGNABP polypeptide are located on one vector.

102. The system of any one of claims 74-100, wherein said system further comprises one or more donor polynucleotides or one or more nucleotide sequences encoding the one or more donor polynucleotides.

103. A pharmaceutical composition comprising the nucleic acid molecule of any one of claims 1- 17, the vector of any one of claims 18-32, the cell of claim 33, the isolated RGNABP polypeptide of any one of claims 43-59, or the system of any one of claims 60-102, and a pharmaceutically acceptable carrier.

104. A method for binding a target sequence of a nucleic acid molecule comprising delivering a system according to any one of claims 74-102, to said target sequence or a cell comprising the target sequence.

105. The method of claim 104, wherein said RGNABP polypeptide or said guide RNA further comprises a detectable label, thereby allowing for detection of said target sequence.

106. The method of claim 104, wherein said guide RNA or said RGNABP polypeptide further comprises an expression modulator, thereby modulating expression of said target sequence or a gene under transcriptional control by said target sequence.

107. A method for cleaving or modifying a target sequence of a nucleic acid molecule comprising delivering a system according to any one of claims 74-102, to said target sequence or a cell comprising the nucleic acid molecule.

108. The method of claim 107, wherein said modified target sequence comprises insertion of heterologous DNA into the target sequence.

109. The method of claim 107, wherein said modified target sequence comprises deletion of at least one nucleotide from the target sequence.

110. The method of claim 107, wherein said modified target sequence comprises mutation of at least one nucleotide in the target sequence.

111. A method for binding a target sequence of a nucleic acid molecule, said method comprising: a) assembling an RNA-guided nucleic acid-binding protein (RGNABP) ribonucleotide complex in vitro by combining: i) one or more guide RNAs capable of hybridizing to the target sequence; and ii) an RGNABP polypeptide comprising an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 1-4; under conditions suitable for formation of the RGNABP ribonucleotide complex; and b) contacting said target sequence or a cell comprising said target sequence with the in vitro- assembled RGNABP ribonucleotide complex; wherein the one or more guide RNAs hybridize to the target sequence, thereby directing said RGNABP polypeptide to bind to said target sequence.

112. The method of claim 111, wherein said RGNABP polypeptide or said guide RNA further comprises a detectable label, thereby allowing for detection of said target sequence.

113. The method of claim 111, wherein said guide RNA or said RGNABP polypeptide further comprises an expression modulator, thereby allowing for the modulation of expression of said target sequence.

114. A method for cleaving and/or modifying a target sequence of a nucleic acid molecule, comprising contacting the nucleic acid molecule with: a) an RNA-guided, nucleic acid-binding protein (RGNABP) polypeptide, wherein said RGNABP comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 1, 2, 3, or 4; and b) one or more guide RNAs capable of targeting the RGNABP of (a) to the target sequence; wherein the one or more guide RNAs hybridize to the target sequence, thereby directing said

RGNABP polypeptide to bind to said target sequence and cleavage and/or modification of said target sequence occurs.

115. The method of claim 114, wherein said RGNABP polypeptide is a fusion polypeptide.

116. The method of claim 115, wherein said fusion polypeptide is an RGNABP operably fused to a nuclease domain.

117. The method of any one of claims 114-116, wherein the cleavage by said RGNABP polypeptide generates a double-stranded break.

118. The method of any one of claims 114-116, wherein the cleavage by said RGNABP polypeptide generates a single -stranded break.

119. The method of claim 115, wherein said RGNABP polypeptide is operably fused to a base editing polypeptide.

120. The method of claim 119, wherein the base-editing polypeptide is a deaminase.

121. The method of claim 120, wherein the deaminase is a cytidine deaminase or an adenine deaminase.

122. The method of claim 114, wherein said modified target sequence comprises insertion of heterologous DNA into the target sequence.

123. The method of claim 114, wherein said modified target sequence comprises deletion of at least one nucleotide from the target sequence.

124. The method of claim 114, wherein said modified target sequence comprises mutation of at least one nucleotide in the target sequence.

125. The method of any one of claims 111-124, wherein said RGNABP comprises an amino acid sequence having at least 85% sequence identity to any one of SEQ ID NOs: 1-4.

126. The method of any one of claims 111-124, wherein said RGNABP comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs: 1-4.

127. The method of any one of claims 111-124, wherein said RGNABP comprises an amino acid sequence having at least 95% sequence identity to any one of SEQ ID NOs: 1-4.

128. The method of any one of claims 111-124, wherein said RGNABP comprises an amino acid sequence having 100% sequence identity to any one of SEQ ID NOs: 1-4.

129. The method of any one of claims 111-124, wherein: a) said RGNABP has at least 80% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 80% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 6.

130. The method of any one of claims 111-124, wherein: a) said RGNABP has at least 85% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 85% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 6.

131. The method of any one of claims 111-124, wherein: a) said RGNABP has at least 90% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 90% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 6.

132. The method of any one of claims 111-124, wherein: a) said RGNABP has at least 95% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 5; or b) said RGNABP has at least 95% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 6.

133. The method of any one of claims 111-124, wherein: a) said RGNABP has 100% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 5; or b) said RGNABP has 100% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 6.

134. The method of any one of claims 111-124, wherein said gRNA comprises a crRNA and a tracrRNA.

135. The method of claim 134, wherein: a) said RGNABP has at least 80% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 80% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 70% sequence identity to SEQ ID NO: 8.

136. The method of claim 134, wherein: a) said RGNABP has at least 85% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 85% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 8.

137. The method of claim 134, wherein: a) said RGNABP has at least 90% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 90% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 8.

138. The method of claim 134, wherein: a) said RGNABP has at least 95% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 7; or b) said RGNABP has at least 95% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 8.

139. The method of claim 134, wherein: a) said RGNABP has 100% sequence identity to SEQ ID NO: 1 or 2 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 5 and a tracrRNA comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 7; or b) said RGNABP has 100% sequence identity to SEQ ID NO: 3 or 4 and said gRNA comprises a CRISPR repeat sequence comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 6 and a tracrRNA comprising a nucleotide sequence having 100% sequence identity to SEQ ID NO: 8.

140. The method of any one of claims 134-139, wherein said gRNA is a single guide RNA (sgRNA).

141. The method of any one of claims 134-139, wherein said gRNA is a dual-guide RNA.

142. The method of any one of claims 111-141, wherein said target sequence is located adjacent to a protospacer adjacent motif (PAM).

143. The method of any one of claims 111-141, wherein the target sequence is within a cell.

144. The method of claim 143, wherein the cell is a eukaryotic cell.

145. The method of claim 144, wherein the eukaryotic cell is a plant cell.

146. The method of claim 144, wherein the eukaryotic cell is a mammalian cell.

147. The method of claim 144, wherein the mammalian cell is a human cell.

148. The method of claim 144, wherein the eukaryotic cell is an insect cell.

149. The method of claim 143, wherein the cell is a prokaryotic cell.

150. The method of any one of claims 143-149, further comprising culturing the cell under conditions in which the RGNABP polypeptide is expressed and produces a nucleic acid molecule comprising a modified target sequence; and selecting a cell comprising said modified target sequence.

151. A cell comprising a modified target sequence according to the method of claim 150.

152. The cell of claim 151, wherein the cell is a eukaryotic cell.

153. The cell of claim 151, wherein the eukaryotic cell is a plant cell.

154. A plant comprising the cell of claim 153.

155. A seed comprising the cell of claim 153.

156. The cell of claim 152, wherein the eukaryotic cell is a mammalian cell.

157. The cell of claim 156, wherein said mammalian cell is a human cell.

158. The cell of claim 152, wherein the eukaryotic cell is an insect cell.

159. The cell of claim 151, wherein the cell is a prokaryotic cell.

160. A pharmaceutical composition comprising the cell of any one of claims 152, 156, and 157 and a pharmaceutically acceptable carrier.

161. A method of treating a disease, said method comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition of claim 103 or 160.

162. The method of claim 161, wherein said disease is associated with a causal mutation and said effective amount of said pharmaceutical composition corrects said causal mutation.